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(v1.3.0.9019) small fix

new-mo-algorithm
parent
commit
354c606d6a
  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 2
      R/mo.R
  4. 0
      data-raw/logo.svg
  5. 4
      docs/404.html
  6. 4
      docs/LICENSE-text.html
  7. 4
      docs/articles/index.html
  8. 4
      docs/authors.html
  9. 4
      docs/index.html
  10. 10
      docs/news/index.html
  11. 2
      docs/pkgdown.yml
  12. 4
      docs/reference/index.html
  13. 4
      docs/survey.html

2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9018
Version: 1.3.0.9019
Date: 2020-09-14
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# AMR 1.3.0.9018
# AMR 1.3.0.9019
## <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!

2
R/mo.R

@ -314,7 +314,7 @@ exec_as.mo <- function(x, @@ -314,7 +314,7 @@ exec_as.mo <- function(x,
res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
if (NROW(res_df) > 1) {
# 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])
if (length(res) == 0) {

0
man/figures/logo.svg → data-raw/logo.svg

Before

Width:  |  Height:  |  Size: 222 KiB

After

Width:  |  Height:  |  Size: 222 KiB

4
docs/404.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="https://msberends.github.io/AMR/extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

4
docs/LICENSE-text.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

4
docs/articles/index.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

4
docs/authors.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

4
docs/index.html

@ -24,7 +24,7 @@ @@ -24,7 +24,7 @@
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
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]>
<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>
@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

10
docs/news/index.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>
@ -236,9 +236,9 @@ @@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309018" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9018">
<a href="#amr-1309018" class="anchor"></a>AMR 1.3.0.9018<small> Unreleased </small>
<div id="amr-1309019" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9019">
<a href="#amr-1309019" class="anchor"></a>AMR 1.3.0.9019<small> Unreleased </small>
</h1>
<div id="last-updated-14-september-2020" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml

@ -2,7 +2,7 @@ pandoc: 2.7.3 @@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-14T10:20Z
last_built: 2020-09-14T11:57Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

4
docs/reference/index.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

4
docs/survey.html

@ -49,7 +49,7 @@ @@ -49,7 +49,7 @@
<script src="extra.js"></script>
<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 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

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