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doc fix

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dr. M.S. (Matthijs) Berends
2022-10-10 21:38:39 +02:00
parent 955f9d7020
commit 57d66cd9d0
4 changed files with 15 additions and 11 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.2.9012 Version: 1.8.2.9013
Date: 2022-10-10 Date: 2022-10-10
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 1.8.2.9012 # AMR 1.8.2.9013
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!

12
R/add_custom_antimicrobials.R
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@@ -27,9 +27,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== # # ==================================================================== #
#' Add Manual Antimicrobials to This Package #' Add Custom Antimicrobials to This Package
#' #'
#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package. #' With [add_custom_antimicrobials()] you can add your own custom antimicrobial codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name" #' @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, although this requires to load the `AMR` package at every start-up: #' @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:
#' #'
@@ -55,15 +55,17 @@
#' as.ab("test") #' as.ab("test")
#' ) #' )
#' #'
#' # now add a manual entry - it will be considered by as.ab() and #' # now add a custom entry - it will be considered by as.ab() and
#' # all ab_*() functions #' # all ab_*() functions
#' add_custom_antimicrobials( #' add_custom_antimicrobials(
#' data.frame(ab = "TEST", #' data.frame(ab = "TEST",
#' name = "Test Antibiotic", #' name = "Test Antibiotic",
#' # you can add any property present in the
#' # 'antibiotics' data set, such as 'group':
#' group = "Test Group") #' group = "Test Group")
#' ) #' )
#' #'
#' "test" is now a new antibiotic: #' # "test" is now a new antibiotic:
#' as.ab("test") #' as.ab("test")
#' ab_name("test") #' ab_name("test")
#' ab_group("test") #' ab_group("test")
@@ -99,5 +101,5 @@ clear_custom_antimicrobials <- function() {
assignInNamespace(x = "AB_lookup", assignInNamespace(x = "AB_lookup",
value = create_AB_lookup(), value = create_AB_lookup(),
ns = asNamespace("AMR")) ns = asNamespace("AMR"))
message_("Manual antimicrobials cleared.") message_("Custom antimicrobials cleared.")
} }

10
man/add_custom_antimicrobials.Rd
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@@ -3,7 +3,7 @@
\name{add_custom_antimicrobials} \name{add_custom_antimicrobials}
\alias{add_custom_antimicrobials} \alias{add_custom_antimicrobials}
\alias{clear_custom_antimicrobials} \alias{clear_custom_antimicrobials}
\title{Add Manual Antimicrobials to This Package} \title{Add Custom Antimicrobials to This Package}
\usage{ \usage{
add_custom_antimicrobials(x) add_custom_antimicrobials(x)
@@ -13,7 +13,7 @@ clear_custom_antimicrobials()
\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"} \item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
} }
\description{ \description{
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own manual antimicrobial codes to the \code{AMR} package. With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial codes to the \code{AMR} package.
} }
\details{ \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, although this requires to load the \code{AMR} package at every start-up: 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:
@@ -38,15 +38,17 @@ suppressWarnings(
as.ab("test") as.ab("test")
) )
# now add a manual entry - it will be considered by as.ab() and # now add a custom entry - it will be considered by as.ab() and
# all ab_*() functions # all ab_*() functions
add_custom_antimicrobials( add_custom_antimicrobials(
data.frame(ab = "TEST", data.frame(ab = "TEST",
name = "Test Antibiotic", name = "Test Antibiotic",
# you can add any property present in the
# 'antibiotics' data set, such as 'group':
group = "Test Group") group = "Test Group")
) )
"test" is now a new antibiotic: # "test" is now a new antibiotic:
as.ab("test") as.ab("test")
ab_name("test") ab_name("test")
ab_group("test") ab_group("test")