suppress print to console by default

Author: Zeyuan-Chen

.Rbuildignore

@@ -13,3 +13,4 @@ LICENSE
 ^vignettes/liu\.rds$
 ^vignettes/hannum\.rds$
 ^CRAN-SUBMISSION$
+^tests/assets$

R/Unico.r

@@ -64,7 +64,7 @@ Unico = function(X, W, C1, C2, fit_tau = FALSE,
                  mean_penalty = 0, var_penalty = 0.01, covar_penalty = 0.01,
                  mean_max_iterations = 2, var_max_iterations = 3, nloptr_opts_algorithm = "NLOPT_LN_COBYLA",
                  max_stds = 2, init_weight = "default", max_u = 1, max_v = 1,
-                 parallel = TRUE, num_cores = NULL, log_file = "Unico.log", verbose = TRUE, debug = FALSE){
+                 parallel = TRUE, num_cores = NULL, log_file = "Unico.log", verbose = FALSE, debug = FALSE){
 
     start_logger(log_file, debug, verbose)
     flog.info("Starting Unico ...")
@@ -263,7 +263,7 @@ Unico = function(X, W, C1, C2, fit_tau = FALSE,
 #'
 #' @export tensor
 tensor = function(X, W, C1, C2, Unico.mdl, parallel = TRUE, num_cores = NULL,
-                  log_file = "Unico.log", verbose = TRUE, debug = FALSE){
+                  log_file = "Unico.log", verbose = FALSE, debug = FALSE){
 
     start_logger(log_file, debug, verbose)
 	  config = config::get(file = system.file("extdata", "config.yml", package = "Unico"), use_parent = FALSE)
@@ -382,7 +382,7 @@ association_parametric = function(X, Unico.mdl, slot_name = "parametric",
                                   Q_max_stds  = Inf,
                                   XQ_max_stds = Inf,
                                   parallel = TRUE, num_cores = NULL,
-                                  log_file = "Unico.log", debug = FALSE, verbose = TRUE){
+                                  log_file = "Unico.log", verbose = FALSE, debug = FALSE){
 
     start_logger(log_file, debug, verbose)
 	  config = config::get(file = system.file("extdata", "config.yml", package = "Unico"), use_parent = FALSE)
@@ -620,7 +620,7 @@ association_asymptotic = function(X, Unico.mdl, slot_name = "asymptotic",
                                   Q_max_stds  = Inf,  #analytical variance
                                   V_min_qlt   = 0.05, #moment condition variance
                                   parallel = TRUE, num_cores = NULL,
-                                  log_file = "Unico.log", debug = FALSE, verbose = TRUE){
+                                  log_file = "Unico.log", verbose = FALSE, debug = FALSE){
 
     start_logger(log_file, debug, verbose)
 	  config = config::get(file = system.file("extdata", "config.yml", package = "Unico"), use_parent = FALSE)
@@ -849,7 +849,7 @@ simulate_data = function(n, m, k, p1, p2,
 												 gammas_mean = 1, gammas_std = 0.1,
 												 betas_mean = 1, betas_std = 0.1,
 												 sigmas_lb = 0, sigmas_ub = 1, taus_std = 0.1,
-												 log_file = "Unico.log", verbose = TRUE){
+												 log_file = "Unico.log", verbose = FALSE){
 	start_logger(log_file, FALSE, verbose)
 	flog.info("Start simulation ...")
 

man/Unico.Rd

@@ -4,10 +4,12 @@ test_that("association testing on cell-type and tissue level covariates has good
 
 	skip_on_cran()
 
-	basedir <- "../assets/"
-
 	#source-specific association
-	sim.data = readRDS(file.path(basedir,"simulation.gammas.10.rds"))
+
+	download.file("https://github.com/cozygene/Unico/raw/main/tests/assets/simulation.gammas.10.rds", "simulation.gammas.10.rds")
+	sim.data = readRDS("simulation.gammas.10.rds")
+	file.remove("simulation.gammas.10.rds")
+
 	Unico.mdl = list()
 	Unico.mdl$params.hat <- Unico(sim.data$X, sim.data$W, C1 = sim.data$C1, C2 = sim.data$C2, parallel = F)
 	Unico.mdl$params.hat = association_parametric(X = sim.data$X, Unico.mdl$params.hat, parallel = F)
@@ -21,9 +23,11 @@ test_that("association testing on cell-type and tissue level covariates has good
 	global.marg.pvals = Unico.mdl$params.hat$parametric$betas_hat_pvals
 	expect_equal(sum(global.marg.pvals < 0.05/(nrow(global.marg.pvals) * ncol(global.marg.pvals)))/(nrow(global.marg.pvals) * ncol(global.marg.pvals)) < 0.05, TRUE)
 
-
 	#non-source-specific association
-	sim.data = readRDS(file.path(basedir,"simulation.betas.10.rds"))
+	download.file("https://github.com/cozygene/Unico/raw/main/tests/assets/simulation.betas.10.rds","simulation.betas.10.rds")
+	sim.data = readRDS("simulation.betas.10.rds")
+	file.remove("simulation.betas.10.rds")
+
 	Unico.mdl = list()
 	Unico.mdl$params.hat <- Unico(sim.data$X, sim.data$W, C1 = sim.data$C1, C2 = sim.data$C2, parallel = F)
 	Unico.mdl$params.hat = association_parametric(X = sim.data$X, Unico.mdl$params.hat, parallel = F)

man/association_asymptotic.Rd

@@ -3,10 +3,20 @@ library(Unico)
 test_that("estimated params and tensors are consisitent with frozen result", {
 	skip_on_cran()
 
-	basedir <- "../assets/"
-	set.seed(2023)
+
+	#basedir <- "../assets"
+	download.file("https://github.com/cozygene/Unico/raw/main/tests/assets/simulation.rds","simulation.rds")
+	download.file("https://github.com/cozygene/Unico/raw/main/tests/assets/frozen.mdl.rds","frozen.mdl.rds")
+
+	sim.data = readRDS("simulation.rds")
+	frozen.mdl = readRDS("frozen.mdl.rds")
+
+	file.remove("simulation.rds")
+	file.remove("frozen.mdl.rds")
+
+
 	#model fit
-	sim.data = readRDS(file.path(basedir,"simulation.rds"))
+	set.seed(2023)
 	Unico.mdl = list()
 	Unico.mdl$params.hat <- Unico(sim.data$X, sim.data$W, C1 = sim.data$C1, C2 = sim.data$C2, parallel = F)
 	n = nrow(sim.data$W)
@@ -16,7 +26,6 @@ test_that("estimated params and tensors are consisitent with frozen result", {
 	p2 = ncol(sim.data$C2)
 
 	# mean check
-	frozen.mdl = readRDS(file.path(basedir,"frozen.mdl.rds"))
 	for (h in 1:k){
 		expect_equal(cor(frozen.mdl$mus_hat[,h], Unico.mdl$params.hat$mus_hat[,h]) > 0.99, TRUE)
 	}

man/association_parametric.Rd

@@ -19,7 +19,7 @@ library(Unico)
 library(matrixStats)
 
 #For visualization in this vignette
-install.packages(c("ggplot2","ggpubr","hexbin", "egg"))
+install.packages(c("ggplot2","ggpubr","hexbin","egg"))
 source("https://github.com/cozygene/Unico/raw/main/vignettes/vignetts.utils.r")
 ```