<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<p>A more convenient function is <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9000</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -217,7 +217,11 @@
<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<ahref="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf">link</a>)</p>
</li>
<li>
<p><code>guideline = "EUCAST3.1"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
</li>
<li>
@ -226,13 +230,14 @@
</li>
<li>
<p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al.(2015) Antimicrobial Resistance and Infection Control 4:7. (<ahref="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</p>
<p>The German national guideline - Mueller et al.(2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
</li>
<li>
<p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]” (<ahref="https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH">link</a>)</p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<ahref="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh">link</a>)</p>
</li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <ahref="https://github.com/msberends/AMR/issues/new"class="uri">https://github.com/msberends/AMR/issues/new</a>.</p>
<spanclass="fu"><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><spanclass="op">(</span><spanclass="op">)</span><spanclass="co"># show frequency table of the result</span>
<spanclass="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
<spanclass="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></div>
<spanclass="co"># Warning in warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", : NA introduced for isolates where the available percentage of antimicrobial</span>
<spanclass="co"># classes was below 50% (set with `pct_required_classes`)</span></pre></div>
<ahref="#last-updated-3-december-2020"class="anchor"></a><small>Last updated: 3 December 2020</small>
<ahref="#last-updated-7-december-2020"class="anchor"></a><small>Last updated: 7 December 2020</small>
</h2>
<divid="new"class="section level3">
<h3class="hasAnchor">
@ -251,42 +251,42 @@
<li>
<p>Function <code><ahref="../reference/is_new_episode.html">is_new_episode()</a></code> to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g.<code><ahref="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code>, <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> and <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code> of the <code>dplyr</code> package:</p>
<p>Functions <code><ahref="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria. They can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p>
<spanclass="co">#> NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div>
</li>
<li>
<p>Function <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <ahref="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020. As with the new <code>mo_is_gram_*()</code> functions, if you have the <code>dplyr</code> package installed the column with microorganisms will be automatically determined when used inside <code>dplyr</code> verbs:</p>
<li><p>Functions <code><ahref="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
<li><p>Function <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <ahref="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
</ul>
</div>
<divid="changed"class="section level3">
<h3class="hasAnchor">
<ahref="#changed"class="anchor"></a>Changed</h3>
<ul>
<li>Reference data used for <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter. This allows for using own interpretation guidelines.</li>
<li>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <ahref="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</li>
<li>Deprecated function <code><ahref="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <ahref="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</li>
<li>Better determination of disk zones and MIC values when running <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
<li>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</li>
<li>Fix for using parameter <code>reference_df</code> in <code><ahref="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</li>
<li>Fix for using <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</li>
<li><p>Reference data used for <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter. This allows for using own interpretation guidelines. The user-set data must have the same structure as <code>rsi_translation</code>.</p></li>
<li>
<code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame will not print a message anymore if the values are already clean R/SI values</li>
<li>Fixed a bug where <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</li>
<li>Fixed a bug where <code><ahref="../reference/as.mo.html">as.mo()</a></code> would not return results for known laboratory codes for microorganisms</li>
<li>Fixed a bug where <code><ahref="../reference/as.ab.html">as.ab()</a></code> would sometimes fail</li>
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><ahref="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data parameter does not need to be set anymore. This is the case for the new functions <code><ahref="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><ahref="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and for the existing functions <code><ahref="../reference/first_isolate.html">first_isolate()</a></code>, <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code>, <code><ahref="../reference/mdro.html">mdro()</a></code>, <code><ahref="../reference/mdro.html">brmo()</a></code>, <code><ahref="../reference/mdro.html">mrgn()</a></code>, <code><ahref="../reference/mdro.html">mdr_tb()</a></code>, <code><ahref="../reference/mdro.html">mdr_cmi2012()</a></code>, <code><ahref="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>. This was already the case for antibiotic selection functions (such as using <code><ahref="../reference/antibiotic_class_selectors.html">penicillins()</a></code> in <code><ahref="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>).</p>
<li><p>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <ahref="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</p></li>
<li><p>Deprecated function <code><ahref="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <ahref="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</p></li>
<li><p>Better determination of disk zones and MIC values when running <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</p></li>
<li><p>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</p></li>
<li><p>Fix for using parameter <code>reference_df</code> in <code><ahref="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</p></li>
<li><p>Fix for using <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</p></li>
