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(v1.5.0.9002) doc update

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dr. M.S. (Matthijs) Berends 2021-01-14 15:51:41 +01:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.5.0.9001 Version: 1.5.0.9002
Date: 2021-01-14 Date: 2021-01-14
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 1.5.0.9001 # AMR 1.5.0.9002
## <small>Last updated: 14 January 2021</small> ## <small>Last updated: 14 January 2021</small>
### New ### New

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R/globals.R
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@ -33,6 +33,7 @@ globalVariables(c(".rowid",
"atc_group2", "atc_group2",
"code", "code",
"data", "data",
"dosage",
"dose", "dose",
"dose_times", "dose_times",
"fullname", "fullname",

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R/isolate_identifier.R
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#' This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available. #' This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
#' @inheritSection lifecycle Maturing lifecycle #' @inheritSection lifecycle Maturing lifecycle
#' @inheritParams eucast_rules #' @inheritParams eucast_rules
#' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglysides()] #' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglycosides()]
#' @export #' @export
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples

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README.md
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<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" /> <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
The latest built **source package** (`AMR_x.x.x.tar.gz`) can be found in folder [/data-raw/](data-raw).
`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.

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docs/404.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/authors.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/index.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/news/index.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509001" class="section level1"> <div id="amr-1509002" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9001"> <h1 class="page-header" data-toc-text="1.5.0.9002">
<a href="#amr-1509001" class="anchor"></a>AMR 1.5.0.9001<small> Unreleased </small> <a href="#amr-1509002" class="anchor"></a>AMR 1.5.0.9002<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-14-january-2021" class="section level2"> <div id="last-updated-14-january-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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docs/pkgdown.yml
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datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-14T13:26Z last_built: 2021-01-14T14:48Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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docs/reference/isolate_identifier.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>
@ -257,7 +257,7 @@
</tr> </tr>
<tr> <tr>
<th>cols_ab</th> <th>cols_ab</th>
<td><p>a character vector of column names of <code>x</code>, or (a combination with) an <a href='[ab_class()]'>antibiotic selector function</a>, such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code> and <code>aminoglysides()</code></p></td> <td><p>a character vector of column names of <code>x</code>, or (a combination with) an <a href='[ab_class()]'>antibiotic selector function</a>, such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code> and <code><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code></p></td>
</tr> </tr>
</table> </table>

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docs/survey.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9002</span>
</span> </span>
</div> </div>

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man/isolate_identifier.Rd
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@ -11,7 +11,7 @@ isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglysides]{aminoglysides()}}} \item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglycosides]{aminoglycosides()}}}
} }
\description{ \description{
This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available. This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.