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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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21
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 (which is now suppressed):
suppressWarnings(
as.ab("test")
)
# returns NA and throws a warning:
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")
}