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(v1.3.0.9019) small fix

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dr. M.S. (Matthijs) Berends 2020-09-14 14:08:07 +02:00
parent 7b6dd676f7
commit 354c606d6a
13 changed files with 23 additions and 23 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.3.0.9018 Version: 1.3.0.9019
Date: 2020-09-14 Date: 2020-09-14
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 1.3.0.9018 # AMR 1.3.0.9019
## <small>Last updated: 14 September 2020</small> ## <small>Last updated: 14 September 2020</small>
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! 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!

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R/mo.R
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@ -314,7 +314,7 @@ exec_as.mo <- function(x,
res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE] res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
if (NROW(res_df) > 1) { if (NROW(res_df) > 1) {
# sort the findings on matching score # sort the findings on matching score
res_df <- res_df[order(mo_matching_score(x_backup[i], res_df[, "fullname", drop = TRUE]), decreasing = TRUE), , drop = FALSE] res_df <- res_df[order(mo_matching_score(input, res_df[, "fullname", drop = TRUE]), decreasing = TRUE), , drop = FALSE]
} }
res <- as.character(res_df[, column, drop = TRUE]) res <- as.character(res_df[, column, drop = TRUE])
if (length(res) == 0) { if (length(res) == 0) {

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man/figures/logo.svg → data-raw/logo.svg
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docs/404.html
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<script src="https://msberends.github.io/AMR/extra.js"></script> <script src="https://msberends.github.io/AMR/extra.js"></script>
<meta property="og:title" content="Page not found (404)" /> <meta property="og:title" content="Page not found (404)" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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<script src="extra.js"></script> <script src="extra.js"></script>
<meta property="og:title" content="License" /> <meta property="og:title" content="License" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Articles" /> <meta property="og:title" content="Articles" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/authors.html
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@ -49,7 +49,7 @@
<script src="extra.js"></script> <script src="extra.js"></script>
<meta property="og:title" content="Citation and Authors" /> <meta property="og:title" content="Citation and Authors" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/index.html
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@ -24,7 +24,7 @@
using evidence-based methods, like those defined by Leclercq et al. (2013) using evidence-based methods, like those defined by Leclercq et al. (2013)
&lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and the Clinical and Laboratory &lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and the Clinical and Laboratory
Standards Institute (2014) &lt;isbn: 1-56238-899-1&gt;."> Standards Institute (2014) &lt;isbn: 1-56238-899-1&gt;.">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@ -43,7 +43,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Changelog" /> <meta property="og:title" content="Changelog" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</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-1309018" class="section level1"> <div id="amr-1309019" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9018"> <h1 class="page-header" data-toc-text="1.3.0.9019">
<a href="#amr-1309018" class="anchor"></a>AMR 1.3.0.9018<small> Unreleased </small> <a href="#amr-1309019" class="anchor"></a>AMR 1.3.0.9019<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-14-september-2020" class="section level2"> <div id="last-updated-14-september-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000 pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: [] articles: []
last_built: 2020-09-14T10:20Z last_built: 2020-09-14T11:57Z
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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@ -49,7 +49,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Function reference" /> <meta property="og:title" content="Function reference" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>

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docs/survey.html
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@ -49,7 +49,7 @@
<script src="extra.js"></script> <script src="extra.js"></script>
<meta property="og:title" content="Survey" /> <meta property="og:title" content="Survey" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -81,7 +81,7 @@
</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">1.3.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9019</span>
</span> </span>
</div> </div>