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(v1.5.0.9010) MDRO vignette update, get_episode for < day
This commit is contained in:
@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9010</span>
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</span>
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</div>
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@ -236,13 +236,13 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1509009" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9009">
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<a href="#amr-1509009" class="anchor"></a>AMR 1.5.0.9009<small> Unreleased </small>
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<div id="amr-1509010" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9010">
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<a href="#amr-1509010" class="anchor"></a>AMR 1.5.0.9010<small> Unreleased </small>
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</h1>
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<div id="last-updated-22-january-2021" class="section level2">
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<div id="last-updated-24-january-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-22-january-2021" class="anchor"></a><small>Last updated: 22 January 2021</small>
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<a href="#last-updated-24-january-2021" class="anchor"></a><small>Last updated: 24 January 2021</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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@ -288,6 +288,7 @@
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<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
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<li>
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<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now returns <code>FALSE</code> immediately if the input does not contain any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
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<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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@ -614,7 +615,7 @@
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<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
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<p>Negative effects of this change are:</p>
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<ul>
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<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
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<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
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<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
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<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
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<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
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@ -951,7 +952,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
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<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
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</li>
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<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
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<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
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<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
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</ul>
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</div>
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@ -1220,7 +1221,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
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<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
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</li>
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<li>Frequency tables (<code>freq()</code>):
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<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
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<ul>
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<li><p>speed improvement for microbial IDs</p></li>
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<li><p>fixed factor level names for R Markdown</p></li>
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@ -1230,12 +1231,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
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<span class="co"># grouped boxplots:</span>
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
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</li>
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</ul>
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@ -1245,7 +1246,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
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</li>
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<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
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<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
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<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
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</li>
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<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
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<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
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@ -1486,7 +1487,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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</li>
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</ul>
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</li>
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<li>Frequency tables (<code>freq()</code> function):
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<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
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<ul>
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<li>
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<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
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@ -1496,15 +1497,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<span class="co"># OLD WAY</span>
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
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<span class="co"># NEW WAY</span>
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
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<span class="co"># Even supports grouping variables:</span>
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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</li>
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<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
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<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
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@ -1587,7 +1588,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
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<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
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<li>
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<p>Frequency tables - <code>freq()</code>:</p>
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<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
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<ul>
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<li>
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<p>Support for grouping variables, test with:</p>
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@ -1595,14 +1596,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<code class="sourceCode R">
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
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</li>
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<li>
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<p>Support for (un)selecting columns:</p>
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<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="va">septic_patients</span> <span class="op">%>%</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
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</li>
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<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
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@ -1620,7 +1621,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
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<li><p>Fix for <code>mo_property</code> not working properly</p></li>
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<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
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<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
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<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
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<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
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<li>
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<p>AI improvements for <code>as.mo</code>:</p>
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@ -1788,13 +1789,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
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<p>For lists, subsetting is possible:</p>
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<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
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<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
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<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
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<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
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<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
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</li>
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</ul>
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</div>
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@ -1868,13 +1869,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<ul>
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<li>A vignette to explain its usage</li>
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<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
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<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
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<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
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</li>
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<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
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</li>
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<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
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</li>
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<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
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<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
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</li>
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<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
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<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
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