diff --git a/DESCRIPTION b/DESCRIPTION index 762e1b42..323f13f6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: spant Type: Package Title: MR Spectroscopy Analysis Tools -Version: 2.22.0 -Date: 2024-07-11 +Version: 2.23.0 +Date: 2024-08-27 Authors@R: c( person("Martin", "Wilson", email = "martin@pipegrep.co.uk", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-2089-3956")), @@ -14,7 +14,7 @@ Description: Tools for reading, visualising and processing Magnetic Resonance . BugReports: https://github.com/martin3141/spant/issues/ License: GPL-3 -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate")) NeedsCompilation: yes LazyData: yes @@ -50,6 +50,7 @@ Suggests: testthat, ragg, doParallel, + parallel, car VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index 4698dd09..06ccada1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -78,6 +78,8 @@ export(bc_poly) export(bc_spline) export(beta2lw) export(bin_spec) +export(calc_basis_corr_mat) +export(calc_basis_crlbs) export(calc_coil_noise_cor) export(calc_coil_noise_sd) export(calc_design_efficiency) diff --git a/NEWS.md b/NEWS.md index e3c3424b..b75425ac 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# spant 2.23.0 +* abfit options for lipid and MM maximum broadening and maximum frequency shift +now default to be the same as the metabolite values unless explicitly changed. +* Added function to calculate the correlation matrix from a basis_set. +* Fix for RDA files where a comma is sometimes used as a decimal point. + # spant 2.22.0 * Added find_bids_mrs and mrs_data2bids helper functions. * Improved handling of CMRR semi-LASER SVS water reference scans. diff --git a/R/abfit.R b/R/abfit.R index c8450d2d..ed1cb4f0 100644 --- a/R/abfit.R +++ b/R/abfit.R @@ -43,6 +43,25 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { mrs_data <- vec2mrs_data(y, fs = acq_paras$fs, ft = acq_paras$ft, ref = acq_paras$ref, nuc = acq_paras$nuc) + # adjust some options if the lcm_compat flag is used + if (!is.null(opts$lb_init)) { + if (opts$lb_init == "lcm_compat") { + hzpppm <- acq_paras$ft * 1e-6 + deext2 <- 2 + opts$lb_init <- deext2 / pi * sqrt(hzpppm / 85.15) + # print(opts$lb_init) + } + } + + if (!is.null(opts$lb_reg)) { + if (opts$lb_reg == "lcm_compat") { + hzpppm <- acq_paras$ft * 1e-6 + desdt2 <- 0.4 + opts$lb_reg <- desdt2 / pi * sqrt(hzpppm / 85.15) + # print(opts$lb_reg) + } + } + #### 1 coarse freq align #### if (opts$pre_align) { max_init_shift_hz <- acq_paras$ft * 1e-6 * opts$max_pre_align_shift @@ -77,10 +96,17 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { # set phase, damping and shift limits for the pre-fit par <- c(0, opts$init_damping, init_shift) upper <- c(opts$max_phase * pi / 180, opts$max_damping, - init_shift + opts$max_shift * acq_paras$ft * 1e-6) + init_shift + opts$max_shift_pre * acq_paras$ft * 1e-6) lower <- c(-opts$max_phase * pi / 180, 0, - init_shift - opts$max_shift * acq_paras$ft * 1e-6) + init_shift - opts$max_shift_pre * acq_paras$ft * 1e-6) + + # apply lb_init to approximate fix stages + if (opts$lb_init_approx_fit) { + lb_init_approx_fit <- opts$lb_init + } else { + lb_init_approx_fit <- NULL + } #### 2 approx iter fit #### # 3 para pre-fit with flexable bl and no broad signals in basis @@ -103,14 +129,24 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { bl_basis_pre_fit <- rbind(sp_bas_pf$bl_bas, sp_bas_pf$deriv_mat * (lambda ^ 0.5)) + metab_basis_pre <- raw_metab_basis + metab_basis_pre_names <- basis$names + # remove broad signal components for the prefit if (opts$remove_lip_mm_prefit) { - broad_indices <- c(grep("^Lip", basis$names), grep("^MM", basis$names)) - metab_basis_pre <- raw_metab_basis[, -broad_indices] - } else { - metab_basis_pre <- raw_metab_basis + broad_indices <- c(grep("^Lip", metab_basis_pre_names), + grep("^MM", metab_basis_pre_names)) + metab_basis_pre <- metab_basis_pre[, -broad_indices] + metab_basis_pre_names <- metab_basis_pre_names[-broad_indices] } + # remove -ve CrCH2 signal for the prefit + # if (opts$remove_m_cr_ch2_prefit) { + # rm_index <- grep("^-CrCH2$", metab_basis_pre_names) + # metab_basis_pre <- metab_basis_pre[, -rm_index] + # metab_basis_pre_names <- metab_basis_pre_names[-rm_index] + # } + # Do a 1D search to improve the starting value of the phase estimate. # Note, this is not part of the published method, but was added in Jan 2021 # to avoid issues with the simplex "prefit" getting stuck in a local minima @@ -125,7 +161,8 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { bl_basis = bl_basis_pre_fit, t = t, f = f, inds = sp_bas_pf$inds, bl_comps = sp_bas_pf$bl_comps, sum_sq = TRUE, ret_full = FALSE, - ahat_calc_method = opts$ahat_calc_method) + ahat_calc_method = opts$ahat_calc_method, + lb_init = lb_init_approx_fit) # find the optimum value and update the starting value for the next step par[1] <- phi_zero[which.min(phase_res)] @@ -140,7 +177,8 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { ctrl, y, metab_basis_pre, bl_basis_pre_fit, t, f, sp_bas_pf$inds, sp_bas_pf$bl_comps, FALSE, FALSE, - opts$ahat_calc_method) + opts$ahat_calc_method, + lb_init_approx_fit) res <- prelim_res } else { @@ -155,7 +193,8 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { inds = sp_bas_pf$inds, bl_comps = sp_bas_pf$bl_comps, sum_sq = TRUE, ret_full = FALSE, - ahat_calc_method = opts$ahat_calc_method) + ahat_calc_method = opts$ahat_calc_method, + lb_init = lb_init_approx_fit) res <- prelim_res res$par <- prelim_res$solution @@ -213,7 +252,9 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { bl_basis = bl_basis_ab, t = t, f = f, inds = sp_bas_ab$inds, bl_comps = sp_bas_ab$bl_comps, sum_sq = FALSE, - ret_full = TRUE, opts$ahat_calc_method) + ret_full = TRUE, + ahat_calc_method = opts$ahat_calc_method, + lb_init = lb_init_approx_fit) resid_spec <- ab_res$resid @@ -284,11 +325,10 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { (lambda ^ 0.5)) # set phase, damping, shift, asym, basis_shift and basis_damping limits - asym_init <- 0 - par <- c(res$par[1], res$par[2], res$par[3], asym_init, rep(0, Nbasis), - rep(opts$lb_init, Nbasis)) + par <- c(res$par[1], res$par[2], res$par[3], asym_init, rep(0, Nbasis), + rep(opts$lb_init, Nbasis)) # find any signals with names starting with Lip or MM as they may have @@ -297,17 +337,37 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { max_basis_shifts <- rep(opts$max_basis_shift, Nbasis) * acq_paras$ft * 1e-6 - max_basis_shifts[broad_indices] <- opts$max_basis_shift_broad * - acq_paras$ft * 1e-6 + if (!is.null(opts$max_basis_shift_broad)) { + max_basis_shifts[broad_indices] <- opts$max_basis_shift_broad * + acq_paras$ft * 1e-6 + } max_basis_dampings <- rep(opts$max_basis_damping, Nbasis) - max_basis_dampings[broad_indices] <- opts$max_basis_damping_broad - upper <- c(opts$max_phase * pi / 180, opts$max_damping, - res$par[3] + opts$max_shift, opts$max_asym, - max_basis_shifts, max_basis_dampings) + if (!is.null(opts$max_basis_damping_broad)) { + max_basis_dampings[broad_indices] <- opts$max_basis_damping_broad + } + + # old method - faster but less accurate in rare cases + # upper <- c(opts$max_phase * pi / 180, opts$max_damping, + # res$par[3] + opts$max_shift_pre, opts$max_asym, + # max_basis_shifts, max_basis_dampings) + # + # lower <- c(-opts$max_phase * pi / 180, 0, + # res$par[3] - opts$max_shift_pre, -opts$max_asym, + # -max_basis_shifts, rep(0, Nbasis)) + + # this is to maintain compatibility with old behaviour + if (is.null(opts$max_shift_fine)) { + opts$max_shift_fine <- opts$max_shift_pre / (acq_paras$ft * 1e-6) + } - lower <- c(-opts$max_phase * pi / 180, 0, res$par[3] -opts$max_shift, + upper <- c(opts$max_phase * pi / 180, opts$max_damping, + res$par[3] + opts$max_shift_fine * acq_paras$ft * 1e-6, + opts$max_asym, max_basis_shifts, max_basis_dampings) + + lower <- c(-opts$max_phase * pi / 180, 0, + res$par[3] - opts$max_shift_fine * acq_paras$ft * 1e-6, -opts$max_asym, -max_basis_shifts, rep(0, Nbasis)) if (opts$phi1_optim) { @@ -336,6 +396,7 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { jac_fn <- abfit_full_num_jac } + # estimate the noise sd if needed if (is.def(opts$freq_reg) | is.def(opts$lb_reg)) { # apply best guess for phase parameter to data y_mod_noise_est <- y * exp(1i * res$par[1]) @@ -357,6 +418,14 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { if (is.def(opts$freq_reg)) { # convert ppm sd to Hz freq_reg_scaled <- noise_sd_est / (opts$freq_reg * acq_paras$ft * 1e-6) + freq_reg_scaled <- rep(freq_reg_scaled, Nbasis) + + if (is.def(opts$freq_reg_naa)) { + # different value for NAA and NAAG + naa_indices <- grep("^NAAG?$", basis$names) + freq_reg_scaled[naa_indices] <- noise_sd_est / + (opts$freq_reg_naa * acq_paras$ft * 1e-6) + } } else { freq_reg_scaled <- NULL } @@ -367,6 +436,31 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { lb_reg_scaled <- NULL } + # useful code to check the jacobian + # num_jac <- abfit_full_num_jac(par, y = y, raw_metab_basis = raw_metab_basis, + # bl_basis = bl_basis_full, t = t, f = f, + # inds = sp_bas_full$inds, + # bl_comps = sp_bas_full$bl_comps, + # sum_sq = FALSE, basis_paras = NULL, + # phi1_optim = opts$phi1_optim, + # ahat_calc_method = opts$ahat_calc_method, + # freq_reg = freq_reg_scaled, + # lb_reg = lb_reg_scaled, + # lb_init = opts$lb_init) + # anal_jac <- abfit_full_anal_jac(par, y = y, + # raw_metab_basis = raw_metab_basis, + # bl_basis = bl_basis_full, t = t, f = f, + # inds = sp_bas_full$inds, + # bl_comps = sp_bas_full$bl_comps, + # sum_sq = FALSE, basis_paras = NULL, + # phi1_optim = opts$phi1_optim, + # ahat_calc_method = opts$ahat_calc_method, + # freq_reg = freq_reg_scaled, + # lb_reg = lb_reg_scaled, + # lb_init = opts$lb_init) + # print(sum((num_jac - anal_jac) ^ 2)) + # image(Mod(anal_jac - num_jac)) + res <- minpack.lm::nls.lm(par, lower, upper, abfit_full_obj, jac_fn, ctrl, y, raw_metab_basis, bl_basis_full, t, f, sp_bas_full$inds, sp_bas_full$bl_comps, FALSE, @@ -448,8 +542,8 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { lb_vec_hz <- res$par[(5 + Nbasis):(4 + 2 * Nbasis)] } - freq_vec <- 2i * pi * freq_vec_hz - lb_vec <- lw2alpha(lb_vec_hz) + freq_vec <- 2i * pi * freq_vec_hz + lb_vec <- lw2alpha(lb_vec_hz) freq_lb_mat <- matrix(freq_vec - lb_vec, nrow = N, ncol = Nbasis, byrow = TRUE) @@ -496,9 +590,12 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { # if maxiters = 0 and maxiters_pre = 0 then we need to calculate the spectral # residual in the final phase if (is.na(diags$res.deviance)) { - diags$res.deviance = sum(res[1:length(sp_bas_final$inds)] ^ 2) + diags$res.deviance <- sum(res[1:length(sp_bas_final$inds)] ^ 2) } + # fit residual of spectral points - no penalty weightings + diags$spec_resid <- sum(res[1:length(sp_bas_final$inds)] ^ 2) + # number of data points used in the fit diags$fit_pts <- length(sp_bas_final$inds) @@ -608,13 +705,13 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #### crlb calc #### # calculate the analytical jacobian for the non-linear parameters - para_crlb <- abfit_full_anal_jac(final_par, y, raw_metab_basis, - bl_basis_final, t, f, sp_bas_final$inds, - sp_bas_final$bl_comps, FALSE, NULL, - opts$phi1_optim, opts$ahat_calc_method, - NULL, NULL, opts$lb_init) - # nb freq_reg, lb_reg not - # included in the crlb calc + para_crlb <- abfit_full_anal_jac(final_par, y, raw_metab_basis, + bl_basis_final, t, f, sp_bas_final$inds, + sp_bas_final$bl_comps, FALSE, NULL, + opts$phi1_optim, opts$ahat_calc_method, + NULL, NULL, opts$lb_init) + # nb freq_reg, lb_reg not + # included in the crlb calc bl_comps_crlb <- sp_bas_final$bl_comps para_crlb <- rbind(Re(para_crlb), matrix(0, nrow = bl_comps_crlb - 2, @@ -754,8 +851,10 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #' @param init_damping initial value of the Gaussian global damping parameter #' (Hz). Very poorly shimmed or high field data may benefit from a larger value. #' @param maxiters The maximum number of iterations to run for the detailed fit. -#' @param max_shift The maximum allowable shift to be applied in the -#' optimisation phase of fitting (ppm). +#' @param max_shift_pre The maximum allowable global shift to be applied in the +#' approximate (pre-fit) phases of analysis (ppm). +#' @param max_shift_fine The maximum allowable global shift to be applied in the +#' detailed fit phase of analysis (ppm). #' @param max_damping maximum permitted value of the global damping parameter #' (Hz). #' @param max_phase the maximum absolute permitted value of the global @@ -794,6 +893,7 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #' @param noise_region spectral region to estimate the noise level (ppm). #' @param optimal_smooth_criterion method to determine the optimal smoothness. #' @param aic_smoothing_factor modification factor for the AIC calculation. +#' Larger values result in less flexible baselines. #' @param anal_jac use a analytical approximation to the jacobian in the #' detailed fitting stage. #' @param pre_fit_ppm_left downfield frequency limit for the fitting range in @@ -805,15 +905,17 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #' @param max_dphi1 maximum allowable change from the initial frequency #' dependant phase term (ms). #' @param max_basis_shift_broad maximum allowable shift for broad signals in the -#' basis (ppm). Determined based on their name beginning with Lip or MM. +#' basis (ppm). Determined based on their name beginning with Lip or MM. The +#' default value is set to max_basis_shift. #' @param max_basis_damping_broad maximum allowable Lorentzian damping for broad #' signals in the basis (Hz). Determined based on their name beginning with Lip -#' or MM. +#' or MM. The default value is set to max_basis_damping. #' @param ahat_calc_method method to calculate the metabolite amplitudes. May be #' one of: "lh_pnnls" or "ls". #' @param prefit_phase_search perform a 1D search for the optimal phase in the #' prefit stage of the algorithm. #' @param freq_reg frequency shift parameter. +#' @param freq_reg_naa frequency shift parameter for NAA and NAAG. #' @param lb_reg individual line broadening parameter. #' @param output_all_paras include more fitting parameters in the fit table, #' e.g. individual shift and damping factors for each basis set element. @@ -824,9 +926,11 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #' @param optim_lw_only optimize the global line-broadening term only. #' @param optim_lw_only_limit limits for the line-breading term as a percentage #' of the starting value when optim_lw_only is TRUE. -#' @param lb_init initial Lorentzian line broadening value for the individual -#' basis signals. Setting to 0 will clash with the minimum allowable value -#' (eg hard constraint) during the detailed fit. +#' @param lb_init initial Lorentzian line broadening value (in Hz) for the +#' individual basis signals. Setting to 0 will clash with the minimum allowable +#' value (eg hard constraint) during the detailed fit. +#' @param lb_init_approx_fit apply lb_init to the basis during the approximate +#' iterative fit. #' @param zf_offset offset in number of data points from the end of the FID to #' zero-fill. Default is NULL and will automatically set this to 50 points when #' the FID distortion flag is set for the mrs_data. @@ -834,9 +938,9 @@ abfit <- function(y, acq_paras, basis, opts = NULL) { #' @examples #' opts <- abfit_opts(ppm_left = 4.2, noise_region = c(-1, -3)) #' @export -abfit_opts <- function(init_damping = 5, maxiters = 1024, max_shift = 0.078, - max_damping = 15, max_phase = 360, lambda = NULL, - ppm_left = 4, ppm_right = 0.2, zp = TRUE, +abfit_opts <- function(init_damping = 5, maxiters = 1024, max_shift_pre = 0.078, + max_shift_fine = NULL, max_damping = 15, max_phase = 360, + lambda = NULL, ppm_left = 4, ppm_right = 0.2, zp = TRUE, bl_ed_pppm = 2.0, auto_bl_flex = TRUE, bl_comps_pppm = 15, export_sp_fit = FALSE, max_asym = 0.25, max_basis_shift = 0.0078, @@ -851,26 +955,31 @@ abfit_opts <- function(init_damping = 5, maxiters = 1024, max_shift = 0.078, aic_smoothing_factor = 5, anal_jac = TRUE, pre_fit_ppm_left = 4, pre_fit_ppm_right = 1.8, phi1_optim = FALSE, phi1_init = 0, max_dphi1 = 0.2, - max_basis_shift_broad = 0.0078, - max_basis_damping_broad = 2, + max_basis_shift_broad = NULL, + max_basis_damping_broad = NULL, ahat_calc_method = "lh_pnnls", prefit_phase_search = TRUE, freq_reg = NULL, - lb_reg = NULL, output_all_paras = FALSE, + freq_reg_naa = NULL, lb_reg = NULL, + output_all_paras = FALSE, output_all_paras_raw = FALSE, input_paras_raw = NULL, optim_lw_only = FALSE, optim_lw_only_limit = 20, - lb_init = 0.001, zf_offset = NULL) { + lb_init = 0.001, lb_init_approx_fit = FALSE, + zf_offset = NULL) { list(init_damping = init_damping, maxiters = maxiters, - max_shift = max_shift, max_damping = max_damping, max_phase = max_phase, - lambda = lambda, ppm_left = ppm_left, ppm_right = ppm_right, zp = zp, - bl_ed_pppm = bl_ed_pppm, auto_bl_flex = auto_bl_flex, + max_shift_pre = max_shift_pre, max_shift_fine = max_shift_fine, + max_damping = max_damping, + max_phase = max_phase, lambda = lambda, ppm_left = ppm_left, + ppm_right = ppm_right, zp = zp, bl_ed_pppm = bl_ed_pppm, + auto_bl_flex = auto_bl_flex, bl_comps_pppm = bl_comps_pppm, export_sp_fit = export_sp_fit, max_asym = max_asym, max_basis_shift = max_basis_shift, max_basis_damping = max_basis_damping, maxiters_pre = maxiters_pre, algo_pre = algo_pre, min_bl_ed_pppm = min_bl_ed_pppm, max_bl_ed_pppm = max_bl_ed_pppm, auto_bl_flex_n = auto_bl_flex_n, pre_fit_bl_ed_pppm = pre_fit_bl_ed_pppm, - remove_lip_mm_prefit = remove_lip_mm_prefit, pre_align = pre_align, + remove_lip_mm_prefit = remove_lip_mm_prefit, + pre_align = pre_align, max_pre_align_shift = max_pre_align_shift, pre_align_ref_freqs = pre_align_ref_freqs, noise_region = noise_region, optimal_smooth_criterion = optimal_smooth_criterion, @@ -882,11 +991,12 @@ abfit_opts <- function(init_damping = 5, maxiters = 1024, max_shift = 0.078, max_basis_damping_broad = max_basis_damping_broad, ahat_calc_method = ahat_calc_method, prefit_phase_search = prefit_phase_search, freq_reg = freq_reg, - lb_reg = lb_reg, output_all_paras = output_all_paras, + freq_reg_naa = freq_reg_naa, lb_reg = lb_reg, + output_all_paras = output_all_paras, output_all_paras_raw = output_all_paras_raw, input_paras_raw = input_paras_raw, optim_lw_only = optim_lw_only, optim_lw_only_limit = optim_lw_only_limit, lb_init = lb_init, - zf_offset = zf_offset) + lb_init_approx_fit = lb_init_approx_fit, zf_offset = zf_offset) } #' Return a list of options for an ABfit analysis to maintain comparability with @@ -968,15 +1078,13 @@ abfit_full_obj <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, # signal estimate Y_hat <- Re(full_bas) %*% ahat + res <- Re(Y[inds]) - Y_hat[1:length(inds)] + if (!is.null(freq_reg)) res <- c(res, freq_reg * freq_shifts) + if (!is.null(lb_reg)) res <- c(res, lb_reg * (lb_vec / pi - lb_init)) + if (sum_sq) { - return(sum((Re(Y[inds]) - Y_hat[1:length(inds)]) ^ 2)) + return(sum(res ^ 2)) } else { - res <- Re(Y[inds]) - Y_hat[1:length(inds)] - - if (!is.null(freq_reg)) res <- c(res, freq_reg * freq_shifts) - - if (!is.null(lb_reg)) res <- c(res, lb_reg * (lb_vec / pi - lb_init)) - return(res) } } @@ -1189,8 +1297,8 @@ abfit_full_anal_jac <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, freq_jac <- -Re(freq_jac[inds,,drop = FALSE]) # multiply by -a * t * pi for basis lw adjustment - lb_vec <- ahat[(bl_comps + 1):length(ahat)] - lb_mat <- matrix(lb_vec, nrow = N, ncol = Nbasis, byrow = TRUE) + lb_vec <- ahat[(bl_comps + 1):length(ahat)] + lb_mat <- matrix(lb_vec, nrow = N, ncol = Nbasis, byrow = TRUE) lb_jac <- -raw_metab_basis_mod * t_mat * lb_mat * pi # back to fd @@ -1199,19 +1307,45 @@ abfit_full_anal_jac <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, # cut out fitting region lb_jac <- -Re(lb_jac[inds,,drop = FALSE]) - # if (is.null(freq_reg)) { + # if (!is.null(freq_reg)) { + # y_hat <- drop(raw_metab_basis_mod %*% ahat[(bl_comps + 1):length(ahat)]) + # y_hat <- y_hat * exp(1i * par[1]) + # y_hat <- y_hat * exp(2i * pi * t * par[3]) + # bl <- drop(bl_basis %*% ahat[1:bl_comps])[1:length(inds)] + # global_paras_jac[, 3] <- c(bl + Re(ft_shift(2i * pi * t * y_hat)[inds]), rep(0, 2*Nbasis)) + # global_paras_jac[, 1] <- c(bl + Re(ft_shift(1i * y_hat)[inds]), rep(0, 2*Nbasis)) + # # global_paras_jac[, 1] <- c(Re(ft_shift(1i * y)[inds]), rep(0, 2*Nbasis)) + # # global_paras_jac[, 3] <- c(Re(ft_shift(2i * pi * t * y)[inds]), rep(0, 2*Nbasis)) + # } + + if (!is.null(freq_reg) | !is.null(lb_reg)) { + if (!is.null(lb_reg)) lb_reg_jac <- lb_reg + if (!is.null(freq_reg)) freq_reg_jac <- freq_reg + if (!is.null(freq_reg)) { + freq_reg_jac_mat <- matrix(0, ncol = Nbasis, nrow = Nbasis) + diag(freq_reg_jac_mat) <- freq_reg_jac + } + if (!is.null(lb_reg)) { + lb_reg_jac_mat <- matrix(0, ncol = Nbasis, nrow = Nbasis) + diag(lb_reg_jac_mat) <- lb_reg_jac + } + zero_jac_mat <- matrix(0, ncol = Nbasis, nrow = Nbasis) + } + if (is.null(freq_reg) & is.null(lb_reg)) { ret_mat <- cbind(global_paras_jac, freq_jac, lb_jac) - } else if (xor(is.null(freq_reg), is.null(lb_reg))) { + } else if (!is.null(freq_reg) & is.null(lb_reg)) { + ret_mat <- cbind(global_paras_jac, + rbind(freq_jac, freq_reg_jac_mat), + rbind(lb_jac, zero_jac_mat)) + } else if (is.null(freq_reg) & !is.null(lb_reg)) { ret_mat <- cbind(global_paras_jac, - rbind(freq_jac, matrix(0, ncol = Nbasis, nrow = Nbasis)), - rbind(lb_jac, matrix(0, ncol = Nbasis, nrow = Nbasis))) + rbind(freq_jac, zero_jac_mat), + rbind(lb_jac, lb_reg_jac_mat)) } else { ret_mat <- cbind(global_paras_jac, - rbind(freq_jac, matrix(0, ncol = Nbasis, - nrow = 2 * Nbasis)), - rbind(lb_jac, matrix(0, ncol = Nbasis, - nrow = 2 * Nbasis))) + rbind(freq_jac, freq_reg_jac_mat, zero_jac_mat), + rbind(lb_jac, zero_jac_mat, lb_reg_jac_mat)) } return(ret_mat) @@ -1219,7 +1353,8 @@ abfit_full_anal_jac <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, # objective function for 3 parameter spline fitting method abfit_3p_obj <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, - bl_comps, sum_sq, ret_full, ahat_calc_method) { + bl_comps, sum_sq, ret_full, ahat_calc_method, + lb_init) { # apply phase parameter to data y <- y * exp(1i * par[1]) @@ -1230,6 +1365,10 @@ abfit_3p_obj <- function(par, y, raw_metab_basis, bl_basis, t, f, inds, # apply damping parameter to basis damp_vec <- exp(-t * t * lw2beta(par[2])) + + # apply lb_init parameter to basis if not NULL + if (!is.null(lb_init)) damp_vec <- damp_vec * exp(-t * lw2alpha(lb_init)) + damp_mat <- matrix(damp_vec, nrow = nrow(raw_metab_basis), ncol = ncol(raw_metab_basis), byrow = F) raw_metab_basis <- raw_metab_basis * damp_mat diff --git a/R/basis_set.R b/R/basis_set.R index c2286019..b91811fa 100644 --- a/R/basis_set.R +++ b/R/basis_set.R @@ -246,11 +246,13 @@ write_basis <- function(basis, basis_file, fwhmba = 0.1) { #' @param amps a vector of scaling factors to apply to each basis element. #' @param shifts a vector of frequency shifts (in ppm) to apply to each basis #' element. +#' @param lbs a vector of Lorentzian line broadening terms (in Hz) to apply to +#' each basis element. #' @return an mrs_data object with basis signals spread across the dynamic #' dimension or summed. #' @export basis2mrs_data <- function(basis, sum_elements = FALSE, amps = NULL, - shifts = NULL) { + shifts = NULL, lbs = NULL) { # TODO nuc is just the default for now res <- mat2mrs_data(t(basis$data), fs = basis$fs, ft = basis$ft, @@ -277,9 +279,17 @@ basis2mrs_data <- function(basis, sum_elements = FALSE, amps = NULL, res <- shift(res, shifts) } + # Lorentzian line broaden basis elements + if (!is.null(lbs)) { + if (n_sigs != length(lbs)) { + stop(paste("Error, length of amps does not match the number of basis elements :", dim(basis$data)[2])) + } + res <- lb(res, lbs, 0) + } + if (sum_elements) res <- sum_dyns(res) - res + return(res) } #' Convert a basis object to a dynamic mrs_data object. @@ -478,3 +488,86 @@ make_basis_from_raw <- function(dir_path, ft, fs, ref) { basis <- mrs_data2basis(mrs_data_dynamic, names = names) return(basis) } + +#' Estimate the CRLB for each element in a basis set. +#' @param basis basis_set object. +#' @param xlim spectral range to use in ppm. +#' @param zf zero-fill the basis set. +#' @param sd standard deviation of the noise. +#' @param bl_comp_pppm number spline baseline components to append per-ppm. +#' @return a vector of predicted errors. +#' @export +calc_basis_crlbs <- function(basis, xlim = c(4, 0.2), zf = TRUE, sd = 1, + bl_comp_pppm = NULL) { + + basis_mrs <- basis2mrs_data(basis) + + if (zf) basis_mrs <- zf(basis_mrs) + + if (is.null(xlim)) { + ppm_sc <- ppm(basis_mrs) + xlim <- c(ppm_sc[1], ppm_sc[length(ppm_sc)]) + basis_mrs <- td2fd(basis_mrs) + } else { + basis_mrs <- crop_spec(basis_mrs, xlim = xlim) + } + + if (is.null(bl_comp_pppm)) { + D <- t(Re(mrs_data2mat(basis_mrs))) + } else { + D <- t(Re(mrs_data2mat(basis_mrs))) + comps <- diff(sort(xlim)) * bl_comp_pppm + sp_basis <- bbase(dim(D)[1], round(comps)) + D <- cbind(D, sp_basis) + } + + F <- (t(D) %*% D) / (sd ^ 2) + + F_inv <- pracma::pinv(F) + + errors <- diag(F_inv) ^ 0.5 + + if (is.null(bl_comp_pppm)) { + names(errors) <- basis$names + } else { + spline_names <- paste("SPLINE", as.character(1:dim(sp_basis)[2]), + sep = "_") + + names(errors) <- c(basis$names, spline_names) + } + + return(errors) +} + +#' Estimate the correlation matrix for a basis set. +#' @param basis basis_set object. +#' @param xlim spectral range to use in ppm. +#' @param zf zero-fill the basis set. +#' @return correlation matrix. +#' @export +calc_basis_corr_mat <- function(basis, xlim = c(4, 0.2), zf = TRUE) { + + basis_mrs <- basis2mrs_data(basis) + + if (zf) basis_mrs <- zf(basis_mrs) + + basis_mrs <- crop_spec(basis_mrs, xlim = xlim) + + D <- t(Re(mrs_data2mat(basis_mrs))) + + F <- (t(D) %*% D) + F_inv <- pracma::pinv(F) + + corr_mat <- matrix(nrow = nrow(F_inv), ncol = ncol(F_inv)) + + for (x in 1:nrow(corr_mat)) { + for (y in 1:ncol(corr_mat)) { + corr_mat[x, y] <- F_inv[x, y] / ((F_inv[x, x] * F_inv[y, y]) ^ 0.5) + } + } + + rownames(corr_mat) <- basis$names + colnames(corr_mat) <- basis$names + + return(corr_mat) +} \ No newline at end of file diff --git a/R/fitting.R b/R/fitting.R index bd03df9f..a08941c2 100644 --- a/R/fitting.R +++ b/R/fitting.R @@ -31,6 +31,8 @@ #' @param w_ref water reference data for concentration scaling (optional). #' @param opts options to pass to the analysis method. #' @param parallel perform analyses in parallel (TRUE or FALSE). +#' @param cl a parallel socket cluster required to run analyses in parallel. +#' Eg, cl <- parallel::makeCluster(4). #' @param time measure the time taken for the analysis to complete #' (TRUE or FALSE). #' @param progress option is passed to plyr::alply function to display a @@ -49,13 +51,12 @@ #' } #' @export fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL, - opts = NULL, parallel = FALSE, time = TRUE, + opts = NULL, parallel = FALSE, cl = NULL, time = TRUE, progress = "text", extra = NULL) { if (inherits(metab, "list")) { if (!is.null(w_ref)) { - # if (class(w_ref) != "list") stop("w_ref is not a list but metab is") if (!inherits(w_ref, "list")) stop("w_ref is not a list but metab is") if (length(metab) != length(w_ref)) { @@ -137,8 +138,7 @@ fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL, acq_paras <- get_acq_paras(metab) - plyr <- TRUE - if (plyr) { + if (!parallel) { result_list <- plyr::alply(metab$data, c(2, 3, 4, 5, 6), abfit, acq_paras, basis, opts, .parallel = parallel, @@ -146,14 +146,23 @@ fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL, .packages = "spant"), .progress = progress, .inform = FALSE) } else { - result_list <- apply(metab$data, c(2, 3, 4, 5, 6), abfit, acq_paras, - basis, opts) + if (is.null(cl)) stop("pass cl argument to fit_mrs for parallel analyses") + result_list <- parallel::parApply(cl, metab$data, c(2, 3, 4, 5, 6), abfit, + acq_paras, basis, opts) labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE) result_list <- result_list[,,,,] attr(result_list, "split_labels") <- labs names(result_list) <- seq_len(nrow(labs)) } + # method using base apply + # result_list <- apply(metab$data, c(2, 3, 4, 5, 6), abfit, acq_paras, + # basis, opts) + # labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE) + # result_list <- result_list[,,,,] + # attr(result_list, "split_labels") <- labs + # names(result_list) <- seq_len(nrow(labs)) + } else if (METHOD == "VARPRO") { # read basis into memory if a file if (is.character(basis)) { @@ -266,12 +275,30 @@ fit_mrs <- function(metab, basis = NULL, method = 'ABFIT', w_ref = NULL, temp_mrs$data = temp_mrs$data[1, 1, 1, 1, 1, 1,] dim(temp_mrs$data) <- c(1, 1, 1, 1, 1, 1, length(temp_mrs$data)) - result_list <- plyr::alply(metab$data, c(2,3,4,5,6), lcmodel_fit, - temp_mrs, basis_file, opts, - .parallel = parallel, - .paropts = list(.inorder = TRUE, - .packages = "spant"), - .progress = progress, .inform = FALSE) + if (!parallel) { + result_list <- plyr::alply(metab$data, c(2, 3, 4, 5, 6), lcmodel_fit, + temp_mrs, basis_file, opts, + .parallel = parallel, + .paropts = list(.inorder = TRUE, + .packages = "spant"), + .progress = progress, .inform = FALSE) + } else { + if (is.null(cl)) stop("pass cl argument to fit_mrs for parallel analyses") + result_list <- parallel::parApply(cl, metab$data, c(2, 3, 4, 5, 6), + lcmodel_fit, temp_mrs, basis_file, opts) + labs <- which(array(TRUE, dim(result_list)), arr.ind = TRUE) + result_list <- result_list[,,,,] + attr(result_list, "split_labels") <- labs + names(result_list) <- seq_len(nrow(labs)) + } + + # result_list <- plyr::alply(metab$data, c(2,3,4,5,6), lcmodel_fit, + # temp_mrs, basis_file, opts, + # .parallel = parallel, + # .paropts = list(.inorder = TRUE, + # .packages = "spant"), + # .progress = progress, .inform = FALSE) + } else if (exists(method)) { message(paste("Using external fit method :", method)) diff --git a/R/mrs_read_rda.R b/R/mrs_read_rda.R index 0a01d2e1..255e2aff 100644 --- a/R/mrs_read_rda.R +++ b/R/mrs_read_rda.R @@ -25,6 +25,9 @@ read_rda <- function(fname, extra) { col_ori <- rep(NA, 3) pos_vec <- rep(NA, 3) + # a fix for when commas are used as decimal points + txt$V2 <- gsub(",", ".", txt$V2) + N <- as.integer(txt$V2[which(txt$V1 == "VectorSize")]) fs <- 1e6 / as.numeric(txt$V2[which(txt$V1 == "DwellTime")]) ft <- 1e6 * as.numeric(txt$V2[which(txt$V1 == "MRFrequency")]) diff --git a/docs/404.html b/docs/404.html index efcfa260..8ea731c0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -25,7 +25,7 @@ - +
@@ -51,7 +55,7 @@
  • @@ -94,7 +98,7 @@
    • - +
    @@ -122,16 +126,20 @@

