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fix for macOS and older tidyr versions

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dr. M.S. (Matthijs) Berends 2018-07-11 12:34:02 +02:00
parent eca406b18b
commit e3e10c2e88
4 changed files with 9 additions and 16 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.2.0.9010 Version: 0.2.0.9010
Date: 2018-07-10 Date: 2018-07-11
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(
@ -44,7 +44,7 @@ Suggests:
covr (>= 3.0.1), covr (>= 3.0.1),
rmarkdown, rmarkdown,
rstudioapi, rstudioapi,
tidyr (>= 0.8.0) tidyr
VignetteBuilder: knitr VignetteBuilder: knitr
URL: https://github.com/msberends/AMR URL: https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues BugReports: https://github.com/msberends/AMR/issues

15
R/freq.R
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@ -166,18 +166,11 @@ frequency_tbl <- function(x,
if (!"tidyr" %in% rownames(installed.packages())) { if (!"tidyr" %in% rownames(installed.packages())) {
stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE) stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE)
} }
values <- x %>% x <- x %>%
as.data.frame(stringsAsFactors = FALSE) %>% as.data.frame(stringsAsFactors = FALSE) %>%
# delete last variable: these are frequencies # paste first two columns
select(-ncol(.)) %>% tidyr::unite(col = "Pasted", 1:2, sep = sep, remove = TRUE)
# paste all other columns: x <- rep(x %>% pull(Pasted), x %>% pull(Freq))
tidyr::unite(sep = sep) %>%
.[, 1]
counts <- x %>%
as.data.frame(stringsAsFactors = FALSE) %>%
# get last variable: these are frequencies
pull(ncol(.))
x <- rep(values, counts)
x.name <- "a `table` object" x.name <- "a `table` object"
cols <- NULL cols <- NULL
mult.columns <- 2 mult.columns <- 2

2
R/globals.R
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@ -30,6 +30,7 @@ globalVariables(c('abname',
'days_diff', 'days_diff',
'fctlvl', 'fctlvl',
'first_isolate_row_index', 'first_isolate_row_index',
'Freq',
'fullname', 'fullname',
'genus', 'genus',
'gramstain', 'gramstain',
@ -46,6 +47,7 @@ globalVariables(c('abname',
'n', 'n',
'na.omit', 'na.omit',
'other_pat_or_mo', 'other_pat_or_mo',
'Pasted',
'patient_id', 'patient_id',
'quantile', 'quantile',
'real_first_isolate', 'real_first_isolate',

2
tests/testthat/test-freq.R
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@ -18,9 +18,7 @@ test_that("frequency table works", {
# factor # factor
expect_output(print(freq(septic_patients$hospital_id))) expect_output(print(freq(septic_patients$hospital_id)))
# table # 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) library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print()) expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())