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fix warnings
This commit is contained in:
@ -289,11 +289,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># resistance of ciprofloxacine per age group</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://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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<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'>%>%</span>
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<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>,
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<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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</span>,
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<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'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
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<span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<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>)
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<span class='co'># }</span></pre>
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@ -362,16 +362,16 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
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<span class='co'># the select function of tidyverse is also supported:</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'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%>%</span>
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<span class='fu'>as.mo</span>()
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<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
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<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%>%</span>
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<span class='fu'>as.mo</span>()
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<span class='co'># although this works easier and does the same:</span>
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<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
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<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'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@ -270,11 +270,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='co'># using dplyr's mutate</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://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_at</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/vars'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
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<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>)
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<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</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://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
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<span class='no'>as.rsi</span>)
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<span class='co'># }</span></pre>
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</div>
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@ -275,7 +275,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
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<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://www.rdocumentation.org/packages/dplyr/topics/n_distinct'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
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<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>
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<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>
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<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>
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@ -314,13 +314,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='fu'><a href='http://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='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>),
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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='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
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<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>
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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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@ -338,13 +338,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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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://www.rdocumentation.org/packages/dplyr/topics/select'>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='http://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'>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://www.rdocumentation.org/packages/dplyr/topics/select'>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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<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'>%>%</span>
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<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'>%>%</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'># }</span></pre>
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@ -222,22 +222,27 @@
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<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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||||
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
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||||
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='st'>"azlo"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>,
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||||
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
|
||||
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>,
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||||
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>,
|
||||
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>,
|
||||
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>, <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>,
|
||||
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>, <span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>,
|
||||
<span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>, <span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='st'>"mezl"</span>,
|
||||
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>, <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>,
|
||||
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>,
|
||||
<span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>, <span class='kw'>oxac</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>,
|
||||
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>, <span class='kw'>pris</span> <span class='kw'>=</span> <span class='st'>"pris"</span>, <span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>,
|
||||
<span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>, <span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>,
|
||||
<span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>, <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>,
|
||||
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
|
||||
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>azlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>mezl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>oxac</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>pris</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>())
|
||||
|
||||
<span class='fu'>EUCAST_rules</span>(<span class='no'>...</span>)
|
||||
|
||||
@ -295,7 +300,7 @@
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
||||
<p>To define antibiotics column names, 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>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>),
|
||||
|
||||
@ -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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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='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='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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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='co'># Which can be shortened to:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</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'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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='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'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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='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>
|
||||
|
||||
