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EUCAST update, as.mo bugfix for empty vlaues

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dr. M.S. (Matthijs) Berends
2019-01-08 16:23:45 +01:00
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<meta property="og:description" content="All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS)." />
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<h1>ITIS: Integrated Taxonomic Information System</h1>
<div class="hidden name"><code>ITIS.Rd</code></div>
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<div class="ref-description">
<p>All taxonomic names of all microorganisms are included in this package, using the authoritative Integrated Taxonomic Information System (ITIS).</p>
</div>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
<p><img src='figures/itis_logo.jpg' height=60px style=margin-bottom:5px /> <br />
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
<p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># Get a note when a species was renamed</span>
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydia psittaci"</span>)
<span class='co'># Note: 'Chlamydia psittaci' (Page, 1968) was renamed</span>
<span class='co'># 'Chlamydophila psittaci' (Everett et al., 1999)</span>
<span class='co'># [1] "C. psittaci"</span>
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
<span class='fu'><a href='mo_property.html'>mo_class</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Gammaproteobacteria"</span>
<span class='fu'><a href='mo_property.html'>mo_family</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Enterobacteriaceae"</span>
<span class='fu'><a href='mo_property.html'>mo_subkingdom</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Negibacteria"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># based on subkingdom</span>
<span class='co'># [1] "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_ref</a></span>(<span class='st'>"E. coli"</span>)
<span class='co'># [1] "Castellani and Chalmers, 1919"</span>
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Cyanobacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span>
<span class='co'># }</span></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#itis">ITIS</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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@ -289,11 +289,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span></pre>

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@ -270,11 +270,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='http://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='no'>as.rsi</span>)
<span class='co'># }</span></pre>
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@ -217,7 +217,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p>
</div>
@ -275,7 +275,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='http://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -314,13 +314,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://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>),
<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'>%&gt;%</span>
<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>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
<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>
<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>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<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 amount of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
@ -338,13 +338,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://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'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span></pre>

128
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@ -289,8 +289,8 @@
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/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. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -302,68 +302,68 @@
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>),
<strong>coli</strong>: colistin (<em>J01XB01</em>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>),
<strong>line</strong>: linezolid (<em>J01XX08</em>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

12
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@ -361,11 +361,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='co'># Which can be shortened to:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@ -376,14 +376,14 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Now let's see if first isolates matter:</span>
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<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'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<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'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span>

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@ -354,7 +354,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
<li><p>Median, using <code><a href='https://www.rdocumentation.org/packages/stats/topics/median'>median</a></code>, with percentage since oldest</p></li>
</ul>
<p>In factors, all factor levels that are not existing in the input data will be dropped.</p>
<p>The function <code>top_freq</code> uses <code><a href='http://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p>
<p>The function <code>top_freq</code> uses <code><a href='https://dplyr.tidyverse.org/reference/top_n.html'>top_n</a></code> internally and will include more than <code>n</code> rows if there are ties.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -378,34 +378,34 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># you could also use `select` or `pull` to get your variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>()
<span class='co'># multiple selected variables will be pasted together</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>left_join_microorganisms</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># group a variable and analyse another</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>gender</span>)
<span class='co'># get top 10 bugs of hospital A as a vector</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>top_freq</span>(<span class='fl'>10</span>)
<span class='co'># save frequency table to an object</span>
<span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>year</span>)
@ -456,11 +456,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># only get selected columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
<span class='co'># check differences between frequency tables</span>

36
docs/reference/ggplot_rsi.html
View File

@ -327,7 +327,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
<span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span>
@ -341,17 +341,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>()
<span class='co'># get only portions and no counts:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
<span class='co'># add other ggplot2 parameters as you like:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
<span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
@ -360,25 +360,25 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># `age_group` is also a function of this package:</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<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'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
@ -388,22 +388,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># determine first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># select this short name and some antiseptic drugs</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='co'># group by MO</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>,