<li><p><code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame will not print a message anymore if the values are already clean R/SI values</p></li>
<li><p>Fixed a bug where <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</p></li>
<li><p>Fixed a bug where <code><ahref="../reference/as.mo.html">as.mo()</a></code> would not return results for known laboratory codes for microorganisms</p></li>
<li><p>Fixed a bug where <code><ahref="../reference/as.ab.html">as.ab()</a></code> would sometimes fail</p></li>
<li><p>If using <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this</p></li>
</ul>
</div>
<divid="other"class="section level3">
@ -313,7 +313,7 @@
<li>
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
<p>Support for using <code>dplyr</code>’s <code><ahref="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
<p>Added intelligent data cleaning to <code><ahref="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
<li><p>Function <code><ahref="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g.health care records, which also corrects for misspelling since it uses <code><ahref="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><ahref="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><ahref="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><ahref="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<spanclass="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
@ -496,7 +496,7 @@
<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>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>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><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>
@ -600,7 +600,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><spanclass="op">(</span><spanclass="va">antibiotic1</span><spanclass="op">:</span><spanclass="va">antibiotic25</span><spanclass="op">)</span>, <spanclass="va">as.rsi</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span><spanclass="op">)</span>
@ -628,7 +628,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><ahref="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
@ -638,7 +638,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><ahref="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
@ -718,7 +718,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Functions <code><ahref="../reference/proportion.html">susceptibility()</a></code> and <code><ahref="../reference/proportion.html">resistance()</a></code> as aliases of <code><ahref="../reference/proportion.html">proportion_SI()</a></code> and <code><ahref="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
@ -746,7 +746,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li>
<p>Added a score (a certainty percentage) to <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <ahref="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
@ -804,13 +804,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e.microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
@ -824,7 +824,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co">#> invalid microorganism code, NA generated</span></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>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>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>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@ -834,7 +834,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><ahref="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<spanclass="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g.Excel with the base R <code><ahref="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<p>Additional way to calculate co-resistance, i.e.when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
@ -882,7 +882,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code><code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
@ -964,7 +964,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><ahref="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><ahref="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
@ -1111,7 +1111,7 @@ 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>freq()</code> for when all values are <code>NA</code>
<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>
<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>
@ -1188,7 +1188,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</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>
<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>
@ -1229,19 +1229,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New function <code><ahref="../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.</p></li>
<li>
<p>New function <code><ahref="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><ahref="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<p>Functions <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><ahref="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
@ -1284,7 +1284,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><ahref="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
@ -1298,7 +1298,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<spanclass="fu"><ahref="../reference/mo_property.html">mo_genus</a></span><spanclass="op">(</span><spanclass="st">"qwerty"</span>, language <spanclass="op">=</span><spanclass="st">"es"</span><spanclass="op">)</span>
<spanclass="co"># Warning: </span>
<spanclass="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
@ -1343,24 +1343,24 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1442,20 +1442,20 @@ 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 parameter <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>
<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></pre></div>
</li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1473,7 +1473,7 @@ 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>top_freq()</code></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><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@ -1532,7 +1532,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<spanclass="fu"><ahref="../reference/mo_property.html">mo_gramstain</a></span><spanclass="op">(</span><spanclass="st">"E. coli"</span>, language <spanclass="op">=</span><spanclass="st">"de"</span><spanclass="op">)</span><spanclass="co"># German</span>
@ -1542,7 +1542,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="fu"><ahref="../reference/mo_property.html">mo_fullname</a></span><spanclass="op">(</span><spanclass="st">"S. group A"</span>, language <spanclass="op">=</span><spanclass="st">"pt"</span><spanclass="op">)</span><spanclass="co"># Portuguese</span>
<spanclass="co"># [1] "Streptococcus grupo A"</span></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
