Fix: CRAN comments

DidierMurilloF · Apr 19, 2023 · d442851 · d442851
1 parent eb6752f
commit d442851
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Showing 15 changed files with 358 additions and 250 deletions.
diff --git a/R/fct_diagonal_arrangement.R b/R/fct_diagonal_arrangement.R
@@ -90,7 +90,7 @@
 #' splitBy = "row", 
 #' blocks = c(150,155,95,200,120),
 #' data = treatment_list
-#'  )
+#' )
 #' spatDB$infoDesign
 #' spatDB$layoutRandom
 #' spatDB$plotsNumber
@@ -99,14 +99,18 @@
 #' # Example 3: Generates a spatial decision block diagonal arrangement design in one location
 #' # with 270 treatments allocated in 3 experiments or blocks for a field with dimensions
 #' # 20 rows x 15 cols in a serpentine arrangement. Which in turn is an augmented block (3 blocks).
-#' spatAB <- diagonal_arrangement(nrows = 20, ncols = 15, lines = 270, 
-#' checks = 4, 
-#' plotNumber = c(1,1001,2001), 
-#' kindExpt = "DBUDC", 
-#' planter = "serpentine",
-#' exptName = c("20WRA", "20WRB", "20WRC"), 
-#' blocks = c(90, 90, 90),
-#' splitBy = "column")
+#' spatAB <- diagonal_arrangement(
+#' nrows = 20, 
+#' ncols = 15, 
+#' lines = 270, 
+#' checks = 4, 
+#' plotNumber = c(1,1001,2001), 
+#' kindExpt = "DBUDC", 
+#' planter = "serpentine",
+#' exptName = c("20WRA", "20WRB", "20WRC"), 
+#' blocks = c(90, 90, 90),
+#' splitBy = "column"
+#' )
 #' spatAB$infoDesign
 #' spatAB$layoutRandom
 #' spatAB$plotsNumber
@@ -142,9 +146,9 @@ diagonal_arrangement <- function(
 
  if (!inherits(plotNumber,"list")) { 
  if (!is.null(plotNumber) && is.numeric(plotNumber)) {
- if(any(plotNumber < 1) || any(diff(plotNumber) < 0)) {
- base::stop('diagonal_arrangement() requires plotNumber to be positive and sorted integers.')
- }
+  if(any(plotNumber < 1) || any(diff(plotNumber) < 0)) {
+  base::stop('diagonal_arrangement() requires plotNumber to be positive and sorted integers.')
+  }
  }
  if(!is.numeric(plotNumber) && !is.integer(plotNumber)) {
  base::stop("plotNumber should be an integer or a numeric vector.")
@@ -528,18 +532,13 @@ diagonal_arrangement <- function(
  data_file = my_data_VLOOKUP, 
  reps = FALSE
  )
- # if (Option_NCD == TRUE) {
- # final_expt_export$CHECKS <- ifelse(
- # final_expt_export$NAME == "Filler", 
- # "NA", 
- # final_expt_export$CHECKS
- # )
- # final_expt_export$EXPT <- ifelse(
- # final_expt_export$EXPT == "Filler", 
- # "NA", 
- # final_expt_export$EXPT
- # )
- # } 
+ if (Option_NCD == TRUE) {
+ final_expt_export$CHECKS <- ifelse(
+ final_expt_export$NAME == "Filler",
+ 0,
+ final_expt_export$CHECKS
+ )
+ }
  return(list(final_expt = final_expt_export))
  }
 