    Page not found (404)

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index 12975bf3..39c50594 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -111,15 +115,19 @@

    Pull requests +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    - - + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index c024836a..9b720e04 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -762,15 +766,19 @@

    License

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/articles/abfit-baseline-opts.html b/docs/articles/abfit-baseline-opts.html index 9da9b524..224cba62 100644 --- a/docs/articles/abfit-baseline-opts.html +++ b/docs/articles/abfit-baseline-opts.html @@ -18,15 +18,13 @@ - - - +
    @@ -52,7 +54,7 @@
  • @@ -95,7 +97,7 @@
    • - +
    @@ -222,9 +224,7 @@

    Custom analyses - -

    +
    @@ -237,16 +237,20 @@

    Custom analyses

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel - - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index cbcb747e..2b1f1a37 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -95,15 +99,19 @@

    All vignettes

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/articles/spant-basis-simulation.html b/docs/articles/spant-basis-simulation.html index e3bc5346..9fc1bdd8 100644 --- a/docs/articles/spant-basis-simulation.html +++ b/docs/articles/spant-basis-simulation.html @@ -18,15 +18,13 @@ - - - +
    @@ -52,7 +54,7 @@
  • @@ -95,7 +97,7 @@
    • - +
    @@ -174,9 +176,7 @@

    Basis simulation - -

    +
    @@ -189,16 +189,20 @@

    Basis simulation

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel - - + + diff --git a/docs/articles/spant-intro.html b/docs/articles/spant-intro.html index f91bcb30..938c488e 100644 --- a/docs/articles/spant-intro.html +++ b/docs/articles/spant-intro.html @@ -18,15 +18,13 @@ - - - +
    @@ -52,7 +54,7 @@
  • @@ -95,7 +97,7 @@
    • - +
    @@ -195,6 +197,7 @@

    Basis simulation 
     fit_res$res_tab
+<<<<<<< HEAD
 #>   X Y Z Dynamic Coil X.CrCH2          Ala          Asp          Cr         GABA
 #> 1 1 1 1       1    1       0 8.133932e-06 3.547065e-05 4.02672e-05 1.697281e-05
 #>            Glc          Gln          GSH          Glu          GPC          Ins
@@ -227,23 +230,74 @@ 
    Basis simulation#> 1            FALSE 7.754368e-05     497       3.8 62.71687 51.3328 1.492722
 #>      tNAA_lw     tCr_lw    tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
 #> 1 0.04562445 0.05189506 0.05438237      -8.900349          -8.944159
+=======
+#>   X Y Z Dynamic Coil X.CrCH2          Ala          Asp           Cr
+#> 1 1 1 1       1    1       0 8.133802e-06 3.547064e-05 4.026719e-05
+#>           GABA          Glc          Gln          GSH          Glu          GPC
+#> 1 1.697276e-05 2.446591e-06 3.036118e-06 2.228048e-05 6.503219e-05 1.606706e-05
+#>            Ins          Lac        Lip09       Lip13a Lip13b Lip20         MM09
+#> 1 5.906155e-05 5.802244e-06 2.387705e-05 2.670583e-06      0     0 9.630767e-06
+#>           MM12         MM14         MM17         MM20          NAA        NAAG
+#> 1 6.511376e-06 2.603852e-05 2.238403e-05 9.203742e-05 6.011109e-05 1.53653e-05
+#>   PCh          PCr         sIns Tau         tNAA         tCr         tCho
+#> 1   0 2.101921e-05 6.504096e-06   0 7.547639e-05 6.12864e-05 1.606706e-05
+#>           Glx        tLM09        tLM13        tLM20   X.CrCH2.sd       Ala.sd
+#> 1 6.80683e-05 3.350782e-05 3.522048e-05 9.203742e-05 2.386862e-06 4.343934e-06
+#>         Asp.sd        Cr.sd      GABA.sd       Glc.sd       Gln.sd       GSH.sd
+#> 1 9.235327e-06 3.689004e-06 4.574399e-06 4.421682e-06 5.083001e-06 2.020427e-06
+#>         Glu.sd       GPC.sd       Ins.sd       Lac.sd     Lip09.sd    Lip13a.sd
+#> 1 5.082976e-06 2.602652e-06 2.093225e-06 5.301706e-06 4.119256e-06 1.328304e-05
+#>      Lip13b.sd     Lip20.sd      MM09.sd      MM12.sd      MM14.sd      MM17.sd
+#> 1 6.474468e-06 7.510908e-06 3.827554e-06 4.594028e-06 7.223426e-06 3.811301e-06
+#>        MM20.sd       NAA.sd      NAAG.sd       PCh.sd       PCr.sd      sIns.sd
+#> 1 8.595853e-06 1.017711e-06 1.208984e-06 2.236874e-06 3.084599e-06 7.240069e-07
+#>         Tau.sd      tNAA.sd       tCr.sd      tCho.sd      Glx.sd     tLM09.sd
+#> 1 3.759957e-06 7.031382e-07 5.890482e-07 2.110662e-07 3.16966e-06 1.006794e-06
+#>       tLM13.sd     tLM20.sd    phase       lw       shift      asym
+#> 1 1.573147e-06 3.016809e-06 11.10963 5.023682 -0.00376505 0.1771067
+#>   res.deviance res.niter res.info
+#> 1 7.307671e-05        28        2
+#>                                                        res.message bl_ed_pppm
+#> 1 Relative error between `par' and the solution is at most `ptol'.   2.364083
+#>   max_bl_flex_used    full_res   spec_resid fit_pts ppm_range      SNR      SRR
+#> 1            FALSE 7.75437e-05 7.307671e-05     497       3.8 62.71686 51.33279
+#>        FQN    tNAA_lw     tCr_lw    tCho_lw auto_bl_crit_7 auto_bl_crit_5.901
+#> 1 1.492722 0.04562445 0.05189506 0.05438237      -8.900349          -8.944159
+>>>>>>> devel
 #>   auto_bl_crit_4.942 auto_bl_crit_4.12 auto_bl_crit_3.425 auto_bl_crit_2.844
 #> 1          -8.977355         -9.000064          -9.013367           -9.02055
 #>   auto_bl_crit_2.364 auto_bl_crit_1.969 auto_bl_crit_1.647 auto_bl_crit_1.384
 #> 1          -9.024177          -9.023462          -9.009854          -8.958654
 #>   auto_bl_crit_1.17 auto_bl_crit_0.997 auto_bl_crit_0.856 auto_bl_crit_0.743
+<<<<<<< HEAD
 #> 1         -8.844271          -8.690744          -8.562631          -8.485471
 #>   auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
 #> 1          -8.447136          -8.430174          -8.423053         -8.420086
+=======
+#> 1         -8.844271          -8.690744           -8.56263          -8.485471
+#>   auto_bl_crit_0.654 auto_bl_crit_0.593 auto_bl_crit_0.558 auto_bl_crit_0.54
+#> 1          -8.447135          -8.430173          -8.423052         -8.420085
+>>>>>>> devel
 #>   auto_bl_crit_0.532 auto_bl_crit_0.529
 #> 1          -8.418839          -8.418312

    Note that signal names appended with “.sd” are the CRLB estimates for the uncertainty (standard deviation) in the metabolite quantity estimate. e.g. to calculate the percentage s.d. for tNAA:

    +<<<<<<< HEAD 
     fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
 #> [1] 0.9316001

    Spectral SNR:

    +======= +
    +fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
+#> [1] 0.9316002
    +

    Spectral SNR:

    +
    +fit_res$res_tab$SNR
+#> [1] 62.71686
    +

    Linewidth of the tNAA resonance in PPM:

    +>>>>>>> devel 
     fit_res$res_tab$SNR
 #> [1] 62.71687
    @@ -265,6 +319,7 @@

    Ratios to total-creatineprint(t(amps)) #> [,1] #> X.CrCH2 0.00000000 +<<<<<<< HEAD #> Ala 0.13272001 #> Asp 0.57876874 #> Cr 0.65703313 @@ -298,6 +353,41 @@

    Ratios to total-creatine#> tLM09 0.54674163 #> tLM13 0.57468844 #> tLM20 1.50175937

    +======= +#> Ala 0.13271789 +#> Asp 0.57876852 +#> Cr 0.65703306 +#> GABA 0.27694176 +#> Glc 0.03992062 +#> Gln 0.04953983 +#> GSH 0.36354693 +#> Glu 1.06111932 +#> GPC 0.26216353 +#> Ins 0.96369742 +#> Lac 0.09467424 +#> Lip09 0.38959787 +#> Lip13a 0.04357545 +#> Lip13b 0.00000000 +#> Lip20 0.00000000 +#> MM09 0.15714362 +#> MM12 0.10624504 +#> MM14 0.42486612 +#> MM17 0.36523650 +#> MM20 1.50175914 +#> NAA 0.98082262 +#> NAAG 0.25071302 +#> PCh 0.00000000 +#> PCr 0.34296694 +#> sIns 0.10612625 +#> Tau 0.00000000 +#> tNAA 1.23153565 +#> tCr 1.00000000 +#> tCho 0.26216353 +#> Glx 1.11065914 +#> tLM09 0.54674149 +#> tLM13 0.57468661 +#> tLM20 1.50175914
    +>>>>>>> devel

    Water reference scaling, AKA “absolute-quantification” @@ -327,7 +417,11 @@

    Water reference sca 
     fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
 fit_res_molar$res_tab$tNAA
+<<<<<<< HEAD
 #> [1] 6.826336
    +======= +#> [1] 6.826335

    +>>>>>>> devel

    Note, while “absolute” units are attractive, a large number of assumptions about metabolite and water relaxation rates are necessary to arrive at these mM estimates. If you’re not confident at being able to @@ -340,9 +434,7 @@

    Water reference sca + @@ -355,16 +447,20 @@

    Water reference sca

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png index 11e79ce5..cceccee8 100644 Binary files a/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/spant-intro_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/spant-metabolite-simulation.html b/docs/articles/spant-metabolite-simulation.html index 564fa989..0b599b16 100644 --- a/docs/articles/spant-metabolite-simulation.html +++ b/docs/articles/spant-metabolite-simulation.html @@ -18,15 +18,13 @@ - - - +
    @@ -52,7 +54,7 @@
  • @@ -95,7 +97,7 @@
    • - +
    @@ -290,9 +292,7 @@

    Custom molecules - -

    +
    @@ -305,16 +305,20 @@

    Custom molecules

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel - - + + diff --git a/docs/articles/spant-preprocessing.html b/docs/articles/spant-preprocessing.html index 9544cf71..2a477a86 100644 --- a/docs/articles/spant-preprocessing.html +++ b/docs/articles/spant-preprocessing.html @@ -18,15 +18,13 @@ - - - +
    @@ -52,7 +54,7 @@
  • @@ -95,7 +97,7 @@
    • - +
    @@ -164,9 +166,7 @@

    Reading raw data and plotting - -

    +
    @@ -179,16 +179,20 @@

    Reading raw data and plotting

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel - - + + diff --git a/docs/authors.html b/docs/authors.html index 34e6b241..a7fe7801 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -72,17 +76,17 @@

    Authors and Citation

    - +

    • Martin Wilson. Maintainer, author.

    • -

      Yong Wang. Contributor. +

      Yong Wang. Contributor.

    • -

      John Muschelli. Contributor. +

      John Muschelli. Contributor.

    @@ -140,15 +144,19 @@

    Citation

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/index.html b/docs/index.html index c58968f6..1cf2cb48 100644 --- a/docs/index.html +++ b/docs/index.html @@ -26,7 +26,7 @@ - +
    @@ -52,7 +56,7 @@
  • @@ -95,7 +99,7 @@
    • - +
    @@ -265,16 +269,20 @@

    Developers

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 45dd152f..63380a9d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -73,7 +77,17 @@

    Changelog

    +<<<<<<< HEAD

    spant 2.22.0

    +======= +

    spant 2.23.0

    +
    • abfit options for lipid and MM maximum broadening and maximum frequency shift now default to be the same as the metabolite values unless explicitly changed.
      • +
    • Added function to calculate the correlation matrix from a basis_set.
      • +
    • Fix for RDA files where a comma is sometimes used as a decimal point.
      • +
    +
    +

    spant 2.22.02024-07-11

    +>>>>>>> devel
    • Added find_bids_mrs and mrs_data2bids helper functions.
    • Improved handling of CMRR semi-LASER SVS water reference scans.
    • Added functions for GLS coil combination.
      • @@ -590,15 +604,19 @@

      spant 0.1.02

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 8099ddc1..9f9c389c 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,9 @@ pandoc: 3.1.11 +<<<<<<< HEAD pkgdown: 2.0.9 +======= +pkgdown: 2.1.0 +>>>>>>> devel pkgdown_sha: ~ articles: abfit-baseline-opts: abfit-baseline-opts.html @@ -7,8 +11,11 @@ articles: spant-intro: spant-intro.html spant-metabolite-simulation: spant-metabolite-simulation.html spant-preprocessing: spant-preprocessing.html +<<<<<<< HEAD last_built: 2024-07-11T11:18Z +======= +last_built: 2024-08-27T13:06Z +>>>>>>> devel urls: reference: https://martin3141.github.io/spant/reference article: https://martin3141.github.io/spant/articles - diff --git a/docs/reference/Arg.mrs_data.html b/docs/reference/Arg.mrs_data.html index 4eba752f..21cf298b 100644 --- a/docs/reference/Arg.mrs_data.html +++ b/docs/reference/Arg.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,21 @@

    Apply Arg operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Arg(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Arg operator.

    +

    MRS data following Arg operator.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Conj.mrs_data.html b/docs/reference/Conj.mrs_data.html index 10ea0ef1..c5ff53bb 100644 --- a/docs/reference/Conj.mrs_data.html +++ b/docs/reference/Conj.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,21 @@

    Apply Conj operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Conj(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Conj operator.

    +

    MRS data following Conj operator.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Im.mrs_data.html b/docs/reference/Im.mrs_data.html index e0e26588..efda9d95 100644 --- a/docs/reference/Im.mrs_data.html +++ b/docs/reference/Im.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,21 @@

    Apply Im operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Im(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Im operator.

    +

    MRS data following Im operator.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Imzap.html b/docs/reference/Imzap.html index cf1b088d..d24f6216 100644 --- a/docs/reference/Imzap.html +++ b/docs/reference/Imzap.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,11 +89,13 @@

    Complex rounding function taken from complexplus package to reduce the numbe

    Arguments

    -
    x
    + + +
    x

    a scalar or vector, real or complex.

    -
    tol
    +
    tol

    a tolerance, 10^-6 by default. Prevents possible numerical problems. Can be set to 0 if desired.

    @@ -107,15 +113,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    - - + + diff --git a/docs/reference/Mod.mrs_data.html b/docs/reference/Mod.mrs_data.html index 4c762948..10f3097a 100644 --- a/docs/reference/Mod.mrs_data.html +++ b/docs/reference/Mod.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,21 @@

    Apply Mod operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Mod(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Mod operator.

    +

    MRS data following Mod operator.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Ncoils.html b/docs/reference/Ncoils.html index 09d22662..8b9e62a0 100644 --- a/docs/reference/Ncoils.html +++ b/docs/reference/Ncoils.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of coil elements in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Ndyns.html b/docs/reference/Ndyns.html index 26ca34a7..5cbcc56c 100644 --- a/docs/reference/Ndyns.html +++ b/docs/reference/Ndyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of dynamic scans in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Npts.html b/docs/reference/Npts.html index 7e8af89e..e6a89329 100644 --- a/docs/reference/Npts.html +++ b/docs/reference/Npts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the number of data points in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    number of data points.

    +

    number of data points.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Nspec.html b/docs/reference/Nspec.html index ff6c4dcd..51bdc1c0 100644 --- a/docs/reference/Nspec.html +++ b/docs/reference/Nspec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of spectra in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Ntrans.html b/docs/reference/Ntrans.html index 32ae3ad6..2493e772 100644 --- a/docs/reference/Ntrans.html +++ b/docs/reference/Ntrans.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of acquired transients for an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Nx.html b/docs/reference/Nx.html index 461192b3..4c619b3e 100644 --- a/docs/reference/Nx.html +++ b/docs/reference/Nx.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of x locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Ny.html b/docs/reference/Ny.html index 530efde4..dd95a54b 100644 --- a/docs/reference/Ny.html +++ b/docs/reference/Ny.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of y locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Nz.html b/docs/reference/Nz.html index 15295f98..6b13ee79 100644 --- a/docs/reference/Nz.html +++ b/docs/reference/Nz.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Return the total number of z locations in an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/Re.mrs_data.html b/docs/reference/Re.mrs_data.html index 37608c36..792e2b27 100644 --- a/docs/reference/Re.mrs_data.html +++ b/docs/reference/Re.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,21 @@

    Apply Re operator to an MRS dataset.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 Re(z)

    Arguments

    -
    z
    + + +
    z

    MRS data.

    Value

    - - -

    MRS data following Re operator.

    +

    MRS data following Re operator.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/abfit_opts.html b/docs/reference/abfit_opts.html index 5524db43..91e4014c 100644 --- a/docs/reference/abfit_opts.html +++ b/docs/reference/abfit_opts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -81,7 +85,8 @@

    Return a list of options for an ABfit analysis.

    abfit_opts(
   init_damping = 5,
   maxiters = 1024,
-  max_shift = 0.078,
+  max_shift_pre = 0.078,
+  max_shift_fine = NULL,
   max_damping = 15,
   max_phase = 360,
   lambda = NULL,
@@ -114,11 +119,12 @@ 
    Return a list of options for an ABfit analysis.
    
   phi1_optim = FALSE,
   phi1_init = 0,
   max_dphi1 = 0.2,
-  max_basis_shift_broad = 0.0078,
-  max_basis_damping_broad = 2,
+  max_basis_shift_broad = NULL,
+  max_basis_damping_broad = NULL,
   ahat_calc_method = "lh_pnnls",
   prefit_phase_search = TRUE,
   freq_reg = NULL,
+  freq_reg_naa = NULL,
   lb_reg = NULL,
   output_all_paras = FALSE,
   output_all_paras_raw = FALSE,
@@ -126,227 +132,255 @@ 
    Return a list of options for an ABfit analysis.
    
   optim_lw_only = FALSE,
   optim_lw_only_limit = 20,
   lb_init = 0.001,
+<<<<<<< HEAD
+=======
+  lb_init_approx_fit = FALSE,
+>>>>>>> devel
   zf_offset = NULL
 )

    Arguments

    -
    init_damping
    + + +
    init_damping

    initial value of the Gaussian global damping parameter (Hz). Very poorly shimmed or high field data may benefit from a larger value.

    -
    maxiters
    +
    maxiters

    The maximum number of iterations to run for the detailed fit.

    -
    max_shift
    -

    The maximum allowable shift to be applied in the -optimisation phase of fitting (ppm).

    +
    max_shift_pre
    +

    The maximum allowable global shift to be applied in the +approximate (pre-fit) phases of analysis (ppm).

    + + +
    max_shift_fine
    +

    The maximum allowable global shift to be applied in the +detailed fit phase of analysis (ppm).

    -
    max_damping
    +
    max_damping

    maximum permitted value of the global damping parameter (Hz).

    -
    max_phase
    +
    max_phase

    the maximum absolute permitted value of the global zero-order phase term (degrees). Note, the prefit_phase_search option is not constrained by this term.

    -
    lambda
    +
    lambda

    manually set the the baseline smoothness parameter.

    -
    ppm_left
    +
    ppm_left

    downfield frequency limit for the fitting range (ppm).

    -
    ppm_right
    +
    ppm_right

    upfield frequency limit for the fitting range (ppm).

    -
    zp
    +
    zp

    zero pad the data to twice the original length before fitting.

    -
    bl_ed_pppm
    +
    bl_ed_pppm

    manually set the the baseline smoothness parameter (ED per ppm).

    -
    auto_bl_flex
    +
    auto_bl_flex

    automatically determine the level of baseline smoothness.

    -
    bl_comps_pppm
    +
    bl_comps_pppm

    spline basis density (signals per ppm).

    -
    export_sp_fit
    +
    export_sp_fit

    add the fitted spline functions to the fit result.

    -
    max_asym
    +
    max_asym

    maximum allowable value of the asymmetry parameter.

    -
    max_basis_shift
    +
    max_basis_shift

    maximum allowable frequency shift for individual basis signals (ppm).

    -
    max_basis_damping
    +
    max_basis_damping

    maximum allowable Lorentzian damping factor for individual basis signals (Hz).

    -
    maxiters_pre
    +
    maxiters_pre

    maximum iterations for the coarse (pre-)fit.

    -
    algo_pre
    +
    algo_pre

    optimisation method for the coarse (pre-)fit.

    -
    min_bl_ed_pppm
    +
    min_bl_ed_pppm

    minimum value for the candidate baseline flexibility analyses (ED per ppm).

    -
    max_bl_ed_pppm
    +
    max_bl_ed_pppm

    minimum value for the candidate baseline flexibility analyses (ED per ppm).

    -
    auto_bl_flex_n
    +
    auto_bl_flex_n

    number of candidate baseline analyses to perform.

    -
    pre_fit_bl_ed_pppm
    +
    pre_fit_bl_ed_pppm

    level of baseline flexibility to use in the coarse fitting stage of the algorithm (ED per ppm).

    -
    remove_lip_mm_prefit
    +
    remove_lip_mm_prefit

    remove broad signals in the coarse fitting stage of the algorithm.

    -
    pre_align
    +
    pre_align

    perform a pre-alignment step before coarse fitting.

    -
    max_pre_align_shift
    +
    max_pre_align_shift

    maximum allowable shift in the pre-alignment step (ppm).

    -
    pre_align_ref_freqs
    +
    pre_align_ref_freqs

    a vector of prominent spectral frequencies used in the pre-alignment step (ppm).

    -
    noise_region
    +
    noise_region

    spectral region to estimate the noise level (ppm).

    -
    optimal_smooth_criterion
    +
    optimal_smooth_criterion

    method to determine the optimal smoothness.

    -
    aic_smoothing_factor
    -

    modification factor for the AIC calculation.

    +
    aic_smoothing_factor
    +

    modification factor for the AIC calculation. +Larger values result in less flexible baselines.

    -
    anal_jac
    +
    anal_jac

    use a analytical approximation to the jacobian in the detailed fitting stage.

    -
    pre_fit_ppm_left
    +
    pre_fit_ppm_left

    downfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

    -
    pre_fit_ppm_right
    +
    pre_fit_ppm_right

    upfield frequency limit for the fitting range in the coarse fitting stage of the algorithm (ppm).

    -
    phi1_optim
    +
    phi1_optim

    apply and optimise a frequency dependant phase term.

    -
    phi1_init
    +
    phi1_init

    initial value for the frequency dependant phase term (ms).

    -
    max_dphi1
    +
    max_dphi1

    maximum allowable change from the initial frequency dependant phase term (ms).

    -
    max_basis_shift_broad
    +
    max_basis_shift_broad

    maximum allowable shift for broad signals in the -basis (ppm). Determined based on their name beginning with Lip or MM.

    +basis (ppm). Determined based on their name beginning with Lip or MM. The +default value is set to max_basis_shift.

    -
    max_basis_damping_broad
    +
    max_basis_damping_broad

    maximum allowable Lorentzian damping for broad signals in the basis (Hz). Determined based on their name beginning with Lip -or MM.

    +or MM. The default value is set to max_basis_damping.

    -
    ahat_calc_method
    +
    ahat_calc_method

    method to calculate the metabolite amplitudes. May be one of: "lh_pnnls" or "ls".

    -
    prefit_phase_search
    +

    perform a 1D search for the optimal phase in the prefit stage of the algorithm.

    -
    freq_reg
    +
    freq_reg

    frequency shift parameter.

    -
    lb_reg
    +
    freq_reg_naa
    +

    frequency shift parameter for NAA and NAAG.

    + + +
    lb_reg

    individual line broadening parameter.

    -
    output_all_paras
    +
    output_all_paras

    include more fitting parameters in the fit table, e.g. individual shift and damping factors for each basis set element.

    -
    output_all_paras_raw
    +
    output_all_paras_raw

    include raw fitting parameters in the fit table. For advanced diagnostic use only.

    -
    input_paras_raw
    +
    input_paras_raw

    input raw fitting parameters. For advanced diagnostic use only.

    -
    optim_lw_only
    +
    optim_lw_only

    optimize the global line-broadening term only.

    -
    optim_lw_only_limit
    +
    optim_lw_only_limit

    limits for the line-breading term as a percentage of the starting value when optim_lw_only is TRUE.

    -
    lb_init
    -

    initial Lorentzian line broadening value for the individual -basis signals. Setting to 0 will clash with the minimum allowable value -(eg hard constraint) during the detailed fit.

    +
    lb_init
    +

    initial Lorentzian line broadening value (in Hz) for the +individual basis signals. Setting to 0 will clash with the minimum allowable +value (eg hard constraint) during the detailed fit.

    + + +
    lb_init_approx_fit
    +

    apply lb_init to the basis during the approximate +iterative fit.

    + + +
    zf_offset
    +

    offset in number of data points from the end of the FID to +zero-fill. Default is NULL and will automatically set this to 50 points when +the FID distortion flag is set for the mrs_data.

    zf_offset
    @@ -357,9 +391,7 @@

    Arguments

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -379,15 +411,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/abfit_opts_v1_9_0.html b/docs/reference/abfit_opts_v1_9_0.html index 975f7a0a..04268252 100644 --- a/docs/reference/abfit_opts_v1_9_0.html +++ b/docs/reference/abfit_opts_v1_9_0.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Return a list of options for an ABfit analysis to maintain comparability wit

    Arguments

    -
    ...
    + + +
    ...

    arguments passed to abfit_opts.

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/acquire.html b/docs/reference/acquire.html index 7c41ae1c..05f23aaf 100644 --- a/docs/reference/acquire.html +++ b/docs/reference/acquire.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Simulate pulse sequence acquisition.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rec_phase
    +
    rec_phase

    receiver phase in degrees.

    -
    tol
    +
    tol

    ignore resonance amplitudes below this threshold.

    -
    detect
    +
    detect

    detection nuclei.

    -
    amp_scale
    +
    amp_scale

    scaling factor for the output amplitudes.

    Value

    - - -

    a list of resonance amplitudes and frequencies.

    +

    a list of resonance amplitudes and frequencies.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/add_noise.html b/docs/reference/add_noise.html index c2ded890..9ba363ba 100644 --- a/docs/reference/add_noise.html +++ b/docs/reference/add_noise.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Add noise to an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to add noise to.

    -
    sd
    +
    sd

    standard deviation of the noise.

    -
    fd
    +
    fd

    generate the noise samples in the frequency-domain (TRUE) or time-domain (FALSE). This is required since the absolute value of the standard deviation of noise samples changes when data is Fourier transformed.

    @@ -99,9 +105,7 @@

    Arguments

    Value

    - - -

    mrs_data object with additive normally distributed noise.

    +

    mrs_data object with additive normally distributed noise.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/add_noise_spec_snr.html b/docs/reference/add_noise_spec_snr.html index 92a0fab3..4785a76b 100644 --- a/docs/reference/add_noise_spec_snr.html +++ b/docs/reference/add_noise_spec_snr.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -88,31 +92,35 @@

    Add noise to an mrs_data object to match a given SNR.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to add noise to.

    -
    target_snr
    +
    target_snr

    desired spectral SNR, note this assumes the input data is noise-free, eg simulated data. Note the SNR is estimated from the first scan in the dataset and the same noise level is added to all spectra.

    -
    sig_region
    +
    sig_region

    spectral limits to search for the strongest spectral data point.

    +<<<<<<< HEAD
    ref_data
    +======= +
    ref_data
    +>>>>>>> devel

    measure the signal from the first scan in this reference data and apply the same target noise level to mrs_data.

    Value

    - - -

    mrs_data object with additive normally distributed noise.

    +

    mrs_data object with additive normally distributed noise.

    @@ -127,15 +135,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/align.html b/docs/reference/align.html index 53697923..a2a458ae 100644 --- a/docs/reference/align.html +++ b/docs/reference/align.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,46 +96,46 @@

    Align spectra to a reference frequency using a convolution based method.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be aligned.

    -
    ref_freq
    +
    ref_freq

    reference frequency in ppm units. More than one frequency may be specified.

    -
    ref_amp
    +
    ref_amp

    amplitude value for the reference signal. More than one value may be specified to match the number of ref_freq signals.

    -
    zf_factor
    +
    zf_factor

    zero filling factor to increase alignment resolution.

    -
    lb
    +
    lb

    line broadening to apply to the reference signal.

    -
    max_shift
    +
    max_shift

    maximum allowable shift in Hz.

    -
    ret_df
    +
    ret_df

    return frequency shifts in addition to aligned data (logical).

    -
    mean_dyns
    +
    mean_dyns

    align the mean spectrum and apply the same shift to each dynamic.

    Value

    - - -

    aligned data object.

    +

    aligned data object.

    @@ -146,15 +150,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/apodise_xy.html b/docs/reference/apodise_xy.html index 9f622f56..8144cf92 100644 --- a/docs/reference/apodise_xy.html +++ b/docs/reference/apodise_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,27 @@

    Apodise MRSI data in the x-y direction with a k-space filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    +<<<<<<< HEAD
    func
    +======= +
    func
    +>>>>>>> devel

    must be "hamming", "hanning" or "gaussian".

    -
    w
    +
    w

    the reciprocal of the standard deviation for the Gaussian function.

    Value

    - - -

    apodised data.

    +

    apodised data.

    @@ -114,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/append_basis.html b/docs/reference/append_basis.html index c32f7be3..58f87125 100644 --- a/docs/reference/append_basis.html +++ b/docs/reference/append_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Combine a pair of basis set objects.

    Arguments

    -
    basis_a
    + + +
    basis_a

    first basis.

    -
    basis_b
    +
    basis_b

    second basis.

    Value

    - - -

    combined basis set object.

    +

    combined basis set object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/append_coils.html b/docs/reference/append_coils.html index 99c8c3cf..6316e4ec 100644 --- a/docs/reference/append_coils.html +++ b/docs/reference/append_coils.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Append MRS data across the coil dimension, assumes they matched across the o

    Arguments

    -
    ...
    + + +
    ...

    MRS data objects as arguments, or a list of MRS data objects.

    Value

    - - -

    a single MRS data object with the input objects concatenated together.

    +

    a single MRS data object with the input objects concatenated together.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/append_dyns.html b/docs/reference/append_dyns.html index 5ff13ef0..9012cac6 100644 --- a/docs/reference/append_dyns.html +++ b/docs/reference/append_dyns.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Append MRS data across the dynamic dimension, assumes they matched across th

    Arguments

    -
    ...
    + + +
    ...

    MRS data objects as arguments, or a list of MRS data objects.

    Value

    - - -

    a single MRS data object with the input objects concatenated together.

    +

    a single MRS data object with the input objects concatenated together.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/append_regs.html b/docs/reference/append_regs.html index d1389c8f..148ffbbc 100644 --- a/docs/reference/append_regs.html +++ b/docs/reference/append_regs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Append multiple regressor data frames into a single data frame.

    Arguments

    -
    ...
    + + +
    ...

    input regressor data frames.

    Value

    - - -

    output regressor data frame.

    +

    output regressor data frame.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/apply_axes.html b/docs/reference/apply_axes.html index b5a7e296..8f1baf51 100644 --- a/docs/reference/apply_axes.html +++ b/docs/reference/apply_axes.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Apply a function over specified array axes.

    Arguments

    -
    x
    + + +
    x

    an array.

    -
    axes
    +
    axes

    a vector of axes to apply fun over.

    -
    fun
    +
    fun

    function to be applied.

    -
    ...
    +
    ...

    optional arguments to fun.

    Value

    - - -

    array.

    +

    array.

    @@ -130,15 +134,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/apply_mrs.html b/docs/reference/apply_mrs.html index 1e2ea9ed..f34191b5 100644 --- a/docs/reference/apply_mrs.html +++ b/docs/reference/apply_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,25 @@

    Apply a function across given dimensions of a MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    dims
    +
    dims

    dimensions to apply the function.

    -
    fun
    +
    fun

    name of the function.

    -
    ...
    +
    ...

    arguments to the function.

    -
    data_only
    +
    data_only

    return an array rather than an MRS data object.

    @@ -116,15 +122,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/apply_pulse.html b/docs/reference/apply_pulse.html index 17c6e3ae..5277105c 100644 --- a/docs/reference/apply_pulse.html +++ b/docs/reference/apply_pulse.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,35 +87,35 @@

    Simulate an RF pulse on a single spin.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    spin_n
    +
    spin_n

    spin index.

    -
    angle
    +
    angle

    RF flip angle in degrees.

    -
    nuc
    +
    nuc

    nucleus influenced by the pulse.

    -
    xy
    +
    xy

    x or y pulse.

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -126,15 +130,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/array2mrs_data.html b/docs/reference/array2mrs_data.html index c5f77129..2e7ca3d6 100644 --- a/docs/reference/array2mrs_data.html +++ b/docs/reference/array2mrs_data.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -93,39 +97,47 @@

    Convert a 7 dimensional array in into a mrs_data object. The array dimension

    Arguments

    -
    data_array
    + + +
    data_array

    7d data array.

    +<<<<<<< HEAD
    mrs_data

    example data to copy acquisition parameters from.

    fs
    +======= +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs
    +>>>>>>> devel

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    nucleus that is resonant at the transmitter frequency.

    -
    fd
    +
    fd

    flag to indicate if the matrix is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -140,15 +152,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/auto_phase.html b/docs/reference/auto_phase.html index 1a2257fc..c1c1c981 100644 --- a/docs/reference/auto_phase.html +++ b/docs/reference/auto_phase.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,27 +91,27 @@

    Perform zeroth-order phase correction based on the minimisation of the squar

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    xlim
    +
    xlim

    frequency range (default units of PPM) to including in the phase.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    -
    ret_phase
    +
    ret_phase

    return phase values (logical).

    Value

    - - -

    MRS data object and phase values (optional).

    +

    MRS data object and phase values (optional).

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/back_extrap_ar.html b/docs/reference/back_extrap_ar.html index 11dcc697..790e3383 100644 --- a/docs/reference/back_extrap_ar.html +++ b/docs/reference/back_extrap_ar.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,38 +94,38 @@

    Back extrapolate time-domain data points using an autoregressive model.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    extrap_pts
    +
    extrap_pts

    number of points to extrapolate.

    -
    pred_pts
    +
    pred_pts

    number of points to base the extrapolation on.

    -
    method
    +
    method

    character string specifying the method to fit the model. Must be one of the strings in the default argument (the first few characters are sufficient). Defaults to "burg".

