* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@ -7,10 +7,10 @@
@@ -7,10 +7,10 @@
* Added data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
* Existing data set `example_isolates` now reflects the latest EUCAST rules
* Added argument `only_rsi_columns` for some functions, which defaults to `FALSE`, to indicate if the functions must only be applied to columns that are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
* All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglocysides()`, `carbapenems()`, `penicillins()`)
* All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglocysides()`, `filter_carbapenems()`, `filter_penicillins()`)
* All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglycosides()`, `carbapenems()`, `penicillins()`)
* All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglycosides()`, `filter_carbapenems()`, `filter_penicillins()`)
* `eucast_rules()`
* `mdro()` (including wrappers such as `brmo()`, `mrgn` and `eucast_exceptional_phenotypes()`)
* `mdro()` (including wrappers such as `brmo()`, `mrgn()` and `eucast_exceptional_phenotypes()`)
* `guess_ab_col()`
* Functions `oxazolidinones()` (an antibiotic selector function) and `filter_oxazolidinones()` (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
@ -20,7 +20,7 @@ This package is fully independent of any other R package and works on Windows, m
@@ -20,7 +20,7 @@ This package is fully independent of any other R package and works on Windows, m
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package.
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to our university's Gitea server (https://git.web.rug.nl/P281424/AMR) and to GitLab (https://gitlab.com/msberends/AMR).*
### How to get this package
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
<ahref="#last-updated-9-february-2021"class="anchor"></a><small>Last updated: 9 February 2021</small>
<ahref="#last-updated-17-february-2021"class="anchor"></a><small>Last updated: 17 February 2021</small>
</h2>
<divid="new"class="section level3">
<h3class="hasAnchor">
@ -259,11 +259,11 @@
@@ -259,11 +259,11 @@
<li>
<p>Added argument <code>only_rsi_columns</code> for some functions, which defaults to <code>FALSE</code>, to indicate if the functions must only be applied to columns that are of class <code><rsi></code> (i.e., transformed with <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:</p>
<ul>
<li>All antibiotic selector functions (<code><ahref="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code>aminoglocysides()</code>, <code><ahref="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><ahref="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
<li>All antibiotic filter functions (<code><ahref="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code>filter_aminoglocysides()</code>, <code><ahref="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><ahref="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
<li>All antibiotic selector functions (<code><ahref="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code><ahref="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>, <code><ahref="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><ahref="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
<li>All antibiotic filter functions (<code><ahref="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code><ahref="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>, <code><ahref="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><ahref="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
<code><ahref="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><ahref="../reference/mdro.html">brmo()</a></code>, <code>mrgn</code> and <code><ahref="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
<code><ahref="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><ahref="../reference/mdro.html">brmo()</a></code>, <code><ahref="../reference/mdro.html">mrgn()</a></code> and <code><ahref="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
<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>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<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>
<li><del>All functions from the <code>mo_*</code> family (like <code><ahref="../reference/mo_property.html">mo_name()</a></code> and <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
<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>
@ -988,7 +988,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -988,7 +988,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co">#> invalid microorganism code, NA generated</span></code></pre></div>
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g.<code><ahref="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
</li>
<li><p>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <ahref="https://github.com/msberends/clean"><code>clean</code></a> (<ahref="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><ahref="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>
<li><p>Function <code>freq()</code> has moved to a new package, <ahref="https://github.com/msberends/clean"><code>clean</code></a> (<ahref="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>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@ -1257,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1257,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><ahref="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
@ -1267,12 +1267,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1267,12 +1267,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1282,7 +1282,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1282,7 +1282,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><ahref="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -1523,7 +1523,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1523,7 +1523,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -1533,15 +1533,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1533,15 +1533,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@ -1624,7 +1624,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1624,7 +1624,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
<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>
@ -1632,14 +1632,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1632,14 +1632,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/select.html">select</a></span><spanclass="op">(</span><spanclass="op">-</span><spanclass="va">count</span>, <spanclass="op">-</span><spanclass="va">cum_count</span><spanclass="op">)</span><spanclass="co"># only get item, percent, cum_percent</span></code></pre></div>
</li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1657,7 +1657,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1657,7 +1657,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@ -1825,13 +1825,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1825,13 +1825,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1905,13 +1905,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@@ -1905,13 +1905,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><ahref="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.5.0.9016</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.5.0.9019</span>
</span>
</div>
@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
@@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<spanclass='co'># See ?example_isolates.</span>
<spanclass='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
@ -85,7 +85,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
@@ -85,7 +85,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
# See ?example_isolates.
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
example_isolates[, c(carbapenems())]
example_isolates[, carbapenems()]
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