@@ -678,6 +677,12 @@ unrep_data_parameters <- function(
  base::stop("Input data should have 4 columns: LOCATION, ENTRY, NAME")
  }
  colnames(gen_list) <- c("LOCATION", "ENTRY", "NAME")
+ if (length(gen_list$ENTRY) != length(unique(gen_list$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(gen_list$NAME) != length(unique(gen_list$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  # Create a space in memory for the locations data entry list
  list_locs <- setNames(
  object = vector(mode = "list", length = l), 
@@ -695,16 +700,34 @@ unrep_data_parameters <- function(
  data_entry <- list_locs[[location]]
  data_entry_UP <- na.omit(data_entry[,1:2]) 
  colnames(data_entry_UP) <- c("ENTRY", "NAME")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  } else if (is.list(data)) {
  list_locs <- data
  data_entry <- list_locs[[location]]
  data_entry_UP <- na.omit(data_entry[ ,1:2]) 
  colnames(data_entry_UP) <- c("ENTRY", "NAME")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  }
  } else {
  data_entry <- data
  data_entry_UP <- na.omit(data_entry[,1:2]) 
  colnames(data_entry_UP) <- c("ENTRY", "NAME")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  }
  ##############################################################################################
  # Check if the data entry is a data frame
@@ -727,6 +750,12 @@ unrep_data_parameters <- function(
  data_entry_UP <- na.omit(data_entry[,1:2]) 
  data_entry_UP$BLOCK <- c(rep("ALL", checks), rep(1:length(blocks), times = blocks))
  colnames(data_entry_UP) <- c("ENTRY", "NAME", "BLOCK")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  B <- data_entry_UP[(checks + 1):nrow(data_entry_UP),]
  Block_levels <- suppressWarnings(as.numeric(levels(as.factor(B$BLOCK))))
  Block_levels <- na.omit(Block_levels)
@@ -764,6 +793,12 @@ unrep_data_parameters <- function(
  NAME = NAME
  )
  colnames(data_entry_UP) <- c("ENTRY", "NAME")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  if (nrow(data_entry_UP) != (lines + checks)) base::stop("nrows data != of lines + checks")
  } else if (kindExpt == "DBUDC") {
  if (is.null(blocks)) {
@@ -780,6 +815,12 @@ unrep_data_parameters <- function(
  )
  data_entry_UP$BLOCK <- c(rep("ALL", checks), rep(1:length(blocks), times = blocks))
  colnames(data_entry_UP) <- c("ENTRY", "NAME", "BLOCK")
+ if (length(data_entry_UP$ENTRY) != length(unique(data_entry_UP$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(data_entry_UP$NAME) != length(unique(data_entry_UP$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  Blocks <- length(blocks)
  if (Option_NCD == TRUE) {
  data_entry1 <- data_entry_UP[(length(checksEntries) + 1):nrow(data_entry_UP), ] # checksEntries intead of checks

diff --git a/R/fct_do_optim.R b/R/fct_do_optim.R
@@ -29,7 +29,7 @@
 #' @examples 
 #' sparse_example <- do_optim(
 #' design = "sparse",
-#' lines = 180, 
+#' lines = 120, 
 #' l = 4, 
 #' copies_per_entry = 3, 
 #' add_checks = TRUE, 
@@ -294,9 +294,9 @@ do_optim <- function(
 #' 
 #' @examples
 #' sparse <- sparse_allocation(
-#' lines = 260, 
-#' l = 5, 
-#' copies_per_entry = 4, 
+#' lines = 120, 
+#' l = 4, 
+#' copies_per_entry = 3, 
 #' checks = 4, 
 #' locationNames = c("LOC1", "LOC2", "LOC3", "LOC4", "LOC5"), 
 #' seed = 1234

diff --git a/R/fct_optimized_arrangement.R b/R/fct_optimized_arrangement.R
@@ -45,6 +45,7 @@
 #' @examples
 #' # Example 1: Generates a spatial unreplicated optimized arrangement design in one location
 #' # with 120 genotypes + 20 check plots (4 checks) for a field with dimension 14 rows x 10 cols.
+#' \dontrun{
 #' optim_unrep1 <- optimized_arrangement(
 #' nrows = 14, 
 #' ncols = 10, 
@@ -61,10 +62,12 @@
 #' optim_unrep1$layoutRandom
 #' optim_unrep1$plotNumber
 #' head(optim_unrep1$fieldBook, 12)
+#' }
 #' 
 #' # Example 2: Generates a spatial unreplicated optimized arrangement design in one location
 #' # with 200 genotypes + 20 check plots (4 checks) for a field with dimension 10 rows x 22 cols.
 #' # As example, we set up the data option with the entries list.
+#' \dontrun{
 #' checks <- 4
 #' list_checks <- paste("CH", 1:checks, sep = "")
 #' treatments <- paste("G", 5:204, sep = "")
@@ -86,6 +89,7 @@
 #' optim_unrep2$layoutRandom
 #' optim_unrep2$plotNumber
 #' head(optim_unrep2$fieldBook,12)
+#' }
 #' 
 #' @export
 optimized_arrangement <- function(
@@ -221,6 +225,12 @@ optimized_arrangement <- function(
  gen_list <- gen_list[, 1:3]
  gen_list <- na.omit(gen_list)
  colnames(gen_list) <- c("ENTRY", "NAME", "REPS")
+ if (length(gen_list$ENTRY) != length(unique(gen_list$ENTRY))) {
+ stop("Please ensure all ENTRIES in data are distinct.")
+ }
+ if (length(gen_list$NAME) != length(unique(gen_list$NAME))) {
+ stop("Please ensure all NAMES in data are distinct.")
+ }
  if (any(gen_list$ENTRY < 1) || any(gen_list$REPS < 1)) {
  base::stop("Negatives number are not allowed in the data.")
  }