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(v3.0.0.9027) skimr update and as.ab warning - fixes #234, fixes #232

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dr. M.S. (Matthijs) Berends
2025-09-10 13:32:52 +02:00
parent d5a568318b
commit 4d7c4ca52c
13 changed files with 92 additions and 58 deletions
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33
R/sir.R
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@@ -1974,33 +1974,18 @@ freq.sir <- function(x, ...) {
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
get_skimmers.sir <- function(column) {
# get the variable name 'skim_variable'
name_call <- function(.data) {
calls <- sys.calls()
frms <- sys.frames()
calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
ind <- which(calls_txt %like% "skim_variable")[1L]
vars <- tryCatch(eval(parse(text = ".data$skim_variable$sir"), envir = frms[[ind]]),
error = function(e) NULL
)
tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL, info = FALSE),
error = function(e) NA_character_
)
} else {
NA_character_
}
}
# TODO add here in AMR 3.1.0 details about guideline
skimr::sfl(
skim_type = "sir",
ab_name = name_call,
count_R = count_R,
count_S = count_susceptible,
# guideline = function(x) "EUCAST 2025", # or "Multiple"
# origin = function(x) "MIC", # or "Multiple"
count_S = count_S,
count_I = count_I,
prop_R = ~ proportion_R(., minimum = 0),
prop_S = ~ susceptibility(., minimum = 0),
prop_I = ~ proportion_I(., minimum = 0)
count_R = count_R,
prop_S = ~ round(proportion_S(., minimum = 0) * 100, 1),
prop_I = ~ round(proportion_I(., minimum = 0) * 100, 1),
prop_R = ~ round(proportion_R(., minimum = 0) * 100, 1),
hist = ~ skimr::inline_hist(as.double(stats::na.omit(.)), 3)
)
}