things to fix before resubmitting to CRAN

DESCRIPTION

@@ -22,19 +22,27 @@ Authors@R: c(
            role = "ctb",
            email = "[email protected]",
            comment = c(ORCID = "0000-0002-9866-7051")),
+    person(given = "Jitao David",
+           family = "Zhang",
+           role = c("aut", "cph"),
+           email = "[email protected]",
+           comment = c(ORCID="0000-0002-3085-0909")),
     person(given = "Balazs",
            family = "Banfai",
            role = c("aut", "cph"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-0422-7977")),
     person(given = "F. Hoffman-La Roche", role = c("cph", "fnd")))
 Description:
-    Reducing batch effect by intelligently assigning samples to batches.
-    Batch-effect have a strong influence in data analysis, especially when
-    samples-to-batches assignment is coinciding with contrast groups.
-    By defining your batch container and a scoring function reflecting
-    the contrasts, you can assign samples in such a way that the potential
-    batch-effect has minimal effect on the comparison of interest.
+    Intelligently assign samples to batches in order to reduce batch effects.
+    Batch effects can have a significant impact on data analysis, especially
+    when the assignment of samples to batches coincides with the contrast
+    groups being studied. By defining a batch container and a scoring function
+    that reflects the contrasts, this package allows users to assign samples in
+    a way that minimizes the potential impact of batch effects on the
+    comparison of interest. Among other functionality, we provide an
+    implementation for OSAT score by Yan et al. (2012,
+    <doi:10.1186/1471-2164-13-689>).
 License: MIT + file LICENSE
 URL: https://bedapub.github.io/designit/, https://github.com/BEDApub/designit/
 BugReports: https://github.com/BEDApub/designit/issues
@@ -51,7 +59,6 @@ Imports:
     assertthat,
     stringr,
     R6,
-    ineq,
     data.table,
     stats
 Suggests: 

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
-COPYRIGHT HOLDER: Iakov I. Davydov, Juliane Siebourg-Polster, Guido Steiner, Balazs Banfai, F. Hoffman-La Roche
+YEAR: 2024
+COPYRIGHT HOLDER: designit authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 Iakov I. Davydov, Juliane Siebourg-Polster, Guido Steiner, Balazs Banfai, F. Hoffman-La Roche
+Copyright (c) 2024 designit authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,7 +1,10 @@
 # designit (development version)
 
-* remove magrittr, glue, checkmate, forcats, and tidyselect dependencies
+* remove magrittr, glue, checkmate, forcats, ineq, and tidyselect dependencies
 * minimum R version 4.1.0 (for the native pipe and lambda functions)
+* remove several unexported functions
+* BatchContainer trace saves the random seed as well as RNG kind
+* preparing for CRAN resumbission
 
 # designit 0.4.1
 

R/optimize.R

@@ -197,9 +197,16 @@ optimize_design <- function(batch_container, samples = NULL,
     start_assignment_vec = list(batch_container$assignment)
   )
 
-  # based on https://stat.ethz.ch/pipermail/r-help/2007-September/141717.html
-  if (!exists(".Random.seed")) stats::runif(1)
+  # saving the current random seed for reproducibility
+  if (!exists(".Random.seed", .GlobalEnv)) {
+    # Sets the default random number generator and initializes
+    # .Random.seed in the global environment.
+    # This doesn't affect the way random seed would have been set in
+    # downstream functions such as `sample()`.
+    set.seed(NULL)
+  }
   trace$seed <- list(.Random.seed)
+  trace$rng_kind <- list(RNGkind())
 
   if (is.null(samples)) {
     assertthat::assert_that(batch_container$has_samples,

R/plot.R

@@ -85,7 +85,7 @@ plot_design <- function(.tbl, ..., .color, .alpha = NULL) {
 #'   .color = Treatment, .alpha = Timepoint
 #' )
 #'
-#' \dontrun{
+#' \donttest{
 #' plot_plate(bc$get_samples(),
 #'   plate = plate, column = column, row = row,
 #'   .color = Treatment, .pattern = Timepoint