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(v0.7.1.9005) new rsi calculations, atc class removal

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dr. M.S. (Matthijs) Berends
2019-07-01 14:03:15 +02:00
parent 65c6702b21
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78 changed files with 1169 additions and 911 deletions
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docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</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">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -322,12 +322,9 @@ This function uses intelligent rules to help getting fast and logical results. I
</ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human non-pathogenic microorganisms.</p>
<p><strong>Uncertain results</strong> <br />
The algorithm can additionally use three different levels of uncertainty to guess valid results. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> will skip all of these additional rules:</p><ul>
<li><p>(uncertainty level 1): It tries to look for only matching genera</p></li>
<li><p>(uncertainty level 1): It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
<li><p>(uncertainty level 2): It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 2): It strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It strips off words from the start one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It tries any part of the name</p></li>
<li><p>(uncertainty level 1): It tries to look for only matching genera, previously accepted (but now invalid) taxonomic names and misspelled input</p></li>
<li><p>(uncertainty level 2): It removed parts between brackets, strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It strips off words from the start one by one and tries any part of the name</p></li>
</ul>
<p>You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
<p>Examples:</p><ul>