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replace T with TRUE to pass check
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@richardli
richardli committed Nov 9, 2023
1 parent b4af5ac commit 0aeb3e5
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34 changes: 17 additions & 17 deletions R/smoothArea.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
#' data(DemoMap2)
#' library(survey)
#' des0 <- svydesign(ids = ~clustid+id, strata = ~strata,
#' weights = ~weights, data = DemoData2, nest = T)
#' weights = ~weights, data = DemoData2, nest = TRUE)
#' Xmat <- aggregate(age~region, data = DemoData2, FUN = mean)
#'
#' # EXAMPLE 1: Continuous response model
Expand Down Expand Up @@ -118,15 +118,15 @@ smoothArea <- function(formula,
# known domain sizes
if (!is.null(domain.size)) {
direct.est <-
survey::svyby(resp.frm, domain, design = design, svytotal, na.rm = T)
survey::svyby(resp.frm, domain, design = design, svytotal, na.rm = TRUE)
direct.est$domain.size <-
domain.size[match(direct.est[, 1], domain.size[, 1]), 2]
direct.est[, 2] = direct.est[, 2] / direct.est$domain.size
direct.est[, 3] = (direct.est[, 3] / direct.est$domain.size) ^ 2
direct.est <- direct.est[, 1:3]
} else {
direct.est <-
survey::svyby(resp.frm, domain, design = design, svymean, na.rm = T)
survey::svyby(resp.frm, domain, design = design, svymean, na.rm = TRUE)
direct.est[, 3] <- direct.est[, 3] ^ 2
}
} else {
Expand Down Expand Up @@ -165,10 +165,10 @@ smoothArea <- function(formula,
mod.X.domain <- X.domain
mod.X.domain$domain <- X.domain[[domain.var]]
mod.X.domain <- mod.X.domain[, names(mod.X.domain) != domain.var]
mod.dat <- merge(mod.dat, mod.X.domain, by = "domain", all.y = T)
mod.dat <- merge(mod.dat, mod.X.domain, by = "domain", all.y = TRUE)
direct.est <-
merge(direct.est, data.frame(domain = mod.X.domain$domain),
by = "domain", all.y = T)
by = "domain", all.y = TRUE)
direct.est$method = "Direct"
} else if(!is.null(adj.mat)) {
if (any(is.na(match(mod.dat$domain, rownames(adj.mat))))) {
Expand All @@ -180,10 +180,10 @@ smoothArea <- function(formula,
}
mod.dat <-
merge(mod.dat, data.frame(domain = rownames(adj.mat)),
by = "domain", all.y = T)
by = "domain", all.y = TRUE)
direct.est <-
merge(direct.est, data.frame(domain = rownames(adj.mat)),
by = "domain", all.y = T)
by = "domain", all.y = TRUE)
direct.est$method = "Direct"
}
mod.dat$domain.id <- 1:nrow(mod.dat)
Expand Down Expand Up @@ -260,12 +260,12 @@ smoothArea <- function(formula,
data.frame(domain = mod.dat$domain,
mean = rowMeans(iid.model.mat),
median = apply(iid.model.mat, 1,
function(x) median(x, na.rm = T)),
function(x) median(x, na.rm = TRUE)),
var = apply(iid.model.mat, 1, var),
lower = apply(iid.model.mat, 1,
function(x) quantile(x, (1-level)/2, na.rm = T)),
function(x) quantile(x, (1-level)/2, na.rm = TRUE)),
upper = apply(iid.model.mat, 1,
function(x) quantile(x, 1-(1-level)/2, na.rm = T)),
function(x) quantile(x, 1-(1-level)/2, na.rm = TRUE)),
method = paste0("Area level model: IID"))

