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new antibiotics
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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</span>
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</div>
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@ -146,7 +146,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</a>
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</li>
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<li>
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<a href="../reference/atc_property.html">
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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@ -257,8 +257,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<span class='fu'>n_rsi</span>(<span class='no'>...</span>)
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<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
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<span class='st'>"official"</span>), <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
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<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -277,7 +277,11 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</tr>
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<tr>
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<th>translate_ab</th>
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<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
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<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property</a></code></p></td>
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</tr>
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<tr>
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<th>language</th>
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<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
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</tr>
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<tr>
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<th>combine_IR</th>
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@ -315,55 +319,55 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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?<span class='no'>septic_patients</span>
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<span class='co'># Count resistant isolates</span>
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<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='co'># Or susceptible isolates</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='co'># Count all available isolates</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='co'># Since n_rsi counts available isolates, you can</span>
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<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
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<span class='co'># This results in the same:</span>
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
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<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
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<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
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<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),
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<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>CIP</span>),
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
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<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
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<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
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<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
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<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1342 (71.4%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># S = 1342 (71.4%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># S = 1372 (74.0%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
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<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1660 (92.3%)</span>
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<span class='fu'>count_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># S = 1660 (92.3%)</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1798</span>
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<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
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<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
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<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
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<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='co'># It also supports grouping variables</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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