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add labels_rsi_count

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dr. M.S. (Matthijs) Berends
2018-09-16 22:11:17 +02:00
parent b792a2754e
commit db14781593
16 changed files with 110 additions and 29 deletions
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6
R/count.R
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@ -146,6 +146,10 @@ count_S <- function(...) {
count_df <- function(data,
translate_ab = getOption("get_antibiotic_names", "official")) {
if (!"data.frame" %in% class(data)) {
stop("`count_df` must be called on a data.frame")
}
if (data %>% select_if(is.rsi) %>% ncol() == 0) {
stop("No columns with class 'rsi' found. See ?as.rsi.")
}
@ -177,7 +181,7 @@ count_df <- function(data,
res <- bind_rows(resS, resI, resR) %>%
mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
tidyr::gather(Antibiotic, Count, -Interpretation, -data.groups)
tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
if (!translate_ab == FALSE) {
if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {