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documentation fix

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dr. M.S. (Matthijs) Berends 2022-10-10 21:03:39 +02:00
parent 3deeedc4b6
commit 955f9d7020
5 changed files with 28 additions and 18 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.2.9011
Version: 1.8.2.9012
Date: 2022-10-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9011
# AMR 1.8.2.9012
This version will eventually become v2.0! We're happy to reach a new major milestone soon!

2
R/ab_property.R
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@ -458,7 +458,7 @@ ab_validate <- function(x, property, ...) {
} else {
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::antibiotics[1, property, drop = TRUE],
tryCatch(x[1L] %in% AB_lookup[1, property, drop = TRUE],
error = function(e) stop(e$message, call. = FALSE)
)

17
R/add_custom_antimicrobials.R
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@ -31,9 +31,13 @@
#'
#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @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:
#' @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:
#'
#' ```r
#' # Open .Rprofile file
#' utils::file.edit("~/.Rprofile")
#'
#' # Add custom antibiotic codes:
#' library(AMR)
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
@ -46,12 +50,12 @@
#' @rdname add_custom_antimicrobials
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning:
#' # returns NA and throws a warning (which is now suppressed):
#' suppressWarnings(
#' as.ab("test")
#' )
#'
#' # now a manual entry - it will be considered by as.ab() and
#' # now add a manual entry - it will be considered by as.ab() and
#' # all ab_*() functions
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
@ -63,7 +67,8 @@
#' as.ab("test")
#' ab_name("test")
#' ab_group("test")
#' }
#'
#' ab_info("test")
add_custom_antimicrobials <- function(x) {
meet_criteria(x, allow_class = "data.frame")
stop_ifnot(all(c("ab", "name") %in% colnames(x)),

19
man/add_custom_antimicrobials.Rd
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@ -16,9 +16,13 @@ clear_custom_antimicrobials()
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package.
}
\details{
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:
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:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{library(AMR)
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
utils::file.edit("~/.Rprofile")
# Add custom antibiotic codes:
library(AMR)
add_custom_antimicrobials(
data.frame(ab = "TEST",
name = "Test Antibiotic",
@ -29,12 +33,12 @@ 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:
# returns NA and throws a warning (which is now suppressed):
suppressWarnings(
as.ab("test")
)
# now a manual entry - it will be considered by as.ab() and
# now add a manual entry - it will be considered by as.ab() and
# all ab_*() functions
add_custom_antimicrobials(
data.frame(ab = "TEST",
@ -46,5 +50,6 @@ add_custom_antimicrobials(
as.ab("test")
ab_name("test")
ab_group("test")
}
ab_info("test")
}