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(v1.2.0.9011) mo_domain(), improved error handling

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dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
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27
R/mdro.R
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@ -106,15 +106,13 @@ mdro <- function(x,
}
}
if (!is.data.frame(x)) {
stop("`x` must be a data frame.", call. = FALSE)
}
stop_ifnot(is.data.frame(x), "`x` must be a data.frame")
stop_if(any(dim(x) == 0), "`x` must contain rows and columns")
# force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE)
if (!is.numeric(pct_required_classes)) {
stop("`pct_required_classes` must be numeric.", call. = FALSE)
}
stop_ifnot(is.numeric(pct_required_classes), "`pct_required_classes` must be numeric")
if (pct_required_classes > 1) {
# allow pct_required_classes = 75 -> pct_required_classes = 0.75
pct_required_classes <- pct_required_classes / 100
@ -124,9 +122,7 @@ mdro <- function(x,
warning("Using `country` is deprecated, use `guideline` instead. Please see ?mdro.", call. = FALSE)
guideline <- list(...)$country
}
if (length(guideline) > 1) {
stop("`guideline` must be a length one character string.", call. = FALSE)
}
stop_ifnot(length(guideline) == 1, "`guideline` must be of length 1")
if (is.null(guideline)) {
# default to the paper by Magiorakos et al. (2012)
@ -138,9 +134,8 @@ mdro <- function(x,
if (tolower(guideline) == "de") {
guideline <- "MRGN"
}
if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb", "cmi2012")) {
stop("invalid guideline: ", guideline, call. = FALSE)
}
stop_ifnot(tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb", "cmi2012"),
"invalid guideline: ", guideline)
guideline <- list(code = tolower(guideline))
# try to find columns based on type
@ -154,9 +149,7 @@ mdro <- function(x,
x$mo <- as.mo("Mycobacterium tuberculosis")
col_mo <- "mo"
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
stop_if(is.null(col_mo), "`col_mo` must be set")
if (guideline$code == "cmi2012") {
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
@ -417,9 +410,7 @@ mdro <- function(x,
RFP <- cols_ab["RFP"]
abx_tb <- c(CAP, ETH, GAT, INH, PZA, RIF, RIB, RFP)
abx_tb <- abx_tb[!is.na(abx_tb)]
if (guideline$code == "tb" & length(abx_tb) == 0) {
stop("No antimycobacterials found in data set.", call. = FALSE)
}
stop_if(guideline$code == "tb" & length(abx_tb) == 0, "no antimycobacterials found in data set")
if (combine_SI == TRUE) {
search_result <- "R"