@ -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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='no'>left_join_microorganisms</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%>%</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'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</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='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</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='co'># check differences between frequency tables</span>
|
||||
|
||||
@ -216,7 +216,7 @@
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> functions.</p>
|
||||
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> functions.</p>
|
||||
|
||||
</div>
|
||||
|
||||
@ -307,10 +307,10 @@
|
||||
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='abname.html'>abname</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p>
|
||||
<p><strong>The functions</strong><br />
|
||||
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
|
||||
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
|
||||
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
|
||||
<p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
|
||||
<p><code>scale_rsi_colours</code> sets colours to the bars: green for S, yellow for I and red for R, using <code>scale_brewer</code>.</p>
|
||||
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://www.rdocumentation.org/packages/ggplot2/topics/theme'>theme</a></code> with minimal distraction.</p>
|
||||
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></code> with minimal distraction.</p>
|
||||
<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>geom_text</a></code></p>
|
||||
<p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%>%</code>). See Examples.</p>
|
||||
|
||||
@ -327,12 +327,12 @@ 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://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</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'>geom_rsi</span>()
|
||||
|
||||
<span class='co'># prettify the plot using some additional functions:</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"nitr"</span>, <span class='st'>"fosf"</span>, <span class='st'>"trim"</span>, <span class='st'>"cipr"</span>)]
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
|
||||
<span class='fu'>geom_rsi</span>() +
|
||||
<span class='fu'>scale_y_percent</span>() +
|
||||
<span class='fu'>scale_rsi_colours</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</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'>%>%</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>,
|
||||
@ -360,56 +360,56 @@ 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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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'>%>%</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='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'>%>%</span>
|
||||
<span class='co'># `age_group` is also a function of this package:</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</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'>%>%</span>
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
|
||||
<span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>%>%</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'>%>%</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>) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
|
||||
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>)
|
||||
|
||||
<span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</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='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</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'>%>%</span>
|
||||
<span class='co'># filter on top three bacterial ID's</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>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>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># determine first isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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='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'>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'>%>%</span>
|
||||
<span class='co'># filter on first isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='co'># get short MO names (like "E. coli")</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</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'>%>%</span>
|
||||
<span class='co'># select this short name and some antiseptic drugs</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>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'>%>%</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'>%>%</span>
|
||||
<span class='co'># group by MO</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</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'>%>%</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>,
|
||||
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
|
||||
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='st'>"Only First Isolates, CoNS grouped according to Becker et al. (2014)"</span>,
|
||||
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Microorganisms"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
|
||||
293
docs/reference/guess_ab.html
Normal file
293
docs/reference/guess_ab.html
Normal file
@ -0,0 +1,293 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Guess antibiotic column — guess_ab • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- sticky kit -->
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<h1>Guess antibiotic column</h1>
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<div class="hidden name"><code>guess_ab.Rd</code></div>
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<p>This tries to find a column name in a data set based on information from the <code><a href='antibiotics.html'>antibiotics</a></code> data set.</p>
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||||
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||||
<pre class="usage"><span class='fu'>guess_ab</span>(<span class='kw'>tbl</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</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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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
|
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<th>tbl</th>
|
||||
<td><p>a <code>data.frame</code></p></td>
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||||
</tr>
|
||||
<tr>
|
||||
<th>col</th>
|
||||
<td><p>a character to look for</p></td>
|
||||
</tr>
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<tr>
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<th>verbose</th>
|
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<td><p>a logical to indicate whether additional info should be printed</p></td>
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<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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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>
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<li><a href="#arguments">Arguments</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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@ -240,7 +240,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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||||
<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 'Chlamydophila psittaci' (Everett et al., 1999)</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>
|
||||
|
||||
@ -220,13 +220,17 @@
|
||||
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||||
</div>
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||||
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||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
|
||||
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='st'>"pita"</span>,
|
||||
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>,
|
||||
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>,
|
||||
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
|
||||
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>,
|
||||
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>),
|
||||
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"pita"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>),
|
||||
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"tetr"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"coli"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
|
||||
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
@ -320,8 +324,8 @@ 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'># set key antibiotics to a new variable</span>
|
||||
<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
|
||||
<span class='co'># now calculate first isolates</span>
|
||||
<span class='kw'>first_regular</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_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
|
||||
<span class='co'># and first WEIGHTED isolates</span>