    -
    rem_add
    +
    rem_add

    remove additional points from the end of the FID to maintain the original length of the dataset. Default to TRUE.

    -
    ...
    +
    ...

    additional arguments to specific methods, see ?ar.

    Value

    - - -

    back extrapolated data.

    +

    back extrapolated data.

    @@ -136,15 +140,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/basis2dyn_mrs_data.html b/docs/reference/basis2dyn_mrs_data.html index ef466e85..80b8fcfa 100644 --- a/docs/reference/basis2dyn_mrs_data.html +++ b/docs/reference/basis2dyn_mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Convert a basis object to a dynamic mrs_data object.

    Arguments

    -
    basis
    + + +
    basis

    basis set object.

    -
    amps
    +
    amps

    a data frame with each column corresponding to a basis element and each row corresponding to each dynamic scan.

    -
    tr
    +
    tr

    the dataset repetition time in seconds.

    Value

    - - -

    a dynamic mrs_data object.

    +

    a dynamic mrs_data object.

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/basis2mrs_data.html b/docs/reference/basis2mrs_data.html index dd0f65d9..fe710559 100644 --- a/docs/reference/basis2mrs_data.html +++ b/docs/reference/basis2mrs_data.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -80,33 +84,44 @@

    Convert a basis object to an mrs_data object - where basis signals are sprea

    - 
    basis2mrs_data(basis, sum_elements = FALSE, amps = NULL, shifts = NULL)
    + 
    basis2mrs_data(
+  basis,
+  sum_elements = FALSE,
+  amps = NULL,
+  shifts = NULL,
+  lbs = NULL
+)

    Arguments

    -
    basis
    + + +
    basis

    basis set object.

    -
    sum_elements
    +
    sum_elements

    return the sum of basis elements (logical)

    -
    amps
    +
    amps

    a vector of scaling factors to apply to each basis element.

    -
    shifts
    +
    shifts

    a vector of frequency shifts (in ppm) to apply to each basis element.

    + +
    lbs
    +

    a vector of Lorentzian line broadening terms (in Hz) to apply to +each basis element.

    +

    Value

    - - -

    an mrs_data object with basis signals spread across the dynamic +

    an mrs_data object with basis signals spread across the dynamic dimension or summed.

    @@ -122,15 +137,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bbase.html b/docs/reference/bbase.html index 96320692..fb69df5f 100644 --- a/docs/reference/bbase.html +++ b/docs/reference/bbase.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,23 +89,23 @@

    Generate a spline basis, slightly adapted from : "Splines, knots, and penalt

    Arguments

    -
    N
    + + +
    N

    number of data points.

    -
    number
    +
    number

    number of spline functions.

    -
    deg
    +
    deg

    spline degree : deg = 1 linear, deg = 2 quadratic, deg = 3 cubic.

    Value

    - - -

    spline basis as a matrix.

    +

    spline basis as a matrix.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bc_als.html b/docs/reference/bc_als.html index d2463a11..09652dc8 100644 --- a/docs/reference/bc_als.html +++ b/docs/reference/bc_als.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,28 +89,28 @@

    Baseline correction using the ALS method.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    lambda
    +
    lambda

    controls the baseline flexibility.

    -
    p
    +
    p

    controls the penalty for negative data points.

    -
    ret_bc_only
    +
    ret_bc_only

    return the baseline corrected data only. When FALSE the baseline estimate and input data will be returned.

    Value

    - - -

    baseline corrected data.

    +

    baseline corrected data.

    @@ -121,15 +125,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bc_constant.html b/docs/reference/bc_constant.html index 4869e72d..6e27f5ed 100644 --- a/docs/reference/bc_constant.html +++ b/docs/reference/bc_constant.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Remove a constant baseline offset based on a reference spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range containing a flat baseline region to measure the offset.

    Value

    - - -

    baseline corrected data.

    +

    baseline corrected data.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bc_gauss.html b/docs/reference/bc_gauss.html index 29fee72a..d5b57ebe 100644 --- a/docs/reference/bc_gauss.html +++ b/docs/reference/bc_gauss.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Apply and subtract a Gaussian smoother in the spectral domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    Value

    - - -

    smoother subtracted data.

    +

    smoother subtracted data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bc_poly.html b/docs/reference/bc_poly.html index 50b824de..488abbd4 100644 --- a/docs/reference/bc_poly.html +++ b/docs/reference/bc_poly.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Fit and subtract a polynomial to each spectrum in a dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    p_deg
    +
    p_deg

    polynomial degree.

    Value

    - - -

    polynomial subtracted data.

    +

    polynomial subtracted data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bc_spline.html b/docs/reference/bc_spline.html index 33239c4a..b44a93a9 100644 --- a/docs/reference/bc_spline.html +++ b/docs/reference/bc_spline.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Fit and subtract a smoothing spline to each spectrum in a dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    spar
    +
    spar

    smoothing parameter typically between 0 and 1.

    -
    nknots
    +
    nknots

    number of spline knots.

    Value

    - - -

    smoothing spline subtracted data.

    +

    smoothing spline subtracted data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/beta2lw.html b/docs/reference/beta2lw.html index d6afbc92..2df9a7d7 100644 --- a/docs/reference/beta2lw.html +++ b/docs/reference/beta2lw.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Covert a beta value in the time-domain to an equivalent linewidth in Hz: x *

    Arguments

    -
    beta
    + + +
    beta

    beta damping value.

    Value

    - - -

    linewidth value in Hz.

    +

    linewidth value in Hz.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/bin_spec.html b/docs/reference/bin_spec.html index 66a23cce..19601cba 100644 --- a/docs/reference/bin_spec.html +++ b/docs/reference/bin_spec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Bin equally spaced spectral regions.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be "binned".

    -
    width
    +
    width

    bin width.

    -
    unit
    +
    unit

    bin width unit, can be "ppm" (default) or "pts".

    Value

    - - -

    binned mrs_data object.

    +

    binned mrs_data object.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_basis_corr_mat.html b/docs/reference/calc_basis_corr_mat.html new file mode 100644 index 00000000..25eed3ef --- /dev/null +++ b/docs/reference/calc_basis_corr_mat.html @@ -0,0 +1,128 @@ + +Estimate the correlation matrix for a basis set. — calc_basis_corr_mat • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Estimate the correlation matrix for a basis set.

    + Source: R/basis_set.R + +
    + +
    +

    Estimate the correlation matrix for a basis set.

    +
    + +
    + 
    calc_basis_corr_mat(basis, xlim = c(4, 0.2), zf = TRUE)
    +
    + +
    +

    Arguments

    + + +
    basis
    +

    basis_set object.

    + + +
    xlim
    +

    spectral range to use in ppm.

    + + +
    zf
    +

    zero-fill the basis set.

    + +
    +
    +

    Value

    +

    correlation matrix.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/calc_basis_crlbs.html b/docs/reference/calc_basis_crlbs.html new file mode 100644 index 00000000..9b8b0c37 --- /dev/null +++ b/docs/reference/calc_basis_crlbs.html @@ -0,0 +1,142 @@ + +Estimate the CRLB for each element in a basis set. — calc_basis_crlbs • Spectroscopy Analysis Tools (spant) + + +
    +
    + + + +
    +
    +
    +

    Estimate the CRLB for each element in a basis set.

    + Source: R/basis_set.R + +
    + +
    +

    Estimate the CRLB for each element in a basis set.

    +
    + +
    + 
    calc_basis_crlbs(
+  basis,
+  xlim = c(4, 0.2),
+  zf = TRUE,
+  sd = 1,
+  bl_comp_pppm = NULL
+)
    +
    + +
    +

    Arguments

    + + +
    basis
    +

    basis_set object.

    + + +
    xlim
    +

    spectral range to use in ppm.

    + + +
    zf
    +

    zero-fill the basis set.

    + + +
    sd
    +

    standard deviation of the noise.

    + + +
    bl_comp_pppm
    +

    number spline baseline components to append per-ppm.

    + +
    +
    +

    Value

    +

    a vector of predicted errors.

    +
    + +
    + +
    + + +
    +

    Developed by Martin Wilson.

    +
    + +
    +

    Site built with pkgdown 2.1.0.

    +
    + +
    + + + + + + + + diff --git a/docs/reference/calc_coil_noise_cor.html b/docs/reference/calc_coil_noise_cor.html index 935cf09f..e4e58d8a 100644 --- a/docs/reference/calc_coil_noise_cor.html +++ b/docs/reference/calc_coil_noise_cor.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the noise correlation between coil elements.

    Arguments

    -
    noise_data
    + + +
    noise_data

    mrs_data object with one FID for each coil element.

    Value

    - - -

    correlation matrix.

    +

    correlation matrix.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_coil_noise_sd.html b/docs/reference/calc_coil_noise_sd.html index d5f47a93..4c4a4218 100644 --- a/docs/reference/calc_coil_noise_sd.html +++ b/docs/reference/calc_coil_noise_sd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the noise standard deviation for each coil element.

    Arguments

    -
    noise_data
    + + +
    noise_data

    mrs_data object with one FID for each coil element.

    Value

    - - -

    array of standard deviations.

    +

    array of standard deviations.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_design_efficiency.html b/docs/reference/calc_design_efficiency.html index 2975440c..eb470b7a 100644 --- a/docs/reference/calc_design_efficiency.html +++ b/docs/reference/calc_design_efficiency.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Calculate the efficiency of a regressor data frame.

    Arguments

    -
    regressor_df
    + + +
    regressor_df

    input regressor data frame.

    -
    contrasts
    +
    contrasts

    a vector of contrast values.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_ed_from_lambda.html b/docs/reference/calc_ed_from_lambda.html index 7962e054..99ea03e7 100644 --- a/docs/reference/calc_ed_from_lambda.html +++ b/docs/reference/calc_ed_from_lambda.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Calculate the effective dimensions of a spline smoother from lambda.

    Arguments

    -
    spline_basis
    + + +
    spline_basis

    spline basis.

    -
    deriv_mat
    +
    deriv_mat

    derivative matrix.

    -
    lambda
    +
    lambda

    smoothing parameter.

    Value

    - - -

    the effective dimension value.

    +

    the effective dimension value.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_peak_info_vec.html b/docs/reference/calc_peak_info_vec.html index 03813eb8..16a4310b 100644 --- a/docs/reference/calc_peak_info_vec.html +++ b/docs/reference/calc_peak_info_vec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Calculate the FWHM of a peak from a vector of intensity values.

    Arguments

    -
    data_pts
    + + +
    data_pts

    input vector.

    -
    interp_f
    +
    interp_f

    interpolation factor to improve the FWHM estimate.

    Value

    - - -

    a vector of: x position of the highest data point, maximum peak +

    a vector of: x position of the highest data point, maximum peak value in the y axis, FWHM in the units of data points.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_sd_poly.html b/docs/reference/calc_sd_poly.html index c2f6d1eb..55b500d2 100644 --- a/docs/reference/calc_sd_poly.html +++ b/docs/reference/calc_sd_poly.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Perform a polynomial fit, subtract and return the standard deviation of the

    Arguments

    -
    y
    + + +
    y

    array.

    -
    degree
    +
    degree

    polynomial degree.

    Value

    - - -

    standard deviation of the fit residuals.

    +

    standard deviation of the fit residuals.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_spec_diff.html b/docs/reference/calc_spec_diff.html index 3d40524a..e258f6bb 100644 --- a/docs/reference/calc_spec_diff.html +++ b/docs/reference/calc_spec_diff.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Calculate the sum of squares differences between two mrs_data objects.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    ref
    +
    ref

    reference mrs_data object to calculate differences.

    -
    xlim
    +
    xlim

    spectral limits to perform calculation.

    Value

    - - -

    an array of the sum of squared difference values.

    +

    an array of the sum of squared difference values.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/calc_spec_snr.html b/docs/reference/calc_spec_snr.html index 972912a0..34e74a11 100644 --- a/docs/reference/calc_spec_snr.html +++ b/docs/reference/calc_spec_snr.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -92,39 +96,39 @@

    Calculate the spectral SNR.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    sig_region
    +
    sig_region

    a ppm region to define where the maximum signal value should be estimated.

    -
    noise_region
    +
    noise_region

    a ppm region to defined where the noise level should be estimated.

    -
    p_order
    +
    p_order

    polynomial order to fit to the noise region before estimating the standard deviation.

    -
    interp_f
    +
    interp_f

    interpolation factor to improve detection of the highest signal value.

    -
    full_output
    +
    full_output

    output signal, noise and SNR values separately.

    Value

    - - -

    an array of SNR values.

    +

    an array of SNR values.

    Details

    @@ -145,15 +149,19 @@

    Details

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/check_lcm.html b/docs/reference/check_lcm.html index 685324ee..99fb5614 100644 --- a/docs/reference/check_lcm.html +++ b/docs/reference/check_lcm.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,15 +98,19 @@

    Check LCModel can be run

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/check_tqn.html b/docs/reference/check_tqn.html index 4bfd1977..aef1d677 100644 --- a/docs/reference/check_tqn.html +++ b/docs/reference/check_tqn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,15 +98,19 @@

    Check the TARQUIN binary can be run

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/circ_mask.html b/docs/reference/circ_mask.html index 4634256d..dad70c51 100644 --- a/docs/reference/circ_mask.html +++ b/docs/reference/circ_mask.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Create a logical circular mask spanning the full extent of an n x n matrix.<

    Arguments

    -
    d
    + + +
    d

    diameter of the mask.

    -
    n
    +
    n

    number of matrix rows and columns.

    -
    offset
    +
    offset

    offset the mask centre in matrix dimension units.

    Value

    - - -

    logical n x n mask matrix.

    +

    logical n x n mask matrix.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/coherence_filter.html b/docs/reference/coherence_filter.html index 852d1489..8d49462c 100644 --- a/docs/reference/coherence_filter.html +++ b/docs/reference/coherence_filter.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Zero all coherence orders other than the one supplied as an argument.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    order
    +
    order

    coherence order to keep (default is 0).

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/collapse_to_dyns.fit_result.html b/docs/reference/collapse_to_dyns.fit_result.html new file mode 100644 index 00000000..63b1d1c8 --- /dev/null +++ b/docs/reference/collapse_to_dyns.fit_result.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/collapse_to_dyns.html b/docs/reference/collapse_to_dyns.html index 7668cb08..83bf2ca6 100644 --- a/docs/reference/collapse_to_dyns.html +++ b/docs/reference/collapse_to_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -80,28 +84,28 @@

    Collapse MRS data by concatenating spectra along the dynamic dimension.

    collapse_to_dyns(x, rm_masked = FALSE)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 collapse_to_dyns(x, rm_masked = FALSE)
 
-# S3 method for fit_result
+# S3 method for class 'fit_result'
 collapse_to_dyns(x, rm_masked = FALSE)

    Arguments

    -
    x
    + + +
    x

    data object to be collapsed (mrs_data or fit_result object).

    -
    rm_masked
    +
    rm_masked

    remove masked dynamics from the output.

    Value

    - - -

    collapsed data with spectra or fits concatenated along the dynamic +

    collapsed data with spectra or fits concatenated along the dynamic dimension.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/collapse_to_dyns.mrs_data.html b/docs/reference/collapse_to_dyns.mrs_data.html new file mode 100644 index 00000000..63b1d1c8 --- /dev/null +++ b/docs/reference/collapse_to_dyns.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/comb_coils.html b/docs/reference/comb_coils.html index 9253b058..98cd6580 100644 --- a/docs/reference/comb_coils.html +++ b/docs/reference/comb_coils.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -98,55 +102,55 @@

    Combine coil data based on the first data point of a reference signal.

    Arguments

    -
    metab
    + + +
    metab

    MRS data containing metabolite data.

    -
    ref
    +
    ref

    MRS data containing reference data (optional).

    -
    noise
    +
    noise

    MRS data from a noise scan (optional).

    -
    scale
    +
    scale

    option to rescale coil elements based on the first data point (logical).

    -
    scale_method
    +
    scale_method

    one of "sig_noise_sq", "sig_noise" or "sig".

    -
    sum_coils
    +
    sum_coils

    sum the coil elements as a final step (logical).

    -
    noise_region
    +
    noise_region

    the spectral region (in ppm) to estimate the noise.

    -
    average_ref_dyns
    +
    average_ref_dyns

    take the mean of the reference scans in the dynamic dimension before use.

    -
    ref_pt_index
    +
    ref_pt_index

    time-domain point to use for estimating phase and scaling values.

    -
    ret_metab_only
    +
    ret_metab_only

    return the metabolite data only, even if reference data has been specified.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -161,15 +165,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/comb_coils_mrsi_gls.html b/docs/reference/comb_coils_mrsi_gls.html index dd0d2285..57bc19d2 100644 --- a/docs/reference/comb_coils_mrsi_gls.html +++ b/docs/reference/comb_coils_mrsi_gls.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -85,24 +105,42 @@

    Combine MRSI coil data using the GLS method presented by An et al JMRI 37:14

    Arguments

    +<<<<<<< HEAD
    metab

    MRSI data containing metabolite data.

    noise_pts
    +======= + + +
    metab
    +

    MRSI data containing metabolite data.

    + + +
    noise_pts
    +>>>>>>> devel

    number of points from the end of the FIDs to use for noise covariance estimation.

    +<<<<<<< HEAD
    noise_mrs
    +======= +
    noise_mrs
    +>>>>>>> devel

    MRS data containing noise information for each coil.

    Value

    +<<<<<<< HEAD

    coil combined MRSI data.

    +======= +

    coil combined MRSI data.

    +>>>>>>> devel

    @@ -117,15 +155,26 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/comb_coils_svs_gls.html b/docs/reference/comb_coils_svs_gls.html index 05b14d6d..92247de5 100644 --- a/docs/reference/comb_coils_svs_gls.html +++ b/docs/reference/comb_coils_svs_gls.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -91,6 +111,7 @@

    Combine SVS coil data using the GLS method presented by An et al JMRI 37:144

    Arguments

    +<<<<<<< HEAD
    metab

    MRS data containing metabolite data.

    @@ -100,23 +121,48 @@

    Arguments

    noise_pts
    +======= + + +
    metab
    +

    MRS data containing metabolite data.

    + + +
    ref
    +

    MRS data containing reference data (optional).

    + + +
    noise_pts
    +>>>>>>> devel

    number of points from the end of the FIDs to use for noise covariance estimation.

    +<<<<<<< HEAD
    noise_mrs

    MRS data containing noise information for each coil.

    use_mean_sens
    +======= +
    noise_mrs
    +

    MRS data containing noise information for each coil.

    + + +
    use_mean_sens
    +>>>>>>> devel

    use the dynamic mean to estimate coil sensitivities.

    Value

    +<<<<<<< HEAD

    coil combined MRS data.

    +======= +

    coil combined MRS data.

    +>>>>>>> devel

    @@ -131,15 +177,26 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/comb_fit_list_fit_tables.html b/docs/reference/comb_fit_list_fit_tables.html index 098dea6e..8896b41b 100644 --- a/docs/reference/comb_fit_list_fit_tables.html +++ b/docs/reference/comb_fit_list_fit_tables.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,39 +94,39 @@

    Combine all fitting data points from a list of fits into a single data frame

    Arguments

    -
    fit_list
    + + +
    fit_list

    list of fit_result objects.

    -
    add_extra
    +
    add_extra

    add variables in the extra data frame to the output (TRUE).

    -
    harmonise_ppm
    +
    harmonise_ppm

    ensure the ppm scale for each fit is identical to the first.

    -
    inc_basis_sigs
    +
    inc_basis_sigs

    include the individual fitting basis signals in the output table, defaults to FALSE.

    -
    inc_indices
    +
    inc_indices

    include indices such as X, Y and coil in the output, defaults to TRUE. These are generally not useful for SVS analysis.

    -
    add_res_id
    +
    add_res_id

    add a res_id column to the output to distinguish between datasets.

    Value

    - - -

    a data frame containing the fit data points.

    +

    a data frame containing the fit data points.

    @@ -137,15 +141,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/comb_fit_list_result_tables.html b/docs/reference/comb_fit_list_result_tables.html index 82008f85..a2aa1be5 100644 --- a/docs/reference/comb_fit_list_result_tables.html +++ b/docs/reference/comb_fit_list_result_tables.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Combine the fit result tables from a list of fit results.

    Arguments

    -
    fit_list
    + + +
    fit_list

    a list of fit_result objects.

    -
    add_extra
    +
    add_extra

    add variables in the extra data frame to the output (TRUE).

    -
    add_res_id
    +
    add_res_id

    add a res_id column to the output to distinguish between datasets.

    Value

    - - -

    a data frame combine all fit result tables with an additional id +

    a data frame combine all fit result tables with an additional id column to differentiate between data sets. Any variables in the extra data frame may be optionally added to the result.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/comb_fit_tables.html b/docs/reference/comb_fit_tables.html index 5ab0b533..4329524b 100644 --- a/docs/reference/comb_fit_tables.html +++ b/docs/reference/comb_fit_tables.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Combine all fitting data points into a single data frame.

    Arguments

    -
    fit_res
    + + +
    fit_res

    a single fit_result object.

    -
    inc_basis_sigs
    +
    inc_basis_sigs

    include the individual fitting basis signals in the output table, defaults to FALSE.

    -
    inc_indices
    +
    inc_indices

    include indices such as X, Y and coil in the output, defaults to TRUE. These are generally not useful for SVS analysis.

    Value

    - - -

    a data frame containing the fit data points.

    +

    a data frame containing the fit data points.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/comb_metab_ref.html b/docs/reference/comb_metab_ref.html index ac6d5555..61628f4a 100644 --- a/docs/reference/comb_metab_ref.html +++ b/docs/reference/comb_metab_ref.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Combine a reference and metabolite mrs_data object.

    Arguments

    -
    metab
    + + +
    metab

    metabolite mrs_data object.

    -
    ref
    +
    ref

    reference mrs_data object.

    Value

    - - -

    combined metabolite and reference mrs_data object.

    +

    combined metabolite and reference mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/conv_mrs.html b/docs/reference/conv_mrs.html index 298e9810..0079ca2a 100644 --- a/docs/reference/conv_mrs.html +++ b/docs/reference/conv_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Convolve two MRS data objects.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be convolved.

    -
    conv
    +
    conv

    convolution data stored as an mrs_data object.

    Value

    - - -

    convolved data.

    +

    convolved data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_basis.html b/docs/reference/crop_basis.html index 8193c2fe..5fffdc11 100644 --- a/docs/reference/crop_basis.html +++ b/docs/reference/crop_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Crop basis_set object based on a frequency range.

    Arguments

    -
    basis
    + + +
    basis

    basis_set object to be cropped in the spectral dimension.

    -
    xlim
    +
    xlim

    range of values to crop in the spectral dimension eg xlim = c(4, 0.2).

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_spec.html b/docs/reference/crop_spec.html index be5e2e87..3dad07e3 100644 --- a/docs/reference/crop_spec.html +++ b/docs/reference/crop_spec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Crop mrs_data object based on a frequency range.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    range of values to crop in the spectral dimension eg xlim = c(4, 0.2).

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_td_pts.html b/docs/reference/crop_td_pts.html index c810fa4b..02db8ea9 100644 --- a/docs/reference/crop_td_pts.html +++ b/docs/reference/crop_td_pts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Crop mrs_data object data points in the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    start
    +
    start

    starting data point (defaults to 1).

    -
    end
    +
    end

    ending data point (defaults to the last saved point).

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_td_pts_end.html b/docs/reference/crop_td_pts_end.html index 45fd251f..ddd110fc 100644 --- a/docs/reference/crop_td_pts_end.html +++ b/docs/reference/crop_td_pts_end.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Crop mrs_data object data points at the end of the FID.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of points to remove from the end of the FID.

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_td_pts_pot.html b/docs/reference/crop_td_pts_pot.html index 4e2c39de..7390cada 100644 --- a/docs/reference/crop_td_pts_pot.html +++ b/docs/reference/crop_td_pts_pot.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,15 +91,15 @@

    Crop mrs_data object data points in the time-domain rounding do

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    cropped mrs_data object.

    +

    cropped mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crop_xy.html b/docs/reference/crop_xy.html index dd9fe0cf..2e38399c 100644 --- a/docs/reference/crop_xy.html +++ b/docs/reference/crop_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Crop an MRSI dataset in the x-y direction

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_dim
    +
    x_dim

    x dimension output length.

    -
    y_dim
    +
    y_dim

    y dimension output length.

    Value

    - - -

    selected subset of MRS data.

    +

    selected subset of MRS data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/crossprod_3d.html b/docs/reference/crossprod_3d.html index eaf22eac..95267292 100644 --- a/docs/reference/crossprod_3d.html +++ b/docs/reference/crossprod_3d.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Compute the vector cross product between vectors x and y. Adapted from http:

    Arguments

    -
    x
    + + +
    x

    vector of length 3.

    -
    y
    +
    y

    vector of length 3.

    Value

    - - -

    vector cross product of x and y.

    +

    vector cross product of x and y.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/decimate_mrs_fd.html b/docs/reference/decimate_mrs_fd.html index 98287067..9a7def9a 100644 --- a/docs/reference/decimate_mrs_fd.html +++ b/docs/reference/decimate_mrs_fd.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Decimate an MRS signal to half the original sampling frequency by filtering

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    decimated data at half the original sampling frequency.

    +

    decimated data at half the original sampling frequency.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/decimate_mrs_td.html b/docs/reference/decimate_mrs_td.html index bf9b87d6..f3ac72fa 100644 --- a/docs/reference/decimate_mrs_td.html +++ b/docs/reference/decimate_mrs_td.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Decimate an MRS signal by filtering in the time domain before downsampling.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    q
    +
    q

    integer factor to downsample by (default = 2).

    -
    n
    +
    n

    filter order used in the downsampling.

    -
    ftype
    +
    ftype

    filter type, "iir" or "fir".

    Value

    - - -

    decimated data.

    +

    decimated data.

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/deconv_mrs.html b/docs/reference/deconv_mrs.html index 61ad2631..3468f9e1 100644 --- a/docs/reference/deconv_mrs.html +++ b/docs/reference/deconv_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Deconvolve two MRS data objects.

    Arguments

    -
    mrs_data_a
    + + +
    mrs_data_a

    MRS data to be deconvolved.

    -
    mrs_data_b
    +
    mrs_data_b

    MRS data to be deconvolved.

    Value

    - - -

    deconvolved data.

    +

    deconvolved data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/def_N.html b/docs/reference/def_N.html index 204d145b..7b57f2fb 100644 --- a/docs/reference/def_N.html +++ b/docs/reference/def_N.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return the default number of data points in the spectral dimension.

    Value

    - - -

    number of data points in the spectral dimension.

    +

    number of data points in the spectral dimension.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/def_acq_paras.html b/docs/reference/def_acq_paras.html index b06e4d22..d9e52f60 100644 --- a/docs/reference/def_acq_paras.html +++ b/docs/reference/def_acq_paras.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -91,31 +95,31 @@

    Return (and optionally modify using the input arguments) a list of the defau

    Arguments

    -
    ft
    + + +
    ft

    specify the transmitter frequency in Hz.

    -
    fs
    +
    fs

    specify the sampling frequency in Hz.

    -
    N
    +
    N

    specify the number of data points in the spectral dimension.

    -
    ref
    +
    ref

    specify the reference value for ppm scale.

    -
    nuc
    +
    nuc

    specify the resonant nucleus.

    Value

    - - -

    A list containing the following elements:

    • ft transmitter frequency in Hz.

      • +

      A list containing the following elements:

      • ft transmitter frequency in Hz.

      • fs sampling frequency in Hz.

      • N number of data points in the spectral dimension.

      • ref reference value for ppm scale.

        • @@ -134,15 +138,19 @@

        Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    - - + + diff --git a/docs/reference/def_fs.html b/docs/reference/def_fs.html index 0e67eb9e..14a64bcf 100644 --- a/docs/reference/def_fs.html +++ b/docs/reference/def_fs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return the default sampling frequency in Hz.

    Value

    - - -

    sampling frequency in Hz.

    +

    sampling frequency in Hz.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/def_ft.html b/docs/reference/def_ft.html index cb7a33fb..3bc225a4 100644 --- a/docs/reference/def_ft.html +++ b/docs/reference/def_ft.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return the default transmitter frequency in Hz.

    Value

    - - -

    transmitter frequency in Hz.

    +

    transmitter frequency in Hz.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/def_nuc.html b/docs/reference/def_nuc.html index addd88b8..cea3c2c2 100644 --- a/docs/reference/def_nuc.html +++ b/docs/reference/def_nuc.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return the default nucleus.

    Value

    - - -

    number of data points in the spectral dimension.

    +

    number of data points in the spectral dimension.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/def_ref.html b/docs/reference/def_ref.html index 0ff90af1..aebc7dc7 100644 --- a/docs/reference/def_ref.html +++ b/docs/reference/def_ref.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return the default reference value for ppm scale.

    Value

    - - -

    reference value for ppm scale.

    +

    reference value for ppm scale.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/dicom_reader.html b/docs/reference/dicom_reader.html index 0d19c93c..a9d06bfd 100644 --- a/docs/reference/dicom_reader.html +++ b/docs/reference/dicom_reader.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -92,28 +96,28 @@

    A very simple DICOM reader.

    Arguments

    -
    input
    + + +
    input

    either a file path or raw binary object.

    -
    tags
    +
    tags

    a named list of tags to be extracted from the file. eg tags <- list(spec_data = "7FE1,1010", pat_name = "0010,0010")

    -
    endian
    +
    endian

    can be "little" or "big".

    -
    debug
    +
    debug

    print out some debugging information, can be "little" or "big".

    Value

    - - -

    a list with the same structure as the input, but with tag codes +

    a list with the same structure as the input, but with tag codes replaced with the corresponding data in a raw format.

    @@ -129,15 +133,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/diff_mrs.html b/docs/reference/diff_mrs.html index 9f4e07b3..ec823a9d 100644 --- a/docs/reference/diff_mrs.html +++ b/docs/reference/diff_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Apply the diff operator to an MRS dataset in the FID/spectral dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    ...
    +
    ...

    additional arguments to the diff function.

    Value

    - - -

    MRS data following diff operator.

    +

    MRS data following diff operator.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/downsample_mrs_fd.html b/docs/reference/downsample_mrs_fd.html index abb34365..7dbf0e34 100644 --- a/docs/reference/downsample_mrs_fd.html +++ b/docs/reference/downsample_mrs_fd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    downsampled data.

    +

    downsampled data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/downsample_mrs_td.html b/docs/reference/downsample_mrs_td.html index c8464ac5..cf6e347b 100644 --- a/docs/reference/downsample_mrs_td.html +++ b/docs/reference/downsample_mrs_td.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,15 +91,15 @@

    Downsample an MRS signal by a factor of 2 by removing every other data point

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    downsampled data.

    +

    downsampled data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/dyn_acq_times.html b/docs/reference/dyn_acq_times.html index 7ec68388..571acb1b 100644 --- a/docs/reference/dyn_acq_times.html +++ b/docs/reference/dyn_acq_times.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,28 +89,40 @@

    Return a time scale vector of acquisition times for a dynamic MRS scan. The

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans
    +======= +
    Ntrans
    +>>>>>>> devel

    number of dynamic scans acquired.

    Value

    - - -

    time scale vector in units of seconds.

    +

    time scale vector in units of seconds.

    @@ -121,15 +137,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ecc.html b/docs/reference/ecc.html index cdfbcfef..ef1110f3 100644 --- a/docs/reference/ecc.html +++ b/docs/reference/ecc.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Eddy current correction.

    Arguments

    -
    metab
    + + +
    metab

    MRS data to be corrected.

    -
    ref
    +
    ref

    reference dataset.

    -
    rev
    +
    rev

    reverse the correction.

    Value

    - - -

    corrected data in the time domain.

    +

    corrected data in the time domain.

    Details

    @@ -120,15 +124,19 @@

    Details

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/elliptical_mask.html b/docs/reference/elliptical_mask.html index 0e8f2c72..be25a02d 100644 --- a/docs/reference/elliptical_mask.html +++ b/docs/reference/elliptical_mask.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,39 +87,39 @@

    Create an elliptical mask stored as a matrix of logical values.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of ellipse in the x direction in units of pixels.

    -
    y0
    +
    y0

    centre of ellipse in the y direction in units of pixels.

    -
    xr
    +
    xr

    radius in the x direction in units of pixels.

    -
    yr
    +
    yr

    radius in the y direction in units of pixels.

    -
    angle
    +
    angle

    angle of rotation in degrees.

    Value

    - - -

    logical mask matrix with dimensions fov_yN x fov_xN.

    +

    logical mask matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +134,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/est_noise_sd.html b/docs/reference/est_noise_sd.html index 287ec04c..3b006a9d 100644 --- a/docs/reference/est_noise_sd.html +++ b/docs/reference/est_noise_sd.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,29 +89,29 @@

    Estimate the standard deviation of the noise from a segment of an mrs_data o

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    n
    +
    n

    number of data points (taken from the end of array) to use in the estimation.

    -
    offset
    +
    offset

    number of final points to exclude from the calculation.

    -
    p_order
    +
    p_order

    polynomial order to fit to the data before estimating the standard deviation.

    Value

    - - -

    standard deviation array.

    +

    standard deviation array.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fd2td.html b/docs/reference/fd2td.html index fb55edd9..ed920335 100644 --- a/docs/reference/fd2td.html +++ b/docs/reference/fd2td.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Transform frequency-domain data to the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data in frequency-domain representation.

    Value

    - - -

    MRS data in time-domain representation.

    +

    MRS data in time-domain representation.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fd_conv_filt.html b/docs/reference/fd_conv_filt.html index daf83ea8..82ad011d 100644 --- a/docs/reference/fd_conv_filt.html +++ b/docs/reference/fd_conv_filt.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Frequency-domain convolution based filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    K
    +
    K

    window width in data points.

    -
    ext
    +
    ext

    point separation for linear extrapolation.

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fd_gauss_smo.html b/docs/reference/fd_gauss_smo.html index 0e6f1a96..23d659e0 100644 --- a/docs/reference/fd_gauss_smo.html +++ b/docs/reference/fd_gauss_smo.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Apply a Gaussian smoother in the spectral domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object.

    -
    smo_ppm_sd
    +
    smo_ppm_sd

    Gaussian smoother sd in ppm units.

    Value

    - - -

    spectrally smoothed data.

    +

    spectrally smoothed data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/find_bids_mrs.html b/docs/reference/find_bids_mrs.html index ec9106b3..f6b4cdd7 100644 --- a/docs/reference/find_bids_mrs.html +++ b/docs/reference/find_bids_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,23 @@

    Search for MRS data files in a BIDS filesystem structure.

    Arguments

    -
    path
    + + +
    path

    path to the directory containing the BIDS structure.

    +<<<<<<< HEAD
    output_full_path
    +======= +
    output_full_path
    +>>>>>>> devel

    output the full normalised data paths.

    Value

    - - -

    data frame containing full paths and information on each MRS file.

    +

    data frame containing full paths and information on each MRS file.

    @@ -110,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/find_mrs_files.html b/docs/reference/find_mrs_files.html index 675c6ef0..3952ebff 100644 --- a/docs/reference/find_mrs_files.html +++ b/docs/reference/find_mrs_files.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Find valid MRS data files recursively from a directory path.

