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dr. M.S. (Matthijs) Berends 2022-12-10 10:09:57 +01:00
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DESCRIPTION
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Package: AMR
Version: 1.8.2.9059
Date: 2022-12-09
Version: 1.8.2.9060
Date: 2022-12-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 1.8.2.9059
# AMR 1.8.2.9060
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
### Breaking
* Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
* **Removed all species of the taxonomic kingdom Chromista** from the package. This was done for multiple reasons:
* CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them
* Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package
* Chromista are almost never clinically relevant, thus lacking the secondary scope of this package
@ -16,8 +16,8 @@ This version will eventually become v2.0! We're happy to reach a new major miles
### New
* **EUCAST 2022 and CLSI 2022 guidelines** have been added for `as.rsi()`. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for `eucast_rules()` to apply EUCAST Expert Rules.
* Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.
* **All new algorithm for `as.mo()`** (and thus all `mo_*()` functions) while still following our original set-up as described in our recently submitted JSS paper (DOI [10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)).
* Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages. The automatic language determination will give a note on systems in supported languages.
* **All new algorithm for `as.mo()`** (and thus all `mo_*()` functions) while still following our original set-up as described in our recently published JSS paper (DOI [10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)).
* A new argument `keep_synonyms` allows to *not* correct for updated taxonomy, in favour of the now deleted argument `allow_uncertain`
* It has increased tremendously in speed and returns generally more consequent results
* Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new `mo_reset_session()` function.

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R/translate.R
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#' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
#'
#' **To silence language notes when this package loads** on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this:
#' To permanently silence the once-per-session language notes on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this:
#'
#' ```r
#' # Open .Rprofile file
#' utils::file.edit("~/.Rprofile")
#'
#' # Add e.g. Italian support to that file using:
#' # Then add e.g. Italian support to that file using:
#' options(AMR_locale = "Italian")
#' ```
#'
@ -84,11 +84,11 @@
#' set_AMR_locale("Deutsch")
#' set_AMR_locale("German")
#' set_AMR_locale("de")
#' ab_name("amoxi/clav")
#' ab_name("amox/clav")
#'
#' # reset to system default
#' reset_AMR_locale()
#' ab_name("amoxi/clav")
#' ab_name("amox/clav")
get_AMR_locale <- function() {
# a message for this will be thrown in translate_into_language() if outcome is non-English
if (!is.null(getOption("AMR_locale", default = NULL))) {

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man/translate.Rd
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@ -27,12 +27,12 @@ For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_na
\details{
The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
\strong{To silence language notes when this package loads} on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
To permanently silence the once-per-session language notes on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
utils::file.edit("~/.Rprofile")
# Add e.g. Italian support to that file using:
# Then add e.g. Italian support to that file using:
options(AMR_locale = "Italian")
}\if{html}{\out{</div>}}
@ -76,9 +76,9 @@ mo_name("Coagulase-negative Staphylococcus (CoNS)")
set_AMR_locale("Deutsch")
set_AMR_locale("German")
set_AMR_locale("de")
ab_name("amoxi/clav")
ab_name("amox/clav")
# reset to system default
reset_AMR_locale()
ab_name("amoxi/clav")
ab_name("amox/clav")
}