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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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8
R/first_isolate.R
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@ -256,7 +256,7 @@ first_isolate <- function(x = NULL,
if (method == "phenotype-based" & !any_col_contains_rsi) {
method <- "episode-based"
}
if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
if (info == TRUE & message_not_thrown_before("first_isolate", "method")) {
message_(paste0("Determining first isolates ",
ifelse(method %in% c("episode-based", "phenotype-based"),
ifelse(is.infinite(episode_days),
@ -360,7 +360,7 @@ first_isolate <- function(x = NULL,
testcodes_exclude <- NULL
}
# remove testcodes
if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate", "excludingtestcodes")) {
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
add_fn = font_black,
as_note = FALSE)
@ -373,7 +373,7 @@ first_isolate <- function(x = NULL,
# filter on specimen group and keyantibiotics when they are filled in
if (!is.null(specimen_group)) {
check_columns_existance(col_specimen, x)
if (info == TRUE & message_not_thrown_before("first_isolate.excludingspecimen")) {
if (info == TRUE & message_not_thrown_before("first_isolate", "excludingspecimen")) {
message_("Excluding other than specimen group '", specimen_group, "'",
add_fn = font_black,
as_note = FALSE)
@ -445,7 +445,7 @@ first_isolate <- function(x = NULL,
# Analysis of first isolate ----
if (!is.null(col_keyantimicrobials)) {
if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
if (info == TRUE & message_not_thrown_before("first_isolate", "type")) {
if (type == "keyantimicrobials") {
message_("Basing inclusion on key antimicrobials, ",
ifelse(ignore_I == FALSE, "not ", ""),