P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 06:02:01 +02:00
Code Releases Activity

(v0.7.1.9063) septic_patients -> example_isolates

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
Download Patch File Download Diff File Expand all files Collapse all files

40
docs/reference/count.html
View File

@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9063</span>
</span>
</div>
@ -356,29 +356,29 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span>
<span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='co'># Count resistant isolates</span>
<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># Or susceptible isolates</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># Since n_rsi counts available isolates, you can</span>
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
<span class='co'># This results in the same:</span>
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='portion.html'>portion_SI</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='portion.html'>portion_SI</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>CIP</span>),
@ -390,24 +390,24 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `portion_SI` calculates percentages right away instead.</span>
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>example_isolates</span>,
<span class='fu'>count_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1764</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>example_isolates</span>,
<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1936</span>
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</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'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)