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filter_ab_class fix

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dr. M.S. (Matthijs) Berends 2019-03-06 09:32:48 +01:00
parent 74e0ae21fd
commit 5c7a061a5d
6 changed files with 137 additions and 93 deletions
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.5.0.9021 Version: 0.5.0.9021
Date: 2019-03-05 Date: 2019-03-06
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

24
NEWS.md
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@ -20,11 +20,33 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
This data is updated annually - check the included version with the new function `catalogue_of_life_version()`. This data is updated annually - check the included version with the new function `catalogue_of_life_version()`.
* Due to this change, some `mo` codes changed (e.g. *Streptococcus* changed from `B_STRPTC` to `B_STRPT`). A translation table is used internally to support older microorganism IDs, so users will not notice this difference. * Due to this change, some `mo` codes changed (e.g. *Streptococcus* changed from `B_STRPTC` to `B_STRPT`). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.
* New function `mo_rank()` for the taxonomic rank (genus, species, infraspecies, etc.) * New function `mo_rank()` for the taxonomic rank (genus, species, infraspecies, etc.)
* New function `mo_url()` to get the URL to the Catalogue of Life * New function `mo_url()` to get the direct URL of a species from the Catalogue of Life
* Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network): * Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network):
* Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically. * Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically.
* This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the `antibiotics` data set now contains a column `ears_net`. * This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the `antibiotics` data set now contains a column `ears_net`.
* The function `as.mo()` now knows all WHONET species abbreviations too, because more than 1,600 microbial abbreviations were added to the `microorganisms.codes` data set. * The function `as.mo()` now knows all WHONET species abbreviations too, because more than 1,600 microbial abbreviations were added to the `microorganisms.codes` data set.
* New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:
```r
filter_aminoglycosides()
filter_carbapenems()
filter_cephalosporins()
filter_1st_cephalosporins()
filter_2nd_cephalosporins()
filter_3rd_cephalosporins()
filter_4th_cephalosporins()
filter_fluoroquinolones()
filter_glycopeptides()
filter_macrolides()
filter_tetracyclines()
```
The `antibiotics` data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the `antibiotics` data set.
For example:
```r
septic_patients %>% filter_glycopeptides(result = "R")
# Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R
septic_patients %>% filter_glycopeptides(result = "R", scope = "all")
# Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R
```
* All `ab_*` functions are deprecated and replaced by `atc_*` functions: * All `ab_*` functions are deprecated and replaced by `atc_*` functions:
```r ```r
ab_property -> atc_property() ab_property -> atc_property()

5
R/filter_ab_class.R
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@ -27,8 +27,9 @@
#' @param result an antibiotic result: S, I or R (or a combination of more of them) #' @param result an antibiotic result: S, I or R (or a combination of more of them)
#' @param scope the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"} #' @param scope the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}
#' @param ... parameters passed on to \code{\link[dplyr]{filter_at}} #' @param ... parameters passed on to \code{\link[dplyr]{filter_at}}
#' @details The \code{\code{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set. #' @details The \code{\link{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
#' @rdname filter_ab_class #' @rdname filter_ab_class
#' @keywords filter fillter_class
#' @importFrom dplyr filter_at %>% select vars any_vars all_vars #' @importFrom dplyr filter_at %>% select vars any_vars all_vars
#' @importFrom crayon bold blue #' @importFrom crayon bold blue
#' @export #' @export
@ -89,7 +90,7 @@ filter_ab_class <- function(tbl,
scope_fn <- all_vars scope_fn <- all_vars
} }
message(blue(paste0("Filtering on ", atc_groups, ": ", scope, " of ", message(blue(paste0("Filtering on ", atc_groups, ": ", scope, " of ",
paste(bold(vars_df), collapse = scope_txt), operator, toString(result)))) paste(bold(paste0("`", vars_df, "`")), collapse = scope_txt), operator, toString(result))))
tbl %>% tbl %>%
filter_at(.vars = vars(vars_df), filter_at(.vars = vars(vars_df),
.vars_predicate = scope_fn(. %in% result), .vars_predicate = scope_fn(. %in% result),

191
docs/news/index.html
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@ -259,10 +259,10 @@
<p>The responsible author(s) and year of scientific publication</p> <p>The responsible author(s) and year of scientific publication</p>
This data is updated annually - check the included version with the new function <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</li> This data is updated annually - check the included version with the new function <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</li>
<li>Due to this change, some <code>mo</code> codes changed (e.g. <em>Streptococcus</em> changed from <code>B_STRPTC</code> to <code>B_STRPT</code>). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.</li> <li>Due to this change, some <code>mo</code> codes changed (e.g. <em>Streptococcus</em> changed from <code>B_STRPTC</code> to <code>B_STRPT</code>). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.</li>
<li>New function <code><a href="../reference/mo_property.html">mo_rank()</a></code> for the taxonomic rank (genus, species, infraspecies, etc.)</li>
<li>New function <code><a href="../reference/mo_property.html">mo_url()</a></code> to get the direct URL of a species from the Catalogue of Life</li>
</ul> </ul>
</li> </li>
<li>New function <code><a href="../reference/mo_property.html">mo_rank()</a></code> for the taxonomic rank (genus, species, infraspecies, etc.)</li>
<li>New function <code><a href="../reference/mo_property.html">mo_url()</a></code> to get the URL to the Catalogue of Life</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network): <li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul> <ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li> <li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
@ -271,14 +271,33 @@ This data is updated annually - check the included version with the new function
</ul> </ul>
</li> </li>
<li> <li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb1-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb1-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb1-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
<a class="sourceLine" id="cb1-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
<a class="sourceLine" id="cb1-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
