From c312da79c907d722d1c4eb406b065303bcce6a5d Mon Sep 17 00:00:00 2001
From: "Zhian N. Kamvar" <zkamvar@gmail.com>
Date: Sat, 12 May 2018 17:21:30 -0700
Subject: [PATCH] update error message for shufflepop

---
 R/sample_schemes.r             | 23 ++++++-----------------
 tests/testthat/test-sampling.R |  1 +
 2 files changed, 7 insertions(+), 17 deletions(-)

diff --git a/R/sample_schemes.r b/R/sample_schemes.r
index 4963c30e..abda0553 100755
--- a/R/sample_schemes.r
+++ b/R/sample_schemes.r
@@ -101,15 +101,12 @@ shufflepop <- function(pop, method=1){
   METHODS = c("permute alleles", "parametric bootstrap",
               "non-parametric bootstrap", "multilocus")
   if (all((1:4)!=method)) {
-    cat("1 = Permute Alleles (maintain allelic structure)\n")
-    cat("2 = Parametric Bootstrap (simulate new population based on allelic frequency)\n")
-    cat("3 = Non-Parametric Bootstrap (simulate new population)\n")
-    cat("4 = Multilocus style (maintain heterozygosity and allelic structure)\n")
-    cat("Select an integer (1, 2, 3, or 4): ")
-    method <- as.integer(readLines(n = 1))
-  }
-  if (all((1:4)!=method)){
-    stop ("Non convenient method number")
+    msg <- paste("Method", method, "is not defined. Please choose a defined method:\n\n",
+                 "1 = Permute Alleles (maintain allelic structure)\n",
+                 "2 = Parametric Bootstrap (simulate new population based on allelic frequency)\n",
+                 "3 = Non-Parametric Bootstrap (simulate new population)\n",
+                 "4 = Multilocus style (maintain heterozygosity and allelic structure)\n")
+    stop(msg)
   }
   if(pop@type == "PA"){
     if(method == 1 | method == 4){
@@ -137,14 +134,6 @@ shufflepop <- function(pop, method=1){
   return(pop)
 }
 
-#==============================================================================#
-# Shuffling function that never panned out. The idea was to provide a way to 
-# utilize these bootstrap methods for any statistic. 
-#==============================================================================#
-shufflefunk <- function(pop, FUN, sample=1, method=1, ...){
-  FUN <- match.fun(FUN)
-  lapply(1:sample, function(x) FUN(shufflepop(pop, method=method), ...))
-}
 #==============================================================================#
 # .sampling will reshuffle the alleles per individual, per locus via the 
 # .single.sampler function, which is described below. It will then calculate the
diff --git a/tests/testthat/test-sampling.R b/tests/testthat/test-sampling.R
index 305b1050..189cb520 100644
--- a/tests/testthat/test-sampling.R
+++ b/tests/testthat/test-sampling.R
@@ -44,6 +44,7 @@ test_that("shuffling methods work for PA data", {
 	expect_is(shufflepop(Aeut, method = 2), "genind")
 	expect_is(shufflepop(Aeut, method = 3), "genind")
 	expect_is(shufflepop(Aeut, method = 4), "genind")
+	expect_error(shufflepop(Aeut, method = 5), "Method 5 is not defined")
 
 	A10 <- Aeut[sample(nInd(Aeut), 10)]
 	expect_is(poppr(A10, sample = 9, method = 1, quiet = TRUE, hist = FALSE, sublist = "Total"), "popprtable")