    Arguments

    -
    dir
    + + +
    dir

    a directory path.

    Value

    - - -

    a vector of valid MRS data files.

    +

    a vector of valid MRS data files.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_amps.html b/docs/reference/fit_amps.html index af27c9c7..47231500 100644 --- a/docs/reference/fit_amps.html +++ b/docs/reference/fit_amps.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -88,28 +92,28 @@

    Extract the fit amplitudes from an object of class fit_result.<

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    inc_index
    +
    inc_index

    include columns for the voxel index.

    -
    sort_names
    +
    sort_names

    sort the basis set names alphabetically.

    -
    append_common_1h_comb
    +
    append_common_1h_comb

    append commonly used 1H metabolite combinations eg tNAA = NAA + NAAG.

    Value

    - - -

    a dataframe of amplitudes.

    +

    a dataframe of amplitudes.

    @@ -124,15 +128,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_diags.html b/docs/reference/fit_diags.html index b7ce449b..bd0bdc8c 100644 --- a/docs/reference/fit_diags.html +++ b/docs/reference/fit_diags.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Calculate diagnostic information for object of class fit_result

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    amps
    +
    amps

    known metabolite amplitudes.

    Value

    - - -

    a dataframe of diagnostic information.

    +

    a dataframe of diagnostic information.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_mrs.html b/docs/reference/fit_mrs.html index e088a98f..ec92d17f 100644 --- a/docs/reference/fit_mrs.html +++ b/docs/reference/fit_mrs.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -89,6 +93,7 @@

    Perform a fit based analysis of MRS data.

    w_ref = NULL, opts = NULL, parallel = FALSE, + cl = NULL, time = TRUE, progress = "text", extra = NULL @@ -97,53 +102,58 @@

    Perform a fit based analysis of MRS data.

    Arguments

    -
    metab
    + + +
    metab

    metabolite data.

    -
    basis
    +
    basis

    basis class object or character vector to basis file in LCModel .basis format.

    -
    method
    +
    method

    'ABFIT' (default), 'VARPRO', 'VARPRO_3P', 'TARQUIN' or 'LCMODEL'.

    -
    w_ref
    +
    w_ref

    water reference data for concentration scaling (optional).

    -
    opts
    +
    opts

    options to pass to the analysis method.

    -
    parallel
    +
    parallel

    perform analyses in parallel (TRUE or FALSE).

    -
    time
    +
    cl
    +

    a parallel socket cluster required to run analyses in parallel. +Eg, cl <- parallel::makeCluster(4).

    + + +
    time

    measure the time taken for the analysis to complete (TRUE or FALSE).

    -
    progress
    +
    progress

    option is passed to plyr::alply function to display a progress bar during fitting. Default value is "text", set to "none" to disable.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    Value

    - - -

    MRS analysis object.

    +

    MRS analysis object.

    Details

    @@ -169,10 +179,10 @@

    Examples

    fname <- system.file("extdata", "philips_spar_sdat_WS.SDAT", package =
 "spant")
 svs <- read_mrs(fname)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 basis <- sim_basis_1h_brain_press(svs)
 fit_result <- fit_mrs(svs, basis)
-}
+} # }
    @@ -187,15 +197,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_res2csv.html b/docs/reference/fit_res2csv.html index 120f0d35..05b14b50 100644 --- a/docs/reference/fit_res2csv.html +++ b/docs/reference/fit_res2csv.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Write fit results table to a csv file.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit result object.

    -
    fname
    +
    fname

    filename of csv file.

    -
    unscaled
    +
    unscaled

    output the unscaled result table (default = FALSE).

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_t1_ti_array.html b/docs/reference/fit_t1_ti_array.html index c8e26e48..f42c9fe5 100644 --- a/docs/reference/fit_t1_ti_array.html +++ b/docs/reference/fit_t1_ti_array.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,37 +94,37 @@

    Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes.

    Arguments

    -
    ti_vec
    + + +
    ti_vec

    vector of TI values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T1 value.

    -
    upper
    +
    upper

    maximum allowable T1 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +140,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_t1_tr_array.html b/docs/reference/fit_t1_tr_array.html index 0a1f6cf3..4fc881dd 100644 --- a/docs/reference/fit_t1_tr_array.html +++ b/docs/reference/fit_t1_tr_array.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,37 +94,37 @@

    Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes.

    Arguments

    -
    tr_vec
    + + +
    tr_vec

    vector of TR values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T1 value.

    -
    upper
    +
    upper

    maximum allowable T1 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +140,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fit_t2_te_array.html b/docs/reference/fit_t2_te_array.html index 75983e35..56ce5e67 100644 --- a/docs/reference/fit_t2_te_array.html +++ b/docs/reference/fit_t2_te_array.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,37 +94,37 @@

    Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes.

    Arguments

    -
    te_vec
    + + +
    te_vec

    vector of TE values in seconds.

    -
    amp_vec
    +
    amp_vec

    vector of amplitudes.

    -
    lower
    +
    lower

    minimum allowable T2 value.

    -
    upper
    +
    upper

    maximum allowable T2 value.

    -
    output_fit_res
    +
    output_fit_res

    temporal resolution (seconds) of the ideal output relaxation curve.

    -
    ret_full
    +
    ret_full

    return full fitting information including ideal relaxation curve.

    Value

    - - -

    a list containing relaxation parameters and an ideal curve for fit +

    a list containing relaxation parameters and an ideal curve for fit evaluation.

    @@ -136,15 +140,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fp_phase.html b/docs/reference/fp_phase.html index 5053cca5..e08f5061 100644 --- a/docs/reference/fp_phase.html +++ b/docs/reference/fp_phase.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the phase of the first data point in the time-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    phase values in degrees.

    +

    phase values in degrees.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fp_phase_correct.html b/docs/reference/fp_phase_correct.html index 8859b25b..0a1df591 100644 --- a/docs/reference/fp_phase_correct.html +++ b/docs/reference/fp_phase_correct.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Perform a zeroth order phase correction based on the phase of the first data

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ret_phase
    +
    ret_phase

    return phase values (logical).

    Value

    - - -

    corrected data or a list with corrected data and optional phase +

    corrected data or a list with corrected data and optional phase values.

    @@ -113,15 +117,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fp_scale.html b/docs/reference/fp_scale.html index 32d84dc2..2b30a4f6 100644 --- a/docs/reference/fp_scale.html +++ b/docs/reference/fp_scale.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Scale the first time-domain data point in an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    scale
    +
    scale

    scaling value, defaults to 0.5.

    Value

    - - -

    scaled mrs_data object.

    +

    scaled mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/fs.html b/docs/reference/fs.html index cd022581..742d76ec 100644 --- a/docs/reference/fs.html +++ b/docs/reference/fs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the sampling frequency in Hz of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    sampling frequency in Hz.

    +

    sampling frequency in Hz.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ft_dyns.html b/docs/reference/ft_dyns.html index b8838eba..a47a5263 100644 --- a/docs/reference/ft_dyns.html +++ b/docs/reference/ft_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,28 +87,28 @@

    Apply the Fourier transform over the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data where the dynamic dimension is in the time-domain.

    -
    ft_shift
    +
    ft_shift

    apply FT shift to the output, default is FALSE.

    -
    ret_mod
    +
    ret_mod

    return the modulus out the transform, default is FALSE.

    -
    fd
    +
    fd

    transform the chemical shift axis to the frequency domain first, default is TRUE.

    Value

    - - -

    transformed MRS data.

    +

    transformed MRS data.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ft_shift.html b/docs/reference/ft_shift.html index a91d15c4..1951b339 100644 --- a/docs/reference/ft_shift.html +++ b/docs/reference/ft_shift.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Perform a fft and ffshift on a vector.

    Arguments

    -
    vec_in
    + + +
    vec_in

    vector input.

    Value

    - - -

    output vector.

    +

    output vector.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ft_shift_mat.html b/docs/reference/ft_shift_mat.html index 46b6e787..5c3d8b11 100644 --- a/docs/reference/ft_shift_mat.html +++ b/docs/reference/ft_shift_mat.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Perform a fft and fftshift on a matrix with each column replaced by its shif

    Arguments

    -
    mat_in
    + + +
    mat_in

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gausswin_2d.html b/docs/reference/gausswin_2d.html index b7240d20..66c2a491 100644 --- a/docs/reference/gausswin_2d.html +++ b/docs/reference/gausswin_2d.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,39 +87,39 @@

    Create a two dimensional Gaussian window function stored as a matrix.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of window function in the x direction in units of pixels. Note, only integer values are applied.

    -
    y0
    +
    y0

    centre of window function in the y direction in units of pixels. Note, only integer values are applied.

    -
    xw
    +
    xw

    the reciprocal of the standard deviation of the Gaussian window in x direction.

    -
    yw
    +
    yw

    the reciprocal of the standard deviation of the Gaussian window in y direction.

    Value

    - - -

    matrix with dimensions fov_yN x fov_xN.

    +

    matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +134,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_F.html b/docs/reference/gen_F.html index 2bdbe201..8ef33256 100644 --- a/docs/reference/gen_F.html +++ b/docs/reference/gen_F.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Generate the F product operator.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    op
    +
    op

    operator, one of "x", "y", "z", "p", "m".

    -
    detect
    +
    detect

    detection nuclei.

    Value

    - - -

    F product operator matrix.

    +

    F product operator matrix.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_F_xy.html b/docs/reference/gen_F_xy.html index 34e0242c..f129c701 100644 --- a/docs/reference/gen_F_xy.html +++ b/docs/reference/gen_F_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Generate the Fxy product operator with a specified phase.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    phase
    +
    phase

    phase angle in degrees.

    -
    detect
    +
    detect

    detection nuclei.

    Value

    - - -

    product operator matrix.

    +

    product operator matrix.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_I.html b/docs/reference/gen_I.html index 3b071790..e554d67f 100644 --- a/docs/reference/gen_I.html +++ b/docs/reference/gen_I.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Generate the I product operator for a single spin.

    Arguments

    -
    n
    + + +
    n

    spin index number for the required operator.

    -
    spin_num
    +
    spin_num

    vector of spin numbers in the system.

    -
    op
    +
    op

    operator, one of "x", "y", "z", "p", "m".

    Value

    - - -

    I product operator matrix.

    +

    I product operator matrix.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_baseline_reg.html b/docs/reference/gen_baseline_reg.html index 6c061185..7059dcea 100644 --- a/docs/reference/gen_baseline_reg.html +++ b/docs/reference/gen_baseline_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,28 +87,40 @@

    Generate baseline regressor.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object for timing information.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans
    +======= +
    Ntrans
    +>>>>>>> devel

    number of dynamic scans acquired.

    Value

    - - -

    a single baseline regressor with value of 1.

    +

    a single baseline regressor with value of 1.

    @@ -119,15 +135,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_bold_reg.html b/docs/reference/gen_bold_reg.html index e8755630..5258ceba 100644 --- a/docs/reference/gen_bold_reg.html +++ b/docs/reference/gen_bold_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,53 +98,69 @@

    Generate BOLD regressors.

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans

    number of dynamic scans acquired.

    match_tr
    +======= +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    match_tr
    +>>>>>>> devel

    match the output to the input mrs_data.

    -
    dt
    +
    dt

    timing resolution for internal calculations.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    BOLD regressor data frame.

    +

    BOLD regressor data frame.

    @@ -155,15 +175,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_conv_reg.html b/docs/reference/gen_conv_reg.html index 2a62bfc6..d1d07c8d 100644 --- a/docs/reference/gen_conv_reg.html +++ b/docs/reference/gen_conv_reg.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -96,53 +100,69 @@

    Generate regressors by convolving a specified response function with a stimu

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans

    number of dynamic scans acquired.

    resp_fn
    +======= +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    resp_fn
    +>>>>>>> devel

    a data frame specifying the response function to be convolved.

    -
    match_tr
    +
    match_tr

    match the output to the input mrs_data.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    BOLD regressor data frame.

    +

    BOLD regressor data frame.

    @@ -157,15 +177,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_group_reg.html b/docs/reference/gen_group_reg.html index 7cbe328f..b9d154ed 100644 --- a/docs/reference/gen_group_reg.html +++ b/docs/reference/gen_group_reg.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -83,11 +103,21 @@

    Expand a regressor matrix for a group analysis.

    Arguments

    +<<<<<<< HEAD
    regressor_df

    input regressor data frame.

    n
    +======= + + +
    regressor_df
    +

    input regressor data frame.

    + + +
    n
    +>>>>>>> devel

    number of datasets n the group.

    @@ -104,15 +134,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/gen_impulse_reg.html b/docs/reference/gen_impulse_reg.html index b31ec7ff..1a8fb594 100644 --- a/docs/reference/gen_impulse_reg.html +++ b/docs/reference/gen_impulse_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,36 +94,48 @@

    Generate impulse regressors.

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans
    +======= +
    Ntrans
    +>>>>>>> devel

    number of dynamic scans acquired.

    Value

    - - -

    impulse regressors data frame.

    +

    impulse regressors data frame.

    @@ -134,15 +150,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_poly_reg.html b/docs/reference/gen_poly_reg.html index e90af45c..fb4b30ad 100644 --- a/docs/reference/gen_poly_reg.html +++ b/docs/reference/gen_poly_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,6 +87,7 @@

    Generate polynomial regressors.

    Arguments

    +<<<<<<< HEAD
    degree

    the degree of the polynomial.

    @@ -96,19 +101,38 @@

    Arguments

    Ndyns
    +======= + + +
    degree
    +

    the degree of the polynomial.

    + + +
    mrs_data
    +

    mrs_data object for timing information.

    + + +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans
    +======= +
    Ntrans
    +>>>>>>> devel

    number of dynamic scans acquired.

    Value

    - - -

    polynomial regressors.

    +

    polynomial regressors.

    @@ -123,15 +147,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gen_trap_reg.html b/docs/reference/gen_trap_reg.html index d624f730..fdd87b5e 100644 --- a/docs/reference/gen_trap_reg.html +++ b/docs/reference/gen_trap_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -99,74 +103,90 @@

    Generate trapezoidal regressors.

    Arguments

    -
    onset
    + + +
    onset

    stimulus onset in seconds.

    -
    duration
    +
    duration

    stimulus duration in seconds.

    -
    trial_type
    +
    trial_type

    string label for the stimulus.

    -
    mrs_data
    +
    mrs_data

    mrs_data object for timing information.

    +<<<<<<< HEAD
    tr

    repetition time.

    Ndyns
    +======= +
    tr
    +

    repetition time.

    + + +
    Ndyns
    +>>>>>>> devel

    number of dynamic scans stored, potentially less than Ntrans if block averaging has been performed.

    +<<<<<<< HEAD
    Ntrans

    number of dynamic scans acquired.

    rise_t
    +======= +
    Ntrans
    +

    number of dynamic scans acquired.

    + + +
    rise_t
    +>>>>>>> devel

    time to reach a plateau from baseline in seconds.

    -
    fall_t
    +
    fall_t

    time to fall from plateau level back to baseline in seconds.

    -
    exp_fall
    +
    exp_fall

    model an exponential fall instead of linear.

    -
    exp_fall_power
    +
    exp_fall_power

    exponential fall power.

    -
    smo_sigma
    +
    smo_sigma

    standard deviation of Gaussian smoothing kernel in seconds. Set to NULL to disable (default behavior).

    -
    match_tr
    +
    match_tr

    match the output to the input mrs_data.

    -
    dt
    +
    dt

    timing resolution for internal calculations.

    -
    normalise
    +
    normalise

    normalise the response function to have a maximum value of one.

    Value

    - - -

    trapezoidal regressor data frame.

    +

    trapezoidal regressor data frame.

    @@ -181,15 +201,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_brain_basis_names.html b/docs/reference/get_1h_brain_basis_names.html index 0f940926..d10c53fe 100644 --- a/docs/reference/get_1h_brain_basis_names.html +++ b/docs/reference/get_1h_brain_basis_names.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,25 +89,25 @@

    Return a character vector of common 1H molecules found in healthy human brai

    Arguments

    -
    add
    + + +
    add

    optional character vector of additional molecular names. Eg c("asc", "gly", "peth").

    -
    remove
    +
    remove

    optional character vector of molecular names to remove from the set. Eg c("m_cr_ch2").

    -
    inc_lip_mm
    +
    inc_lip_mm

    include Lipid and MM basis signals.

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras.html b/docs/reference/get_1h_brain_basis_paras.html index b368775c..150bf218 100644 --- a/docs/reference/get_1h_brain_basis_paras.html +++ b/docs/reference/get_1h_brain_basis_paras.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,24 +89,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v1.html b/docs/reference/get_1h_brain_basis_paras_v1.html index bc93db65..a042f453 100644 --- a/docs/reference/get_1h_brain_basis_paras_v1.html +++ b/docs/reference/get_1h_brain_basis_paras_v1.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,24 +89,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v2.html b/docs/reference/get_1h_brain_basis_paras_v2.html index 0ca888f5..da73164c 100644 --- a/docs/reference/get_1h_brain_basis_paras_v2.html +++ b/docs/reference/get_1h_brain_basis_paras_v2.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,24 +89,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_brain_basis_paras_v3.html b/docs/reference/get_1h_brain_basis_paras_v3.html index 8209ebe2..fe46863c 100644 --- a/docs/reference/get_1h_brain_basis_paras_v3.html +++ b/docs/reference/get_1h_brain_basis_paras_v3.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,24 +89,24 @@

    Return a list of mol_parameter objects suitable for 1H brain MR

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    metab_lw
    +
    metab_lw

    linewidth of metabolite signals (Hz).

    -
    lcm_compat
    +
    lcm_compat

    when TRUE, lipid, MM and -CrCH molecules will be excluded from the output.

    Value

    - - -

    list of mol_parameter objects.

    +

    list of mol_parameter objects.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_braino_basis_names.html b/docs/reference/get_1h_braino_basis_names.html index 6be8043e..dd75ac8b 100644 --- a/docs/reference/get_1h_braino_basis_names.html +++ b/docs/reference/get_1h_braino_basis_names.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,9 +87,7 @@

    Return a character vector of molecules included in the GE BRAINO phantom.

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -100,15 +102,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_1h_spectre_basis_names.html b/docs/reference/get_1h_spectre_basis_names.html index 1a559f2e..d8f23776 100644 --- a/docs/reference/get_1h_spectre_basis_names.html +++ b/docs/reference/get_1h_spectre_basis_names.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,9 +89,7 @@

    Return a character vector of molecules included in the Gold Star Phantoms SP

    Value

    - - -

    a character vector of molecule names.

    +

    a character vector of molecule names.

    @@ -102,15 +104,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_2d_psf.html b/docs/reference/get_2d_psf.html index 96dc300b..8f7c43c5 100644 --- a/docs/reference/get_2d_psf.html +++ b/docs/reference/get_2d_psf.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -89,32 +93,32 @@

    Get the point spread function (PSF) for a 2D phase encoded MRSI scan.

    Arguments

    -
    FOV
    + + +
    FOV

    field of view in mm.

    -
    mat_size
    +
    mat_size

    acquisition matrix size (not interpolated).

    -
    sampling
    +
    sampling

    can be either "circ" for circular or "rect" for rectangular.

    -
    hamming
    +
    hamming

    should Hamming k-space weighting be applied (default FALSE).

    -
    ensure_odd
    +
    ensure_odd

    add 1mm to the FOV when required to ensure the output pdf has odd dimensions. Required when using get_mrsi2d_seg.

    Value

    - - -

    A matrix of the PSF with 1mm resolution.

    +

    A matrix of the PSF with 1mm resolution.

    @@ -129,15 +133,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_acq_paras.html b/docs/reference/get_acq_paras.html index 3050cfff..ef96e673 100644 --- a/docs/reference/get_acq_paras.html +++ b/docs/reference/get_acq_paras.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return acquisition parameters from a MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    list of acquisition parameters.

    +

    list of acquisition parameters.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_basis_subset.html b/docs/reference/get_basis_subset.html index 08340cca..98b4fcb8 100644 --- a/docs/reference/get_basis_subset.html +++ b/docs/reference/get_basis_subset.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Return a subset of the input basis.

    Arguments

    -
    basis
    + + +
    basis

    input basis.

    -
    names
    +
    names

    basis set elements to keep in the returned object.

    -
    invert
    +
    invert

    set to true to return all basis elements except those given in the names argument.

    Value

    - - -

    a subset of the input basis.

    +

    a subset of the input basis.

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_dyns.html b/docs/reference/get_dyns.html index f9ef2c85..18186b58 100644 --- a/docs/reference/get_dyns.html +++ b/docs/reference/get_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Extract a subset of dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be returned.

    Value

    - - -

    MRS data containing the subset of requested dynamics.

    +

    MRS data containing the subset of requested dynamics.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_even_dyns.html b/docs/reference/get_even_dyns.html index 8869a5aa..29d2a1f0 100644 --- a/docs/reference/get_even_dyns.html +++ b/docs/reference/get_even_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return even numbered dynamic scans starting from 1 (2,4,6...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data containing even numbered scans.

    +

    dynamic MRS data containing even numbered scans.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_fh_dyns.html b/docs/reference/get_fh_dyns.html index e040408f..77e173df 100644 --- a/docs/reference/get_fh_dyns.html +++ b/docs/reference/get_fh_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the first half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    first half of the dynamic series.

    +

    first half of the dynamic series.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_fit_map.html b/docs/reference/get_fit_map.html index 0a20e465..45357702 100644 --- a/docs/reference/get_fit_map.html +++ b/docs/reference/get_fit_map.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Get a data array from a fit result.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    name
    +
    name

    name of the quantity to plot, eg "tNAA".

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_fp.html b/docs/reference/get_fp.html index f6a7c7e3..196703f4 100644 --- a/docs/reference/get_fp.html +++ b/docs/reference/get_fp.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the first time-domain data point.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    first time-domain data point.

    +

    first time-domain data point.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_guassian_pulse.html b/docs/reference/get_guassian_pulse.html index a6b1117c..220ea59e 100644 --- a/docs/reference/get_guassian_pulse.html +++ b/docs/reference/get_guassian_pulse.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Generate a gaussian pulse shape.

    Arguments

    -
    angle
    + + +
    angle

    pulse angle in degrees.

    -
    n
    +
    n

    number of points to generate.

    -
    trunc
    +
    trunc

    percentage truncation factor.

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_head_dyns.html b/docs/reference/get_head_dyns.html index b3eea046..14a796df 100644 --- a/docs/reference/get_head_dyns.html +++ b/docs/reference/get_head_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Return the first scans of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    n
    +
    n

    the number of dynamic scans to return.

    Value

    - - -

    first scans of a dynamic series.

    +

    first scans of a dynamic series.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_lcm_cmd.html b/docs/reference/get_lcm_cmd.html index df411eaf..7429341b 100644 --- a/docs/reference/get_lcm_cmd.html +++ b/docs/reference/get_lcm_cmd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,15 +98,19 @@

    Print the command to run the LCModel command-line program.

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_metab.html b/docs/reference/get_metab.html index e4777661..5ef3e36f 100644 --- a/docs/reference/get_metab.html +++ b/docs/reference/get_metab.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Extract the metabolite component from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    metabolite component.

    +

    metabolite component.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mol_names.html b/docs/reference/get_mol_names.html index 44c0460f..6b9c3dad 100644 --- a/docs/reference/get_mol_names.html +++ b/docs/reference/get_mol_names.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,9 +89,7 @@

    Return a character array of names that may be used with the get_mol_pa

    Value

    - - -

    a character array of names.

    +

    a character array of names.

    @@ -102,15 +104,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mol_paras.html b/docs/reference/get_mol_paras.html index e8050702..485c7a14 100644 --- a/docs/reference/get_mol_paras.html +++ b/docs/reference/get_mol_paras.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Get a mol_parameters object for a named molecule.

    Arguments

    -
    name
    + + +
    name

    the name of the molecule.

    -
    ...
    +
    ...

    arguments to pass to molecule definition function.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mrs_affine.html b/docs/reference/get_mrs_affine.html index 1f4c519f..f8b909eb 100644 --- a/docs/reference/get_mrs_affine.html +++ b/docs/reference/get_mrs_affine.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Generate an affine for nifti generation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    input data.

    -
    x_pos
    +
    x_pos

    x_position coordinate.

    -
    y_pos
    +
    y_pos

    y_position coordinate.

    -
    z_pos
    +
    z_pos

    z_position coordinate.

    Value

    - - -

    affine matrix.

    +

    affine matrix.

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mrsi2d_seg.html b/docs/reference/get_mrsi2d_seg.html index 99e56c11..738e5362 100644 --- a/docs/reference/get_mrsi2d_seg.html +++ b/docs/reference/get_mrsi2d_seg.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,25 +89,25 @@

    Calculate the partial volume estimates for each voxel in a 2D MRSI dataset.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data with multiple voxels in the x-y dimension.

    -
    mri_seg
    +
    mri_seg

    MRI data with values corresponding to the segmentation class. Must be 1mm isotropic resolution.

    -
    ker
    +
    ker

    MRSI PSF kernel in the x-y direction compatible with the mmand package, eg: mmand::shapeKernel(c(10, 10), type = "box").

    Value

    - - -

    a data frame of partial volume estimates and individual segmentation +

    a data frame of partial volume estimates and individual segmentation maps.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mrsi_voi.html b/docs/reference/get_mrsi_voi.html index 6fdf6e33..994fefec 100644 --- a/docs/reference/get_mrsi_voi.html +++ b/docs/reference/get_mrsi_voi.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,28 +87,28 @@

    Generate a MRSI VOI from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    map
    +
    map

    optional voi intensity map.

    -
    ker
    +
    ker

    kernel to rescale the map data to the target_mri. Default value is mmand::boxKernel(), use mmand::mnKernel() for a smoothed map.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mrsi_voxel.html b/docs/reference/get_mrsi_voxel.html index 9f082f05..ba9a7ad2 100644 --- a/docs/reference/get_mrsi_voxel.html +++ b/docs/reference/get_mrsi_voxel.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Generate a MRSI voxel from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    x_pos
    +
    x_pos

    x voxel coordinate.

    -
    y_pos
    +
    y_pos

    y voxel coordinate.

    -
    z_pos
    +
    z_pos

    z voxel coordinate.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_mrsi_voxel_xy_psf.html b/docs/reference/get_mrsi_voxel_xy_psf.html index 1af5dfd5..6fe772f0 100644 --- a/docs/reference/get_mrsi_voxel_xy_psf.html +++ b/docs/reference/get_mrsi_voxel_xy_psf.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Generate a MRSI voxel PSF from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    -
    x_pos
    +
    x_pos

    x voxel coordinate.

    -
    y_pos
    +
    y_pos

    y voxel coordinate.

    -
    z_pos
    +
    z_pos

    z voxel coordinate.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_odd_dyns.html b/docs/reference/get_odd_dyns.html index 498c924f..0e9caef8 100644 --- a/docs/reference/get_odd_dyns.html +++ b/docs/reference/get_odd_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return odd numbered dynamic scans starting from 1 (1,3,5...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data containing odd numbered scans.

    +

    dynamic MRS data containing odd numbered scans.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_ref.html b/docs/reference/get_ref.html index 9cf13eab..f23191c7 100644 --- a/docs/reference/get_ref.html +++ b/docs/reference/get_ref.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Extract the reference component from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    reference component.

    +

    reference component.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_seg_ind.html b/docs/reference/get_seg_ind.html index 68eaa5f1..bd389804 100644 --- a/docs/reference/get_seg_ind.html +++ b/docs/reference/get_seg_ind.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Get the indices of data points lying between two values (end > x > sta

    Arguments

    -
    scale
    + + +
    scale

    full list of values.

    -
    start
    +
    start

    smallest value in the subset.

    -
    end
    +
    end

    largest value in the subset.

    Value

    - - -

    set of indices.

    +

    set of indices.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_sh_dyns.html b/docs/reference/get_sh_dyns.html index 8ea1d7be..0f3ce73d 100644 --- a/docs/reference/get_sh_dyns.html +++ b/docs/reference/get_sh_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the second half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    second half of the dynamic series.

    +

    second half of the dynamic series.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_slice.html b/docs/reference/get_slice.html index 1fb729cc..559fd5ad 100644 --- a/docs/reference/get_slice.html +++ b/docs/reference/get_slice.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Return a single slice from a larger MRSI dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    -
    z_pos
    +
    z_pos

    the z index to extract.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_spin_num.html b/docs/reference/get_spin_num.html index acff1245..f48b0f1e 100644 --- a/docs/reference/get_spin_num.html +++ b/docs/reference/get_spin_num.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the spin number for a given nucleus.

    Arguments

    -
    nucleus
    + + +
    nucleus

    nucleus name, eg "1H".

    Value

    - - -

    spin number.

    +

    spin number.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_subset.html b/docs/reference/get_subset.html index ecab116c..44e651e5 100644 --- a/docs/reference/get_subset.html +++ b/docs/reference/get_subset.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,44 +96,44 @@

    Extract a subset of MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_set
    +
    x_set

    x indices to include in the output (default all).

    -
    y_set
    +
    y_set

    y indices to include in the output (default all).

    -
    z_set
    +
    z_set

    z indices to include in the output (default all).

    -
    dyn_set
    +
    dyn_set

    dynamic indices to include in the output (default all).

    -
    coil_set
    +
    coil_set

    coil indices to include in the output (default all).

    -
    fd_set
    +
    fd_set

    frequency domain data indices to include in the output (default all).

    -
    td_set
    +
    td_set

    time-domain indices to include in the output (default all).

    Value

    - - -

    selected subset of MRS data.

    +

    selected subset of MRS data.

    @@ -144,15 +148,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_svs_voi.html b/docs/reference/get_svs_voi.html index 97437d5d..088c8d0e 100644 --- a/docs/reference/get_svs_voi.html +++ b/docs/reference/get_svs_voi.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Generate a SVS acquisition volume from an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    target_mri
    +
    target_mri

    optional image data to match the intended volume space.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_tail_dyns.html b/docs/reference/get_tail_dyns.html index cee1cec3..b8609163 100644 --- a/docs/reference/get_tail_dyns.html +++ b/docs/reference/get_tail_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Return the last scans of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    n
    +
    n

    the number of dynamic scans to return.

    Value

    - - -

    last scans of a dynamic series.

    +

    last scans of a dynamic series.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_td_amp.html b/docs/reference/get_td_amp.html index 5e2b5814..988cb426 100644 --- a/docs/reference/get_td_amp.html +++ b/docs/reference/get_td_amp.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,28 +89,28 @@

    Return an array of amplitudes derived from fitting the initial points in the

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    nstart
    +
    nstart

    first data point to fit.

    -
    nend
    +
    nend

    last data point to fit.

    -
    method
    +
    method

    method for measuring the amplitude, one of "poly", spline" or exp".

    Value

    - - -

    array of amplitudes.

    +

    array of amplitudes.

    @@ -121,15 +125,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_tqn_cmd.html b/docs/reference/get_tqn_cmd.html index f7df7ab4..9ad3b7b0 100644 --- a/docs/reference/get_tqn_cmd.html +++ b/docs/reference/get_tqn_cmd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,15 +98,19 @@

    Print the command to run the TARQUIN command-line program.

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_uncoupled_mol.html b/docs/reference/get_uncoupled_mol.html index 5fd5cb69..14d35556 100644 --- a/docs/reference/get_uncoupled_mol.html +++ b/docs/reference/get_uncoupled_mol.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -93,40 +97,40 @@

    Generate a mol_parameters object for a simple spin system with

    Arguments

    -
    name
    + + +
    name

    abbreviated name of the molecule.

    -
    chem_shift
    +
    chem_shift

    chemical shift of the resonance (PPM).

    -
    nucleus
    +
    nucleus

    nucleus (1H, 31P...).

    -
    scale_factor
    +
    scale_factor

    multiplicative scaling factor. Note, this value can be made complex to adjust the phase of the resonance.

    -
    lw
    +
    lw

    linewidth in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    -
    full_name
    +
    full_name

    long name of the molecule (optional).

    Value

    - - -

    mol_parameters object.

    +

    mol_parameters object.

    @@ -141,15 +145,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_voi_cog.html b/docs/reference/get_voi_cog.html index 996dcf87..5cd06b6f 100644 --- a/docs/reference/get_voi_cog.html +++ b/docs/reference/get_voi_cog.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the centre of gravity for an image containing 0 and 1's.

    Arguments

    -
    voi
    + + +
    voi

    nifti object.

    Value

    - - -

    triplet of x,y,z coordinates.

    +

    triplet of x,y,z coordinates.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_voi_seg.html b/docs/reference/get_voi_seg.html index 261f5aa2..5d1a2e90 100644 --- a/docs/reference/get_voi_seg.html +++ b/docs/reference/get_voi_seg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Return the white matter, gray matter and CSF composition of a volume.

    Arguments

    -
    voi
    + + +
    voi

    volume data as a nifti object.

    -
    mri_seg
    +
    mri_seg

    segmented brain volume as a nifti object.

    Value

    - - -

    a vector of partial volumes expressed as percentages.

    +

    a vector of partial volumes expressed as percentages.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_voi_seg_psf.html b/docs/reference/get_voi_seg_psf.html index 7982a0a4..717726ff 100644 --- a/docs/reference/get_voi_seg_psf.html +++ b/docs/reference/get_voi_seg_psf.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Return the white matter, gray matter and CSF composition of a volume.

    Arguments

    -
    psf
    + + +
    psf

    volume data as a nifti object.

    -
    mri_seg
    +
    mri_seg

    segmented brain volume as a nifti object.

    Value

    - - -

    a vector of partial volumes expressed as percentages.

    +

    a vector of partial volumes expressed as percentages.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/get_voxel.html b/docs/reference/get_voxel.html index 93a4b392..024b7506 100644 --- a/docs/reference/get_voxel.html +++ b/docs/reference/get_voxel.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,35 +87,35 @@

    Return a single voxel from a larger mrs dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    x_pos
    +
    x_pos

    the x index to plot.

    -
    y_pos
    +
    y_pos

    the y index to plot.

    -
    z_pos
    +
    z_pos

    the z index to plot.

    -
    dyn
    +
    dyn

    the dynamic index to plot.

    -
    coil
    +
    coil

    the coil element number to plot.

    Value

    - - -

    MRS data.

    +

    MRS data.

    @@ -126,15 +130,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/glm_spec.html b/docs/reference/glm_spec.html index e767ecbf..0295d48a 100644 --- a/docs/reference/glm_spec.html +++ b/docs/reference/glm_spec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,28 @@

    Perform a GLM analysis of dynamic MRS data in the spectral domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    single-voxel dynamics MRS data.

    -
    regressor_df
    +
    regressor_df

    a data frame containing temporal regressors to be applied to each spectral datapoint.

    +<<<<<<< HEAD
    full_output
    +======= +
    full_output
    +>>>>>>> devel

    append mrs_data and regressor_df to the output list.

    Value

    - - -

    list of statistical results.

    +

    list of statistical results.

    @@ -115,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/glm_spec_fmrs_fl.html b/docs/reference/glm_spec_fmrs_fl.html index 30584e18..4fc7ee83 100644 --- a/docs/reference/glm_spec_fmrs_fl.html +++ b/docs/reference/glm_spec_fmrs_fl.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -91,21 +111,36 @@

    Perform first-level spectral GLM analysis of an fMRS dataset.

