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Package: AMR
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Version: 1.8.2.9011
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Version: 1.8.2.9012
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Date: 2022-10-10
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 1.8.2.9011
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# AMR 1.8.2.9012
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -458,7 +458,7 @@ ab_validate <- function(x, property, ...) {
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} else {
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# try to catch an error when inputting an invalid argument
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% AMR::antibiotics[1, property, drop = TRUE],
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tryCatch(x[1L] %in% AB_lookup[1, property, drop = TRUE],
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error = function(e) stop(e$message, call. = FALSE)
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)
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@ -31,9 +31,13 @@
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#'
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#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
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#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
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#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, for example:
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#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, although this requires to load the `AMR` package at every start-up:
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#'
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#' ```r
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#' # Open .Rprofile file
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#' utils::file.edit("~/.Rprofile")
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#'
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#' # Add custom antibiotic codes:
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#' library(AMR)
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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@ -46,12 +50,12 @@
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#' @rdname add_custom_antimicrobials
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#' @export
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#' @examples
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#' \donttest{
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#' # returns NA and throws a warning (which is now suppressed):
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#' suppressWarnings(
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#' as.ab("test")
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#' )
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#'
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#' # returns NA and throws a warning:
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#' as.ab("test")
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#'
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#' # now a manual entry - it will be considered by as.ab() and
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#' # now add a manual entry - it will be considered by as.ab() and
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#' # all ab_*() functions
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#' add_custom_antimicrobials(
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#' data.frame(ab = "TEST",
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@ -63,7 +67,8 @@
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#' as.ab("test")
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#' ab_name("test")
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#' ab_group("test")
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#' }
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#'
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#' ab_info("test")
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add_custom_antimicrobials <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot(all(c("ab", "name") %in% colnames(x)),
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@ -16,9 +16,13 @@ clear_custom_antimicrobials()
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With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
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}
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\details{
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Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, for example:
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Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{library(AMR)
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
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utils::file.edit("~/.Rprofile")
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# Add custom antibiotic codes:
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library(AMR)
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add_custom_antimicrobials(
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data.frame(ab = "TEST",
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name = "Test Antibiotic",
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@ -29,12 +33,12 @@ add_custom_antimicrobials(
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Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to clear the previously added antimicrobials.
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}
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\examples{
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\donttest{
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# returns NA and throws a warning (which is now suppressed):
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suppressWarnings(
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as.ab("test")
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)
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# returns NA and throws a warning:
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as.ab("test")
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# now a manual entry - it will be considered by as.ab() and
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# now add a manual entry - it will be considered by as.ab() and
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# all ab_*() functions
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add_custom_antimicrobials(
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data.frame(ab = "TEST",
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@ -46,5 +50,6 @@ add_custom_antimicrobials(
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as.ab("test")
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ab_name("test")
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ab_group("test")
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}
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ab_info("test")
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}
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