6
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@ -221,7 +221,7 @@
<tbody>
<tr>
<th colspan="2">
<h2 id="section-backround-information" class="hasAnchor"><a href="#section-backround-information" class="anchor"></a>Backround information</h2>
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
<p class="section-desc"><p>Some pages about our package and its external sources.</p></p>
</th>
</tr>
@ -234,7 +234,7 @@
</tr><tr>
<td>
<p><code><a href="itis.html">itis</a></code> </p>
<p><code><a href="ITIS.html">ITIS</a></code> </p>
</td>
<td><p>ITIS: Integrated Taxonomic Information System</p></td>
</tr>
@ -513,7 +513,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-backround-information">Backround information</a></li>
<li><a href="#section-background-information">Background information</a></li>
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
<li><a href="#section-analysing-your-data">Analysing your data</a></li>

4
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@ -249,13 +249,13 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters to pass on to <code>dplyr::<a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code>.</p></td>
<td><p>other parameters to pass on to <code>dplyr::<a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> As opposed to the <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> functions of <code>dplyr</code>, characters vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='http://dplyr.tidyverse.org/reference/join.html'>join</a></code> for more information.</p>
<p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code> functions of <code>dplyr</code>, characters vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/join.html'>join</a></code> for more information.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
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@ -288,7 +288,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
<span class='co'># }</span></pre>
</div>

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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab.html'>guess_ab</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<em>J01CR02</em>),
<strong>amik</strong>: amikacin (<em>J01GB06</em>),
<strong>amox</strong>: amoxicillin (<em>J01CA04</em>),
<strong>ampi</strong>: ampicillin (<em>J01CA01</em>),
<strong>azit</strong>: azithromycin (<em>J01FA10</em>),
<strong>azlo</strong>: azlocillin (<em>J01CA09</em>),
<strong>aztr</strong>: aztreonam (<em>J01DF01</em>),
<strong>cefa</strong>: cefaloridine (<em>J01DB02</em>),
<strong>cfep</strong>: cefepime (<em>J01DE01</em>),
<strong>cfot</strong>: cefotaxime (<em>J01DD01</em>),
<strong>cfox</strong>: cefoxitin (<em>J01DC01</em>),
<strong>cfra</strong>: cefradine (<em>J01DB09</em>),
<strong>cfta</strong>: ceftazidime (<em>J01DD02</em>),
<strong>cftr</strong>: ceftriaxone (<em>J01DD04</em>),
<strong>cfur</strong>: cefuroxime (<em>J01DC02</em>),
<strong>chlo</strong>: chloramphenicol (<em>J01BA01</em>),
<strong>cipr</strong>: ciprofloxacin (<em>J01MA02</em>),
<strong>clar</strong>: clarithromycin (<em>J01FA09</em>),
<strong>clin</strong>: clindamycin (<em>J01FF01</em>),
<strong>clox</strong>: flucloxacillin (<em>J01CF05</em>),
<strong>coli</strong>: colistin (<em>J01XB01</em>),
<strong>czol</strong>: cefazolin (<em>J01DB04</em>),
<strong>dapt</strong>: daptomycin (<em>J01XX09</em>),
<strong>doxy</strong>: doxycycline (<em>J01AA02</em>),
<strong>erta</strong>: ertapenem (<em>J01DH03</em>),
<strong>eryt</strong>: erythromycin (<em>J01FA01</em>),
<strong>fosf</strong>: fosfomycin (<em>J01XX01</em>),
<strong>fusi</strong>: fusidic acid (<em>J01XC01</em>),
<strong>gent</strong>: gentamicin (<em>J01GB03</em>),
<strong>imip</strong>: imipenem (<em>J01DH51</em>),
<strong>kana</strong>: kanamycin (<em>J01GB04</em>),
<strong>levo</strong>: levofloxacin (<em>J01MA12</em>),
<strong>linc</strong>: lincomycin (<em>J01FF02</em>),
<strong>line</strong>: linezolid (<em>J01XX08</em>),
<strong>mero</strong>: meropenem (<em>J01DH02</em>),
<strong>mezl</strong>: mezlocillin (<em>J01CA10</em>),
<strong>mino</strong>: minocycline (<em>J01AA08</em>),
<strong>moxi</strong>: moxifloxacin (<em>J01MA14</em>),
<strong>nali</strong>: nalidixic acid (<em>J01MB02</em>),
<strong>neom</strong>: neomycin (<em>J01GB05</em>),
<strong>neti</strong>: netilmicin (<em>J01GB07</em>),
<strong>nitr</strong>: nitrofurantoin (<em>J01XE01</em>),
<strong>norf</strong>: norfloxacin (<em>J01MA06</em>),
<strong>novo</strong>: novobiocin (an ATCvet code: <em>QJ01XX95</em>),
<strong>oflo</strong>: ofloxacin (<em>J01MA01</em>),
<strong>peni</strong>: penicillin (<em>J01RA01</em>),
<strong>pipe</strong>: piperacillin (<em>J01CA12</em>),
<strong>pita</strong>: piperacillin+tazobactam (<em>J01CR05</em>),
<strong>poly</strong>: polymyxin B (<em>J01XB02</em>),
<strong>pris</strong>: pristinamycin (<em>J01FG01</em>),
<strong>qida</strong>: quinupristin/dalfopristin (<em>J01FG02</em>),
<strong>rifa</strong>: rifampicin (<em>J04AB02</em>),
<strong>roxi</strong>: roxithromycin (<em>J01FA06</em>),
<strong>siso</strong>: sisomicin (<em>J01GB08</em>),
<strong>teic</strong>: teicoplanin (<em>J01XA02</em>),
<strong>tetr</strong>: tetracycline (<em>J01AA07</em>),
<strong>tica</strong>: ticarcillin (<em>J01CA13</em>),
<strong>tige</strong>: tigecycline (<em>J01AA12</em>),
<strong>tobr</strong>: tobramycin (<em>J01GB01</em>),
<strong>trim</strong>: trimethoprim (<em>J01EA01</em>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<em>J01EE01</em>),
<strong>vanc</strong>: vancomycin (<em>J01XA01</em>).</p>
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
<strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
<strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
<strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
<strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
<strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
<strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
<strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
<strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
<strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
<strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
<strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
<strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
<strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
<strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
<strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
<strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
<strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
<strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
<strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
<strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
<strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
<strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
<strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
<strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
<strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
<strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
<strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
<strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
<strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
<strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
<strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
<strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
<strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
<strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
<strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
<strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
<strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
<strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
<strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
<strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
<strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
<strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
<strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
<strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
<strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
<strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
<strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
<strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
<strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
<strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
<strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
<strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
<strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
<strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
<strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
<strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
<strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
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@ -216,7 +216,7 @@
<div class="ref-description">
<p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p>
<p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='AMR-deprecated.html'>guess_mo</a></code>.</p>
</div>

