From e3e10c2e882d36970de6cce01609e57ac9febd9e Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Wed, 11 Jul 2018 12:34:02 +0200
Subject: [PATCH] fix for macOS and older tidyr versions

---
 DESCRIPTION                |  4 ++--
 R/freq.R                   | 15 ++++-----------
 R/globals.R                |  2 ++
 tests/testthat/test-freq.R |  4 +---
 4 files changed, 9 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4549789c..6a3c0aba 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.2.0.9010
-Date: 2018-07-10
+Date: 2018-07-11
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -44,7 +44,7 @@ Suggests:
     covr (>= 3.0.1),
     rmarkdown,
     rstudioapi,
-    tidyr (>= 0.8.0)
+    tidyr
 VignetteBuilder: knitr
 URL: https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues
diff --git a/R/freq.R b/R/freq.R
index e7cb4f71..6665500b 100755
--- a/R/freq.R
+++ b/R/freq.R
@@ -166,18 +166,11 @@ frequency_tbl <- function(x,
     if (!"tidyr" %in% rownames(installed.packages())) {
       stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE)
     }
-    values <- x %>%
+    x <- x %>%
       as.data.frame(stringsAsFactors = FALSE) %>%
-      # delete last variable: these are frequencies
-      select(-ncol(.)) %>%
-      # paste all other columns:
-      tidyr::unite(sep = sep) %>%
-      .[, 1]
-    counts <- x %>%
-      as.data.frame(stringsAsFactors = FALSE) %>%
-      # get last variable: these are frequencies
-      pull(ncol(.))
-    x <- rep(values, counts)
+      # paste first two columns
+      tidyr::unite(col = "Pasted", 1:2, sep = sep, remove = TRUE)
+    x <- rep(x %>% pull(Pasted), x %>% pull(Freq))
     x.name <- "a `table` object"
     cols <- NULL
     mult.columns <- 2
diff --git a/R/globals.R b/R/globals.R
index 1bfa1f5f..bb1e3503 100755
--- a/R/globals.R
+++ b/R/globals.R
@@ -30,6 +30,7 @@ globalVariables(c('abname',
                   'days_diff',
                   'fctlvl',
                   'first_isolate_row_index',
+                  'Freq',
                   'fullname',
                   'genus',
                   'gramstain',
@@ -46,6 +47,7 @@ globalVariables(c('abname',
                   'n',
                   'na.omit',
                   'other_pat_or_mo',
+                  'Pasted',
                   'patient_id',
                   'quantile',
                   'real_first_isolate',
diff --git a/tests/testthat/test-freq.R b/tests/testthat/test-freq.R
index d4770978..be3de4c3 100755
--- a/tests/testthat/test-freq.R
+++ b/tests/testthat/test-freq.R
@@ -18,9 +18,7 @@ test_that("frequency table works", {
   # factor
   expect_output(print(freq(septic_patients$hospital_id)))
   # table
-  #if (Sys.info()['sysname'] %in% c("Windows", "Linux")) {
-    expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
-  #}
+  expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
 
   library(dplyr)
   expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())