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(v1.7.1.9000) ab_class update, unit tests

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dr. M.S. (Matthijs) Berends
2021-06-04 21:07:55 +02:00
parent 7e70403efb
commit 1908e7cc7a
34 changed files with 365 additions and 1368 deletions
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14
R/aa_helper_functions.R
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@ -506,7 +506,7 @@ dataset_UTF8_to_ASCII <- function(df) {
# for eucast_rules() and mdro(), creates markdown output with URLs and names
create_eucast_ab_documentation <- function() {
x <- trimws(unique(toupper(unlist(strsplit(eucast_rules_file$then_change_these_antibiotics, ",")))))
x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
ab <- character()
for (val in x) {
if (val %in% ls(envir = asNamespace("AMR"))) {
@ -713,9 +713,10 @@ meet_criteria <- function(object,
return(invisible())
}
get_current_data <- function(arg_name, call) {
# check if retrieved before, then get it from package environment
if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
get_current_data <- function(arg_name, call, reuse_equal_call = TRUE) {
# check if retrieved before, then get it from package environment to improve speed
if (reuse_equal_call == TRUE &&
identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
return(pkg_env$get_current_data.out)
}
@ -735,9 +736,10 @@ get_current_data <- function(arg_name, call) {
if (getRversion() < "3.2") {
# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
# R-3.2 was released in April 2015
if (is.na(arg_name)) {
# like in carbapenems() etc.
warning_("this function can only be used in R >= 3.2", call = call)
# such as for carbapenems() etc.
warning_("this function requires R version 3.2 or later - you have ", R.version.string, call = call)
return(data.frame())
} else {
# mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ]