Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
stop_ifnot(col_mo%in%colnames(x),"column '",col_mo,"' (`col_mo`) not found")
if (guideline$code=="cmi2012"){
guideline$name<-"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
# this will save the uncertain items as attribute, so they can be bound to `uncertainties` in the uncertain_fn() function
x<-structure(x,uncertainties=uncertainties)
}
if (old_mo_warning==TRUE&property!="mo"){
warning("The input contained old microorganism IDs from previous versions of this package.\nPlease use `as.mo()` on these old IDs to transform them to the new format.\nSUPPORT FOR THIS WILL BE DROPPED IN A FUTURE VERSION.",call.=FALSE)
cat(font_blue("Scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name.\n"))
cat(font_blue(strwrap(c("Scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Furthermore, an indication is given about the likelihood of the match - the more transformations are needed for coercion, the more unlikely the result.")),collapse="\n"))
#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
#'
#' ## Changing the default language
#' The system language will be used at default (as returned by [Sys.getenv("LANG")] or, if `LANG` is not set, [Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
#' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
#'
#' 1. Setting the R option `AMR_locale`, e.g. by running `options(AMR_locale = "de")`
#' 2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9018</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9020</span>
</span>
</div>
@ -252,7 +252,7 @@
<p>Please suggest your own translations <ahref='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3>Changing the default language</h3>
<p>The system language will be used at default (as returned by Sys.getenv("LANG") or, if <code>LANG</code> is not set, <code><ahref='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol>
<p>The system language will be used at default (as returned by <code><ahref='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><ahref='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol>
<li><p>Setting the R option <code>AMR_locale</code>, e.g. by running <code><ahref='https://rdrr.io/r/base/options.html'>options(AMR_locale = "de")</a></code></p></li>
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory</p></li>
@ -18,7 +18,7 @@ Currently supported languages are: Dutch, English, French, German, Italian, Port
Please suggest your own translations \href{https://github.com/msberends/AMR/issues/new?title=Translations}{by creating a new issue on our repository}.
\subsection{Changing the default language}{
The system language will be used at default (as returned by \link{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale()}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
The system language will be used at default (as returned by \code{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale()}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
\enumerate{
\item Setting the R option \code{AMR_locale}, e.g. by running \code{options(AMR_locale = "de")}
\item Setting the system variable \code{LANGUAGE} or \code{LANG}, e.g. by adding \code{LANGUAGE="de_DE.utf8"} to your \code{.Renviron} file in your home directory
