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(v1.4.0.9041) updates based on review

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dr. M.S. (Matthijs) Berends
2020-12-17 16:22:25 +01:00
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commit 81af41da3a
74 changed files with 710 additions and 627 deletions
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9041</span>
</span>
</div>
@ -91,14 +91,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<ul class="nav navbar-nav">
<li>
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Home
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How to
@ -107,77 +107,77 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
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Conduct AMR analysis
</a>
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<li>
<a href="../articles/resistance_predict.html">
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Predict antimicrobial resistance
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Data sets for download / own use
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<a href="../articles/PCA.html">
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Conduct principal component analysis for AMR
</a>
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<li>
<a href="../articles/MDR.html">
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<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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<a href="../reference/mo_property.html">
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Get properties of a microorganism
</a>
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Get properties of an antibiotic
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Other: benchmarks
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@ -186,21 +186,21 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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Manual
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Authors
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Changelog
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@ -209,14 +209,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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Survey
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@ -287,7 +287,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Use a value</p></td>
<td><p>a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code></p></td>
</tr>
<tr>
<th>language</th>
@ -295,7 +295,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</tr>
<tr>
<th>combine_SI</th>
<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>