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(v0.9.0.9017) documentation fix

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dr. M.S. (Matthijs) Berends 2020-01-27 19:30:26 +01:00
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commit 1b80773c22
12 changed files with 16 additions and 17 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 0.9.0.9016 Version: 0.9.0.9017
Date: 2020-01-27 Date: 2020-01-27
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 0.9.0.9016 # AMR 0.9.0.9017
## <small>Last updated: 27-Jan-2020</small> ## <small>Last updated: 27-Jan-2020</small>
### New ### New

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R/data.R
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#' - `disk_dose`\cr Dose of the used disk diffusion method #' - `disk_dose`\cr Dose of the used disk diffusion method
#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimeters that leads to "S" #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimeters that leads to "S"
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimeters that leads to "R" #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimeters that leads to "R"
#' @details The repository of this `AMR` package contains a file comprising this exact data set: [https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt]. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. #' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
"rsi_translation" "rsi_translation"

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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.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
</span> </span>
</div> </div>

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docs/authors.html
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@ -84,7 +84,7 @@
</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-9-0-9016" class="section level1"> <div id="amr-0-9-0-9017" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-9-0-9016" class="anchor"></a>AMR 0.9.0.9016<small> Unreleased </small> <a href="#amr-0-9-0-9017" class="anchor"></a>AMR 0.9.0.9017<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-27-jan-2020" class="section level2"> <div id="last-updated-27-jan-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -1459,7 +1459,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9016">0.9.0.9016</a></li> <li><a href="#amr-0-9-0-9017">0.9.0.9017</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li> <li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
</span> </span>
</div> </div>

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docs/reference/rsi_translation.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">0.9.0.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
</span> </span>
</div> </div>
@ -255,7 +255,7 @@
</ul> </ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p> <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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man/rsi_translation.Rd
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@ -23,7 +23,7 @@ rsi_translation
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values. Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
} }
\details{ \details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \link{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
} }
\section{Read more on our website!}{ \section{Read more on our website!}{