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pm fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-08 16:51:41 +01:00
parent 822e9de82c
commit aa48c6bf53
11 changed files with 211 additions and 186 deletions
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6
R/antibiogram.R
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@ -334,6 +334,9 @@ antibiogram <- function(x,
FUN = function(x) x)
counts <- out
out$numerator <- ifelse(isTRUE(combine_SI), out$S + out$I, out$S)
out$minimum <- minimum
# regroup for summarising
if (isTRUE(has_syndromic_group)) {
colnames(out)[1] <- "syndromic_group"
@ -348,7 +351,6 @@ antibiogram <- function(x,
}
out <- out %>%
mutate(numerator = ifelse(isTRUE(combine_SI), S + I, S)) %>%
summarise(SI = ifelse(total >= minimum, numerator / total, NA_real_)) %>%
filter(!is.na(SI))
@ -504,7 +506,7 @@ autoplot.antibiogram <- function(object, ...) {
#' @rdname antibiogram
print.antibiogram <- function(x, as_kable = !interactive(), ...) {
meet_criteria(as_kable, allow_class = "logical", has_length = 1)
if (isTRUE(as_kable)) {
if (isTRUE(as_kable) && !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
stop_ifnot_installed("knitr")
kable <- import_fn("kable", "knitr", error_on_fail = TRUE)
kable(x, ...)