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param rules for EUCAST

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dr. M.S. (Matthijs) Berends
2018-10-18 12:10:10 +02:00
parent 693f64bdbf
commit 0ef91be3ac
7 changed files with 1431 additions and 1348 deletions
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2441
R/eucast.R
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27
R/freq.R
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@ -59,6 +59,7 @@
#' @importFrom dplyr %>% select pull n_distinct group_by arrange desc mutate summarise n_distinct tibble
#' @importFrom utils browseVignettes installed.packages
#' @importFrom hms is.hms
#' @importFrom crayon red silver
#' @keywords summary summarise frequency freq
#' @rdname freq
#' @name freq
@ -321,13 +322,24 @@ frequency_tbl <- function(x,
} else {
header <- header %>% paste0(markdown_line, 'Class: ', class(x) %>% rev() %>% paste(collapse = " > "))
if (!mode(x) %in% class(x)) {
header <- header %>% paste0(" (", mode(x), ")")
header <- header %>% paste0(silver(paste0(" (", mode(x), ")")))
}
}
NAs_to_red <- function(x) {
if (!x %in% c("0", "0.00%")) {
red(x)
} else {
x
}
}
header <- header %>% paste0(markdown_line, '\nLength: ', (NAs %>% length() + x %>% length()) %>% format(),
' (of which NA: ', NAs %>% length() %>% format(),
' = ', (NAs %>% length() / (NAs %>% length() + x %>% length())) %>% percent(force_zero = TRUE, round = digits) %>% sub('NaN', '0', ., fixed = TRUE), ')')
' (of which NA: ', NAs %>% length() %>% format() %>% NAs_to_red(),
' = ', (NAs %>% length() / (NAs %>% length() + x %>% length())) %>%
percent(force_zero = TRUE, round = digits) %>%
sub('NaN', '0', ., fixed = TRUE) %>%
NAs_to_red(), ')')
header <- header %>% paste0(markdown_line, '\nUnique: ', x %>% n_distinct() %>% format())
if (NROW(x) > 0 & any(class(x) == "character")) {
@ -570,6 +582,7 @@ diff.frequency_tbl <- function(x, y, ...) {
#' @exportMethod print.frequency_tbl
#' @importFrom knitr kable
#' @importFrom dplyr n_distinct
#' @importFrom crayon bold
#' @export
print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default = 15), ...) {
@ -602,7 +615,13 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
}
}
cat("Frequency table", title, "\n")
title <- paste("Frequency table", title)
if (opt$tbl_format == "pandoc") {
title <- bold(title) # only bold in regular printing
}
cat(title, "\n")
if (!is.null(opt$header)) {
cat(opt$header)