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Merge branch 'main' of https://github.com/msberends/AMR into main

# Conflicts:
#	DESCRIPTION
#	R/add_custom_antimicrobials.R
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dr. M.S. (Matthijs) Berends 2022-10-11 10:53:51 +02:00
commit dfae4c7e7d
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
Version: 1.8.2.9013
Version: 1.8.2.9014
Date: 2022-10-11
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 1.8.2.9013
# AMR 1.8.2.9014
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/ #
# ==================================================================== #
#' 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"
#' @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")
#' )
#'
#' # 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
#' add_custom_antimicrobials(
#' data.frame(ab = "TEST",
#' name = "Test Antibiotic",
#' # you can add any property present in the
#' # 'antibiotics' data set, such as 'group':
#' group = "Test Group")
#' )
#'
#' "test" is now a new antibiotic:
#' # "test" is now a new antibiotic:
#' as.ab("test")
#' ab_name("test")
#' ab_group("test")
@ -128,5 +130,5 @@ clear_custom_antimicrobials <- function() {
value = create_AB_lookup(),
ns = asNamespace("AMR"))
AMR_env$custom_ab_codes <- character(0)
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}
\alias{add_custom_antimicrobials}
\alias{clear_custom_antimicrobials}
\title{Add Manual Antimicrobials to This Package}
\title{Add Custom Antimicrobials to This Package}
\usage{
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"}
}
\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{
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")
)
# 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
add_custom_antimicrobials(
data.frame(ab = "TEST",
name = "Test Antibiotic",
# you can add any property present in the
# 'antibiotics' data set, such as 'group':
group = "Test Group")
)
"test" is now a new antibiotic:
# "test" is now a new antibiotic:
as.ab("test")
ab_name("test")
ab_group("test")