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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

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dr. M.S. (Matthijs) Berends
2021-11-28 23:01:26 +01:00
parent 9a2c431e16
commit 694cf5ba77
72 changed files with 780 additions and 669 deletions
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9
docs/reference/eucast_rules.html
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@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.7.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
</span>
</div>
@ -247,7 +247,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
version_breakpoints <span class='op'>=</span> <span class='fl'>11</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.3</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
custom_rules <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -285,7 +285,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr>
<tr>
<th>version_expertrules</th>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".</p></td>
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></td>
</tr>
<tr>
<th>ampc_cephalosporin_resistance</th>
@ -321,6 +321,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; doi: <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>10.1111/j.1469-0691.2011.03703.x</a></p></li>
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
@ -434,7 +435,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">