<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Function reference • AMR (for R)</title> <!-- favicons --> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"> <link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" /> <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" /> <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" /> <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" /> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" 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class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">AMR (for R)</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9047</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../index.html"> <span class="fa fa-home"></span> Home </a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <span class="fa fa-question-circle"></span> How to <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/AMR.html"> <span class="fa fa-directions"></span> Conduct AMR analysis </a> </li> <li> <a href="../articles/resistance_predict.html"> <span class="fa fa-dice"></span> Predict antimicrobial resistance </a> </li> <li> <a href="../articles/MDR.html"> <span class="fa fa-skull-crossbones"></span> Determine multi-drug resistance (MDR) </a> </li> <li> <a href="../articles/WHONET.html"> <span class="fa fa-globe-americas"></span> Work with WHONET data </a> </li> <li> <a href="../articles/SPSS.html"> <span class="fa fa-file-upload"></span> Import data from SPSS/SAS/Stata </a> </li> <li> <a href="../articles/EUCAST.html"> <span class="fa fa-exchange-alt"></span> Apply EUCAST rules </a> </li> <li> <a href="../reference/mo_property.html"> <span class="fa fa-bug"></span> Get properties of a microorganism </a> </li> <li> <a href="../reference/ab_property.html"> <span class="fa fa-capsules"></span> Get properties of an antibiotic </a> </li> <li> <a href="../articles/freq.html"> <span class="fa fa-sort-amount-down"></span> Create frequency tables </a> </li> <li> <a href="../articles/G_test.html"> <span class="fa fa-clipboard-check"></span> Use the G-test </a> </li> <li> <a href="../articles/benchmarks.html"> <span class="fa fa-shipping-fast"></span> Other: benchmarks </a> </li> </ul> </li> <li> <a href="../reference/"> <span class="fa fa-book-open"></span> Manual </a> </li> <li> <a href="../authors.html"> <span class="fa fa-users"></span> Authors </a> </li> <li> <a href="../news/"> <span class="far fa far fa-newspaper"></span> Changelog </a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://gitlab.com/msberends/AMR"> <span class="fab fa fab fa-gitlab"></span> Source Code </a> </li> <li> <a href="../LICENSE-text.html"> <span class="fa fa-book"></span> Licence </a> </li> </ul> <form class="navbar-form navbar-right" role="search"> <div class="form-group"> <input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off"> </div> </form> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> <table class="ref-index"> <colgroup> <col class="alias" /> <col class="title" /> </colgroup> <tbody> <tr> <th colspan="2"> <h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2> <p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p> </th> </tr> <tr> <td> <p><code><a href="AMR.html">AMR</a></code> </p> </td> <td><p>The <code>AMR</code> Package</p></td> </tr><tr> <td> <p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p> </td> <td><p>The Catalogue of Life</p></td> </tr><tr> <td> <p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p> </td> <td><p>Version info of included Catalogue of Life</p></td> </tr><tr> <td> <p><code><a href="WHOCC.html">WHOCC</a></code> </p> </td> <td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2> <p class="section-desc"><p>Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a>.</p></p> </th> </tr> <tr> <td> <p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p> </td> <td><p>Transform to antibiotic ID</p></td> </tr><tr> <td> <p><code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p> </td> <td><p>Transform to ATC code</p></td> </tr><tr> <td> <p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p> </td> <td><p>Class 'disk'</p></td> </tr><tr> <td> <p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p> </td> <td><p>Class 'mic'</p></td> </tr><tr> <td> <p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p> </td> <td><p>Transform to microorganism ID</p></td> </tr><tr> <td> <p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p> </td> <td><p>Class 'rsi'</p></td> </tr><tr> <td> <p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p> </td> <td><p>Use predefined reference data set</p></td> </tr><tr> <td> <p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_rules_file()</a></code> </p> </td> <td><p>EUCAST rules</p></td> </tr><tr> <td> <p><code><a href="rsi_translation.html">rsi_translation</a></code> </p> </td> <td><p>Data set for RSI interpretation</p></td> </tr><tr> <td> <p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p> </td> <td><p>Guess antibiotic column</p></td> </tr><tr> <td> <p><code><a href="read.4D.html">read.4D()</a></code> </p> </td> <td><p>Read data from 4D