    Arguments

    +<<<<<<< HEAD
    regressor_df
    +======= + + +
    regressor_df
    +>>>>>>> devel

    a data frame containing temporal regressors to be applied to each spectral datapoint.

    +<<<<<<< HEAD
    analysis_dir
    +======= +
    analysis_dir
    +>>>>>>> devel

    directory containing preprocessed data generated by the preproc_svs_dataset function.

    +<<<<<<< HEAD
    exclude_labels
    +======= +
    exclude_labels
    +>>>>>>> devel

    vector of labels of scans to exclude, eg poor quality data.

    +<<<<<<< HEAD
    labels

    labels to describe each data set.

    @@ -119,6 +154,21 @@

    Arguments

    return_results
    +======= +
    labels
    +

    labels to describe each data set.

    + + +
    xlim
    +

    spectral range to include in the analysis.

    + + +
    vline
    +

    vertical lines to add to the plot.

    + + +
    return_results
    +>>>>>>> devel

    function will return key outputs, defaults to FALSE.

    @@ -135,15 +185,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/glm_spec_fmrs_group.html b/docs/reference/glm_spec_fmrs_group.html index 527478e5..1a4c1166 100644 --- a/docs/reference/glm_spec_fmrs_group.html +++ b/docs/reference/glm_spec_fmrs_group.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -88,22 +108,40 @@

    Perform group-level spectral GLM analysis of an fMRS dataset.

    Arguments

    +<<<<<<< HEAD
    regressor_df
    +======= + + +
    regressor_df
    +>>>>>>> devel

    a data frame containing temporal regressors to be applied to each spectral datapoint.

    +<<<<<<< HEAD
    analysis_dir
    +======= +
    analysis_dir
    +>>>>>>> devel

    directory containing preprocessed data generated by the preproc_svs_dataset function.

    +<<<<<<< HEAD
    exclude_labels
    +======= +
    exclude_labels
    +>>>>>>> devel

    vector of labels of scans to exclude, eg poor quality data.

    +<<<<<<< HEAD
    labels
    +======= +
    labels
    +>>>>>>> devel

    labels to describe each data set.

    @@ -120,15 +158,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/glm_spec_group_linhyp.html b/docs/reference/glm_spec_group_linhyp.html index 747860d9..b2e83dd5 100644 --- a/docs/reference/glm_spec_group_linhyp.html +++ b/docs/reference/glm_spec_group_linhyp.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -83,11 +103,21 @@

    Test a group-level spectral GLM linear hypothesis.

    Arguments

    +<<<<<<< HEAD
    hmat

    linear hypothesis matrix.

    analysis_dir
    +======= + + +
    hmat
    +

    linear hypothesis matrix.

    + + +
    analysis_dir
    +>>>>>>> devel

    directory containing preprocessed data generated by the preproc_svs_dataset function.

    @@ -105,15 +135,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/grid_shift_xy.html b/docs/reference/grid_shift_xy.html index d0e05b1d..a5381a82 100644 --- a/docs/reference/grid_shift_xy.html +++ b/docs/reference/grid_shift_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Grid shift MRSI data in the x/y dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data in the spatial domain.

    -
    x_shift
    +
    x_shift

    shift to apply in the x-direction in units of voxels.

    -
    y_shift
    +
    y_shift

    shift to apply in the y-direction in units of voxels.

    Value

    - - -

    shifted data.

    +

    shifted data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gridplot.html b/docs/reference/gridplot.html index 54e40afe..ffb1ad08 100644 --- a/docs/reference/gridplot.html +++ b/docs/reference/gridplot.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Arrange spectral plots in a grid.

    Arguments

    -
    x
    + + +
    x

    object for plotting.

    -
    ...
    +
    ...

    arguments to be passed to methods.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/gridplot.mrs_data.html b/docs/reference/gridplot.mrs_data.html index 8d68edae..1c0c0df9 100644 --- a/docs/reference/gridplot.mrs_data.html +++ b/docs/reference/gridplot.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,7 +82,7 @@

    Arrange spectral plots in a grid.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 gridplot(
   x,
   rows = NA,
@@ -93,36 +97,38 @@ 
    Arrange spectral plots in a grid.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    rows
    
+
    rows
    
 
    number of grid rows.
    
 
 
-
    cols
    
+
    cols
    
 
    number of grid columns.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    oma
    
+
    oma
    
 
    outer margin area.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -139,15 +145,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/hsvd.html b/docs/reference/hsvd.html index 41c28be8..3055013e 100644 --- a/docs/reference/hsvd.html +++ b/docs/reference/hsvd.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -89,27 +93,27 @@

    HSVD of an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object to be decomposed.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor.

    Value

    - - -

    basis matrix and signal table.

    +

    basis matrix and signal table.

    @@ -124,15 +128,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/hsvd_filt.html b/docs/reference/hsvd_filt.html index 1d5d953d..d3046f4d 100644 --- a/docs/reference/hsvd_filt.html +++ b/docs/reference/hsvd_filt.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -97,41 +101,41 @@

    HSVD based signal filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    xlim
    +
    xlim

    frequency range to filter, default units are Hz which can be changed to ppm using the "scale" argument.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor.

    -
    scale
    +
    scale

    either "hz" or "ppm" to set the frequency units of xlim.

    -
    return_model
    +
    return_model

    by default the filtered spectrum is returned. Set return_model to TRUE to return the HSVD model of the data.

    Value

    - - -

    filtered data or model depending on the return_model argument.

    +

    filtered data or model depending on the return_model argument.

    @@ -146,15 +150,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/hsvd_vec.html b/docs/reference/hsvd_vec.html index b960d9d5..67be18a9 100644 --- a/docs/reference/hsvd_vec.html +++ b/docs/reference/hsvd_vec.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -89,32 +93,32 @@

    HSVD of a complex vector.

    Arguments

    -
    y
    + + +
    y

    time domain signal to be filtered as a vector.

    -
    fs
    +
    fs

    sampling frequency of y.

    -
    comps
    +
    comps

    number of Lorentzian components to use for modelling.

    -
    irlba
    +
    irlba

    option to use irlba SVD (logical).

    -
    max_damp
    +
    max_damp

    maximum allowable damping factor. Default value of 0 ensures resultant model is damped.

    Value

    - - -

    basis matrix and signal table.

    +

    basis matrix and signal table.

    @@ -129,15 +133,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/hz.html b/docs/reference/hz.html index 39f31a26..69e23d0e 100644 --- a/docs/reference/hz.html +++ b/docs/reference/hz.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Return the frequency scale of an MRS dataset in Hz.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    Value

    - - -

    frequency scale.

    +

    frequency scale.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ift_shift.html b/docs/reference/ift_shift.html index 168b58dd..d9c15357 100644 --- a/docs/reference/ift_shift.html +++ b/docs/reference/ift_shift.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Perform an iffshift and ifft on a vector.

    Arguments

    -
    vec_in
    + + +
    vec_in

    vector input.

    Value

    - - -

    output vector.

    +

    output vector.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ift_shift_mat.html b/docs/reference/ift_shift_mat.html index 22a75c11..12129b50 100644 --- a/docs/reference/ift_shift_mat.html +++ b/docs/reference/ift_shift_mat.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Perform an ifft and ifftshift on a matrix with each column replaced by its s

    Arguments

    -
    mat_in
    + + +
    mat_in

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/image.mrs_data.html b/docs/reference/image.mrs_data.html index 79eb6371..03522c45 100644 --- a/docs/reference/image.mrs_data.html +++ b/docs/reference/image.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,7 +82,7 @@

    Image plot method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 image(
   x,
   xlim = NULL,
@@ -105,59 +109,62 @@ 
    Image plot method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    col
    
+
    col
    
 
    Colour map to use, defaults to viridis.
    
 
 
-
    plot_dim
    
+
    plot_dim
    
 
    the dimension to display on the y-axis, can be one of: "dyn",
 "time_sec", x", "y", "z", "coil" or NULL. If NULL (the default) all spectra
 are collapsed into the dynamic dimension and displayed.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    y_ticks
    
+
    y_ticks
    
 
    a vector of indices specifying where to place additional red
 tick marks.
    
 
 
+<<<<<<< HEAD
 
    hline
    
 
    add a horizontal line at the specified value.
    
 
@@ -180,14 +187,38 @@ 
    Arguments
    
 
 
    vline_col
    
 
    colour for the vertical line.
    
+=======
+
    hline
    
+
    add a horizontal line at the specified value.
    
+
+
+
    hline_lty
    
+
    linetype for the horizontal line.
    
+>>>>>>> devel
+
+
+
    hline_col
    
+
    colour for the horizontal line.
    
+
+
+
    vline
    
+
    add a vertical line at the specified value.
    
+
+
+
    vline_lty
    
+
    linetype for the vertical line.
    
+
+
+
    vline_col
    
+
    colour for the vertical line.
    
 
 
-
    legend
    
+
    legend
    
 
    add a colour bar to the plot using the imagePlot function
 from the fields package.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -204,15 +235,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/img2kspace_xy.html b/docs/reference/img2kspace_xy.html index 4b47cc32..c1d4a779 100644 --- a/docs/reference/img2kspace_xy.html +++ b/docs/reference/img2kspace_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Transform 2D MRSI data to k-space in the x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data.

    Value

    - - -

    k-space data.

    +

    k-space data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 689c02a5..4a940014 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,13 @@ +<<<<<<< HEAD Function reference • Spectroscopy Analysis Tools (spant)Package index • Spectroscopy Analysis Tools (spant) - +
    @@ -28,7 +36,7 @@
    • - +
    @@ -239,6 +247,14 @@

    All functions bin_spec()

    Bin equally spaced spectral regions.

    + +

    calc_basis_corr_mat()

    + +

    Estimate the correlation matrix for a basis set.

    + +

    calc_basis_crlbs()

    + +

    Estimate the CRLB for each element in a basis set.

    calc_coil_noise_cor()

    @@ -1524,15 +1540,19 @@

    All functions
    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    - - + + diff --git a/docs/reference/int_spec.html b/docs/reference/int_spec.html index 783325a8..3760b0a5 100644 --- a/docs/reference/int_spec.html +++ b/docs/reference/int_spec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Integrate a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    Value

    - - -

    an array of integral values.

    +

    an array of integral values.

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/interleave_dyns.html b/docs/reference/interleave_dyns.html index 441eff27..c7b55648 100644 --- a/docs/reference/interleave_dyns.html +++ b/docs/reference/interleave_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Interleave the first and second half of a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    interleaved data.

    +

    interleaved data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/inv_even_dyns.html b/docs/reference/inv_even_dyns.html index dcb781dc..c30cabb3 100644 --- a/docs/reference/inv_even_dyns.html +++ b/docs/reference/inv_even_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Invert even numbered dynamic scans starting from 1 (2,4,6...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data with inverted even numbered scans.

    +

    dynamic MRS data with inverted even numbered scans.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/inv_odd_dyns.html b/docs/reference/inv_odd_dyns.html index 78d64660..9b111dfd 100644 --- a/docs/reference/inv_odd_dyns.html +++ b/docs/reference/inv_odd_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Invert odd numbered dynamic scans starting from 1 (1,3,5...).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    dynamic MRS data with inverted odd numbered scans.

    +

    dynamic MRS data with inverted odd numbered scans.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/is.def.html b/docs/reference/is.def.html index a67b9eba..00b05f2d 100644 --- a/docs/reference/is.def.html +++ b/docs/reference/is.def.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Check if an object is defined, which is the same as being not NULL.

    Arguments

    -
    x
    + + +
    x

    object to test for being NULL.

    Value

    - - -

    logical value.

    +

    logical value.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/is_fd.html b/docs/reference/is_fd.html index 18a193aa..0b44a5c4 100644 --- a/docs/reference/is_fd.html +++ b/docs/reference/is_fd.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Check if the chemical shift dimension of an MRS data object is in the freque

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    logical value.

    +

    logical value.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/kspace2img_xy.html b/docs/reference/kspace2img_xy.html index 8f0664b0..9a3bb8d2 100644 --- a/docs/reference/kspace2img_xy.html +++ b/docs/reference/kspace2img_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Transform 2D MRSI data from k-space to image space in the x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    2D MRSI data.

    Value

    - - -

    MRSI data in image space.

    +

    MRSI data in image space.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/l2_reg.html b/docs/reference/l2_reg.html index 21aa9849..52aa0d6d 100644 --- a/docs/reference/l2_reg.html +++ b/docs/reference/l2_reg.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -94,47 +98,47 @@

    Perform l2 regularisation artefact suppression.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    input data for artefact suppression.

    -
    thresh
    +
    thresh

    threshold parameter to extract lipid signals from mrs_data based on the spectral integration of the thresh_xlim region in magnitude mode.

    -
    b
    +
    b

    regularisation parameter.

    -
    A
    +
    A

    set of spectra containing the artefact basis signals. The thresh parameter is ignored when A is specified.

    -
    xlim
    +
    xlim

    spectral limits in ppm to restrict the reconstruction range. Defaults to the full spectral width.

    -
    thresh_xlim
    +
    thresh_xlim

    spectral limits in ppm to integrate for the threshold map.

    -
    A_append
    +
    A_append

    additional spectra to append to the A basis.

    -
    ret_norms
    +
    ret_norms

    return the residual norm and solution norms.

    Value

    - - -

    l2 reconstructed mrs_data object.

    +

    l2 reconstructed mrs_data object.

    @@ -149,15 +153,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/lb.basis_set.html b/docs/reference/lb.basis_set.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.basis_set.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lb.html b/docs/reference/lb.html index 272f1966..948cd64e 100644 --- a/docs/reference/lb.html +++ b/docs/reference/lb.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -80,35 +84,35 @@

    Apply line-broadening (apodisation) to MRS data or basis object.

    lb(x, lb, lg = 1)
 
-# S3 method for list
+# S3 method for class 'list'
 lb(x, lb, lg = 1)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 lb(x, lb, lg = 1)
 
-# S3 method for basis_set
+# S3 method for class 'basis_set'
 lb(x, lb, lg = 1)

    Arguments

    -
    x
    + + +
    x

    input mrs_data or basis_set object.

    -
    lb
    +
    lb

    amount of line-broadening in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    Value

    - - -

    line-broadened data.

    +

    line-broadened data.

    @@ -123,15 +127,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/lb.list.html b/docs/reference/lb.list.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.list.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lb.mrs_data.html b/docs/reference/lb.mrs_data.html new file mode 100644 index 00000000..9db2e0f7 --- /dev/null +++ b/docs/reference/lb.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/lofdc.html b/docs/reference/lofdc.html index 31347a25..b109e947 100644 --- a/docs/reference/lofdc.html +++ b/docs/reference/lofdc.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,39 +95,39 @@

    Correct linear frequency drift.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    max_hz_s
    +
    max_hz_s

    the maximum drift rate to search over.

    -
    tr
    +
    tr

    mrs_data repetition time.

    -
    ret_corr_only
    +
    ret_corr_only

    return the corrected mrs_data object only.

    -
    outlier_thresh
    +
    outlier_thresh

    threshold to remove outliers.

    -
    xlim
    +
    xlim

    spectral width (in ppm) to evaluate outliers.

    -
    order
    +
    order

    correction order.

    Value

    - - -

    drift corrected mrs_data object.

    +

    drift corrected mrs_data object.

    @@ -138,15 +142,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/lw2alpha.html b/docs/reference/lw2alpha.html index 25da229b..42f45ce5 100644 --- a/docs/reference/lw2alpha.html +++ b/docs/reference/lw2alpha.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie:

    Arguments

    -
    lw
    + + +
    lw

    linewidth in Hz.

    Value

    - - -

    beta damping value.

    +

    beta damping value.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/lw2beta.html b/docs/reference/lw2beta.html index cc5e4bbd..4a82e2cf 100644 --- a/docs/reference/lw2beta.html +++ b/docs/reference/lw2beta.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Covert a linewidth in Hz to an equivalent beta value in the time-domain ie:

    Arguments

    -
    lw
    + + +
    lw

    linewidth in Hz.

    Value

    - - -

    beta damping value.

    +

    beta damping value.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/make_basis_from_raw.html b/docs/reference/make_basis_from_raw.html index 069f8086..117d3c80 100644 --- a/docs/reference/make_basis_from_raw.html +++ b/docs/reference/make_basis_from_raw.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,28 +89,28 @@

    Make a basis-set object from a directory containing LCModel formatted RAW fi

    Arguments

    -
    dir_path
    + + +
    dir_path

    path to the directory containing LCModel RAW files. One file per signal.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    Value

    - - -

    a basis-set object.

    +

    a basis-set object.

    @@ -121,15 +125,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_dyns.html b/docs/reference/mask_dyns.html index 3b27106c..377742dd 100644 --- a/docs/reference/mask_dyns.html +++ b/docs/reference/mask_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Mask an MRS dataset in the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    mask
    +
    mask

    vector of boolean values specifying the dynamics to mask, where a value of TRUE indicates the spectrum should be removed.

    Value

    - - -

    masked dataset.

    +

    masked dataset.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_fit_res.html b/docs/reference/mask_fit_res.html index ebd91a99..606a9a91 100644 --- a/docs/reference/mask_fit_res.html +++ b/docs/reference/mask_fit_res.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Mask fit result spectra depending on a vector of bool values.

    Arguments

    -
    fit_result
    + + +
    fit_result

    fit result object to be masked.

    -
    mask_vec
    +
    mask_vec

    a Boolean vector with the same number of rows as there are rows in the results table.

    -
    amps_only
    +
    amps_only

    only mask the amplitude and associated error estimate columns.

    Value

    - - -

    a masked fit result object.

    +

    a masked fit result object.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_xy.html b/docs/reference/mask_xy.html index b0d38619..66e37b7e 100644 --- a/docs/reference/mask_xy.html +++ b/docs/reference/mask_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Mask an MRSI dataset in the x-y direction

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    x_dim
    +
    x_dim

    x dimension output length.

    -
    y_dim
    +
    y_dim

    y dimension output length.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_xy_corners.html b/docs/reference/mask_xy_corners.html index 2d13839d..efde8336 100644 --- a/docs/reference/mask_xy_corners.html +++ b/docs/reference/mask_xy_corners.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Mask the four corners of an MRSI dataset in the x-y plane.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_xy_ellipse.html b/docs/reference/mask_xy_ellipse.html index e2e749ef..c4f84807 100644 --- a/docs/reference/mask_xy_ellipse.html +++ b/docs/reference/mask_xy_ellipse.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Mask the voxels outside an elliptical region spanning the MRSI dataset in th

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    Value

    - - -

    masked MRS data.

    +

    masked MRS data.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mask_xy_mat.html b/docs/reference/mask_xy_mat.html index e80665b6..98a24815 100644 --- a/docs/reference/mask_xy_mat.html +++ b/docs/reference/mask_xy_mat.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Mask a 2D MRSI dataset in the x-y dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    mask
    +
    mask

    matrix of boolean values specifying the voxels to mask, where a value of TRUE indicates the voxel should be removed.

    -
    value
    +
    value

    the value to set masked data to (usually NA or 0).

    Value

    - - -

    masked dataset.

    +

    masked dataset.

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mat2mrs_data.html b/docs/reference/mat2mrs_data.html index ae55665f..4b07206d 100644 --- a/docs/reference/mat2mrs_data.html +++ b/docs/reference/mat2mrs_data.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -93,39 +97,47 @@

    Convert a matrix (with spectral points in the column dimension and dynamics

    Arguments

    -
    mat
    + + +
    mat

    data matrix.

    +<<<<<<< HEAD
    mrs_data

    example data to copy acquisition parameters from.

    fs
    +======= +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs
    +>>>>>>> devel

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    -
    fd
    +
    fd

    flag to indicate if the matrix is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -140,15 +152,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/matexp.html b/docs/reference/matexp.html index d784516b..569ed954 100644 --- a/docs/reference/matexp.html +++ b/docs/reference/matexp.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Matrix exponential function taken from complexplus package to reduce the num

    Arguments

    -
    x
    + + +
    x

    a square complex matrix.

    Value

    - - -

    the matrix exponential of x.

    +

    the matrix exponential of x.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/max_mrs.html b/docs/reference/max_mrs.html index c627faec..4f34b976 100644 --- a/docs/reference/max_mrs.html +++ b/docs/reference/max_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Apply the max operator to an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    MRS data following max operator.

    +

    MRS data following max operator.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/max_mrs_interp.html b/docs/reference/max_mrs_interp.html index 52e63f3e..ed85e5aa 100644 --- a/docs/reference/max_mrs_interp.html +++ b/docs/reference/max_mrs_interp.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Apply the max operator to an interpolated MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    interp_f
    +
    interp_f

    interpolation factor.

    Value

    - - -

    Array of maximum values (real only).

    +

    Array of maximum values (real only).

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean.list.html b/docs/reference/mean.list.html index 048306fd..7c495704 100644 --- a/docs/reference/mean.list.html +++ b/docs/reference/mean.list.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,25 +82,25 @@

    Calculate the mean spectrum from an mrs_data object.

    - 
    # S3 method for list
+    
    # S3 method for class 'list'
 mean(x, ...)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    ...
    +
    ...

    other arguments to pass to the colMeans function.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean.mrs_data.html b/docs/reference/mean.mrs_data.html index 79515014..6839d70e 100644 --- a/docs/reference/mean.mrs_data.html +++ b/docs/reference/mean.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,25 +82,25 @@

    Calculate the mean spectrum from an mrs_data object.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 mean(x, ...)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    ...
    +
    ...

    other arguments to pass to the colMeans function.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean_dyn_blocks.html b/docs/reference/mean_dyn_blocks.html index 4c042448..9ebda1e6 100644 --- a/docs/reference/mean_dyn_blocks.html +++ b/docs/reference/mean_dyn_blocks.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Calculate the mean of adjacent dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    block_size
    +
    block_size

    number of adjacent dynamics scans to average over.

    Value

    - - -

    dynamic data averaged in blocks.

    +

    dynamic data averaged in blocks.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean_dyn_pairs.html b/docs/reference/mean_dyn_pairs.html index 1a241126..5d27251f 100644 --- a/docs/reference/mean_dyn_pairs.html +++ b/docs/reference/mean_dyn_pairs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the pairwise means across a dynamic data set.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    mean dynamic data of adjacent dynamic pairs.

    +

    mean dynamic data of adjacent dynamic pairs.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean_dyns.html b/docs/reference/mean_dyns.html index 0daa27df..07e2ea71 100644 --- a/docs/reference/mean_dyns.html +++ b/docs/reference/mean_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Calculate the mean dynamic data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be averaged.

    Value

    - - -

    mean dynamic data.

    +

    mean dynamic data.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean_mrs_list.html b/docs/reference/mean_mrs_list.html index 10d842c0..ecacd3b1 100644 --- a/docs/reference/mean_mrs_list.html +++ b/docs/reference/mean_mrs_list.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the mean of a list of mrs_data objects.

    Arguments

    -
    mrs_list
    + + +
    mrs_list

    list of mrs_data objects.

    Value

    - - -

    mean mrs_data object.

    +

    mean mrs_data object.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mean_vec_blocks.html b/docs/reference/mean_vec_blocks.html index dd78b122..da217a87 100644 --- a/docs/reference/mean_vec_blocks.html +++ b/docs/reference/mean_vec_blocks.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Calculate the mean of adjacent blocks in a vector.

    Arguments

    -
    x
    + + +
    x

    input vector.

    -
    block_size
    +
    block_size

    number of adjacent elements to average over.

    Value

    - - -

    vector data averaged in blocks.

    +

    vector data averaged in blocks.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/median_dyns.html b/docs/reference/median_dyns.html index 9a085b10..0e2c5447 100644 --- a/docs/reference/median_dyns.html +++ b/docs/reference/median_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the median dynamic data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    median dynamic data.

    +

    median dynamic data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mod_td.html b/docs/reference/mod_td.html index 141ef09e..07c3f551 100644 --- a/docs/reference/mod_td.html +++ b/docs/reference/mod_td.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Apply the Modulus operator to the time-domain MRS signal.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data input.

    Value

    - - -

    time-domain modulus of input.

    +

    time-domain modulus of input.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mrs_data2basis.html b/docs/reference/mrs_data2basis.html index 11797b91..c7bc7bea 100644 --- a/docs/reference/mrs_data2basis.html +++ b/docs/reference/mrs_data2basis.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Convert an mrs_data object to basis object - where basis signals are spread

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    mrs_data object with basis signals spread across the dynamic dimension.

    -
    names
    +
    names

    list of names corresponding to basis signals.

    Value

    - - -

    basis set object.

    +

    basis set object.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mrs_data2bids.html b/docs/reference/mrs_data2bids.html index 557d3adb..5d19d16e 100644 --- a/docs/reference/mrs_data2bids.html +++ b/docs/reference/mrs_data2bids.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -100,6 +120,7 @@

    Create a BIDS file structure from a vector of MRS data paths or list of mrs_

    Arguments

    +<<<<<<< HEAD
    mrs_data

    vector of MRS data paths or list of mrs_data objects.

    @@ -109,17 +130,35 @@

    Arguments

    suffix
    +======= + + +
    mrs_data
    +

    vector of MRS data paths or list of mrs_data objects.

    + + +
    output_dir
    +

    the base directory to create the BIDS structure.

    + + +
    suffix
    +>>>>>>> devel

    optional vector of file suffixes. Default behaviour is to automatically determine these from the input data, however it is recommended that they are specified to allow more efficient skipping of existing data.

    +<<<<<<< HEAD
    sub
    +======= +
    sub
    +>>>>>>> devel

    optional vector of subject labels. If not specified, these will be automatically generated as a series of increasing zero-padded integer values corresponding to the mrs_data input indices.

    +<<<<<<< HEAD
    ses

    optional vector of session labels.

    @@ -157,6 +196,45 @@

    Arguments

    skip_existing
    +======= +
    ses
    +

    optional vector of session labels.

    + + +
    task
    +

    optional vector of task labels.

    + + +
    acq
    +

    optional vector of acquisition labels.

    + + +
    nuc
    +

    optional vector of nucleus labels.

    + + +
    voi
    +

    optional vector of volume of interest labels.

    + + +
    rec
    +

    optional vector of reconstruction labels.

    + + +
    run
    +

    optional vector of run indices.

    + + +
    echo
    +

    optional vector of echo time indices.

    + + +
    inv
    +

    optional vector of inversion indices.

    + + +
    skip_existing
    +>>>>>>> devel

    skip any data files that have already been converted. Defaults to TRUE, set to FALSE to force an overwrite of any existing data files.

    @@ -175,15 +253,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/mrs_data2mat.html b/docs/reference/mrs_data2mat.html index 9e47688a..4e242fb6 100644 --- a/docs/reference/mrs_data2mat.html +++ b/docs/reference/mrs_data2mat.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,20 +89,20 @@

    Convert mrs_data object to a matrix, with spectral points in the column dime

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object or list of MRS data objects.

    -
    collapse
    +
    collapse

    collapse all other dimensions along the dynamic dimension, eg a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.

    Value

    - - -

    MRS data matrix.

    +

    MRS data matrix.

    @@ -113,15 +117,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mrs_data2spec_mat.html b/docs/reference/mrs_data2spec_mat.html index 1079b1aa..4e2a2f9c 100644 --- a/docs/reference/mrs_data2spec_mat.html +++ b/docs/reference/mrs_data2spec_mat.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -85,20 +105,34 @@

    Convert mrs_data object to a matrix, with spectral points in the column dime

    Arguments

    +<<<<<<< HEAD
    mrs_data

    MRS data object or list of MRS data objects.

    collapse
    +======= + + +
    mrs_data
    +

    MRS data object or list of MRS data objects.

    + + +
    collapse
    +>>>>>>> devel

    collapse all other dimensions along the dynamic dimension, eg a 16x16 MRSI grid would be first collapsed across 256 dynamic scans.

    Value

    +<<<<<<< HEAD

    MRS data matrix.

    +======= +

    MRS data matrix.

    +>>>>>>> devel

    @@ -113,15 +147,26 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/mrs_data2vec.html b/docs/reference/mrs_data2vec.html index a1fd654d..6fe60349 100644 --- a/docs/reference/mrs_data2vec.html +++ b/docs/reference/mrs_data2vec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,35 +87,35 @@

    Convert mrs_data object to a vector.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    dyn
    +
    dyn

    dynamic index.

    -
    x_pos
    +
    x_pos

    x index.

    -
    y_pos
    +
    y_pos

    y index.

    -
    z_pos
    +
    z_pos

    z index.

    -
    coil
    +
    coil

    coil element index.

    Value

    - - -

    MRS data vector.

    +

    MRS data vector.

    @@ -126,15 +130,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mvfftshift.html b/docs/reference/mvfftshift.html index 976b3410..e455cf7e 100644 --- a/docs/reference/mvfftshift.html +++ b/docs/reference/mvfftshift.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Perform a fftshift on a matrix, with each column replaced by its shifted res

    Arguments

    -
    x
    + + +
    x

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/mvifftshift.html b/docs/reference/mvifftshift.html index 8c6266d4..4710bf7b 100644 --- a/docs/reference/mvifftshift.html +++ b/docs/reference/mvifftshift.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Perform an ifftshift on a matrix, with each column replaced by its shifted r

    Arguments

    -
    x
    + + +
    x

    matrix input.

    Value

    - - -

    output matrix.

    +

    output matrix.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/n2coord.html b/docs/reference/n2coord.html index d070cd0f..0116e5af 100644 --- a/docs/reference/n2coord.html +++ b/docs/reference/n2coord.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Print fit coordinates from a single index.

    Arguments

    -
    n
    + + +
    n

    fit index.

    -
    fit_res
    +
    fit_res

    fit_result object.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/nifti_flip_lr.html b/docs/reference/nifti_flip_lr.html index 19860b3c..3b64bd73 100644 --- a/docs/reference/nifti_flip_lr.html +++ b/docs/reference/nifti_flip_lr.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,15 +91,15 @@

    Flip the x data dimension order of a nifti image. This corresponds to flippi

    Arguments

    -
    x
    + + +
    x

    nifti object to be processed.

    Value

    - - -

    nifti object with reversed x data direction.

    +

    nifti object with reversed x data direction.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/one_page_pdf.html b/docs/reference/one_page_pdf.html index 4bae170e..fdf3f5d7 100644 --- a/docs/reference/one_page_pdf.html +++ b/docs/reference/one_page_pdf.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Export a one-page pdf of a single fit result

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    pdf_out_path
    +
    pdf_out_path

    path to the exported pdf file.

    -
    title
    +
    title

    ouptut title.

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ortho3.html b/docs/reference/ortho3.html index 5d7dd2fd..94e2d564 100644 --- a/docs/reference/ortho3.html +++ b/docs/reference/ortho3.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -99,63 +103,65 @@

    Display an orthographic projection plot of a nifti object.

    Arguments

    -
    underlay
    + + +
    underlay

    underlay image to be shown in grayscale.

    -
    overlay
    +
    overlay

    optional overlay image.

    -
    xyz
    +
    xyz

    x, y, z slice coordinates to display.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    zlim_ol
    +
    zlim_ol

    overlay intensity limits.

    -
    alpha
    +
    alpha

    transparency of overlay.

    -
    col_ol
    +
    col_ol

    colour palette of overlay.

    -
    orient_lab
    +
    orient_lab

    display orientation labels (default TRUE).

    -
    rescale
    +
    rescale

    rescale factor for the underlay and overlay images.

    -
    crosshairs
    +
    crosshairs

    display the crosshairs (default TRUE).

    -
    ch_lwd
    +
    ch_lwd

    crosshair linewidth.

    -
    colourbar
    +
    colourbar

    display a colourbar for the overlay (default TRUE).

    -
    bg
    +
    bg

    plot background colour.

    -
    mar
    +
    mar

    plot margins.

    -
    smallplot
    +
    smallplot

    smallplot option for positioning the colourbar.

    @@ -172,15 +178,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ortho3_inter.html b/docs/reference/ortho3_inter.html index 15948899..992d6173 100644 --- a/docs/reference/ortho3_inter.html +++ b/docs/reference/ortho3_inter.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,31 +95,33 @@

    Display an interactive orthographic projection plot of a nifti object.

    Arguments

    -
    underlay
    + + +
    underlay

    underlay image to be shown in grayscale.

    -
    overlay
    +
    overlay

    optional overlay image.

    -
    xyz
    +
    xyz

    x, y, z slice coordinates to display.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    zlim_ol
    +
    zlim_ol

    overlay intensity limits.

    -
    alpha
    +
    alpha

    transparency of overlay.

    -
    ...
    +
    ...

    other options to be passed to the ortho3 function.

    @@ -132,15 +138,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/peak_info.html b/docs/reference/peak_info.html index 41c8ffaf..fec6ff63 100644 --- a/docs/reference/peak_info.html +++ b/docs/reference/peak_info.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -91,33 +95,33 @@

    Search for the highest peak in a spectral region and return the frequency, h

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    an object of class mrs_data.

    -
    xlim
    +
    xlim

    frequency range (default units of PPM) to search for the highest peak.

    -
    interp_f
    +
    interp_f

    interpolation factor, defaults to 4x.

    -
    scale
    +
    scale

    the units to use for the frequency scale, can be one of: "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "real", "imag" or "mod".

    Value

    - - -

    list of arrays containing the highest peak frequency, height and FWHM +

    list of arrays containing the highest peak frequency, height and FWHM in units of PPM and Hz.

    @@ -133,15 +137,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/pg_extrap_xy.html b/docs/reference/pg_extrap_xy.html index 992be757..b038cc50 100644 --- a/docs/reference/pg_extrap_xy.html +++ b/docs/reference/pg_extrap_xy.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -95,37 +99,37 @@

    Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    img_mask
    +
    img_mask

    a boolean matrix of voxels with strong signals to be extrapolated. Must be twice the dimensions of the input data.

    -
    kspace_mask
    +
    kspace_mask

    a boolean matrix of kspace points that have been sampled. Typically a circle for MRSI, but defaults to the full rectangular area of k-space covered by the input data. Must match the x-y dimensions of the input data.

    -
    intensity_thresh
    +
    intensity_thresh

    used to define img_mask based on the strength of the signal in each voxel. Defaults to intensities greater than 15% of the maximum. Ignored if img_mask is specified as argument.

    -
    iters
    +
    iters

    number of iterations to perform.

    Value

    - - -

    extrapolated mrs_data object.

    +

    extrapolated mrs_data object.

    @@ -140,15 +144,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/phase.html b/docs/reference/phase.html index f2d35f4f..a863b66e 100644 --- a/docs/reference/phase.html +++ b/docs/reference/phase.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Apply phasing parameters to MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    zero_order
    +
    zero_order

    zero'th order phase term in degrees.

    -
    first_order
    +
    first_order

    first order (frequency dependent) phase term in ms.

    Value

    - - -

    MRS data with applied phase parameters.

    +

    MRS data with applied phase parameters.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/phase_ref_1h_brain.html b/docs/reference/phase_ref_1h_brain.html index 8707a74a..156697ed 100644 --- a/docs/reference/phase_ref_1h_brain.html +++ b/docs/reference/phase_ref_1h_brain.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -85,24 +105,42 @@

    Corrected zero order phase and chemical shift offset in 1H MRS data from the

    Arguments

    +<<<<<<< HEAD
    mrs_data

    MRS data to be corrected.

    mean_ref
    +======= + + +
    mrs_data
    +

    MRS data to be corrected.

