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patient ID in first isolate

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-03-11 17:13:19 +01:00
parent 7ad8635994
commit 9179e98e12
4 changed files with 8 additions and 7 deletions
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4
R/first_isolate.R
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@ -350,7 +350,7 @@ first_isolate <- function(x = NULL,
x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE])
x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
x$newvar_date <- x[, col_date, drop = TRUE]
x$newvar_patient_id <- x[, col_patient_id, drop = TRUE]
x$newvar_patient_id <- as.character(x[, col_patient_id, drop = TRUE])
if (is.null(col_testcode)) {
testcodes_exclude <- NULL
@ -378,7 +378,7 @@ first_isolate <- function(x = NULL,
}
}
if (!is.null(col_keyantimicrobials)) {
x$newvar_key_ab <- x[, col_keyantimicrobials, drop = TRUE]
x$newvar_key_ab <- as.character(x[, col_keyantimicrobials, drop = TRUE])
}
if (is.null(testcodes_exclude)) {

7
R/proportion.R
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@ -303,13 +303,14 @@ sir_confidence_interval <- function(...,
}
if (isTRUE(as_percent)) {
out <- percentage(out, digits = 1)
} else {
out <- round(out, digits = 3)
}
if (!isFALSE(collapse) && length(out) > 1) {
if (is.numeric(out)) {
out <- round(out, digits = 3)
}
out <- paste(out, collapse = ifelse(isTRUE(collapse), "-", collapse))
}
if (n < minimum) {
warning_("Introducing NA: ",
ifelse(n == 0, "no", paste("only", n)),