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fix veterinary for R<4

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dr. M.S. (Matthijs) Berends
2024-02-24 19:26:35 +01:00
parent 35963ca3dc
commit b303662ec6
4 changed files with 12 additions and 10 deletions
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12
R/sir.R
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@ -526,7 +526,7 @@ as.sir.data.frame <- function(x,
meet_criteria(include_screening, allow_class = "logical", has_length = 1)
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1)
meet_criteria(host, allow_class = "character", allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE)
x.bak <- x
for (i in seq_len(ncol(x))) {
# don't keep factors, overwriting them is hard
@ -545,8 +545,8 @@ as.sir.data.frame <- function(x,
if (breakpoint_type == "animal") {
if (is.null(host)) {
host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE)
} else if (length(host) == 1 && host %in% colnames(x)) {
host <- x[[host]]
} else if (length(host) == 1 && as.character(host) %in% colnames(x)) {
host <- x[[as.character(host)]]
}
}
@ -745,7 +745,7 @@ get_guideline <- function(guideline, reference_data) {
}
convert_host <- function(x, lang = get_AMR_locale()) {
x <- trimws2(tolower(x))
x <- trimws2(tolower(as.character(x)))
x_out <- rep(NA_character_, length(x))
# this order is based on: clinical_breakpoints |> filter(type == "animal") |> count(host, sort = TRUE)
x_out[is.na(x_out) & (x %like% "dog|canine" | x %like% translate_AMR("dog|dogs|canine", lang))] <- "dogs"
@ -785,7 +785,7 @@ as_sir_method <- function(method_short,
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
check_reference_data(reference_data, .call_depth = -2)
meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1, .call_depth = -2)
meet_criteria(host, allow_class = "character", allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
# backward compatibilty
dots <- list(...)
@ -804,7 +804,7 @@ as_sir_method <- function(method_short,
}
}
} else {
if (!is.null(host) && !all(toupper(host) %in% c("HUMAN", "ECOFF"))) {
if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
if (message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
message_("Assuming `breakpoint_type = \"animal\"`, since `host` is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set `guideline = \"CLSI\"`?", ""), "\n\n")
}