    + + +
    mean_ref
    +>>>>>>> devel

    apply the phase and offset of the mean spectrum to all others. Default is FALSE.

    +<<<<<<< HEAD
    ret_corr_only
    +======= +
    ret_corr_only
    +>>>>>>> devel

    return the corrected data only.

    Value

    +<<<<<<< HEAD

    corrected MRS data.

    +======= +

    corrected MRS data.

    +>>>>>>> devel

    @@ -117,15 +155,26 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/plot.fit_result.html b/docs/reference/plot.fit_result.html index 836a53ee..54946129 100644 --- a/docs/reference/plot.fit_result.html +++ b/docs/reference/plot.fit_result.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,7 +82,7 @@

    Plot the fitting results of an object of class fit_result.

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 plot(
   x,
   dyn = 1,
@@ -106,91 +110,93 @@ 
    Plot the fitting results of an object of class fit_result.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    fit_result object.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    data_only
    
+
    data_only
    
 
    display only the processed data (logical).
    
 
 
-
    label
    
+
    label
    
 
    character string to add to the top left of the plot window.
    
 
 
-
    plot_sigs
    
+
    plot_sigs
    
 
    a character vector of signal names to add to the plot.
    
 
 
-
    n
    
+
    n
    
 
    single index element to plot (overrides other indices when given).
    
 
 
-
    sub_bl
    
+
    sub_bl
    
 
    subtract the baseline from the data and fit (logical).
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    ylim
    
+
    ylim
    
 
    range of values to display on the y-axis, eg ylim = c(0,10).
    
 
 
-
    y_scale
    
+
    y_scale
    
 
    option to display the y-axis values (logical).
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    invert_fit
    
+
    invert_fit
    
 
    show the fit result "upside-down"/
    
 
 
-
    ...
    
+
    ...
    
 
    further arguments to plot method.
    
 
 
    
@@ -207,15 +213,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/plot.mrs_data.html b/docs/reference/plot.mrs_data.html index bb2ec651..3be2e1d6 100644 --- a/docs/reference/plot.mrs_data.html +++ b/docs/reference/plot.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,7 +82,7 @@

    Plotting method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 plot(
   x,
   dyn = 1,
@@ -121,156 +125,158 @@ 
    Plotting method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    fd
    
+
    fd
    
 
    display data in the frequency-domain (default), or time-domain
 (logical).
    
 
 
-
    x_units
    
+
    x_units
    
 
    the units to use for the x-axis, can be one of: "ppm", "hz",
 "points" or "seconds".
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    y_scale
    
+
    y_scale
    
 
    option to display the y-axis values (logical).
    
 
 
-
    x_ax
    
+
    x_ax
    
 
    option to display the x-axis values (logical).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    lwd
    
+
    lwd
    
 
    plot linewidth.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    label
    
+
    label
    
 
    character string to add to the top left of the plot window.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    xaxis_lab
    
+
    xaxis_lab
    
 
    x-axis label.
    
 
 
-
    yaxis_lab
    
+
    yaxis_lab
    
 
    y-axis label.
    
 
 
-
    xat
    
+
    xat
    
 
    x-axis tick label values.
    
 
 
-
    xlabs
    
+
    xlabs
    
 
    x-axis tick labels.
    
 
 
-
    yat
    
+
    yat
    
 
    y-axis tick label values.
    
 
 
-
    ylabs
    
+
    ylabs
    
 
    y-axis tick labels.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    col
    
+
    col
    
 
    set the line colour, eg col = rgb(0.5, 0.5, 0.5).
    
 
 
-
    alpha
    
+
    alpha
    
 
    set the line transparency, eg alpha = 0.5 is 50% transparency.
 Overrides any transparency levels set by col.
    
 
 
-
    bl_lty
    
+
    bl_lty
    
 
    linetype for the y = 0 baseline trace. A default value NULL
 results in no baseline being plotted.
    
 
 
-
    hline
    
+
    hline
    
 
    add a horizontal line at the specified value.
    
 
 
-
    hline_lty
    
+
    hline_lty
    
 
    linetype for the horizontal line.
    
 
 
-
    hline_col
    
+
    hline_col
    
 
    colour for the horizontal line.
    
 
 
-
    vline
    
+
    vline
    
 
    add a vertical line at the specified value.
    
 
 
-
    vline_lty
    
+
    vline_lty
    
 
    linetype for the vertical line.
    
 
 
-
    vline_col
    
+
    vline_col
    
 
    colour for the vertical line.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the plot method.
    
 
 
    
@@ -287,15 +293,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_bc.html b/docs/reference/plot_bc.html index b48142cc..43e8ca45 100644 --- a/docs/reference/plot_bc.html +++ b/docs/reference/plot_bc.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Convenience function to plot a baseline estimate with the original data.

    Arguments

    -
    orig_data
    + + +
    orig_data

    the original data.

    -
    bc_data
    +
    bc_data

    the baseline corrected data.

    -
    ...
    +
    ...

    other arguments to pass to the stackplot function.

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_reg.html b/docs/reference/plot_reg.html index 2addb2f6..0d59af08 100644 --- a/docs/reference/plot_reg.html +++ b/docs/reference/plot_reg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Plot regressors as an image.

    Arguments

    -
    regressor_df
    + + +
    regressor_df

    input regressor data frame.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_slice_fit.html b/docs/reference/plot_slice_fit.html index 57f1af8a..4825864c 100644 --- a/docs/reference/plot_slice_fit.html +++ b/docs/reference/plot_slice_fit.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,29 +94,31 @@

    Plot a 2D slice from an MRSI fit result object.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    map
    +
    map

    fit result values to display as a colour map. Can be specified as a character string or array of numeric values. Defaults to "tNAA".

    -
    map_denom
    +
    map_denom

    fit result values to divide the map argument by. Can be specified as a character string (eg "tCr") or array of numeric values.

    -
    slice
    +
    slice

    slice to plot in the z direction.

    -
    zlim
    +
    zlim

    range of values to plot.

    -
    interp
    +
    interp

    interpolation factor.

    @@ -129,15 +135,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_slice_fit_inter.html b/docs/reference/plot_slice_fit_inter.html index da105a7d..65009ccb 100644 --- a/docs/reference/plot_slice_fit_inter.html +++ b/docs/reference/plot_slice_fit_inter.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,33 +95,35 @@

    Plot a 2D slice from an MRSI fit result object.

    Arguments

    -
    fit_res
    + + +
    fit_res

    fit_result object.

    -
    map
    +
    map

    fit result values to display as a colour map. Can be specified as a character string or array of numeric values. Defaults to "tNAA".

    -
    map_denom
    +
    map_denom

    fit result values to divide the map argument by. Can be specified as a character string (eg "tCr") or array of numeric values.

    -
    slice
    +
    slice

    slice to plot in the z direction.

    -
    zlim
    +
    zlim

    range of values to plot.

    -
    interp
    +
    interp

    interpolation factor.

    -
    xlim
    +
    xlim

    spectral plot limits for the x axis.

    @@ -134,15 +140,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_slice_map.html b/docs/reference/plot_slice_map.html index ffb2a134..53bd6680 100644 --- a/docs/reference/plot_slice_map.html +++ b/docs/reference/plot_slice_map.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -95,48 +99,50 @@

    Plot a slice from a 7 dimensional array.

    Arguments

    -
    data
    + + +
    data

    7d array of values to be plotted.

    -
    zlim
    +
    zlim

    smallest and largest values to be plotted.

    -
    mask_map
    +
    mask_map

    matching map with logical values to indicate if the corresponding values should be plotted.

    -
    mask_cutoff
    +
    mask_cutoff

    minimum values to plot (as a percentage of the maximum).

    -
    interp
    +
    interp

    map interpolation factor.

    -
    slice
    +
    slice

    the slice index to plot.

    -
    dyn
    +
    dyn

    the dynamic index to plot.

    -
    coil
    +
    coil

    the coil element number to plot.

    -
    ref
    +
    ref

    reference index to plot.

    -
    denom
    +
    denom

    map to use as a denominator.

    -
    horizontal
    +
    horizontal

    display the colourbar horizontally (logical).

    @@ -153,15 +159,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_slice_map_inter.html b/docs/reference/plot_slice_map_inter.html index 90968f66..9c56b8f4 100644 --- a/docs/reference/plot_slice_map_inter.html +++ b/docs/reference/plot_slice_map_inter.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -100,62 +104,64 @@

    Plot an interactive slice map from a data array where voxels can be selected

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    spectral data.

    -
    map
    +
    map

    array of values to be plotted, defaults to the integration of the modulus of the full spectral width.

    -
    xlim
    +
    xlim

    spectral region to plot.

    -
    slice
    +
    slice

    the slice index to plot.

    -
    zlim
    +
    zlim

    smallest and largest values to be plotted.

    -
    mask_map
    +
    mask_map

    matching map with logical values to indicate if the corresponding values should be plotted.

    -
    denom
    +
    denom

    map to use as a denominator.

    -
    mask_cutoff
    +
    mask_cutoff

    minimum values to plot (as a percentage of the maximum).

    -
    interp
    +
    interp

    map interpolation factor.

    -
    mode
    +
    mode

    representation of the complex spectrum to be plotted, can be one of: "re", "im", "mod" or "arg".

    -
    y_scale
    +
    y_scale

    option to display the y-axis values (logical).

    -
    ylim
    +
    ylim

    intensity range to plot.

    -
    coil
    +
    coil

    coil element to plot.

    -
    fd
    +
    fd

    display data in the frequency-domain (default), or time-domain (logical).

    @@ -173,15 +179,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    - - + + diff --git a/docs/reference/plot_spec_sd.html b/docs/reference/plot_spec_sd.html index 95514562..2cdd56e2 100644 --- a/docs/reference/plot_spec_sd.html +++ b/docs/reference/plot_spec_sd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,21 @@

    Plot the spectral standard deviation.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be plotted.

    -
    xlim
    +
    xlim

    plotting limits in ppm.

    -
    scale_sd
    +
    scale_sd

    scaling factor for the standard deviation trace.

    -
    ...
    +
    ...

    other arguments passed to the stackplot function.

    @@ -112,15 +118,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_voi_overlay.html b/docs/reference/plot_voi_overlay.html index bbbbf35e..cc9e52ef 100644 --- a/docs/reference/plot_voi_overlay.html +++ b/docs/reference/plot_voi_overlay.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,25 @@

    Plot a volume as an image overlay.

    Arguments

    -
    mri
    + + +
    mri

    image data as a nifti object or path to data file.

    -
    voi
    +
    voi

    volume data as a nifti object or path to data file.

    -
    export_path
    +
    export_path

    optional path to save the image in png format.

    -
    zlim
    +
    zlim

    underlay intensity limits.

    -
    ...
    +
    ...

    additional arguments to the ortho3 function.

    @@ -116,15 +122,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/plot_voi_overlay_seg.html b/docs/reference/plot_voi_overlay_seg.html index 0e800ff2..1e237de0 100644 --- a/docs/reference/plot_voi_overlay_seg.html +++ b/docs/reference/plot_voi_overlay_seg.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,21 @@

    Plot a volume as an overlay on a segmented brain volume.

    Arguments

    -
    mri_seg
    + + +
    mri_seg

    segmented brain volume as a nifti object.

    -
    voi
    +
    voi

    volume data as a nifti object.

    -
    export_path
    +
    export_path

    optional path to save the image in png format.

    -
    ...
    +
    ...

    additional arguments to the ortho3 function.

    @@ -112,15 +118,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ppm.fit_result.html b/docs/reference/ppm.fit_result.html new file mode 100644 index 00000000..9251b9b6 --- /dev/null +++ b/docs/reference/ppm.fit_result.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/ppm.html b/docs/reference/ppm.html index ee4696e2..2733d58c 100644 --- a/docs/reference/ppm.html +++ b/docs/reference/ppm.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -80,44 +84,44 @@

    Return the ppm scale of an MRS dataset or fit result.

    ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)
 
-# S3 method for fit_result
+# S3 method for class 'fit_result'
 ppm(x, ft = NULL, ref = NULL, fs = NULL, N = NULL)

    Arguments

    -
    x
    + + +
    x

    MRS dataset of fit result.

    -
    ft
    +
    ft

    transmitter frequency in Hz, does not apply when the object is a fit result.

    -
    ref
    +
    ref

    reference value for ppm scale, does not apply when the object is a fit result.

    -
    fs
    +
    fs

    sampling frequency in Hz, does not apply when the object is a fit result.

    -
    N
    +
    N

    number of data points in the spectral dimension, does not apply when the object is a fit result.

    Value

    - - -

    ppm scale.

    +

    ppm scale.

    @@ -132,15 +136,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ppm.mrs_data.html b/docs/reference/ppm.mrs_data.html new file mode 100644 index 00000000..9251b9b6 --- /dev/null +++ b/docs/reference/ppm.mrs_data.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/precomp.html b/docs/reference/precomp.html index df3d2c6c..e21833e2 100644 --- a/docs/reference/precomp.html +++ b/docs/reference/precomp.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,17 @@

    Save function results to file and load on subsequent calls to avoid repeat c

    Arguments

    -
    file
    + + +
    file

    file name to write the results.

    -
    fun
    +
    fun

    function to run.

    -
    ...
    +
    ...

    arguments to be passed to fun.

    @@ -110,15 +116,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/preproc_svs.html b/docs/reference/preproc_svs.html index 244d9b3a..a96a133c 100644 --- a/docs/reference/preproc_svs.html +++ b/docs/reference/preproc_svs.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -83,6 +103,7 @@

    Preprocess and perform quality assessment of a single SVS data set.

    Arguments

    +<<<<<<< HEAD
    path

    path to the fMRS data file or IMA directory.

    @@ -96,6 +117,23 @@

    Arguments

    ref_inds
    +======= + + +
    path
    +

    path to the fMRS data file or IMA directory.

    + + +
    label
    +

    a label to describe the data set.

    + + +
    output_dir
    +

    output directory.

    + + +
    ref_inds
    +>>>>>>> devel

    a vector of 1-based indices for any water reference dynamic scans.

    @@ -113,15 +151,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/preproc_svs_dataset.html b/docs/reference/preproc_svs_dataset.html index 07c3a29b..fc2ba596 100644 --- a/docs/reference/preproc_svs_dataset.html +++ b/docs/reference/preproc_svs_dataset.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -91,6 +111,7 @@

    Preprocess and perform quality assessment of one or more SVS data sets.

    Arguments

    +<<<<<<< HEAD
    paths

    paths to the fMRS data file or IMA directory.

    @@ -104,20 +125,49 @@

    Arguments

    exclude_labels
    +======= + + +
    paths
    +

    paths to the fMRS data file or IMA directory.

    + + +
    labels
    +

    labels to describe each data set.

    + + +
    output_dir
    +

    output directory.

    + + +
    exclude_labels
    +>>>>>>> devel

    vector of labels of scans to exclude, eg poor quality data.

    +<<<<<<< HEAD
    overwrite

    overwrite saved results, defaults to FALSE.

    ref_inds
    +======= +
    overwrite
    +

    overwrite saved results, defaults to FALSE.

    + + +
    ref_inds
    +>>>>>>> devel

    a vector of 1-based indices for any water reference dynamic scans.

    +<<<<<<< HEAD
    return_results
    +======= +
    return_results
    +>>>>>>> devel

    function will return key outputs, defaults to FALSE.

    @@ -134,15 +184,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/print.fit_result.html b/docs/reference/print.fit_result.html index 5f434e57..1901e445 100644 --- a/docs/reference/print.fit_result.html +++ b/docs/reference/print.fit_result.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,17 +82,19 @@

    Print a summary of an object of class fit_result.

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 print(x, ...)

    Arguments

    -
    x
    + + +
    x

    fit_result object.

    -
    ...
    +
    ...

    further arguments.

    @@ -105,15 +111,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/print.mrs_data.html b/docs/reference/print.mrs_data.html index e1561eb2..64923f52 100644 --- a/docs/reference/print.mrs_data.html +++ b/docs/reference/print.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,21 +82,23 @@

    Print a summary of mrs_data parameters.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 print(x, full = FALSE, ...)

    Arguments

    -
    x
    + + +
    x

    mrs_data object.

    -
    full
    +
    full

    print all parameters (default FALSE).

    -
    ...
    +
    ...

    further arguments.

    @@ -109,15 +115,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/qn_states.html b/docs/reference/qn_states.html index d7aa6715..5da7126a 100644 --- a/docs/reference/qn_states.html +++ b/docs/reference/qn_states.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Get the quantum coherence matrix for a spin system.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    Value

    - - -

    quantum coherence number matrix.

    +

    quantum coherence number matrix.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rats.html b/docs/reference/rats.html index 93585e08..69d3fbcc 100644 --- a/docs/reference/rats.html +++ b/docs/reference/rats.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -103,95 +107,95 @@

    Robust Alignment to a Target Spectrum (RATS).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ref
    +
    ref

    optional MRS data to use as a reference, the mean of all dynamics is used if this argument is not supplied.

    -
    xlim
    +
    xlim

    optional frequency range to perform optimisation, set to NULL to use the full range.

    -
    max_shift
    +
    max_shift

    maximum allowable frequency shift in Hz.

    -
    p_deg
    +
    p_deg

    polynomial degree used for baseline modelling. Negative values disable baseline modelling.

    -
    sp_N
    +
    sp_N

    number of spline functions, note the true number will be sp_N + sp_deg.

    -
    sp_deg
    +
    sp_deg

    degree of spline functions.

    -
    max_t
    +
    max_t

    truncate the FID when longer than max_t to reduce time taken, set to NULL to use the entire FID.

    -
    basis_type
    +
    basis_type

    may be one of "poly" or "spline".

    -
    rescale_output
    +
    rescale_output

    rescale the bl_matched_spec and bl output to improve consistency between dynamic scans.

    -
    phase_corr
    +
    phase_corr

    apply phase correction (in addition to frequency). TRUE by default.

    -
    ret_corr_only
    +
    ret_corr_only

    return the corrected mrs_data object only.

    -
    zero_freq_shift_t0
    +
    zero_freq_shift_t0

    perform a linear fit to the frequency shifts and set the (linearly modeled) shift to be 0 Hz for the first dynamic scan.

    -
    remove_freq_outliers
    +
    remove_freq_outliers

    remove dynamics based on their frequency shift.

    -
    freq_outlier_thresh
    +
    freq_outlier_thresh

    threshold to remove frequency outliers.

    -
    remove_phase_outliers
    +
    remove_phase_outliers

    remove dynamics based on their phase shift.

    -
    phase_outlier_thresh
    +
    phase_outlier_thresh

    threshold to remove phase outliers.

    -
    remove_amp_outliers
    +
    remove_amp_outliers

    remove dynamics based on their amplitude change.

    -
    amp_outlier_thresh
    +
    amp_outlier_thresh

    threshold to remove amplitude outliers.

    Value

    - - -

    a list containing the corrected data; phase and shift values in units +

    a list containing the corrected data; phase and shift values in units of degrees and Hz respectively.

    @@ -207,15 +211,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/re_weighting.html b/docs/reference/re_weighting.html index 8b0b070a..e7179d09 100644 --- a/docs/reference/re_weighting.html +++ b/docs/reference/re_weighting.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Apply a weighting to the FID to enhance spectral resolution.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be enhanced.

    -
    re
    +
    re

    resolution enhancement factor (rising exponential factor).

    -
    alpha
    +
    alpha

    alpha factor (Gaussian decay)

    Value

    - - -

    resolution enhanced mrs_data.

    +

    resolution enhanced mrs_data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/readNifti.html b/docs/reference/readNifti.html new file mode 100644 index 00000000..3d3d7357 --- /dev/null +++ b/docs/reference/readNifti.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/read_basis.html b/docs/reference/read_basis.html index eb6f8557..af4fdc6e 100644 --- a/docs/reference/read_basis.html +++ b/docs/reference/read_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Read a basis file in LCModel .basis format.

    Arguments

    -
    basis_file
    + + +
    basis_file

    path to basis file.

    -
    ref
    +
    ref

    assumed ppm reference value.

    -
    sort_basis
    +
    sort_basis

    sort the basis set based on signal names.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_ima_coil_dir.html b/docs/reference/read_ima_coil_dir.html index 4f073cd8..c26faa62 100644 --- a/docs/reference/read_ima_coil_dir.html +++ b/docs/reference/read_ima_coil_dir.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,24 +91,24 @@

    Read a directory containing Siemens MRS IMA files and combine along the coil

    Arguments

    -
    dir
    + + +
    dir

    data directory path.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    -
    verbose
    +
    verbose

    output extra information to the console.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_ima_dyn_dir.html b/docs/reference/read_ima_dyn_dir.html index 881ec855..bfc6b46e 100644 --- a/docs/reference/read_ima_dyn_dir.html +++ b/docs/reference/read_ima_dyn_dir.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,24 +91,24 @@

    Read a directory containing Siemens MRS IMA files and combine along the dyna

    Arguments

    -
    dir
    + + +
    dir

    data directory path.

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    -
    verbose
    +
    verbose

    output extra information to the console.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_lcm_coord.html b/docs/reference/read_lcm_coord.html index 8c56374c..30e9dc73 100644 --- a/docs/reference/read_lcm_coord.html +++ b/docs/reference/read_lcm_coord.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Read an LCModel formatted coord file containing fit information.

    Arguments

    -
    coord_f
    + + +
    coord_f

    path to the coord file.

    Value

    - - -

    list containing a table of fit point and results structure containing +

    list containing a table of fit point and results structure containing signal amplitudes, errors and fitting diagnostics.

    @@ -107,15 +111,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_mrs.html b/docs/reference/read_mrs.html index 2cf36b20..97a680fb 100644 --- a/docs/reference/read_mrs.html +++ b/docs/reference/read_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -95,54 +99,60 @@

    Read MRS data from a file.

    Arguments

    -
    fname
    + + +
    fname

    filename of the dpt format MRS data.

    -
    format
    +
    format

    string describing the data format. Must be one of the following : "spar_sdat", "rda", "dicom", "twix", "pfile", "list_data", "paravis", "dpt", "lcm_raw", "rds", "nifti", "varian", "jmrui_txt". If not specified, the format will be guessed from the filename extension.

    -
    ft
    +
    ft

    transmitter frequency in Hz (required for list_data format).

    -
    fs
    +
    fs

    sampling frequency in Hz (required for list_data format).

    -
    ref
    +
    ref

    reference value for ppm scale (required for list_data format).

    -
    n_ref_scans
    +
    n_ref_scans

    override the number of water reference scans detected in the file header (GE p-file only).

    -
    full_fid
    +
    full_fid

    export all data points, including those before the start of the FID (default = FALSE), TWIX format only.

    -
    omit_svs_ref_scans
    +
    omit_svs_ref_scans

    remove any reference scans sometimes saved in SVS twix data (default = TRUE).

    -
    verbose
    +
    verbose

    print data file information (default = FALSE).

    -
    extra
    +
    extra

    an optional data frame to provide additional variables for use in subsequent analysis steps, eg id or grouping variables.

    +<<<<<<< HEAD
    fid_filt_dist
    +======= +
    fid_filt_dist
    +>>>>>>> devel

    indicate if the data has a distorted FID due to a brick-wall filter being used to downsample the data. Default is to auto detect this from the data, but TRUE or FALSE options can be given to override @@ -151,9 +161,7 @@

    Arguments

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    @@ -191,15 +199,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_mrs_tqn.html b/docs/reference/read_mrs_tqn.html index 84bdaf3a..3cc1d208 100644 --- a/docs/reference/read_mrs_tqn.html +++ b/docs/reference/read_mrs_tqn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,40 +87,40 @@

    Read MRS data using the TARQUIN software package.

    Arguments

    -
    fname
    + + +
    fname

    the filename containing the MRS data.

    -
    fname_ref
    +
    fname_ref

    a second filename containing reference MRS data.

    -
    format
    +
    format

    format of the MRS data. Can be one of the following: siemens, philips, ge, dcm, dpt, rda, lcm, varian, bruker, jmrui_txt.

    -
    id
    +
    id

    optional ID string.

    -
    group
    +
    group

    optional group string.

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    Examples

    fname <- system.file("extdata","philips_spar_sdat_WS.SDAT",package="spant")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 mrs_data <- read_mrs_tqn(fname, format="philips")
-}
+} # }
    @@ -131,15 +135,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_pulse_ascii.html b/docs/reference/read_pulse_ascii.html index ab11c9cc..c877f566 100644 --- a/docs/reference/read_pulse_ascii.html +++ b/docs/reference/read_pulse_ascii.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Read an ASCII formatted pulse file.

    Arguments

    -
    fname
    + + +
    fname

    ASCII formatted pulse file path.

    -
    deg2rad
    +
    deg2rad

    convert phase values stored in degrees to radians.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_pulse_bruker.html b/docs/reference/read_pulse_bruker.html index dbe9073b..ec3e45e8 100644 --- a/docs/reference/read_pulse_bruker.html +++ b/docs/reference/read_pulse_bruker.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Read a Bruker formatted pulse file

    Arguments

    -
    fname
    + + +
    fname

    Bruker formatted pulse file path.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_pulse_pta.html b/docs/reference/read_pulse_pta.html index a0fac3c3..504161fa 100644 --- a/docs/reference/read_pulse_pta.html +++ b/docs/reference/read_pulse_pta.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Read a .pta formatted pulse file compatible with Siemens PulseTool.

    Arguments

    -
    fname
    + + +
    fname

    pta formatted pulse file path.

    Value

    - - -

    pulse waveform and header.

    +

    pulse waveform and header.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_siemens_txt_hdr.html b/docs/reference/read_siemens_txt_hdr.html index 3a17d87c..e9db06f9 100644 --- a/docs/reference/read_siemens_txt_hdr.html +++ b/docs/reference/read_siemens_txt_hdr.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Read the text format header found in Siemens IMA and TWIX data files.

    Arguments

    -
    input
    + + +
    input

    file name to read or raw data.

    -
    version
    +
    version

    software version, can be "vb" or "vd".

    -
    verbose
    +
    verbose

    print information to the console.

    -
    offset
    +
    offset

    offset to begin searching for the text header.

    Value

    - - -

    a list of parameter values

    +

    a list of parameter values

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_tqn_fit.html b/docs/reference/read_tqn_fit.html index a1630420..229fbef7 100644 --- a/docs/reference/read_tqn_fit.html +++ b/docs/reference/read_tqn_fit.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,22 +87,22 @@

    Reader for csv fit results generated by TARQUIN.

    Arguments

    -
    fit_f
    + + +
    fit_f

    TARQUIN fit file.

    Value

    - - -

    A data frame of the fit data points.

    +

    A data frame of the fit data points.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 fit <- read_tqn_fit(system.file("extdata","fit.csv",package="spant"))
-}
+} # }
    @@ -113,15 +117,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/read_tqn_result.html b/docs/reference/read_tqn_result.html index 68a3e98c..921e68e3 100644 --- a/docs/reference/read_tqn_result.html +++ b/docs/reference/read_tqn_result.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,26 +87,26 @@

    Reader for csv results generated by TARQUIN.

    Arguments

    -
    result_f
    + + +
    result_f

    TARQUIN result file.

    -
    remove_rcs
    +
    remove_rcs

    omit row, column and slice ids from output.

    Value

    - - -

    list of amplitudes, crlbs and diagnostics.

    +

    list of amplitudes, crlbs and diagnostics.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 result <- read_tqn_result(system.file("extdata","result.csv",package="spant"))
-}
+} # }
    @@ -117,15 +121,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/recon_imag.html b/docs/reference/recon_imag.html index 5bc3b1eb..4177457f 100644 --- a/docs/reference/recon_imag.html +++ b/docs/reference/recon_imag.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Reconstruct complex time-domain data from the real part of frequency-domain

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    reconstructed MRS data.

    +

    reconstructed MRS data.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/recon_imag_vec.html b/docs/reference/recon_imag_vec.html index 93d04faa..3a7e3aac 100644 --- a/docs/reference/recon_imag_vec.html +++ b/docs/reference/recon_imag_vec.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Reconstruct complex time-domain data from the real part of frequency-domain

    Arguments

    -
    data
    + + +
    data

    data points in the frequency domain.

    Value

    - - -

    reconstructed signal.

    +

    reconstructed signal.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/recon_twix_2d_mrsi.html b/docs/reference/recon_twix_2d_mrsi.html index 05a046c7..08f7c977 100644 --- a/docs/reference/recon_twix_2d_mrsi.html +++ b/docs/reference/recon_twix_2d_mrsi.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Reconstruct 2D MRSI data from a twix file loaded with read_mrs.

    Arguments

    -
    twix_mrs
    + + +
    twix_mrs

    raw dynamic data.

    Value

    - - -

    reconstructed data.

    +

    reconstructed data.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rectangular_mask.html b/docs/reference/rectangular_mask.html index 6e469bc9..5b0af670 100644 --- a/docs/reference/rectangular_mask.html +++ b/docs/reference/rectangular_mask.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,39 +87,39 @@

    Create a rectangular mask stored as a matrix of logical values.

    Arguments

    -
    xN
    + + +
    xN

    number of pixels in the x dimension.

    -
    yN
    +
    yN

    number of pixels in the y dimension.

    -
    x0
    +
    x0

    centre of rectangle in the x direction in units of pixels.

    -
    y0
    +
    y0

    centre of rectangle in the y direction in units of pixels.

    -
    xw
    +
    xw

    width in the x direction in units of pixels.

    -
    yw
    +
    yw

    width in the y direction in units of pixels.

    -
    angle
    +
    angle

    angle of rotation in degrees.

    Value

    - - -

    logical mask matrix with dimensions fov_yN x fov_xN.

    +

    logical mask matrix with dimensions fov_yN x fov_xN.

    @@ -130,15 +134,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index a59e8379..cc06d58e 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -10,7 +10,7 @@ - +
    @@ -35,7 +39,7 @@
    • - +
    @@ -103,15 +107,19 @@

    Objects exported from other packages

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rep_array_dim.html b/docs/reference/rep_array_dim.html index 48c0a5ed..728455e0 100644 --- a/docs/reference/rep_array_dim.html +++ b/docs/reference/rep_array_dim.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Repeat an array over a given dimension.

    Arguments

    -
    x
    + + +
    x

    array.

    -
    rep_dim
    +
    rep_dim

    dimension to extend.

    -
    n
    +
    n

    number of times to repeat.

    Value

    - - -

    extended array.

    +

    extended array.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rep_dyn.html b/docs/reference/rep_dyn.html index 89a4bb9b..014a7a0f 100644 --- a/docs/reference/rep_dyn.html +++ b/docs/reference/rep_dyn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Replicate a scan in the dynamic dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be replicated.

    -
    times
    +
    times

    number of times to replicate.

    Value

    - - -

    replicated data object.

    +

    replicated data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rep_mrs.html b/docs/reference/rep_mrs.html index becb8f00..b0f602d5 100644 --- a/docs/reference/rep_mrs.html +++ b/docs/reference/rep_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,39 +95,39 @@

    Replicate a scan over a given dimension.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be replicated.

    -
    x_rep
    +
    x_rep

    number of x replications.

    -
    y_rep
    +
    y_rep

    number of y replications.

    -
    z_rep
    +
    z_rep

    number of z replications.

    -
    dyn_rep
    +
    dyn_rep

    number of dynamic replications.

    -
    coil_rep
    +
    coil_rep

    number of coil replications.

    -
    warn
    +
    warn

    print a warning when the data dimensions do not change.

    Value

    - - -

    replicated data object.

    +

    replicated data object.

    @@ -138,15 +142,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/resample_basis.html b/docs/reference/resample_basis.html index c7a6222a..817982f3 100644 --- a/docs/reference/resample_basis.html +++ b/docs/reference/resample_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Resample a basis-set to match a mrs_data acquisition.

    Arguments

    -
    basis
    + + +
    basis

    the basis to be resampled.

    -
    mrs_data
    +
    mrs_data

    the mrs_data to match the number of data points and sampling frequency.

    -
    ref_freq_match
    +
    ref_freq_match

    apply a frequency shift to the basis to match the reference frequency (usually 4.65 or 4.68) of the mrs_data.

    Value

    - - -

    resampled basis set object.

    +

    resampled basis set object.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/resample_img.html b/docs/reference/resample_img.html index b0cc8f71..43f3c24f 100644 --- a/docs/reference/resample_img.html +++ b/docs/reference/resample_img.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Resample an image to match a target image space.

    Arguments

    -
    source
    + + +
    source

    image data as a nifti object.

    -
    target
    +
    target

    image data as a nifti object.

    -
    interp
    +
    interp

    interpolation parameter, see nifyreg.linear definition.

    Value

    - - -

    resampled image data as a nifti object.

    +

    resampled image data as a nifti object.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/resample_voi.html b/docs/reference/resample_voi.html index a29ab096..c0db6943 100644 --- a/docs/reference/resample_voi.html +++ b/docs/reference/resample_voi.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Resample a VOI to match a target image space using nearest-neighbour interpo

    Arguments

    -
    voi
    + + +
    voi

    volume data as a nifti object.

    -
    mri
    +
    mri

    image data as a nifti object.

    Value

    - - -

    volume data as a nifti object.

    +

    volume data as a nifti object.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/reslice_to_mrs.html b/docs/reference/reslice_to_mrs.html index db8b48fe..fe74f820 100644 --- a/docs/reference/reslice_to_mrs.html +++ b/docs/reference/reslice_to_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Reslice a nifti object to match the orientation of mrs data.

    Arguments

    -
    mri
    + + +
    mri

    nifti object to be resliced.

    -
    mrs
    +
    mrs

    mrs_data object for the target orientation.

    -
    interp
    +
    interp

    interpolation parameter, see nifyreg.linear definition.

    Value

    - - -

    resliced imaging data.

    +

    resliced imaging data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/reson_table2mrs_data.html b/docs/reference/reson_table2mrs_data.html index c5a2167a..ca8bcd4f 100644 --- a/docs/reference/reson_table2mrs_data.html +++ b/docs/reference/reson_table2mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -87,24 +91,24 @@

    Generate mrs_data from a table of single Lorentzian resonances.

    Arguments

    -
    reson_table
    + + +
    reson_table

    as produced by the hsvd function.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters. See

    -
    back_extrap_pts
    +
    back_extrap_pts

    number of data points to back extrapolate def_acq_paras

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -119,15 +123,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/rm_dyns.html b/docs/reference/rm_dyns.html index 573e1f51..5e3fd437 100644 --- a/docs/reference/rm_dyns.html +++ b/docs/reference/rm_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Remove a subset of dynamic scans.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    subset
    +
    subset

    vector containing indices to the dynamic scans to be removed.

    Value

    - - -

    MRS data without the specified dynamic scans.

    +

    MRS data without the specified dynamic scans.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_molal.html b/docs/reference/scale_amp_molal.html index 7acb8cb0..7e742d2b 100644 --- a/docs/reference/scale_amp_molal.html +++ b/docs/reference/scale_amp_molal.html @@ -9,7 +9,7 @@ - +
    @@ -34,7 +38,7 @@
    • - +
    @@ -105,47 +109,47 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    te
    +
    te

    the MRS TE in seconds.

    -
    tr
    +
    tr

    the MRS TR in seconds.

    -
    water_t1
    +
    water_t1

    assumed water T1 value.

    -
    water_t2
    +
    water_t2

    assumed water T2 value.

