Add omit argument to check_data

Close #49

NEWS.md

@@ -2,6 +2,11 @@
 
 * Check that index used in `inspect` has a valid length, positions and 
   replications matching the data provided.
+
+* `check_data()` gains a new omit argument (#49). 
+   If you relied on positional arguments it will break your scripts. 
+
+* Omitting non existing columns now creates a warning. 
 
 # experDesign 0.3.0
 

R/evaluate_category.R

@@ -77,6 +77,7 @@ evaluate_independence <- function(i, pheno) {
 #' In order to run a successful experiment a good design is needed even before measuring the data.
 #' This functions checks several heuristics for a good experiment and warns if they are not found.
 #' @param pheno Data.frame with the variables of each sample, one row one sample.
+#' @param omit Character vector with the names of the columns to omit.
 #' @param na.omit Check the effects of missing values too.
 #' @return A logical value indicating if everything is alright (TRUE) or not (FALSE).
 #' @export
@@ -91,9 +92,9 @@ evaluate_independence <- function(i, pheno) {
 #' data(survey, package = "MASS")
 #' check_data(survey)
 #' }
-check_data <- function(pheno, na.omit = FALSE) {
+check_data <- function(pheno, omit = NULL, na.omit = FALSE) {
   stopifnot(is.data.frame(pheno) || is.matrix(pheno), is_logical(na.omit))
-  .check_data(pheno = pheno, na.omit = na.omit, verbose = TRUE)
+  .check_data(pheno = omit(pheno, omit), na.omit = na.omit, verbose = TRUE)
 }
 #' @importFrom utils combn
 .check_data <- function(pheno, na.omit = FALSE, verbose = FALSE) {

R/utils.R

@@ -33,6 +33,11 @@ is_cat <- function(x, ...) {
 omit <- function(pheno, omit){
   # Omit columns
   if (!is.null(omit)) {
+    col_diff <- setdiff(omit, colnames(pheno))
+    if (length(col_diff) != 0L) {
+      warning("Columns to omit were not present: ",
+              paste(col_diff, collapse = ", "), ".")
+    }
     pheno[, !colnames(pheno) %in% omit, drop = FALSE]
   } else {
     pheno