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(v1.3.0.9023) optimalisation

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dr. M.S. (Matthijs) Berends
2020-09-19 11:54:01 +02:00
parent 4e40e42011
commit d049cce69b
30 changed files with 104 additions and 578 deletions
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docs/404.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/LICENSE-text.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/articles/index.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/authors.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/index.html
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@ -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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/news/index.html
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@ -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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309022" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9022">
<a href="#amr-1309022" class="anchor"></a>AMR 1.3.0.9022<small> Unreleased </small>
<div id="amr-1309023" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9023">
<a href="#amr-1309023" class="anchor"></a>AMR 1.3.0.9023<small> Unreleased </small>
</h1>
<div id="last-updated-18-september-2020" class="section level2">
<div id="last-updated-19-september-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-18-september-2020" class="anchor"></a><small>Last updated: 18 September 2020</small>
<a href="#last-updated-19-september-2020" class="anchor"></a><small>Last updated: 19 September 2020</small>
</h2>
<p>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!</p>
<div id="new" class="section level3">

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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_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-18T14:05Z
last_built: 2020-09-19T09:53Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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docs/reference/as.mo.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>
@ -376,9 +376,9 @@
<li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
</ol>
<p>$$L' = F - \frac{0.5 \times L}{F}$$</p>
<p>$$L' = F - \frac{0.5L}{F}$$</p>
<p>The final matching score \(M\) is calculated as:
$$M = L' \times \frac{1}{P \times K} * \frac{1}{U}$$</p>
$$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

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docs/reference/index.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>

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docs/reference/mo_matching_score.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>
@ -270,9 +270,9 @@
<li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
</ol>
<p>$$L' = F - \frac{0.5 \times L}{F}$$</p>
<p>$$L' = F - \frac{0.5L}{F}$$</p>
<p>The final matching score \(M\) is calculated as:
$$M = L' \times \frac{1}{P \times K} * \frac{1}{U}$$</p>
$$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)

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docs/survey.html
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</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">1.3.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9023</span>
</span>
</div>