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(v0.7.1.9065) bug-drug fix

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dr. M.S. (Matthijs) Berends
2019-08-27 22:41:09 +02:00
parent f3276592b7
commit 248638ad91
23 changed files with 62 additions and 45 deletions
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15
R/bug_drug_combinations.R
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@ -24,12 +24,14 @@
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @inheritParams rsi_df
#' @importFrom dplyr rename
#' @importFrom tidyr spread
#' @importFrom clean freq
#' @details The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#' @export
#' @rdname bug_drug_combinations
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
#' @examples
@ -65,14 +67,15 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
filter(total >= minimum) %>%
rename(ab = antibiotic)
structure(.Data = x, class = c("bugdrug", class(x)))
structure(.Data = x, class = c("bug_drug_combinations", class(x)))
}
#' @importFrom dplyr everything rename
#' @importFrom tidyr spread
#' @exportMethod format.bugdrug
#' @exportMethod format.bug_drug_combinations
#' @export
format.bugdrug <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
#' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE) {
if (combine_IR == FALSE) {
x$isolates <- x$R
} else {
@ -100,10 +103,10 @@ format.bugdrug <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
y
}
#' @exportMethod print.bugdrug
#' @exportMethod print.bug_drug_combinations
#' @export
#' @importFrom crayon blue
print.bugdrug <- function(x, ...) {
print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing."))
}

2
R/first_isolate.R
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@ -25,7 +25,7 @@
#' @param x a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_mo column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.
#' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)