    -
    metab_t1
    +
    metab_t1

    assumed metabolite T1 value.

    -
    metab_t2
    +
    metab_t2

    assumed metabolite T2 value.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    A fit_result object with a rescaled results table.

    +

    A fit_result object with a rescaled results table.

    @@ -160,15 +164,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_molal_pvc.html b/docs/reference/scale_amp_molal_pvc.html index 4d194abd..c1a2a644 100644 --- a/docs/reference/scale_amp_molal_pvc.html +++ b/docs/reference/scale_amp_molal_pvc.html @@ -8,7 +8,7 @@ - +
    @@ -33,7 +37,7 @@
    • - +
    @@ -93,37 +97,37 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. For example, a voxel containing 100% white matter tissue would use : p_vols = c(WM = 100, GM = 0, CSF = 0).

    -
    te
    +
    te

    the MRS TE in seconds.

    -
    tr
    +
    tr

    the MRS TR in seconds.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    A fit_result object with a rescaled results table.

    +

    A fit_result object with a rescaled results table.

    @@ -138,15 +142,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_molar.html b/docs/reference/scale_amp_molar.html index dc87a338..12fe2028 100644 --- a/docs/reference/scale_amp_molar.html +++ b/docs/reference/scale_amp_molar.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -89,34 +93,34 @@

    Apply water reference scaling to a fitting results object to yield metabolit

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    ref_data
    +
    ref_data

    water reference MRS data object.

    -
    w_att
    +
    w_att

    water attenuation factor (default = 0.7). Assumes water T2 of 80ms and a TE = 30 ms. exp(-30ms / 80ms) ~ 0.7.

    -
    w_conc
    +
    w_conc

    assumed water concentration (default = 35880). Default value corresponds to typical white matter. Set to 43300 for gray matter, and 55556 for phantom measurements.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -131,15 +135,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_molar2molal_pvc.html b/docs/reference/scale_amp_molar2molal_pvc.html index 1b79a8fa..1b62af44 100644 --- a/docs/reference/scale_amp_molar2molal_pvc.html +++ b/docs/reference/scale_amp_molar2molal_pvc.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,30 +89,30 @@

    Convert default LCM/TARQUIN concentration scaling to molal units with partia

    Arguments

    -
    fit_result
    + + +
    fit_result

    a fit_result object to apply partial volume correction.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. For example, a voxel containing 100% white matter tissue would use : p_vols = c(WM = 100, GM = 0, CSF = 0).

    -
    te
    +
    te

    the MRS TE.

    -
    tr
    +
    tr

    the MRS TR.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -123,15 +127,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_ratio.html b/docs/reference/scale_amp_ratio.html index 518b773c..ffea2d25 100644 --- a/docs/reference/scale_amp_ratio.html +++ b/docs/reference/scale_amp_ratio.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,25 +87,25 @@

    Scale fitted amplitudes to a ratio of signal amplitude.

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    name
    +
    name

    the signal name to use as a denominator (usually, "tCr" or "tNAA").

    -
    use_mean_value
    +
    use_mean_value

    scales the result by the mean of the signal when set to TRUE.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_ratio_value.html b/docs/reference/scale_amp_ratio_value.html index 6af8ac51..e860f4da 100644 --- a/docs/reference/scale_amp_ratio_value.html +++ b/docs/reference/scale_amp_ratio_value.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Scale fitted amplitudes to a ratio of signal amplitude.

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    value
    +
    value

    the number use as a denominator.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_amp_water_ratio.html b/docs/reference/scale_amp_water_ratio.html index 35a76b00..0dae8dba 100644 --- a/docs/reference/scale_amp_water_ratio.html +++ b/docs/reference/scale_amp_water_ratio.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude.<

    Arguments

    -
    fit_result
    + + +
    fit_result

    a result object generated from fitting.

    -
    ref_data
    +
    ref_data

    a water reference MRS data object.

    -
    ...
    +
    ...

    additional arguments to get_td_amp function.

    Value

    - - -

    a fit_result object with a rescaled results table.

    +

    a fit_result object with a rescaled results table.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_basis_amp.html b/docs/reference/scale_basis_amp.html index 5a58b5e5..d7321b68 100644 --- a/docs/reference/scale_basis_amp.html +++ b/docs/reference/scale_basis_amp.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Scale a basis object by a scalar.

    Arguments

    -
    basis
    + + +
    basis

    basis_set object to be scaled.

    -
    amp
    +
    amp

    multiplicative factor with length 1.

    Value

    - - -

    basis_set object multiplied by the amplitude scale factor.

    +

    basis_set object multiplied by the amplitude scale factor.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_basis_from_singlet.html b/docs/reference/scale_basis_from_singlet.html index c9a19e77..cd46d35c 100644 --- a/docs/reference/scale_basis_from_singlet.html +++ b/docs/reference/scale_basis_from_singlet.html @@ -9,7 +9,7 @@ - +
    @@ -34,7 +38,7 @@
    • - +
    @@ -95,24 +99,24 @@

    Scale a basis-set to be consistent with spant assumptions for water scaling.

    Arguments

    -
    basis
    + + +
    basis

    basis set to be scaled.

    -
    name
    +
    name

    the name of the singlet to be used as a scaling reference.

    -
    protons
    +
    protons

    the number of MRS visible protons contributing to the singlet resonance.

    Value

    - - -

    a scaled basis.

    +

    a scaled basis.

    @@ -127,15 +131,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_mrs_amp.html b/docs/reference/scale_mrs_amp.html index 990f058a..58099f92 100644 --- a/docs/reference/scale_mrs_amp.html +++ b/docs/reference/scale_mrs_amp.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,20 +87,20 @@

    Scale an mrs_data object by a scalar or vector or amplitudes.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be scaled.

    -
    amp
    +
    amp

    multiplicative factor, must have length equal to 1 or Nspec(mrs_data).

    Value

    - - -

    mrs_data object multiplied by the amplitude scale factor.

    +

    mrs_data object multiplied by the amplitude scale factor.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/scale_spec.html b/docs/reference/scale_spec.html index 6b3ddba4..00b3659c 100644 --- a/docs/reference/scale_spec.html +++ b/docs/reference/scale_spec.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,42 +95,42 @@

    Scale mrs_data to a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    -
    operator
    +
    operator

    can be "sum" (default), "mean", "l2", "max", "min" or "max-min".

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "Hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    -
    mean_dyns
    +
    mean_dyns

    mean the dynamic scans before applying the operator. The same scaling value will be applied to each individual dynamic.

    -
    ret_scale_factor
    +
    ret_scale_factor

    option to return the scaling factor in addition to the scaled data.

    Value

    - - -

    normalised data.

    +

    normalised data.

    @@ -141,15 +145,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sd.html b/docs/reference/sd.html index 3ae4dfd4..44a1e446 100644 --- a/docs/reference/sd.html +++ b/docs/reference/sd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Calculate the standard deviation spectrum from an mrs_data object.

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    na.rm
    +
    na.rm

    remove NA values.

    Value

    - - -

    sd mrs_data object.

    +

    sd mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sd.mrs_data.html b/docs/reference/sd.mrs_data.html index 13bdda85..9c23b926 100644 --- a/docs/reference/sd.mrs_data.html +++ b/docs/reference/sd.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,25 +82,25 @@

    Calculate the standard deviation spectrum from an mrs_data object.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 sd(x, na.rm = FALSE)

    Arguments

    -
    x
    + + +
    x

    object of class mrs_data.

    -
    na.rm
    +
    na.rm

    remove NA values.

    Value

    - - -

    sd mrs_data object.

    +

    sd mrs_data object.

    @@ -111,15 +115,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seconds.html b/docs/reference/seconds.html index 467ee17f..0fa9868c 100644 --- a/docs/reference/seconds.html +++ b/docs/reference/seconds.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return a time scale vector to match the FID of an MRS data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    time scale vector in units of seconds.

    +

    time scale vector in units of seconds.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_cpmg_ideal.html b/docs/reference/seq_cpmg_ideal.html index 45727c86..fa59ccb1 100644 --- a/docs/reference/seq_cpmg_ideal.html +++ b/docs/reference/seq_cpmg_ideal.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    CPMG style sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    echo time in seconds.

    -
    echoes
    +
    echoes

    number of echoes.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_mega_press_ideal.html b/docs/reference/seq_mega_press_ideal.html index a9cd7fa0..05a248e8 100644 --- a/docs/reference/seq_mega_press_ideal.html +++ b/docs/reference/seq_mega_press_ideal.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -94,43 +98,43 @@

    MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editi

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    ed_freq
    +
    ed_freq

    editing pulse frequency in ppm.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    -
    BW
    +
    BW

    editing pulse bandwidth in Hz.

    -
    steps
    +
    steps

    number of hard pulses used to approximate the editing pulse.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -145,15 +149,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_press_2d_shaped.html b/docs/reference/seq_press_2d_shaped.html index 9f76b6e0..afcc419e 100644 --- a/docs/reference/seq_press_2d_shaped.html +++ b/docs/reference/seq_press_2d_shaped.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -96,61 +100,61 @@

    PRESS sequence with shaped refocusing pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    -
    pulse_file
    +
    pulse_file

    path to refocusing pulse file.

    -
    pulse_dur
    +
    pulse_dur

    refocusing pulse duration.

    -
    pulse_file_format
    +
    pulse_file_format

    file format for the refocusing pulse.

    -
    refoc_flip_angle
    +
    refoc_flip_angle

    refocusing pulse flip angle in degrees (defaults to 180).

    -
    xy_pulse_ppm
    +
    xy_pulse_ppm

    a vector of ppm values for the offset of each sub-simulation.

    -
    resamp
    +
    resamp

    option to resample the pulse shape.

    -
    fs_resamp
    +
    fs_resamp

    sampling frequency (Hz) to resample.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -165,15 +169,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_press_ideal.html b/docs/reference/seq_press_ideal.html index 72c3af3d..c295b612 100644 --- a/docs/reference/seq_press_ideal.html +++ b/docs/reference/seq_press_ideal.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    PRESS sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    TE1 sequence parameter in seconds (TE=TE1+TE2).

    -
    TE2
    +
    TE2

    TE2 sequence parameter in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_pulse_acquire.html b/docs/reference/seq_pulse_acquire.html index ad80571e..c5c35ffa 100644 --- a/docs/reference/seq_pulse_acquire.html +++ b/docs/reference/seq_pulse_acquire.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Simple pulse and acquire sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    acquisition nucleus.

    -
    acq_delay
    +
    acq_delay

    delay between excitation and acquisition.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_slaser_ideal.html b/docs/reference/seq_slaser_ideal.html index eb83e8e3..c2fcdf17 100644 --- a/docs/reference/seq_slaser_ideal.html +++ b/docs/reference/seq_slaser_ideal.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,35 +87,35 @@

    sLASER sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE1
    +
    TE1

    first echo time (between exc. and 1st echo) in seconds.

    -
    TE2
    +
    TE2

    second echo time (between 2nd echo and 4th echo) in seconds.

    -
    TE3
    +
    TE3

    third echo time (between 4th echo and 5th echo) in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -126,15 +130,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_spin_echo_ideal.html b/docs/reference/seq_spin_echo_ideal.html index 4248716f..8948e8f5 100644 --- a/docs/reference/seq_spin_echo_ideal.html +++ b/docs/reference/seq_spin_echo_ideal.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Spin echo sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    acquisition nucleus.

    -
    TE
    +
    TE

    echo time in seconds.

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_steam_ideal.html b/docs/reference/seq_steam_ideal.html index 1c8115d7..5f4bcca4 100644 --- a/docs/reference/seq_steam_ideal.html +++ b/docs/reference/seq_steam_ideal.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,29 @@

    STEAM sequence with ideal pulses.

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -111,9 +117,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -128,15 +132,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_steam_ideal_cof.html b/docs/reference/seq_steam_ideal_cof.html index cba7af91..e54e875b 100644 --- a/docs/reference/seq_steam_ideal_cof.html +++ b/docs/reference/seq_steam_ideal_cof.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,27 +89,29 @@

    STEAM sequence with ideal pulses and coherence order filtering to simulate g

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -113,9 +119,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -130,15 +134,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/seq_steam_ideal_young.html b/docs/reference/seq_steam_ideal_young.html index 59770b48..53da07a2 100644 --- a/docs/reference/seq_steam_ideal_young.html +++ b/docs/reference/seq_steam_ideal_young.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -92,27 +96,29 @@

    STEAM sequence with ideal pulses using the z-rotation gradient simulation me

    Arguments

    -
    spin_params
    + + +
    spin_params

    spin system definition.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    TE
    +
    TE

    sequence parameter in seconds.

    -
    TM
    +
    TM

    sequence parameter in seconds.

    -
    amp_scale
    +
    amp_scale

    amplitude scaling factor. Set to 2 (default) to ensure correct scaling for water reference scaling. Set to 1 to maintain the inherent loss of signal associated with STEAM.

    @@ -120,9 +126,7 @@

    Arguments

    Value

    - - -

    list of resonance amplitudes and frequencies.

    +

    list of resonance amplitudes and frequencies.

    @@ -137,15 +141,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_Ntrans.html b/docs/reference/set_Ntrans.html index 6abeeb7f..639ce179 100644 --- a/docs/reference/set_Ntrans.html +++ b/docs/reference/set_Ntrans.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Set the number of transients for an mrs_data object.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    n_trans
    +
    n_trans

    number of acquired transients.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_def_acq_paras.html b/docs/reference/set_def_acq_paras.html index cc2ada9c..505fdf79 100644 --- a/docs/reference/set_def_acq_paras.html +++ b/docs/reference/set_def_acq_paras.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -89,23 +93,25 @@

    Set the default acquisition parameters.

    Arguments

    -
    ft
    + + +
    ft

    transmitter frequency in Hz.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    @@ -122,15 +128,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_lcm_cmd.html b/docs/reference/set_lcm_cmd.html index 42bb2f24..1f1a9df8 100644 --- a/docs/reference/set_lcm_cmd.html +++ b/docs/reference/set_lcm_cmd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Set the command to run the LCModel command-line program.

    Arguments

    -
    cmd
    + + +
    cmd

    path to binary.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_lw.html b/docs/reference/set_lw.html index bb176c62..28fa1290 100644 --- a/docs/reference/set_lw.html +++ b/docs/reference/set_lw.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,32 +87,32 @@

    Apply line-broadening to an mrs_data object to achieve a specified linewidth

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data in.

    -
    lw
    +
    lw

    target linewidth in units of ppm.

    -
    xlim
    +
    xlim

    region to search for peaks to obtain a linewidth estimate.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter.

    -
    mask_narrow
    +
    mask_narrow

    masks spectra where the requested linewidth is too narrow, if set FALSE the spectra are not changed.

    Value

    - - -

    line-broadened data.

    +

    line-broadened data.

    @@ -123,15 +127,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_mask_xy_mat.html b/docs/reference/set_mask_xy_mat.html index 52c4b617..d60dc21e 100644 --- a/docs/reference/set_mask_xy_mat.html +++ b/docs/reference/set_mask_xy_mat.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Set the masked voxels in a 2D MRSI dataset to given spectrum.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data object.

    -
    mask
    +
    mask

    matrix of boolean values specifying the voxels to set, where a value of TRUE indicates the voxel should be set to mask_mrs_data.

    -
    mask_mrs_data
    +
    mask_mrs_data

    the spectral data to be assigned to the masked voxels.

    Value

    - - -

    updated dataset.

    +

    updated dataset.

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_precomp_mode.html b/docs/reference/set_precomp_mode.html index 47c28e3b..e1bb699b 100644 --- a/docs/reference/set_precomp_mode.html +++ b/docs/reference/set_precomp_mode.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Set the precompute mode.

    Arguments

    -
    mode
    + + +
    mode

    can be one of: "default", "overwrite", "clean" or "disabled".

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_precomp_verbose.html b/docs/reference/set_precomp_verbose.html index 9c613505..68a1ca9c 100644 --- a/docs/reference/set_precomp_verbose.html +++ b/docs/reference/set_precomp_verbose.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Set the verbosity of the precompute function.

    Arguments

    -
    verbose
    + + +
    verbose

    can be TRUE or FALSE.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_ref.html b/docs/reference/set_ref.html index 5436dfa2..7f46c46a 100644 --- a/docs/reference/set_ref.html +++ b/docs/reference/set_ref.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Set the ppm reference value (eg ppm value at 0Hz).

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    ref
    +
    ref

    reference value for ppm scale.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_td_pts.html b/docs/reference/set_td_pts.html index 586459ff..dd04214e 100644 --- a/docs/reference/set_td_pts.html +++ b/docs/reference/set_td_pts.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,19 +89,19 @@

    Set the number of time-domain data points, truncating or zero-filling as app

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of data points.

    Value

    - - -

    MRS data with pts data points.

    +

    MRS data with pts data points.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_tqn_cmd.html b/docs/reference/set_tqn_cmd.html index be34269c..4d656806 100644 --- a/docs/reference/set_tqn_cmd.html +++ b/docs/reference/set_tqn_cmd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,7 +87,9 @@

    Set the command to run the TARQUIN command-line program.

    Arguments

    -
    cmd
    + + +
    cmd

    path to binary.

    @@ -100,15 +106,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/set_tr.html b/docs/reference/set_tr.html index 65c9df5f..495efe57 100644 --- a/docs/reference/set_tr.html +++ b/docs/reference/set_tr.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Set the repetition time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    tr
    +
    tr

    repetition time in seconds.

    Value

    - - -

    updated mrs_data set.

    +

    updated mrs_data set.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/shift.html b/docs/reference/shift.html index 034591d0..dbe84d18 100644 --- a/docs/reference/shift.html +++ b/docs/reference/shift.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,23 +87,23 @@

    Apply a frequency shift to MRS data.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    shift
    +
    shift

    frequency shift (in ppm by default).

    -
    units
    +
    units

    of the shift ("ppm" or "hz").

    Value

    - - -

    frequency shifted MRS data.

    +

    frequency shifted MRS data.

    @@ -114,15 +118,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/shift_basis.html b/docs/reference/shift_basis.html index f55a65e0..bc3872fe 100644 --- a/docs/reference/shift_basis.html +++ b/docs/reference/shift_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Apply frequency shifts to basis set signals.

    Arguments

    -
    basis
    + + +
    basis

    the basis to apply the shift to.

    -
    shifts
    +
    shifts

    a vector of frequency shifts to apply in ppm units. Must be the same length as there are basis elements, or one value to be applied to all elements.

    @@ -95,9 +101,7 @@

    Arguments

    Value

    - - -

    modified basis set object.

    +

    modified basis set object.

    @@ -112,15 +116,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_basis.html b/docs/reference/sim_basis.html index bb5fefc6..c2e34095 100644 --- a/docs/reference/sim_basis.html +++ b/docs/reference/sim_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -90,38 +94,38 @@

    Simulate a basis set object.

    Arguments

    -
    mol_list
    + + +
    mol_list

    list of mol_parameter objects. Alternatively, a character vector matching molecules may also be provided. Use the get_mol_names function for a full list of molecules.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    -
    xlim
    +
    xlim

    ppm range limiting signals to be simulated.

    -
    verbose
    +
    verbose

    output simulation progress and timings.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -136,15 +140,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_basis_1h_brain.html b/docs/reference/sim_basis_1h_brain.html index f71ffa0b..59575f22 100644 --- a/docs/reference/sim_basis_1h_brain.html +++ b/docs/reference/sim_basis_1h_brain.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -91,33 +95,33 @@

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRES

    Arguments

    -
    pul_seq
    + + +
    pul_seq

    pulse sequence function to use.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras.

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    lcm_compat
    +
    lcm_compat

    exclude lipid and MM signals for use with default LCModel options.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -132,15 +136,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_basis_1h_brain_press.html b/docs/reference/sim_basis_1h_brain_press.html index 39b907f6..083217fb 100644 --- a/docs/reference/sim_basis_1h_brain_press.html +++ b/docs/reference/sim_basis_1h_brain_press.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -91,33 +95,33 @@

    Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRES

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    lcm_compat
    +
    lcm_compat

    exclude lipid and MM signals for use with default LCModel options.

    -
    TE1
    +
    TE1

    TE1 of PRESS sequence (TE = TE1 + TE2).

    -
    TE2
    +
    TE2

    TE2 of PRESS sequence.

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -132,15 +136,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_basis_mm_lip_lcm.html b/docs/reference/sim_basis_mm_lip_lcm.html index bcd65d9a..f1d379e1 100644 --- a/docs/reference/sim_basis_mm_lip_lcm.html +++ b/docs/reference/sim_basis_mm_lip_lcm.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,16 +89,16 @@

    Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS anal

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras

    Value

    - - -

    basis object.

    +

    basis object.

    @@ -109,15 +113,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_basis_tqn.html b/docs/reference/sim_basis_tqn.html index 6aea77ec..7dc43944 100644 --- a/docs/reference/sim_basis_tqn.html +++ b/docs/reference/sim_basis_tqn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -89,32 +93,34 @@

    Simulate a basis file using TARQUIN.

    Arguments

    -
    fs
    + + +
    fs

    sampling frequency

    -
    ft
    +
    ft

    transmitter frequency

    -
    N
    +
    N

    number of data points

    -
    ref
    +
    ref

    chemical shift reference

    -
    opts
    +
    opts

    list of options to pass to TARQUIN.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 write_basis_tqn('test.basis',mrs_data,c("--echo","0.04"))
-}
+} # }
    @@ -129,15 +135,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_brain_1h.html b/docs/reference/sim_brain_1h.html index 717ee289..1538f40c 100644 --- a/docs/reference/sim_brain_1h.html +++ b/docs/reference/sim_brain_1h.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,57 +98,57 @@

    Simulate MRS data with a similar appearance to normal brain (by default).

    Arguments

    -
    acq_paras
    + + +
    acq_paras

    list of acquisition parameters or an mrs_data object. See def_acq_paras.

    -
    type
    +
    type

    type of spectrum, only "normal" is implemented currently.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    xlim
    +
    xlim

    range of frequencies to simulate in ppm.

    -
    full_output
    +
    full_output

    when FALSE (default) only output the simulated MRS data. When TRUE output a list containing the MRS data, basis set object and corresponding amplitudes.

    -
    amps
    +
    amps

    a vector of basis amplitudes may be specified to modify the output spectrum.

    -
    basis_lb
    +
    basis_lb

    apply additional Gaussian line-broadening to the basis (Hz).

    -
    zero_lip_mm
    +
    zero_lip_mm

    zero the amplitudes of any lipid or macromolecular components based on their name starting with "MM" or "Lip".

    -
    remove_lip_mm
    +
    remove_lip_mm

    remove any lipid or macromolecular basis components based on their name starting with "MM" or "Lip".

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    see full_output option.

    +

    see full_output option.

    @@ -159,15 +163,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_mol.html b/docs/reference/sim_mol.html index 77f76a50..796f7412 100644 --- a/docs/reference/sim_mol.html +++ b/docs/reference/sim_mol.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,43 +96,43 @@

    Simulate a mol_parameter object.

    Arguments

    -
    mol
    + + +
    mol

    mol_parameter object.

    -
    pul_seq
    +
    pul_seq

    pulse sequence function to use.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    xlim
    +
    xlim

    ppm range limiting signals to be simulated.

    -
    ...
    +
    ...

    extra parameters to pass to the pulse sequence function.

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -143,15 +147,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_noise.html b/docs/reference/sim_noise.html index a71477d4..ddc055ce 100644 --- a/docs/reference/sim_noise.html +++ b/docs/reference/sim_noise.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,43 +96,51 @@

    Simulate an mrs_data object containing simulated Gaussian noise.

    Arguments

    -
    sd
    + + +
    sd

    standard deviation of the noise.

    -
    fs
    +
    fs

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    N
    +
    N

    number of data points in the spectral dimension.

    -
    ref
    +
    ref

    reference value for ppm scale.

    +<<<<<<< HEAD
    nuc

    resonant nucleus.

    dyns
    +======= +
    nuc
    +

    resonant nucleus.

    + + +
    dyns
    +>>>>>>> devel

    number of dynamic scans to generate.

    -
    fd
    +
    fd

    return data in the frequency-domain (TRUE) or time-domain (FALSE)

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -143,15 +155,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_resonances.html b/docs/reference/sim_resonances.html index d4f8d7c0..7493cb9f 100644 --- a/docs/reference/sim_resonances.html +++ b/docs/reference/sim_resonances.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -94,54 +98,54 @@

    Simulate a MRS data object containing a set of simulated resonances.

    Arguments

    -
    freq
    + + +
    freq

    resonance frequency.

    -
    amp
    +
    amp

    resonance amplitude.

    -
    lw
    +
    lw

    line width in Hz.

    -
    lg
    +
    lg

    Lorentz-Gauss lineshape parameter (between 0 and 1).

    -
    phase
    +
    phase

    phase in degrees.

    -
    freq_ppm
    +
    freq_ppm

    frequencies are given in ppm units if set to TRUE, otherwise Hz are assumed.

    -
    acq_paras
    +
    acq_paras

    list of acquisition parameters. See def_acq_paras

    -
    fp_scale
    +
    fp_scale

    multiply the first data point by 0.5.

    -
    back_extrap_pts
    +
    back_extrap_pts

    number of data points to back extrapolate.

    -
    sum_resonances
    +
    sum_resonances

    sum all resonances (default is TRUE), otherwise return a dynamic mrs_data object.

    Value

    - - -

    MRS data object.

    +

    MRS data object.

    @@ -161,15 +165,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_th_excit_profile.html b/docs/reference/sim_th_excit_profile.html index e781cab1..cd87f6a4 100644 --- a/docs/reference/sim_th_excit_profile.html +++ b/docs/reference/sim_th_excit_profile.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,23 +89,23 @@

    Simulate an ideal pulse excitation profile by smoothing a top-hat function w

    Arguments

    -
    bw
    + + +
    bw

    top-hat bandwidth (Hz).

    -
    sigma
    +
    sigma

    Gaussian width smoothing parameter (Hz).

    -
    fa
    +
    fa

    intended flip angle of the pulse.

    Value

    - - -

    data frame containing the frequency scale, excitation profile and +

    data frame containing the frequency scale, excitation profile and corresponding flip-angles.

    @@ -117,15 +121,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sim_zero.html b/docs/reference/sim_zero.html index 9fefb5ee..8e9dbb81 100644 --- a/docs/reference/sim_zero.html +++ b/docs/reference/sim_zero.html @@ -17,8 +17,12 @@ Spectroscopy Analysis Tools (spant) +<<<<<<< HEAD <<<<<<< HEAD 2.22.0 +======= + 2.23.0 +>>>>>>> devel ======= 2.23.0 >>>>>>> devel @@ -112,6 +116,7 @@

    Arguments

    reference value for ppm scale.

    +<<<<<<< HEAD <<<<<<< HEAD
    nuc

    resonant nucleus.

    @@ -119,11 +124,16 @@

    Arguments

    dyns
    ======= +======= +>>>>>>> devel
    nuc

    resonant nucleus.

    dyns
    +<<<<<<< HEAD +>>>>>>> devel +======= >>>>>>> devel

    number of dynamic scans to generate.

    @@ -145,11 +155,15 @@

    Value

    +<<<<<<< HEAD <<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    =======

    Site built with pkgdown 2.1.0.

    >>>>>>> devel +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    diff --git a/docs/reference/smooth_dyns.html b/docs/reference/smooth_dyns.html index accf3a51..4bea16bd 100644 --- a/docs/reference/smooth_dyns.html +++ b/docs/reference/smooth_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Smooth data across the dynamic dimension with a Gaussian kernel.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be smoothed.

    -
    sigma
    +
    sigma

    standard deviation of the underlying Gaussian kernel in seconds.

    Value

    - - -

    smoothed mrs_data object.

    +

    smoothed mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sort_basis.html b/docs/reference/sort_basis.html index d25cc006..2839e28d 100644 --- a/docs/reference/sort_basis.html +++ b/docs/reference/sort_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Sort the basis-set elements alphabetically.

    Arguments

    -
    basis
    + + +
    basis

    input basis.

    Value

    - - -

    sorted basis.

    +

    sorted basis.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spant-package.html b/docs/reference/spant-package.html index 90f19ec3..7065532b 100644 --- a/docs/reference/spant-package.html +++ b/docs/reference/spant-package.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -117,15 +121,19 @@

    Author

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spant.html b/docs/reference/spant.html new file mode 100644 index 00000000..8b056250 --- /dev/null +++ b/docs/reference/spant.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/spant_abfit_benchmark.html b/docs/reference/spant_abfit_benchmark.html index 4215c766..c0f4d6fb 100644 --- a/docs/reference/spant_abfit_benchmark.html +++ b/docs/reference/spant_abfit_benchmark.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,17 @@

    Simulate and fit some spectra with ABfit for benchmarking purposes. Basic ti

    Arguments

    -
    noise_reps
    + + +
    noise_reps

    number of spectra to fit with differing noise samples.

    -
    return_res
    +
    return_res

    return a list of fit_result objects.

    -
    opts
    +
    opts

    ABfit options structure.

    @@ -110,15 +116,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spant_mpress_drift.html b/docs/reference/spant_mpress_drift.html index 82137822..34be85e2 100644 --- a/docs/reference/spant_mpress_drift.html +++ b/docs/reference/spant_mpress_drift.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -98,15 +102,19 @@

    Format

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spant_sim_fmrs_dataset.html b/docs/reference/spant_sim_fmrs_dataset.html index 00e48b56..16d181cb 100644 --- a/docs/reference/spant_sim_fmrs_dataset.html +++ b/docs/reference/spant_sim_fmrs_dataset.html @@ -4,7 +4,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -29,7 +37,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -85,7 +105,13 @@

    Simulate an example fMRS dataset for a block design fMRS experiment and expo

    Arguments

    +<<<<<<< HEAD
    output_dir
    +======= + + +
    output_dir
    +>>>>>>> devel

    output directory for the BIDS data. Defaults to : "HOME/sim_fmrs_dataset/data".

    @@ -103,15 +129,26 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel

    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/spant_simulation_benchmark.html b/docs/reference/spant_simulation_benchmark.html index d8cc6841..b861a295 100644 --- a/docs/reference/spant_simulation_benchmark.html +++ b/docs/reference/spant_simulation_benchmark.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,11 +89,13 @@

    Simulate a typical metabolite basis set for benchmarking. Timing metrics wil

    Arguments

    -
    sim_reps
    + + +
    sim_reps

    number of times to simulate the basis set.

    -
    N
    +
    N

    number of FID data points to simulate.

    @@ -106,15 +112,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spec_decomp.html b/docs/reference/spec_decomp.html index 42c4e654..b4c047a0 100644 --- a/docs/reference/spec_decomp.html +++ b/docs/reference/spec_decomp.html @@ -5,7 +5,7 @@ - +
    @@ -30,7 +34,7 @@
    • - +
    @@ -87,27 +91,27 @@

    Decompose an mrs_data object into white and gray matter spectra.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be decomposed into white and gray matter spectra.

    -
    wm
    +
    wm

    vector of white matter contributions to each voxel.

    -
    gm
    +
    gm

    vector of gray matter contributions to each voxel.

    -
    norm_fractions
    +
    norm_fractions

    option to normalise the wm, gm vectors for each voxel.

    Value

    - - -

    a list of two mrs_data objects corresponding to the two tissue types.

    +

    a list of two mrs_data objects corresponding to the two tissue types.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spec_op.html b/docs/reference/spec_op.html index f0d32edf..0df584e3 100644 --- a/docs/reference/spec_op.html +++ b/docs/reference/spec_op.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -89,32 +93,36 @@

    Perform a mathematical operation on a spectral region.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    xlim
    +
    xlim

    spectral range to be integrated (defaults to full range).

    +<<<<<<< HEAD
    operator
    +======= +
    operator
    +>>>>>>> devel

    can be "sum" (default), "mean", "l2", "max", "max_cplx, "min" or "max-min".

    -
    freq_scale
    +
    freq_scale

    units of xlim, can be : "ppm", "hz" or "points".

    -
    mode
    +
    mode

    spectral mode, can be : "re", "im", "mod" or "cplx".

    Value

    - - -

    an array of integral values.

    +

    an array of integral values.

    @@ -129,15 +137,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spin_sys.html b/docs/reference/spin_sys.html index 1eaa9e76..563c688b 100644 --- a/docs/reference/spin_sys.html +++ b/docs/reference/spin_sys.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,31 +87,31 @@

    Create a spin system object for pulse sequence simulation.

    Arguments

    -
    spin_params
    + + +
    spin_params

    an object describing the spin system properties.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    precomp_jc_H
    +
    precomp_jc_H

    use a precomputed J-coupling H matrix to save time.

    -
    precomp_Iz
    +
    precomp_Iz

    use precomputed Iz matrices to save time.

    Value

    - - -

    spin system object.

    +

    spin system object.

    @@ -122,15 +126,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/spm_pve2categorical.html b/docs/reference/spm_pve2categorical.html index 70f10729..f4ddc1d6 100644 --- a/docs/reference/spm_pve2categorical.html +++ b/docs/reference/spm_pve2categorical.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,15 +89,15 @@

    Convert SPM style segmentation files to a single categorical image where the

    Arguments

    -
    fname
    + + +
    fname

    any of the segmentation files (eg c1_MY_T1.nii).

    Value

    - - -

    nifti object.

    +

    nifti object.

    @@ -108,15 +112,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/ssp.html b/docs/reference/ssp.html index c1bbd53e..1838bbdf 100644 --- a/docs/reference/ssp.html +++ b/docs/reference/ssp.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -89,23 +93,23 @@

    Signal space projection method for lipid suppression.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data object.

    -
    comps
    +
    comps

    the number of spatial components to use.

    -
    xlim
    +
    xlim

    spectral range (in ppm) covering the lipid signals.

    Value

    - - -

    lipid suppressed mrs_data object.

    +

    lipid suppressed mrs_data object.

    @@ -120,15 +124,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/stackplot.fit_result.html b/docs/reference/stackplot.fit_result.html index 37b26001..9126f042 100644 --- a/docs/reference/stackplot.fit_result.html +++ b/docs/reference/stackplot.fit_result.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -80,7 +84,7 @@

    Plot the fitting results of an object of class fit_result with

    - 
    # S3 method for fit_result
+    
    # S3 method for class 'fit_result'
 stackplot(
   x,
   xlim = NULL,
@@ -110,103 +114,105 @@ 
    Plot the fitting results of an object of class fit_result with
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    fit_result object.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    y_offset
    
+
    y_offset
    
 
    separate basis signals in the y-axis direction by this value.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    n
    
+
    n
    
 
    single index element to plot (overrides other indices when given).
    
 
 
-
    sub_bl
    
+
    sub_bl
    
 
    subtract the baseline from the data and fit (logical).
    
 
 
-
    labels
    
+
    labels
    
 
    print signal labels at the right side of the plot.
    
 
 
-
    label_names
    
+
    label_names
    
 
    provide a character vector of signal names to replace the
 defaults determined from the basis set.
    
 
 
-
    sig_col
    
+
    sig_col
    
 
    colour of individual signal components.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    omit_signals
    
+
    omit_signals
    
 
    a character vector of basis signal names to be removed
 from the plot.
    
 
 
-
    combine_lipmm
    
+
    combine_lipmm
    
 
    combine all basis signals with names starting with "Lip"
 or "MM".
    