<a class="sourceLine" id="cb1-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<a class="sourceLine" id="cb2-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p> <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_property</a></span>()</a> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_property</a></span>()</a>
<a class="sourceLine" id="cb1-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_name</a></span>()</a> <a class="sourceLine" id="cb3-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_name</a></span>()</a>
<a class="sourceLine" id="cb1-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_official</a></span>()</a> <a class="sourceLine" id="cb3-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_official</a></span>()</a>
<a class="sourceLine" id="cb1-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_trivial_nl</a></span>()</a> <a class="sourceLine" id="cb3-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_trivial_nl</a></span>()</a>
<a class="sourceLine" id="cb1-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_certe</a></span>()</a> <a class="sourceLine" id="cb3-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_certe</a></span>()</a>
<a class="sourceLine" id="cb1-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a> <a class="sourceLine" id="cb3-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a>
<a class="sourceLine" id="cb1-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb3-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li> These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li> <li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li> <li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
@ -290,20 +309,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li> <li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li> <li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p> <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a> <a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div> <a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p> <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># or</span></a> <a class="sourceLine" id="cb5-2" title="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div> <a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<p>is equal to:</p> <p>is equal to:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">septic_patients <span class="op">%&gt;%</span></a> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb6-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb6-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div> <a class="sourceLine" id="cb6-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li> </li>
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code> <li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
</li> </li>
@ -332,10 +351,10 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul> <ul>
<li>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. Properties of these will be translated on foreign systems in all language already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</li> <li>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. Properties of these will be translated on foreign systems in all language already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</li>
</ul> </ul>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># Warning: </span></a> <a class="sourceLine" id="cb7-2" title="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a> <a class="sourceLine" id="cb7-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div> <a class="sourceLine" id="cb7-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
<ul> <ul>
<li>Fix for vector containing only empty values</li> <li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li> <li>Finds better results when input is in other languages</li>
@ -381,19 +400,19 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul> <ul>
<li> <li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p> <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a> <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb6-2" title="2"><span class="co"># OLD WAY</span></a> <a class="sourceLine" id="cb8-2" title="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb6-3" title="3">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb8-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a> <a class="sourceLine" id="cb8-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># NEW WAY</span></a> <a class="sourceLine" id="cb8-6" title="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb6-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb8-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a> <a class="sourceLine" id="cb8-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb6-9" title="9"></a> <a class="sourceLine" id="cb8-9" title="9"></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># Even supports grouping variables:</span></a> <a class="sourceLine" id="cb8-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb6-11" title="11">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb8-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb8-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div> <a class="sourceLine" id="cb8-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
</li> </li>
<li>Header info is now available as a list, with the <code>header</code> function</li> <li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li> <li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@ -467,10 +486,10 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li> <li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li> <li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p> <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a> <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb7-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a> <a class="sourceLine" id="cb9-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a> <a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb7-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div> <a class="sourceLine" id="cb9-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li> <li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li> <li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -483,15 +502,15 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul> <ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb10-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb10-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb11-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div> <a class="sourceLine" id="cb11-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li> </li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code> <li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li> </li>
@ -571,18 +590,18 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li> </li>
