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custom ab fix

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dr. M.S. (Matthijs) Berends 2022-10-15 15:20:13 +02:00
parent 85ed7ea5f0
commit ad68b50ecd
4 changed files with 25 additions and 7 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.2.9016
Date: 2022-10-14
Version: 1.8.2.9018
Date: 2022-10-15
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9016
# AMR 1.8.2.9018
This version will eventually become v2.0! We're happy to reach a new major milestone soon!

21
R/add_custom_antimicrobials.R
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@ -50,6 +50,8 @@
#' @rdname add_custom_antimicrobials
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning (which is now suppressed):
#' suppressWarnings(
#' as.ab("test")
@ -90,6 +92,7 @@
#' ampicillin = as.rsi("R"))
#' x
#' x[, betalactams()]
#' }
add_custom_antimicrobials <- function(x) {
meet_criteria(x, allow_class = "data.frame")
stop_ifnot(all(c("ab", "name") %in% colnames(x)),
@ -107,10 +110,22 @@ add_custom_antimicrobials <- function(x) {
x$loinc <- as.list(x$loinc)
}
AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
class(AMR_env$AB_lookup$ab) <- "character"
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = TRUE)
AMR_env$AB_lookup <- unique(bind_rows(AMR_env$AB_lookup, x))
bind_rows <- import_fn("bind_rowtts", "dplyr", error_on_fail = FALSE)
if (is.null(bind_rows)) {
# do the binding in base R
new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
rownames(new_df) <- NULL
for (col in colnames(x)) {
new_df[, col] <- x[, col, drop = TRUE]
}
AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
} else {
# otherwise use dplyr
AMR_env$AB_lookup <- unique(bind_rows(AMR_env$AB_lookup, x))
}
class(AMR_env$AB_lookup$ab) <- c("ab", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
}

3
man/add_custom_antimicrobials.Rd
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@ -33,6 +33,8 @@ add_custom_antimicrobials(
Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
}
\examples{
\donttest{
# returns NA and throws a warning (which is now suppressed):
suppressWarnings(
as.ab("test")
@ -74,3 +76,4 @@ x <- data.frame(random_column = "test",
x
x[, betalactams()]
}
}