@ -1556,7 +1556,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %>% mutate_if(is.rsi.eligible, as.rsi)</code></p></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 intelligent rules:</p>
<spanclass="fu">microbenchmark</span><spanclass="fu">::</span><spanclass="fu"><ahref="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><spanclass="op">(</span><spanclass="fu"><ahref="../reference/as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="va">thousands_of_E_colis</span><spanclass="op">)</span>, unit <spanclass="op">=</span><spanclass="st">"s"</span><spanclass="op">)</span>
<spanclass="co"># Unit: seconds</span>
@ -1597,7 +1597,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></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>
@ -1613,7 +1613,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></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>
@ -1713,13 +1713,13 @@ 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>freq(table(x, y))</code>
<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>
<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>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
<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>
<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>
<td><p>a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><ahref='https://rdrr.io/r/stats/filter.html'>filter()</a></code>, <code>mutate()</code> and <code>summarise()</code>.</p></td>
<p>The<code>first_isolate()</code> function is a wrapper around the <code><ahref='is_new_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><ahref='is_new_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3class='hasAnchor'id='arguments'><aclass='anchor'href='#arguments'></a>Why this is so important</h3>
@ -378,7 +379,7 @@
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates.</p>
<p>The function <code>filter_first_isolate()</code> is essentially equal to either:</p><pre><spanclass='va'>x</span><spanclass='op'>[</span><spanclass='fu'>first_isolate</span><spanclass='op'>(</span><spanclass='va'>x</span>, <spanclass='va'>...</span><spanclass='op'>)</span>, <spanclass='op'>]</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9030</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -281,48 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimen
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<metaproperty="og:title"content="Key antibiotics for first weighted isolates — key_antibiotics"/>
<metaproperty="og:description"content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates."/>
<metaproperty="og:description"content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first weighted isolates."/>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9030</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<divclass="ref-description">
<p>These function can be used to determine first isolates (see <code><ahref='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p>
<p>These function can be used to determine first isolates (see <code><ahref='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first <em>weighted</em> isolates.</p>
<td><p>a data.frame with antibiotics columns, like <code>AMX</code> or <code>amox</code></p></td>
<td><p>a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
<p>The function <code>key_antibiotics()</code>returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by<code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code>key_antibiotics()</code>function is context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and<code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code><ahref='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See <code><ahref='first_isolate.html'>first_isolate()</a></code> for more info.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are:</p><ul>
<li><p>Amoxicillin</p></li>
@ -395,30 +396,30 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<preclass="examples"><spanclass='co'># `example_isolates` is a dataset available in the AMR package.</span>
<spanclass='co'># See ?example_isolates.</span>
<spanclass='co'># output of the `key_antibiotics` function could be like this:</span>
<spanclass='co'># output of the `key_antibiotics()` function could be like this:</span>
<spanclass='fu'><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><spanclass='op'>(</span>keyab <spanclass='op'>=</span><spanclass='fu'>key_antibiotics</span><spanclass='op'>(</span><spanclass='op'>)</span><spanclass='op'>)</span><spanclass='op'>%>%</span><spanclass='co'># no need to define `x`</span>
<td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
<td><p>a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
</tr>
<tr>
<th>guideline</th>
@ -319,20 +319,21 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or<code>3/4</code>) and percentages (<code>75</code>).</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the<code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).</p>
<p>Currently supported guidelines are (case-insensitive):</p><ul>
<li><p><code>guideline = "CMI2012"</code><br/>
Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<ahref='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<ahref='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.1"</code><br/>
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<ahref='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code><br/>
The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<ahref='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code><br/>
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
<li><p><code>guideline = "BRMO"</code><br/>
The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<ahref='https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh'>link</a>)</p></li>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<ahref='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<ahref='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.1"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<ahref='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code></p>
<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<ahref='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
<li><p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<ahref='https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh'>link</a>)</p></li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <ahref='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
@ -380,10 +381,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<td><p>a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><ahref='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><ahref='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><ahref='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9031</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9032</span>
</span>
</div>
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