2
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@ -216,7 +216,7 @@
<div class="ref-description">
<p>A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='as.mo.html'>guess_mo</a></code>.</p>
<p>A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='AMR-deprecated.html'>guess_mo</a></code>.</p>
</div>

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@ -217,7 +217,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p>
</div>
@ -333,17 +333,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
<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'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<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'>%&gt;%</span>
<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'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
<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 amount of tested isolates!</span>
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
@ -358,8 +358,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<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'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>),
@ -368,22 +368,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://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'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>
<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'>%&gt;%</span>
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
<span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amox</span>, <span class='no'>metr</span>))
<span class='co'># }</span></pre>
</div>

8
docs/reference/resistance_predict.html
View File

@ -311,7 +311,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># or use dplyr so you can actually read it:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>tbl</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Haemophilus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='no'>amcl</span>, <span class='no'>date</span>)
<span class='co'># }</span><span class='co'># NOT RUN {</span>
@ -322,9 +322,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># get bacteria properties like genus and species</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>(<span class='st'>"mo"</span>) <span class='kw'>%&gt;%</span>
<span class='co'># calculate first isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first E. coli isolates</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Escherichia"</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Escherichia"</span>,
<span class='no'>species</span> <span class='kw'>==</span> <span class='st'>"coli"</span>,
<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
<span class='co'># predict resistance of cefotaxime for next years</span>
@ -338,7 +338,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) {
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,