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fix for macOS and older tidyr versions
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 0.2.0.9010
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Version: 0.2.0.9010
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Date: 2018-07-10
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Date: 2018-07-11
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(
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person(
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@ -44,7 +44,7 @@ Suggests:
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covr (>= 3.0.1),
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covr (>= 3.0.1),
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rmarkdown,
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rmarkdown,
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rstudioapi,
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rstudioapi,
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tidyr (>= 0.8.0)
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tidyr
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VignetteBuilder: knitr
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VignetteBuilder: knitr
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URL: https://github.com/msberends/AMR
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URL: https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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BugReports: https://github.com/msberends/AMR/issues
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15
R/freq.R
15
R/freq.R
@ -166,18 +166,11 @@ frequency_tbl <- function(x,
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if (!"tidyr" %in% rownames(installed.packages())) {
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if (!"tidyr" %in% rownames(installed.packages())) {
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stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE)
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stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE)
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}
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}
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values <- x %>%
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x <- x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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# delete last variable: these are frequencies
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# paste first two columns
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select(-ncol(.)) %>%
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tidyr::unite(col = "Pasted", 1:2, sep = sep, remove = TRUE)
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# paste all other columns:
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x <- rep(x %>% pull(Pasted), x %>% pull(Freq))
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tidyr::unite(sep = sep) %>%
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.[, 1]
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counts <- x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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# get last variable: these are frequencies
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pull(ncol(.))
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x <- rep(values, counts)
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x.name <- "a `table` object"
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x.name <- "a `table` object"
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cols <- NULL
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cols <- NULL
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mult.columns <- 2
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mult.columns <- 2
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@ -30,6 +30,7 @@ globalVariables(c('abname',
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'days_diff',
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'days_diff',
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'fctlvl',
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'fctlvl',
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'first_isolate_row_index',
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'first_isolate_row_index',
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'Freq',
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'fullname',
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'fullname',
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'genus',
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'genus',
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'gramstain',
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'gramstain',
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@ -46,6 +47,7 @@ globalVariables(c('abname',
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'n',
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'n',
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'na.omit',
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'na.omit',
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'other_pat_or_mo',
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'other_pat_or_mo',
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'Pasted',
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'patient_id',
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'patient_id',
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'quantile',
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'quantile',
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'real_first_isolate',
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'real_first_isolate',
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@ -18,9 +18,7 @@ test_that("frequency table works", {
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# factor
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# factor
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expect_output(print(freq(septic_patients$hospital_id)))
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expect_output(print(freq(septic_patients$hospital_id)))
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# table
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# table
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#if (Sys.info()['sysname'] %in% c("Windows", "Linux")) {
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expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
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expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
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#}
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library(dplyr)
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library(dplyr)
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expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
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