* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9037</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9038</span>
</span>
</div>
@ -210,27 +210,27 @@ Since you are one of our users, we would like to know how you use the package an
<p>This package is <ahref="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <ahref="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <ahref="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <ahref="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <ahref="./news">actively maintained</a> and is free software (see <ahref="#copyright">Copyright</a>).</p>
<ahref="./countries_large.png"target="_blank"><imgsrc="./countries.png"class="countries_map"></a><strong>Used in 135 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge.
<ahref="./countries_large.png"target="_blank"><imgsrc="./countries.png"class="countries_map"></a><strong>Used in 135 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.
<ahref="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
<divclass="sourceCode"id="cb1"><preclass="sourceCode r"><codeclass="sourceCode r"><spanid="cb1-1"><ahref="#cb1-1"aria-hidden="true"tabindex="-1"></a><spanclass="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
<spanid="cb1-9"><ahref="#cb1-9"aria-hidden="true"tabindex="-1"></a><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column 'mo' as input for mo_is_gram_negative()</span></span>
<spanid="cb1-10"><ahref="#cb1-10"aria-hidden="true"tabindex="-1"></a><spanclass="co">#></span><spanclass="al">NOTE</span><spanclass="co">: Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><ahref="reference/mo_property.html">mo_is_gram_positive()</a></code> and <code><ahref="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><ahref="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><ahref="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <ahref="./reference/microorganisms.html">all microorganisms</a> and <ahref="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><ahref="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><ahref="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><ahref="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <ahref="./reference/microorganisms.html">all microorganisms</a> and <ahref="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="left">mo</th>
@ -253,24 +253,6 @@ Since you are one of our users, we would like to know how you use the package an
@ -455,7 +437,7 @@ Since you are one of our users, we would like to know how you use the package an
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code>summarise()</code>)</li>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
<li>Plot AMR results with <code><ahref="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><ahref="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge.</p><br><br>
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.</p>
</div>
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
@ -36,17 +36,15 @@ example_isolates %>%
#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_positive()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