 
 
-
    combine_metab
    
+
    combine_metab
    
 
    combine all basis signals with names not starting with
 "Lip" or "MM".
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    invert_fit
    
+
    invert_fit
    
 
    show the fit result "upside-down"/
    
 
 
-
    ...
    
+
    ...
    
 
    further arguments to plot method.
    
 
 
    
@@ -223,15 +229,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/stackplot.html b/docs/reference/stackplot.html index 0d626b9a..fa5f073d 100644 --- a/docs/reference/stackplot.html +++ b/docs/reference/stackplot.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Produce a plot with multiple traces.

    Arguments

    -
    x
    + + +
    x

    object for plotting.

    -
    ...
    +
    ...

    arguments to be passed to methods.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/stackplot.mrs_data.html b/docs/reference/stackplot.mrs_data.html index 64eea445..2a2a9b2c 100644 --- a/docs/reference/stackplot.mrs_data.html +++ b/docs/reference/stackplot.mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -78,7 +82,7 @@

    Stackplot plotting method for objects of class mrs_data.

    - 
    # S3 method for mrs_data
+    
    # S3 method for class 'mrs_data'
 stackplot(
   x,
   xlim = NULL,
@@ -114,131 +118,133 @@ 
    Stackplot plotting method for objects of class mrs_data.
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    object of class mrs_data.
    
 
 
-
    xlim
    
+
    xlim
    
 
    the range of values to display on the x-axis, eg xlim = c(4,1).
    
 
 
-
    mode
    
+
    mode
    
 
    representation of the complex numbers to be plotted, can be one
 of: "re", "im", "mod" or "arg".
    
 
 
-
    x_units
    
+
    x_units
    
 
    the units to use for the x-axis, can be one of: "ppm", "hz",
 "points" or "seconds".
    
 
 
-
    fd
    
+
    fd
    
 
    display data in the frequency-domain (default), or time-domain
 (logical).
    
 
 
-
    col
    
+
    col
    
 
    set the colour of the line, eg col = rgb(1, 0, 0, 0.5).
    
 
 
-
    alpha
    
+
    alpha
    
 
    set the line transparency, eg alpha = 0.5 is 50% transparency.
 Overrides any transparency levels set by col.
    
 
 
-
    x_offset
    
+
    x_offset
    
 
    separate plots in the x-axis direction by this value.
 Default value is 0.
    
 
 
-
    y_offset
    
+
    y_offset
    
 
    separate plots in the y-axis direction by this value.
    
 
 
-
    plot_dim
    
+
    plot_dim
    
 
    the dimension to display on the y-axis, can be one of: "dyn",
 "x", "y", "z", "coil" or NULL. If NULL (the default) all spectra will be
 collapsed into the dynamic dimension and displayed.
    
 
 
-
    x_pos
    
+
    x_pos
    
 
    the x index to plot.
    
 
 
-
    y_pos
    
+
    y_pos
    
 
    the y index to plot.
    
 
 
-
    z_pos
    
+
    z_pos
    
 
    the z index to plot.
    
 
 
-
    dyn
    
+
    dyn
    
 
    the dynamic index to plot.
    
 
 
-
    coil
    
+
    coil
    
 
    the coil element number to plot.
    
 
 
-
    bty
    
+
    bty
    
 
    option to draw a box around the plot. See ?par.
    
 
 
-
    labels
    
+
    labels
    
 
    add labels to each data item.
    
 
 
-
    lab_cex
    
+
    lab_cex
    
 
    label size.
    
 
 
-
    bl_lty
    
+
    bl_lty
    
 
    linetype for the y = 0 baseline trace. A default value NULL
 results in no baseline being plotted.
    
 
 
-
    restore_def_par
    
+
    restore_def_par
    
 
    restore default plotting par values after the plot has
 been made.
    
 
 
-
    show_grid
    
+
    show_grid
    
 
    plot gridlines behind the data (logical). Defaults to TRUE.
    
 
 
-
    grid_nx
    
+
    grid_nx
    
 
    number of cells of the grid in x and y direction. When NULL
 the grid aligns with the tick marks on the corresponding default axis (i.e.,
 tickmarks as computed by axTicks). When NA, no grid lines are drawn in the
 corresponding direction.
    
 
 
-
    grid_ny
    
+
    grid_ny
    
 
    as above.
    
 
 
-
    lwd
    
+
    lwd
    
 
    plot linewidth.
    
 
 
-
    vline
    
+
    vline
    
 
    x-value to draw a vertical line.
    
 
 
-
    vline_lty
    
+
    vline_lty
    
 
    linetype for the vertical line.
    
 
 
-
    vline_col
    
+
    vline_col
    
 
    colour for the vertical line.
    
 
 
-
    mar
    
+
    mar
    
 
    option to adjust the plot margins. See ?par.
    
 
 
-
    ...
    
+
    ...
    
 
    other arguments to pass to the matplot method.
    
 
 
    
@@ -255,15 +261,19 @@ 
    Arguments
    
 
    
 
 
    
+<<<<<<< HEAD
   
    Site built with pkgdown 2.0.9.
    
+=======
+  
    Site built with pkgdown 2.1.0.
    
+>>>>>>> devel
    - - + + diff --git a/docs/reference/sub_first_dyn.html b/docs/reference/sub_first_dyn.html index 493b7242..c56f6ce2 100644 --- a/docs/reference/sub_first_dyn.html +++ b/docs/reference/sub_first_dyn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Subtract the first dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the first spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sub_mean_dyns.html b/docs/reference/sub_mean_dyns.html index 221bd0c1..796e803d 100644 --- a/docs/reference/sub_mean_dyns.html +++ b/docs/reference/sub_mean_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Subtract the mean dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the mean spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sub_median_dyns.html b/docs/reference/sub_median_dyns.html index 1e834f14..2b212286 100644 --- a/docs/reference/sub_median_dyns.html +++ b/docs/reference/sub_median_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Subtract the median dynamic spectrum from a dynamic series.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    -
    scale
    +
    scale

    scale factor for the medium spectrum.

    Value

    - - -

    subtracted data.

    +

    subtracted data.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sum_coils.html b/docs/reference/sum_coils.html index e1ab3cc0..aacc9c6b 100644 --- a/docs/reference/sum_coils.html +++ b/docs/reference/sum_coils.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the sum across receiver coil elements.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data split across receiver coil elements.

    Value

    - - -

    sum across coil elements.

    +

    sum across coil elements.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sum_dyns.html b/docs/reference/sum_dyns.html index bbda2ffc..b2a96ad1 100644 --- a/docs/reference/sum_dyns.html +++ b/docs/reference/sum_dyns.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Calculate the sum of data dynamics.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    dynamic MRS data.

    Value

    - - -

    sum of data dynamics.

    +

    sum of data dynamics.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sum_mrs.html b/docs/reference/sum_mrs.html index 3cc3ab9e..11c6568b 100644 --- a/docs/reference/sum_mrs.html +++ b/docs/reference/sum_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Sum two mrs_data objects.

    Arguments

    -
    a
    + + +
    a

    first mrs_data object to be summed.

    -
    b
    +
    b

    second mrs_data object to be summed.

    -
    force
    +
    force

    set to TRUE to force mrs_data objects to be summed, even if they are in different time/frequency domains.

    Value

    - - -

    a + b

    +

    a + b

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/sum_mrs_list.html b/docs/reference/sum_mrs_list.html index c3584348..82d2b428 100644 --- a/docs/reference/sum_mrs_list.html +++ b/docs/reference/sum_mrs_list.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the sum of a list of mrs_data objects.

    Arguments

    -
    mrs_list
    + + +
    mrs_list

    list of mrs_data objects.

    Value

    - - -

    sum mrs_data object.

    +

    sum mrs_data object.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/svs_1h_brain_analysis.html b/docs/reference/svs_1h_brain_analysis.html index dff0ef7d..d19cdea7 100644 --- a/docs/reference/svs_1h_brain_analysis.html +++ b/docs/reference/svs_1h_brain_analysis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -102,89 +106,89 @@

    Standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab
    + + +
    metab

    filepath or mrs_data object containing MRS metabolite data.

    -
    basis
    +
    basis

    basis set object to use for analysis.

    -
    w_ref
    +
    w_ref

    filepath or mrs_data object containing MRS water reference data.

    -
    mri_seg
    +
    mri_seg

    filepath or nifti object containing segmented MRI data.

    -
    mri
    +
    mri

    filepath or nifti object containing anatomical MRI data.

    -
    output_dir
    +
    output_dir

    directory path to output fitting results.

    -
    extra
    +
    extra

    data.frame with one row containing additional information to be attached to the fit results table.

    -
    decimate
    +
    decimate

    option to decimate the input data by a factor of two. The default value of NULL does not perform decimation unless the spectral width is greater than 20 PPM.

    -
    rats_corr
    +
    rats_corr

    option to perform rats correction, defaults to TRUE.

    -
    ecc
    +
    ecc

    option to perform water reference based eddy current correction, defaults to FALSE.

    -
    comb_dyns
    +
    comb_dyns

    option to combine dynamic scans, defaults to TRUE.

    -
    hsvd_filt
    +
    hsvd_filt

    option to apply hsvd water removal, defaults to FALSE.

    -
    scale_amps
    +
    scale_amps

    option to scale metabolite amplitude estimates, defaults to TRUE.

    -
    te
    +
    te

    metabolite mrs data echo time in seconds.

    -
    tr
    +
    tr

    metabolite mrs data repetition time in seconds.

    -
    preproc_only
    +
    preproc_only

    only perform the preprocessing steps and omit fitting. The preprocessed metabolite data will be returned in this case.

    -
    method
    +
    method

    analysis method to use, see fit_mrs help.

    -
    opts
    +
    opts

    options to pass to the analysis method.

    Value

    - - -

    a fit_result or mrs_data object depending on the preproc_only option.

    +

    a fit_result or mrs_data object depending on the preproc_only option.

    @@ -199,15 +203,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/svs_1h_brain_analysis_dev.html b/docs/reference/svs_1h_brain_analysis_dev.html index d71bfea2..fba03b8a 100644 --- a/docs/reference/svs_1h_brain_analysis_dev.html +++ b/docs/reference/svs_1h_brain_analysis_dev.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -99,73 +103,75 @@

    Standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab
    + + +
    metab

    filepath or mrs_data object containing MRS metabolite data.

    -
    w_ref
    +
    w_ref

    filepath or mrs_data object containing MRS water reference data.

    -
    output_dir
    +
    output_dir

    directory path to output fitting results.

    -
    basis
    +
    basis

    precompiled basis set object to use for analysis.

    -
    p_vols
    +
    p_vols

    a numeric vector of partial volumes expressed as percentages. Defaults to 100% white matter. A voxel containing 100% gray matter tissue would use : p_vols = c(WM = 0, GM = 100, CSF = 0).

    -
    append_basis
    +
    append_basis

    names of extra signals to add to the default basis. Eg append_basis = c("peth", "cit"). Cannot be used with precompiled basis sets.

    -
    remove_basis
    +
    remove_basis

    names of signals to remove from the basis. Cannot be used with precompiled basis sets.

    -
    dfp_corr
    +
    dfp_corr

    perform dynamic frequency and phase correction using the RATS method.

    -
    omit_bad_dynamics
    +
    omit_bad_dynamics

    detect and remove bad dynamics.

    -
    te
    +
    te

    metabolite mrs data echo time in seconds. If not supplied this will be guessed from the metab data file.

    -
    tr
    +
    tr

    metabolite mrs data repetition time in seconds. If not supplied this will be guessed from the metab data file.

    -
    output_ratio
    +
    output_ratio

    optional string to specify a metabolite ratio to output. Defaults to "tCr" and multiple metabolites may be specified for multiple outputs. Set as NULL to omit.

    -
    ecc
    +
    ecc

    option to perform water reference based eddy current correction, defaults to FALSE.

    -
    abfit_opts
    +
    abfit_opts

    options to pass to ABfit.

    -
    verbose
    +
    verbose

    output potentially useful information.

    @@ -176,9 +182,9 @@

    Examples

    package = "spant") w_ref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant") -if (FALSE) { +if (FALSE) { # \dontrun{ fit_result <- svs_1h_brain_analysis(metab, w_ref, "fit_res_dir") -} +} # }
    @@ -193,15 +199,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/svs_1h_brain_batch_analysis.html b/docs/reference/svs_1h_brain_batch_analysis.html index 15f7223e..d5bcc3a6 100644 --- a/docs/reference/svs_1h_brain_batch_analysis.html +++ b/docs/reference/svs_1h_brain_batch_analysis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,45 +95,45 @@

    Batch interface to the standard SVS 1H brain analysis pipeline.

    Arguments

    -
    metab_list
    + + +
    metab_list

    list of file paths or mrs_data objects containing MRS metabolite data.

    -
    w_ref_list
    +
    w_ref_list

    list of file paths or mrs_data objects containing MRS water reference data.

    -
    mri_seg_list
    +
    mri_seg_list

    list of file paths or nifti objects containing segmented MRI data.

    -
    mri_list
    +
    mri_list

    list of file paths or nifti objects containing anatomical MRI data.

    -
    output_dir_list
    +
    output_dir_list

    list of directory paths to output fitting results.

    -
    extra
    +
    extra

    a data frame with the same number of rows as metab_list, containing additional information to be attached to the fit results table.

    -
    ...
    +
    ...

    additional options to be passed to the svs_1h_brain_analysis function.

    Value

    - - -

    a list of fit_result objects.

    +

    a list of fit_result objects.

    @@ -144,15 +148,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/t_test_spec.html b/docs/reference/t_test_spec.html index 56a7ea1b..b2f5e2a3 100644 --- a/docs/reference/t_test_spec.html +++ b/docs/reference/t_test_spec.html @@ -3,7 +3,11 @@ +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -28,7 +36,11 @@
    • +<<<<<<< HEAD +======= + +>>>>>>> devel
    @@ -83,19 +103,33 @@

    Perform a t-test on spectral data points.

    Arguments

    +<<<<<<< HEAD
    mrs_data

    an mrs_data object with spectra in the dynamic dimension.

    group
    +======= + + +
    mrs_data
    +

    an mrs_data object with spectra in the dynamic dimension.

    + + +
    group
    +>>>>>>> devel

    vector describing the group membership of each dynamic spectrum.

    Value

    +<<<<<<< HEAD

    a list of statistical results.

    +======= +

    a list of statistical results.

    +>>>>>>> devel
    @@ -110,15 +144,26 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    +<<<<<<< HEAD +======= + + + + +>>>>>>> devel diff --git a/docs/reference/td2fd.html b/docs/reference/td2fd.html index f31ed524..60ca0ef9 100644 --- a/docs/reference/td2fd.html +++ b/docs/reference/td2fd.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Transform time-domain data to the frequency-domain.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data in time-domain representation.

    Value

    - - -

    MRS data in frequency-domain representation.

    +

    MRS data in frequency-domain representation.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/td_conv_filt.html b/docs/reference/td_conv_filt.html index 106b9b00..ed37fc1a 100644 --- a/docs/reference/td_conv_filt.html +++ b/docs/reference/td_conv_filt.html @@ -6,7 +6,7 @@ - +
    @@ -31,7 +35,7 @@
    • - +
    @@ -89,15 +93,17 @@

    Time-domain convolution based filter.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be filtered.

    -
    K
    +
    K

    window width in data points.

    -
    ext
    +
    ext

    point separation for linear extrapolation.

    @@ -114,15 +120,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/tdsr.html b/docs/reference/tdsr.html index 6cc2ee22..82d5407e 100644 --- a/docs/reference/tdsr.html +++ b/docs/reference/tdsr.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,29 +87,29 @@

    Time-domain spectral registration.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data to be corrected.

    -
    ref
    +
    ref

    optional MRS data to use as a reference, the mean of all dynamics is used if this argument is not supplied.

    -
    xlim
    +
    xlim

    optional frequency range to perform optimisation, set to NULL to use the full range.

    -
    max_t
    +
    max_t

    truncate the FID when longer than max_t to reduce time taken.

    Value

    - - -

    a list containing the corrected data; phase and shift values in units +

    a list containing the corrected data; phase and shift values in units of degrees and Hz respectively.

    @@ -121,15 +125,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/te.html b/docs/reference/te.html index 4a65711d..1600b579 100644 --- a/docs/reference/te.html +++ b/docs/reference/te.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the echo time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    echo time in seconds.

    +

    echo time in seconds.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/tr.html b/docs/reference/tr.html index 2e749e02..6740d1a2 100644 --- a/docs/reference/tr.html +++ b/docs/reference/tr.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,15 @@

    Return the repetition time of an MRS dataset.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    Value

    - - -

    repetition time in seconds.

    +

    repetition time in seconds.

    @@ -106,15 +110,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/varpro_3_para_opts.html b/docs/reference/varpro_3_para_opts.html index 52d7cd84..117d9ce2 100644 --- a/docs/reference/varpro_3_para_opts.html +++ b/docs/reference/varpro_3_para_opts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -91,42 +95,42 @@

    Return a list of options for VARPRO based fitting with 3 free parameters.

    Arguments

    -
    nstart
    + + +
    nstart

    position in the time-domain to start fitting, units of data points.

    -
    init_damping
    +
    init_damping

    starting value for the global Gaussian line-broadening term - measured in Hz.

    -
    maxiters
    +
    maxiters

    maximum number of levmar iterations to perform.

    -
    max_shift
    +
    max_shift

    maximum global shift allowed, measured in Hz.

    -
    max_damping
    +
    max_damping

    maximum damping allowed, FWHM measured in Hz.

    -
    anal_jac
    +
    anal_jac

    option to use the analytic or numerical Jacobian (logical).

    -
    bl_smth_pts
    +
    bl_smth_pts

    number of data points to use in the baseline smoothing calculation.

    Value

    - - -

    list of options.

    +

    list of options.

    @@ -141,15 +145,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/varpro_basic_opts.html b/docs/reference/varpro_basic_opts.html index c5104891..ebec1fdf 100644 --- a/docs/reference/varpro_basic_opts.html +++ b/docs/reference/varpro_basic_opts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,27 +87,27 @@

    Return a list of options for a basic VARPRO analysis.

    Arguments

    -
    method
    + + +
    method

    one of "td", "fd", "fd_re".

    -
    nnls
    +
    nnls

    restrict basis amplitudes to non-negative values.

    -
    ppm_left
    +
    ppm_left

    downfield frequency limit for the fitting range (ppm).

    -
    ppm_right
    +
    ppm_right

    upfield frequency limit for the fitting range (ppm).

    Value

    - - -

    full list of options.

    +

    full list of options.

    @@ -118,15 +122,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/varpro_opts.html b/docs/reference/varpro_opts.html index 6332f730..9c8b0aef 100644 --- a/docs/reference/varpro_opts.html +++ b/docs/reference/varpro_opts.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,48 +96,48 @@

    Return a list of options for VARPRO based fitting.

    Arguments

    -
    nstart
    + + +
    nstart

    position in the time-domain to start fitting, units of data points.

    -
    init_g_damping
    +
    init_g_damping

    starting value for the global Gaussian line-broadening term - measured in Hz.

    -
    maxiters
    +
    maxiters

    maximum number of levmar iterations to perform.

    -
    max_shift
    +
    max_shift

    maximum shift allowed to each element in the basis set, measured in Hz.

    -
    max_g_damping
    +
    max_g_damping

    maximum permitted global Gaussian line-broadening.

    -
    max_ind_damping
    +
    max_ind_damping

    maximum permitted Lorentzian line-broadening for each element in the basis set, measured in Hz.

    -
    anal_jac
    +
    anal_jac

    option to use the analytic or numerical Jacobian (logical).

    -
    bl_smth_pts
    +
    bl_smth_pts

    number of data points to use in the baseline smoothing calculation.

    Value

    - - -

    list of options.

    +

    list of options.

    @@ -177,15 +181,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/vec2mrs_data.html b/docs/reference/vec2mrs_data.html index f0d58bf0..83a4c3ed 100644 --- a/docs/reference/vec2mrs_data.html +++ b/docs/reference/vec2mrs_data.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -92,43 +96,55 @@

    Convert a vector into a mrs_data object.

    Arguments

    -
    vec
    + + +
    vec

    the data vector.

    +<<<<<<< HEAD
    mrs_data

    example data to copy acquisition parameters from.

    fs
    +======= +
    mrs_data
    +

    example data to copy acquisition parameters from.

    + + +
    fs
    +>>>>>>> devel

    sampling frequency in Hz.

    -
    ft
    +
    ft

    transmitter frequency in Hz.

    -
    ref
    +
    ref

    reference value for ppm scale.

    -
    nuc
    +
    nuc

    resonant nucleus.

    -
    dyns
    +
    dyns

    replicate the data across the dynamic dimension.

    +<<<<<<< HEAD
    fd
    +======= +
    fd
    +>>>>>>> devel

    flag to indicate if the vector is in the frequency domain (logical).

    Value

    - - -

    mrs_data object.

    +

    mrs_data object.

    @@ -143,15 +159,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/writeNifti.html b/docs/reference/writeNifti.html new file mode 100644 index 00000000..3d3d7357 --- /dev/null +++ b/docs/reference/writeNifti.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/write_basis.html b/docs/reference/write_basis.html index 94c5e021..e3a7ffbf 100644 --- a/docs/reference/write_basis.html +++ b/docs/reference/write_basis.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,15 +87,17 @@

    Write a basis object to an LCModel .basis formatted file.

    Arguments

    -
    basis
    + + +
    basis

    basis object to be exported.

    -
    basis_file
    +
    basis_file

    path to basis file to be generated.

    -
    fwhmba
    +
    fwhmba

    parameter used by LCModel.

    @@ -108,15 +114,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/write_basis_tqn.html b/docs/reference/write_basis_tqn.html index 116c73ec..ced4deb6 100644 --- a/docs/reference/write_basis_tqn.html +++ b/docs/reference/write_basis_tqn.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,26 @@

    Generate a basis file using TARQUIN.

    Arguments

    -
    basis_file
    + + +
    basis_file

    filename of the basis file to be generated.

    -
    metab_data
    +
    metab_data

    MRS data object to match the generated basis parameters.

    -
    opts
    +
    opts

    list of options to pass to TARQUIN.

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 write_basis_tqn('test.basis',mrs_data,c("--echo","0.04"))
-}
+} # }
    @@ -115,15 +121,19 @@

    Examples

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/write_mrs.html b/docs/reference/write_mrs.html index 124b9dc4..357bca87 100644 --- a/docs/reference/write_mrs.html +++ b/docs/reference/write_mrs.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,21 +87,23 @@

    Write MRS data object to file.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    object to be written to file, or list of mrs_data objects.

    -
    fname
    +
    fname

    one or more filenames to output.

    -
    format
    +
    format

    string describing the data format. Must be one of the following : "nifti", "dpt", "lcm_raw", "rds". If not specified, the format will be guessed from the filename extension.

    -
    force
    +
    force

    set to TRUE to overwrite any existing files.

    @@ -114,15 +120,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/write_mrs_nifti.html b/docs/reference/write_mrs_nifti.html index bd3ed4b7..f02e7760 100644 --- a/docs/reference/write_mrs_nifti.html +++ b/docs/reference/write_mrs_nifti.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Write MRS data object to file in NIFTI format.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    object to be written to file.

    -
    fname
    +
    fname

    the filename of the output NIFTI MRS data.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/write_pulse_ascii.html b/docs/reference/write_pulse_ascii.html index 221f8ebb..1aa1bea9 100644 --- a/docs/reference/write_pulse_ascii.html +++ b/docs/reference/write_pulse_ascii.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Write an ASCII formatted pulse file.

    Arguments

    -
    pulse
    + + +
    pulse

    pulse data object.

    -
    path
    +
    path

    file path for export.

    @@ -104,15 +110,19 @@

    Arguments

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/zero_fade_spec.html b/docs/reference/zero_fade_spec.html index c8b572c3..89ade770 100644 --- a/docs/reference/zero_fade_spec.html +++ b/docs/reference/zero_fade_spec.html @@ -4,7 +4,7 @@ - +
    @@ -29,7 +33,7 @@
    • - +
    @@ -85,23 +89,23 @@

    Fade a spectrum to zero by frequency domain multiplication with a tanh funct

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    data to be faded.

    -
    start_ppm
    +
    start_ppm

    start point of the fade in ppm units.

    -
    end_ppm
    +
    end_ppm

    end point of the fade in ppm units.

    Value

    - - -

    modified mrs_data object.

    +

    modified mrs_data object.

    @@ -116,15 +120,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/zero_higher_orders.html b/docs/reference/zero_higher_orders.html index c196526d..48218fbe 100644 --- a/docs/reference/zero_higher_orders.html +++ b/docs/reference/zero_higher_orders.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,24 +87,24 @@

    Zero all coherences including and above a given order.

    Arguments

    -
    sys
    + + +
    sys

    spin system object.

    -
    rho
    +
    rho

    density matrix.

    -
    order
    +
    order

    states higher than or equal to this argument will be set to zero.

    Value

    - - -

    density matrix.

    +

    density matrix.

    @@ -115,15 +119,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/zero_td_pts_end.html b/docs/reference/zero_td_pts_end.html index 71d24ebb..4f54bcc1 100644 --- a/docs/reference/zero_td_pts_end.html +++ b/docs/reference/zero_td_pts_end.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,19 +87,19 @@

    Set mrs_data object data points at the end of the FID to zero.<

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRS data.

    -
    pts
    +
    pts

    number of end points to set to zero.

    Value

    - - -

    modified mrs_data object.

    +

    modified mrs_data object.

    @@ -110,15 +114,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/zf.html b/docs/reference/zf.html index baf50256..dc569b07 100644 --- a/docs/reference/zf.html +++ b/docs/reference/zf.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -80,37 +84,37 @@

    Zero-fill MRS data in the time domain.

    zf(x, factor = 2, offset = 0)
 
-# S3 method for list
+# S3 method for class 'list'
 zf(x, factor = 2, offset = 0)
 
-# S3 method for mrs_data
+# S3 method for class 'mrs_data'
 zf(x, factor = 2, offset = 0)
 
-# S3 method for basis_set
+# S3 method for class 'basis_set'
 zf(x, factor = 2, offset = 0)

    Arguments

    -
    x
    + + +
    x

    input mrs_data or basis_set object.

    -
    factor
    +
    factor

    zero-filling factor, factor of 2 returns a dataset with twice the original data points.

    -
    offset
    +
    offset

    number of points from the end of the FID to insert the zero values.

    Value

    - - -

    zero-filled data.

    +

    zero-filled data.

    @@ -125,15 +129,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/reference/zf.list.html b/docs/reference/zf.list.html new file mode 100644 index 00000000..2da37483 --- /dev/null +++ b/docs/reference/zf.list.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/zf_xy.html b/docs/reference/zf_xy.html index c4104a74..c898d4e5 100644 --- a/docs/reference/zf_xy.html +++ b/docs/reference/zf_xy.html @@ -3,7 +3,7 @@ - +
    @@ -28,7 +32,7 @@
    • - +
    @@ -83,11 +87,13 @@

    Zero-fill MRSI data in the k-space x-y direction.

    Arguments

    -
    mrs_data
    + + +
    mrs_data

    MRSI data.

    -
    factor
    +
    factor

    zero-filling factor, a factor of 2 returns a dataset with twice the original points in the x-y directions. Factors smaller than one are permitted, such that a factor of 0.5 returns half the k-space points in @@ -96,9 +102,7 @@

    Arguments

    Value

    - - -

    zero-filled data.

    +

    zero-filled data.

    @@ -113,15 +117,19 @@

    Value

    +<<<<<<< HEAD

    Site built with pkgdown 2.0.9.

    +======= +

    Site built with pkgdown 2.1.0.

    +>>>>>>> devel
    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 4c39f515..a2209f11 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,3 +1,4 @@ +<<<<<<< HEAD @@ -1218,4 +1219,416 @@ https://martin3141.github.io/spant/reference/zf_xy.html +======= + +https://martin3141.github.io/spant/404.html +https://martin3141.github.io/spant/CONTRIBUTING.html +https://martin3141.github.io/spant/LICENSE-text.html +https://martin3141.github.io/spant/articles/abfit-baseline-opts.html +https://martin3141.github.io/spant/articles/index.html +https://martin3141.github.io/spant/articles/spant-basis-simulation.html +https://martin3141.github.io/spant/articles/spant-intro.html +https://martin3141.github.io/spant/articles/spant-metabolite-simulation.html +https://martin3141.github.io/spant/articles/spant-preprocessing.html +https://martin3141.github.io/spant/authors.html +https://martin3141.github.io/spant/index.html +https://martin3141.github.io/spant/news/index.html 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+https://martin3141.github.io/spant/reference/zero_nzoc.html +https://martin3141.github.io/spant/reference/zero_td_pts_end.html +https://martin3141.github.io/spant/reference/zf.html +https://martin3141.github.io/spant/reference/zf_xy.html +>>>>>>> devel + diff --git a/man/abfit_opts.Rd b/man/abfit_opts.Rd index 41338f04..ae74f838 100644 --- a/man/abfit_opts.Rd +++ b/man/abfit_opts.Rd @@ -7,7 +7,8 @@ abfit_opts( init_damping = 5, maxiters = 1024, - max_shift = 0.078, + max_shift_pre = 0.078, + max_shift_fine = NULL, max_damping = 15, max_phase = 360, lambda = NULL, @@ -40,11 +41,12 @@ abfit_opts( phi1_optim = FALSE, phi1_init = 0, max_dphi1 = 0.2, - max_basis_shift_broad = 0.0078, - max_basis_damping_broad = 2, + max_basis_shift_broad = NULL, + max_basis_damping_broad = NULL, ahat_calc_method = "lh_pnnls", prefit_phase_search = TRUE, freq_reg = NULL, + freq_reg_naa = NULL, lb_reg = NULL, output_all_paras = FALSE, output_all_paras_raw = FALSE, @@ -52,6 +54,7 @@ abfit_opts( optim_lw_only = FALSE, optim_lw_only_limit = 20, lb_init = 0.001, + lb_init_approx_fit = FALSE, zf_offset = NULL ) } @@ -61,8 +64,11 @@ abfit_opts( \item{maxiters}{The maximum number of iterations to run for the detailed fit.} -\item{max_shift}{The maximum allowable shift to be applied in the -optimisation phase of fitting (ppm).} +\item{max_shift_pre}{The maximum allowable global shift to be applied in the +approximate (pre-fit) phases of analysis (ppm).} + +\item{max_shift_fine}{The maximum allowable global shift to be applied in the +detailed fit phase of analysis (ppm).} \item{max_damping}{maximum permitted value of the global damping parameter (Hz).} @@ -126,7 +132,8 @@ the pre-alignment step (ppm).} \item{optimal_smooth_criterion}{method to determine the optimal smoothness.} -\item{aic_smoothing_factor}{modification factor for the AIC calculation.} +\item{aic_smoothing_factor}{modification factor for the AIC calculation. +Larger values result in less flexible baselines.} \item{anal_jac}{use a analytical approximation to the jacobian in the detailed fitting stage.} @@ -145,11 +152,12 @@ coarse fitting stage of the algorithm (ppm).} dependant phase term (ms).} \item{max_basis_shift_broad}{maximum allowable shift for broad signals in the -basis (ppm). Determined based on their name beginning with Lip or MM.} +basis (ppm). Determined based on their name beginning with Lip or MM. The +default value is set to max_basis_shift.} \item{max_basis_damping_broad}{maximum allowable Lorentzian damping for broad signals in the basis (Hz). Determined based on their name beginning with Lip -or MM.} +or MM. The default value is set to max_basis_damping.} \item{ahat_calc_method}{method to calculate the metabolite amplitudes. May be one of: "lh_pnnls" or "ls".} @@ -159,6 +167,8 @@ prefit stage of the algorithm.} \item{freq_reg}{frequency shift parameter.} +\item{freq_reg_naa}{frequency shift parameter for NAA and NAAG.} + \item{lb_reg}{individual line broadening parameter.} \item{output_all_paras}{include more fitting parameters in the fit table, @@ -175,9 +185,12 @@ use only.} \item{optim_lw_only_limit}{limits for the line-breading term as a percentage of the starting value when optim_lw_only is TRUE.} -\item{lb_init}{initial Lorentzian line broadening value for the individual -basis signals. Setting to 0 will clash with the minimum allowable value -(eg hard constraint) during the detailed fit.} +\item{lb_init}{initial Lorentzian line broadening value (in Hz) for the +individual basis signals. Setting to 0 will clash with the minimum allowable +value (eg hard constraint) during the detailed fit.} + +\item{lb_init_approx_fit}{apply lb_init to the basis during the approximate +iterative fit.} \item{zf_offset}{offset in number of data points from the end of the FID to zero-fill. Default is NULL and will automatically set this to 50 points when diff --git a/man/basis2mrs_data.Rd b/man/basis2mrs_data.Rd index 1a9be167..4ece8ba1 100644 --- a/man/basis2mrs_data.Rd +++ b/man/basis2mrs_data.Rd @@ -5,7 +5,13 @@ \title{Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.} \usage{ -basis2mrs_data(basis, sum_elements = FALSE, amps = NULL, shifts = NULL) +basis2mrs_data( + basis, + sum_elements = FALSE, + amps = NULL, + shifts = NULL, + lbs = NULL +) } \arguments{ \item{basis}{basis set object.} @@ -16,6 +22,9 @@ basis2mrs_data(basis, sum_elements = FALSE, amps = NULL, shifts = NULL) \item{shifts}{a vector of frequency shifts (in ppm) to apply to each basis element.} + +\item{lbs}{a vector of Lorentzian line broadening terms (in Hz) to apply to +each basis element.} } \value{ an mrs_data object with basis signals spread across the dynamic diff --git a/man/calc_basis_corr_mat.Rd b/man/calc_basis_corr_mat.Rd new file mode 100644 index 00000000..62f9dd8a --- /dev/null +++ b/man/calc_basis_corr_mat.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/basis_set.R +\name{calc_basis_corr_mat} +\alias{calc_basis_corr_mat} +\title{Estimate the correlation matrix for a basis set.} +\usage{ +calc_basis_corr_mat(basis, xlim = c(4, 0.2), zf = TRUE) +} +\arguments{ +\item{basis}{basis_set object.} + +\item{xlim}{spectral range to use in ppm.} + +\item{zf}{zero-fill the basis set.} +} +\value{ +correlation matrix. +} +\description{ +Estimate the correlation matrix for a basis set. +} diff --git a/man/calc_basis_crlbs.Rd b/man/calc_basis_crlbs.Rd new file mode 100644 index 00000000..e4ca559c --- /dev/null +++ b/man/calc_basis_crlbs.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/basis_set.R +\name{calc_basis_crlbs} +\alias{calc_basis_crlbs} +\title{Estimate the CRLB for each element in a basis set.} +\usage{ +calc_basis_crlbs( + basis, + xlim = c(4, 0.2), + zf = TRUE, + sd = 1, + bl_comp_pppm = NULL +) +} +\arguments{ +\item{basis}{basis_set object.} + +\item{xlim}{spectral range to use in ppm.} + +\item{zf}{zero-fill the basis set.} + +\item{sd}{standard deviation of the noise.} + +\item{bl_comp_pppm}{number spline baseline components to append per-ppm.} +} +\value{ +a vector of predicted errors. +} +\description{ +Estimate the CRLB for each element in a basis set. +}