|
||||
|
||||
@ -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'>%>%</span>
|
||||
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%>%</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'>%>%</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>
|
||||
|
||||
@ -221,21 +221,26 @@
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>amik</span> <span class='kw'>=</span> <span class='st'>"amik"</span>, <span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='st'>"ampi"</span>,
|
||||
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='st'>"azit"</span>, <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='st'>"aztr"</span>, <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='st'>"cefa"</span>, <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='st'>"cfra"</span>,
|
||||
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='st'>"cfep"</span>, <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>, <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"cfox"</span>, <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>,
|
||||
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='st'>"cftr"</span>, <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='st'>"chlo"</span>, <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>,
|
||||
<span class='kw'>clar</span> <span class='kw'>=</span> <span class='st'>"clar"</span>, <span class='kw'>clin</span> <span class='kw'>=</span> <span class='st'>"clin"</span>, <span class='kw'>clox</span> <span class='kw'>=</span> <span class='st'>"clox"</span>, <span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"coli"</span>,
|
||||
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='st'>"czol"</span>, <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='st'>"dapt"</span>, <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='st'>"doxy"</span>, <span class='kw'>erta</span> <span class='kw'>=</span> <span class='st'>"erta"</span>,
|
||||
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>, <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='st'>"fosf"</span>, <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='st'>"fusi"</span>, <span class='kw'>gent</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
|
||||
<span class='kw'>imip</span> <span class='kw'>=</span> <span class='st'>"imip"</span>, <span class='kw'>kana</span> <span class='kw'>=</span> <span class='st'>"kana"</span>, <span class='kw'>levo</span> <span class='kw'>=</span> <span class='st'>"levo"</span>, <span class='kw'>linc</span> <span class='kw'>=</span> <span class='st'>"linc"</span>,
|
||||
<span class='kw'>line</span> <span class='kw'>=</span> <span class='st'>"line"</span>, <span class='kw'>mero</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>metr</span> <span class='kw'>=</span> <span class='st'>"metr"</span>, <span class='kw'>mino</span> <span class='kw'>=</span> <span class='st'>"mino"</span>,
|
||||
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='st'>"moxi"</span>, <span class='kw'>nali</span> <span class='kw'>=</span> <span class='st'>"nali"</span>, <span class='kw'>neom</span> <span class='kw'>=</span> <span class='st'>"neom"</span>, <span class='kw'>neti</span> <span class='kw'>=</span> <span class='st'>"neti"</span>,
|
||||
<span class='kw'>nitr</span> <span class='kw'>=</span> <span class='st'>"nitr"</span>, <span class='kw'>novo</span> <span class='kw'>=</span> <span class='st'>"novo"</span>, <span class='kw'>norf</span> <span class='kw'>=</span> <span class='st'>"norf"</span>, <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='st'>"oflo"</span>,
|
||||
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"peni"</span>, <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='st'>"pipe"</span>, <span class='kw'>pita</span> <span class='kw'>=</span> <span class='st'>"pita"</span>, <span class='kw'>poly</span> <span class='kw'>=</span> <span class='st'>"poly"</span>,
|
||||
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='st'>"qida"</span>, <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='st'>"roxi"</span>, <span class='kw'>siso</span> <span class='kw'>=</span> <span class='st'>"siso"</span>,
|
||||
<span class='kw'>teic</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>tica</span> <span class='kw'>=</span> <span class='st'>"tica"</span>, <span class='kw'>tige</span> <span class='kw'>=</span> <span class='st'>"tige"</span>,
|
||||
<span class='kw'>tobr</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>trim</span> <span class='kw'>=</span> <span class='st'>"trim"</span>, <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>)
|
||||
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>metr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(),
|
||||
<span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>())
|
||||
|
||||
<span class='fu'>brmo</span>(<span class='no'>...</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
|
||||
|
||||
@ -519,7 +524,7 @@
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
||||
<p>To define antibiotics column names, 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>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>),
|
||||
@ -596,7 +601,7 @@ 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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
|
||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
|
||||
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</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'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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='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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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='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='https://www.rdocumentation.org/packages/dplyr/topics/n'>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='http://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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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='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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</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'>%>%</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'>%>%</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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>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='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='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>
|
||||
|
||||
@ -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'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</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='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Haemophilus"</span>) <span class='kw'>%>%</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'>%>%</span>
|
||||
<span class='co'># calculate first isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>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'>%>%</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'>%>%</span>
|
||||
<span class='co'># filter on first E. coli isolates</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Escherichia"</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='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'>%>%</span>
|
||||
<span class='co'># predict resistance of cefotaxime for next years</span>
|
||||
@ -338,27 +338,27 @@ 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'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>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'>%>%</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'>%>%</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>,
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>data</span>,
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar'>geom_col</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>data</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
|
||||
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"grey75"</span>) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_linerange'>geom_errorbar</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
|
||||
<span class='kw'>ymax</span> <span class='kw'>=</span> <span class='no'>se_max</span>),
|
||||
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"grey50"</span>) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
|
||||
<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
|
||||
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"E. coli"</span>))),
|
||||
<span class='kw'>y</span> <span class='kw'>=</span> <span class='st'>"%IR"</span>,
|
||||
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Year"</span>) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggtheme'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
|
||||
}
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user