out$iid.model.est <-
Expand Down Expand Up @@ -320,12 +320,12 @@ smoothArea <- function(formula,
data.frame(domain = mod.dat$domain,
mean = rowMeans(bym2.model.mat),
median = apply(bym2.model.mat, 1,
function(x) median(x, na.rm = T)),
function(x) median(x, na.rm = TRUE)),
var = apply(bym2.model.mat, 1, var),
lower = apply(bym2.model.mat, 1,
function(x) quantile(x, (1-level)/2, na.rm = T)),
function(x) quantile(x, (1-level)/2, na.rm = TRUE)),
upper = apply(bym2.model.mat, 1,
function(x) quantile(x, 1-(1-level)/2, na.rm = T)),
function(x) quantile(x, 1-(1-level)/2, na.rm = TRUE)),
method = paste0("Area level model: BYM2"))
out$bym2.model.est <-
out$bym2.model.est[match(out$direct.est$domain, out$bym2.model.est$domain),]
Expand Down Expand Up @@ -437,7 +437,7 @@ plot.svysae <- function(x, return_list = F, plot.factor = NULL, ...) {
#' data(DemoMap2)
#' library(survey)
#' des0 <- svydesign(ids = ~clustid+id, strata = ~strata,
#' weights = ~weights, data = DemoData2, nest = T)
#' weights = ~weights, data = DemoData2, nest = TRUE)
#' Xmat <- aggregate(age~region, data = DemoData2, FUN = mean)
#'
#' cts.res <- smoothArea(tobacco.use ~ 1,
Expand All @@ -448,7 +448,7 @@ plot.svysae <- function(x, return_list = F, plot.factor = NULL, ...) {
#' pc.alpha = 0.01,
#' pc.u.phi = 0.5,
#' pc.alpha.phi = 2/3,
#' return.samples = T)
#' return.samples = TRUE)
#' compareEstimates(cts.res)
#' }
compareEstimates <- function(x,
Expand Down Expand Up @@ -549,7 +549,7 @@ compareEstimates <- function(x,
#' data(DemoMap2)
#' library(survey)
#' des0 <- svydesign(ids = ~clustid+id, strata = ~strata,
#' weights = ~weights, data = DemoData2, nest = T)
#' weights = ~weights, data = DemoData2, nest = TRUE)
#' Xmat <- aggregate(age~region, data = DemoData2, FUN = mean)
#' geo.data <- sf::st_as_sf(DemoMap2$geo)
#' geo.data$domain <- geo.data$REGNAME
Expand All @@ -561,7 +561,7 @@ compareEstimates <- function(x,
#' pc.alpha = 0.01,
#' pc.u.phi = 0.5,
#' pc.alpha.phi = 2/3,
#' return.samples = T)
#' return.samples = TRUE)
#' mapEstimates(cts.res, geo.data = geo.data, variable = "median")
#' mapEstimates(cts.res, geo.data = geo.data, variable = "var")
#' }
Expand Down
18 changes: 9 additions & 9 deletions R/smoothUnit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
#' data(DemoMap2)
#' library(survey)
#' des0 <- svydesign(ids = ~clustid+id, strata = ~strata,
#' weights = ~weights, data = DemoData2, nest = T)
#' weights = ~weights, data = DemoData2, nest = TRUE)
#'
#' # EXAMPLE 1: Continuous response model
#' cts.res <- smoothUnit(formula = tobacco.use ~ 1,
Expand Down Expand Up @@ -87,14 +87,14 @@ smoothUnit <- function(formula,
# DIRECT ESTIMATES -----------------------------------------------------------
# compute direct estimates (Hajek estimates if domain size unknown)
if (!is.null(domain.size)) {
direct.est <- svyby(resp.frm, domain, design = design, svytotal, na.rm = T)
direct.est <- svyby(resp.frm, domain, design = design, svytotal, na.rm = TRUE)
direct.est$domain.size <-
domain.size$size[match(direct.est[, 1], domain.size[[domain.var]])]
direct.est[, 2] = direct.est[, 2] / direct.est$domain.size
direct.est[, 3] = (direct.est[, 3] / direct.est$domain.size) ^ 2
direct.est <- direct.est[, 1:3]
} else {
direct.est <- svyby(resp.frm, domain, design = design, svymean, na.rm = T)
direct.est <- svyby(resp.frm, domain, design = design, svymean, na.rm = TRUE)
direct.est[, 3] <- direct.est[, 3] ^ 2
}
rownames(direct.est) <- NULL
Expand Down Expand Up @@ -125,7 +125,7 @@ smoothUnit <- function(formula,

direct.est <-
merge(direct.est, data.frame(domain = domain.table$domain),
by = "domain", all.y = T)
by = "domain", all.y = TRUE)
direct.est$method = "Direct"

out$direct.est <- direct.est
Expand Down Expand Up @@ -181,8 +181,8 @@ smoothUnit <- function(formula,
# fit model
mod.frm <- as.formula(ftxt)
fit <- INLA::inla(mod.frm, family = family, data = mod.dat,
control.compute = list(dic = T, mlik = T,
cpo = T, config = TRUE),
control.compute = list(dic = TRUE, mlik = TRUE,
cpo = TRUE, config = TRUE),
control.predictor = list(compute = TRUE),
lincomb = NULL, quantiles = c((1-level)/2, 0.5, 1-(1-level)/2))

Expand Down Expand Up @@ -218,12 +218,12 @@ smoothUnit <- function(formula,
data.frame(domain = domain.table$domain,
mean = rowMeans(est.mat),
median = apply(est.mat, 1,
function(x) median(x, na.rm = T)),
function(x) median(x, na.rm = TRUE)),
var = apply(est.mat, 1, var),
lower = apply(est.mat, 1,
function(x) quantile(x, (1-level)/2, na.rm = T)),
function(x) quantile(x, (1-level)/2, na.rm = TRUE)),
upper = apply(est.mat, 1,
function(x) quantile(x, 1-(1-level)/2, na.rm = T)),
function(x) quantile(x, 1-(1-level)/2, na.rm = TRUE)),
method = paste0("Unit level model: ",
ifelse(is.null(adj.mat), "IID", "BYM2")))
if (return.samples) {
Expand Down
4 changes: 2 additions & 2 deletions man/compareEstimates.Rd
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4 changes: 2 additions & 2 deletions man/mapEstimates.Rd
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2 changes: 1 addition & 1 deletion man/smoothArea.Rd
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2 changes: 1 addition & 1 deletion man/smoothUnit.Rd
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