</ul> </ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p> <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb10-2" title="2"><span class="co"># [1] "Gram negative"</span></a> <a class="sourceLine" id="cb12-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a> <a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb10-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a> <a class="sourceLine" id="cb12-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb10-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a> <a class="sourceLine" id="cb12-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb10-6" title="6"><span class="co"># [1] "Gram negativo"</span></a> <a class="sourceLine" id="cb12-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb10-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a> <a class="sourceLine" id="cb12-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb10-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div> <a class="sourceLine" id="cb12-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p> <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a> <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a> <a class="sourceLine" id="cb13-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb11-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div> <a class="sourceLine" id="cb13-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li> </li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates <li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul> <ul>
@ -593,18 +612,18 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li> </li>
<li> <li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p> <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb12-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a> <a class="sourceLine" id="cb14-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a> <a class="sourceLine" id="cb14-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb12-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a> <a class="sourceLine" id="cb14-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb12-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a> <a class="sourceLine" id="cb14-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb12-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div> <a class="sourceLine" id="cb14-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p> <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a> <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb13-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a> <a class="sourceLine" id="cb15-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb13-3" title="3"><span class="co"># Unit: seconds</span></a> <a class="sourceLine" id="cb15-3" title="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb13-4" title="4"><span class="co"># min median max neval</span></a> <a class="sourceLine" id="cb15-4" title="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb13-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div> <a class="sourceLine" id="cb15-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li> <li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like: <li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@ -632,12 +651,12 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li> <li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li> <li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p> <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a> <div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb14-2" title="2"><span class="co"># [1] "Mupirocin"</span></a> <a class="sourceLine" id="cb16-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb16-3" title="3"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb14-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a> <a class="sourceLine" id="cb16-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb14-5" title="5"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb16-5" title="5"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb14-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div> <a class="sourceLine" id="cb16-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li> </li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li> <li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li> <li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -648,13 +667,13 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li> </li>
<li> <li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p> <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb15-2" title="2"><span class="co"># which is the same as:</span></a> <a class="sourceLine" id="cb17-2" title="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb15-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a> <a class="sourceLine" id="cb17-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb15-4" title="4"></a> <a class="sourceLine" id="cb17-4" title="4"></a>
<a class="sourceLine" id="cb15-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a> <a class="sourceLine" id="cb17-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb15-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a> <a class="sourceLine" id="cb17-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb15-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div> <a class="sourceLine" id="cb17-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li> </li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li> <li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li> <li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@ -668,12 +687,12 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li> </li>
<li> <li>
<p>Support for types (classes) list and matrix for <code>freq</code></p> <p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a> <div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb16-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div> <a class="sourceLine" id="cb18-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p> <p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a> <div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb17-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a> <a class="sourceLine" id="cb19-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb17-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb19-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
</ul> </ul>
</div> </div>

2
docs/reference/filter_ab_class.html
View File

@ -292,7 +292,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code><code>antibiotics</code></code> data set will be searched for <code>ab_class</code> in the columns <code>atc_group1</code> and <code>atc_group2</code> (case-insensitive). Next, <code>tbl</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set.</p> <p>The <code><a href='antibiotics.html'>antibiotics</a></code> data set will be searched for <code>ab_class</code> in the columns <code>atc_group1</code> and <code>atc_group2</code> (case-insensitive). Next, <code>tbl</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>

4
man/filter_ab_class.Rd
View File

@ -54,7 +54,7 @@ filter_tetracyclines(tbl, result = NULL, scope = "any", ...)
Filter on specific antibiotic variables based on their class (ATC groups). Filter on specific antibiotic variables based on their class (ATC groups).
} }
\details{ \details{
The \code{\code{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set. The \code{\link{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
} }
\examples{ \examples{
library(dplyr) library(dplyr)
@ -80,3 +80,5 @@ septic_patients \%>\%
filter_aminoglycosides("R", "any") \%>\% filter_aminoglycosides("R", "any") \%>\%
filter_fluoroquinolones("R", "any") filter_fluoroquinolones("R", "any")
} }
\keyword{fillter_class}
\keyword{filter}