mirror of https://github.com/msberends/AMR.git
patient ID in first isolate
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7ad8635994
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9179e98e12
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Package: AMR
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Package: AMR
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Version: 1.8.2.9150
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Version: 1.8.2.9151
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Date: 2023-03-11
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Date: 2023-03-11
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 1.8.2.9150
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# AMR 1.8.2.9151
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -350,7 +350,7 @@ first_isolate <- function(x = NULL,
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x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE])
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x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE])
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x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
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x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
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x$newvar_date <- x[, col_date, drop = TRUE]
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x$newvar_date <- x[, col_date, drop = TRUE]
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x$newvar_patient_id <- x[, col_patient_id, drop = TRUE]
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x$newvar_patient_id <- as.character(x[, col_patient_id, drop = TRUE])
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if (is.null(col_testcode)) {
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if (is.null(col_testcode)) {
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testcodes_exclude <- NULL
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testcodes_exclude <- NULL
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@ -378,7 +378,7 @@ first_isolate <- function(x = NULL,
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}
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}
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}
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}
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if (!is.null(col_keyantimicrobials)) {
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if (!is.null(col_keyantimicrobials)) {
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x$newvar_key_ab <- x[, col_keyantimicrobials, drop = TRUE]
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x$newvar_key_ab <- as.character(x[, col_keyantimicrobials, drop = TRUE])
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}
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}
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if (is.null(testcodes_exclude)) {
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if (is.null(testcodes_exclude)) {
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@ -303,10 +303,11 @@ sir_confidence_interval <- function(...,
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}
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}
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if (isTRUE(as_percent)) {
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if (isTRUE(as_percent)) {
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out <- percentage(out, digits = 1)
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out <- percentage(out, digits = 1)
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} else {
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out <- round(out, digits = 3)
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}
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}
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if (!isFALSE(collapse) && length(out) > 1) {
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if (!isFALSE(collapse) && length(out) > 1) {
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if (is.numeric(out)) {
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out <- round(out, digits = 3)
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}
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out <- paste(out, collapse = ifelse(isTRUE(collapse), "-", collapse))
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out <- paste(out, collapse = ifelse(isTRUE(collapse), "-", collapse))
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}
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}
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