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(v1.3.0.9009) documentation update

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dr. M.S. (Matthijs) Berends
2020-08-26 16:13:40 +02:00
parent 9b8db57c65
commit 81af0b001c
42 changed files with 53 additions and 40 deletions
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6
R/aa_helper_functions.R
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@ -224,7 +224,7 @@ stop_ifnot_installed <- function(package) {
if (package == "rstudioapi") {
stop("This function only works in RStudio.", call. = FALSE)
} else if (pkg != "base") {
stop("package '", pkg, "' required but not installed.",
stop("This requires the '", pkg, "' package.",
"\nTry to install it with: install.packages(\"", pkg, "\")",
call. = FALSE)
}
@ -240,7 +240,9 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
get(name, envir = asNamespace(pkg)),
error = function(e) {
if (isTRUE(error_on_fail)) {
stop_("function ", name, "() not found in package '", pkg, "'. Please contact the maintainers of the AMR package at https://github.com/msberends/AMR/issues.", call = FALSE)
stop_("function ", name, "() not found in package '", pkg,
"'. Please create an issue at https://github.com/msberends/AMR/issues. Many thanks!",
call = FALSE)
} else {
return(NULL)
}

9
R/ab_class_selectors.R
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@ -21,15 +21,16 @@
#' Antibiotic class selectors
#'
#' Use these selection helpers inside any function that allows [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), like `dplyr::select()` or `tidyr::pivot_longer()`. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' Use these selection helpers inside any function that allows [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html), like `dplyr::select()` or `tidyr::pivot_longer()`. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' @inheritParams filter_ab_class
#' @details All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#' @details All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#'
#' These functions only work if the `tidyselect` package is installed, that comes with the `dplyr` package. An error will be thrown if `tidyselect` package is not installed, or if the functions are used outside a function that allows Tidyverse selections like `select()` or `pivot_longer()`.
#' **N.B. These functions only work if the `tidyselect` package is installed**, that comes with the `dplyr` package. An error will be thrown if the `tidyselect` package is not installed, or if the functions are used outside a function that allows Tidyverse selections like `select()` or `pivot_longer()`.
#' @rdname antibiotic_class_selectors
#' @seealso [filter_ab_class()] for the `filter()` equivalent.
#' @name antibiotic_class_selectors
#' @export
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @examples
#' \dontrun{
@ -58,7 +59,7 @@
#'
#' data.frame(irrelevant = "value",
#' J01CA01 = "S") %>% # ATC code of ampicillin
#' select(penicillins()) # so the 'J01CA01' column is selected
#' select(penicillins()) # the 'J01CA01' column will be selected
#'
#' }
ab_class <- function(ab_class) {

2
R/bug_drug_combinations.R
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@ -51,7 +51,7 @@
#' FUN = mo_gramstain)
#'
#' x <- bug_drug_combinations(example_isolates,
#' FUN = function(x) ifelse(x == "B_ESCHR_COLI",
#' FUN = function(x) ifelse(x == as.mo("E. coli"),
#' "E. coli",
#' "Others"))
#' }