Merge 2-translate-greedyPopMix into develop

NAMESPACE

@@ -52,6 +52,7 @@ importFrom(matlab2r,isspace)
 importFrom(matlab2r,max)
 importFrom(matlab2r,min)
 importFrom(matlab2r,ones)
+importFrom(matlab2r,questdlg)
 importFrom(matlab2r,rand)
 importFrom(matlab2r,repmat)
 importFrom(matlab2r,reshape)

R/findOutRowsFromInd.R

@@ -0,0 +1,26 @@
+findOutRowsFromInd <- function(popnames, rows, ploidisuus = NULL) {
+  if (is.null(ploidisuus)) {
+    ploidisuus <- questdlg(
+      quest = 'Specify the type of individuals in the data',
+      dlgtitle = 'Individual type?',
+      btn = c('Haploid', 'Diploid', 'Tetraploid'),
+      defbtn = 'Diploid'
+    )
+  }
+
+  rowsFromInd <- switch(ploidisuus,
+    'Haploid' = 1,
+    'Diploid' = 2,
+    'Tetraploid' = 4
+  )
+
+  popnames2 <- popnames * NA
+  if (!is.null(popnames)) {
+      for (i in seq_len(size(rows, 1))) {
+          popnames2[i, 1] <- popnames[i, 1]
+          rivi <- rows[i, 1]:rows[i, 2]
+          popnames2[i, 2] <- rivi[rowsFromInd] / rowsFromInd
+      }
+  }
+	return(list(popnames2 = popnames2, rowsFromInd = rowsFromInd))
+}

R/rBAPS-package.R

@@ -5,6 +5,8 @@
 #' @note Found a bug? Want to suggest a feature? Contribute to the scientific
 #' and open source communities by opening an issue on our home page.
 #' Check the "BugReports" field on the package description for the URL.
-#' @importFrom matlab2r blanks cell colon find inputdlg isempty isfield isspace max min ones rand repmat reshape size sortrows squeeze strcmp times zeros
+#' @importFrom matlab2r blanks cell colon find inputdlg
+#' isempty isfield isspace max min ones questdlg rand repmat reshape
+#' size sortrows squeeze strcmp times zeros
 #' @importFrom stats runif
 NULL

tests/testthat/test-greedyPopMix.R

@@ -0,0 +1,11 @@
+context("greedyPopMix functions")
+
+test_that("Auxiliary functions work properly", {
+  x <- matrix(11:16, 3)
+  y <- matrix(2:7, 3)
+  z <- list(
+    popnames2 = matrix(c(11:13, seq(1.5, 2.5, 0.5)), 3),
+    rowsFromInd = 2
+  )
+  expect_equal(findOutRowsFromInd(x, y, "Diploid"), z)
+})