mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 04:02:19 +02:00
(v1.3.0.9001) website update
This commit is contained in:
@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -233,42 +233,42 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>summarise()</code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
|
||||
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
|
||||
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>resistance</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>resistance</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>susceptibility</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>susceptibility</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_R</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_IR</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_I</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_SI</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_S</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>proportion_df</span>(
|
||||
<span class='no'>data</span>,
|
||||
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
|
||||
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
|
||||
<span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
|
||||
<span class='kw'>data</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
minimum = <span class='fl'>30</span>,
|
||||
as_percent = <span class='fl'>FALSE</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>
|
||||
)
|
||||
|
||||
<span class='fu'>rsi_df</span>(
|
||||
<span class='no'>data</span>,
|
||||
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
|
||||
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
|
||||
<span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
|
||||
<span class='kw'>data</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
minimum = <span class='fl'>30</span>,
|
||||
as_percent = <span class='fl'>FALSE</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>
|
||||
)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
@ -336,22 +336,21 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
-------- -------- ---------- ----------- ---------- -----------
|
||||
S or I S or I X X X X
|
||||
R S or I X X X X
|
||||
&lt;NA&gt; S or I X X - -
|
||||
<NA> S or I X X - -
|
||||
S or I R X X X X
|
||||
R R - X - X
|
||||
&lt;NA&gt; R - - - -
|
||||
S or I &lt;NA&gt; X X - -
|
||||
R &lt;NA&gt; - - - -
|
||||
&lt;NA&gt; &lt;NA&gt; - - - -
|
||||
<NA> R - - - -
|
||||
S or I <NA> X X - -
|
||||
R <NA> - - - -
|
||||
<NA> <NA> - - - -
|
||||
--------------------------------------------------------------------
|
||||
</pre>
|
||||
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() + <span class='fu'><a href='count.html'>count_I</a></span>() + <span class='fu'><a href='count.html'>count_R</a></span>() <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() + <span class='fu'>proportion_I</span>() + <span class='fu'>proportion_R</span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>=</span> <span class='fl'>1</span></pre>
|
||||
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &gt;= count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() &gt;= 1
|
||||
</pre>
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>>=</span> <span class='fl'>1</span></pre>
|
||||
|
||||
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
@ -386,84 +385,84 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
|
||||
?<span class='no'>example_isolates</span>
|
||||
<span class='op'>?</span><span class='kw'>example_isolates</span>
|
||||
|
||||
<span class='fu'>resistance</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %R</span>
|
||||
<span class='fu'>susceptibility</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %S+I</span>
|
||||
<span class='fu'>resistance</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %R</span>
|
||||
<span class='fu'>susceptibility</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %S+I</span>
|
||||
|
||||
<span class='co'># be more specific</span>
|
||||
<span class='fu'>proportion_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>proportion_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>proportion_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>proportion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>proportion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>r</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>SI</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
<span class='fu'>proportion_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(r = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>),
|
||||
n = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
SI = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
n1 = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
n2 = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number 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>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>) <span class='co'># %SI = 76.3%</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</span>) <span class='co'># %SI = 75.4%</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># %SI = 94.1%</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1939</span>
|
||||
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>) <span class='co'># %SI = 76.3%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>) <span class='co'># n = 1879</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>) <span class='co'># %SI = 75.4%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>) <span class='co'># n = 1855</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># %SI = 94.1%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># n = 1939</span>
|
||||
|
||||
|
||||
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
|
||||
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
|
||||
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
|
||||
|
||||
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</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'>CIP</span>),
|
||||
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</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'>GEN</span>),
|
||||
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>))
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>))
|
||||
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(cipro_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
cipro_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>),
|
||||
genta_p = <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
genta_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>),
|
||||
combination_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
combination_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>))
|
||||
|
||||
<span class='co'># Get proportions S/I/R immediately of all rsi columns</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
}
|
||||
|
||||
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
|
||||
<span class='co'>if</span> (<span class='fl'>FALSE</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://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://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMX</span>, <span class='no'>MTR</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'>AMX</span>, <span class='no'>MTR</span>))
|
||||
<span class='kw'>my_table</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>genus</span> <span class='op'>==</span> <span class='st'>"Helicobacter"</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(p = <span class='fu'>susceptibility</span>(<span class='kw'>AMX</span>, <span class='kw'>MTR</span>), <span class='co'># amoxicillin with metronidazole</span>
|
||||
n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMX</span>, <span class='kw'>MTR</span>))
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@ -480,7 +479,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user