database</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2> <p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p> </th> </tr> <tr> <td> <p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p> </td> <td><p>Determine first (weighted) isolates</p></td> </tr><tr> <td> <p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p> </td> <td><p>Determine multidrug-resistant organisms (MDRO)</p></td> </tr><tr> <td> <p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p> </td> <td><p>Key antibiotics for first <em>weighted</em> isolates</p></td> </tr><tr> <td> <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p> </td> <td><p>Property of a microorganism</p></td> </tr><tr> <td> <p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p> </td> <td><p>Property of an antibiotic</p></td> </tr><tr> <td> <p><code><a href="age.html">age()</a></code> </p> </td> <td><p>Age in years of individuals</p></td> </tr><tr> <td> <p><code><a href="age_groups.html">age_groups()</a></code> </p> </td> <td><p>Split ages into age groups</p></td> </tr><tr> <td> <p><code><a href="p.symbol.html">p.symbol()</a></code> </p> </td> <td><p>Symbol of a p value</p></td> </tr><tr> <td> <p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p> </td> <td><p>Join a table with <code>microorganisms</code></p></td> </tr><tr> <td> <p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p> </td> <td><p>Get ATC properties from WHOCC website</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2> <p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.</p></p> </th> </tr> <tr> <td> <p><code><a href="availability.html">availability()</a></code> </p> </td> <td><p>Check availability of columns</p></td> </tr><tr> <td> <p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p> </td> <td><p>Count isolates</p></td> </tr><tr> <td> <p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p> </td> <td><p>Calculate resistance of isolates</p></td> </tr><tr> <td> <p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p> </td> <td><p>Filter isolates on result in antibiotic class</p></td> </tr><tr> <td> <p><code><a href="freq.html">freq()</a></code> <code><a href="freq.html">frequency_tbl()</a></code> <code><a href="freq.html">top_freq()</a></code> <code><a href="freq.html">header()</a></code> <code><a href="freq.html">print(<i><freq></i>)</a></code> </p> </td> <td><p>Frequency table</p></td> </tr><tr> <td> <p><code><a href="g.test.html">g.test()</a></code> </p> </td> <td><p><em>G</em>-test for Count Data</p></td> </tr><tr> <td> <p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p> </td> <td><p>AMR plots with <code>ggplot2</code></p></td> </tr><tr> <td> <p><code><a href="kurtosis.html">kurtosis()</a></code> </p> </td> <td><p>Kurtosis of the sample</p></td> </tr><tr> <td> <p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p> </td> <td><p>Predict antimicrobial resistance</p></td> </tr><tr> <td> <p><code><a href="skewness.html">skewness()</a></code> </p> </td> <td><p>Skewness of the sample</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2> <p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p> </th> </tr> <tr> <td> <p><code><a href="antibiotics.html">antibiotics</a></code> </p> </td> <td><p>Data set with ~450 antibiotics</p></td> </tr><tr> <td> <p><code><a href="microorganisms.html">microorganisms</a></code> </p> </td> <td><p>Data set with ~65,000 microorganisms</p></td> </tr><tr> <td> <p><code><a href="septic_patients.html">septic_patients</a></code> </p> </td> <td><p>Data set with 2,000 blood culture isolates from septic patients</p></td> </tr><tr> <td> <p><code><a href="WHONET.html">WHONET</a></code> </p> </td> <td><p>Data set with 500 isolates - WHONET example</p></td> </tr><tr> <td> <p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p> </td> <td><p>Translation table for microorganism codes</p></td> </tr><tr> <td> <p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p> </td> <td><p>Data set with previously accepted taxonomic names</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-other-functions" class="hasAnchor"><a href="#section-other-functions" class="anchor"></a>Other functions</h2> <p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p> </th> </tr> <tr> <td> <p><code><a href="translate.html">get_locale()</a></code> </p> </td> <td><p>Translate strings from AMR package</p></td> </tr><tr> <td> <p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> </p> </td> <td><p>Pattern Matching</p></td> </tr> </tbody><tbody> <tr> <th colspan="2"> <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> <p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p> </th> </tr> <tr> <td> <p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">abname()</a></code> <code><a href="AMR-deprecated.html">atc_property()</a></code> <code><a href="AMR-deprecated.html">atc_official()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">atc_name()</a></code> <code><a href="AMR-deprecated.html">atc_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">atc_tradenames()</a></code> </p> </td> <td><p>Deprecated functions</p></td> </tr> </tbody> </table> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#section-background-information">Background information</a></li> <li><a href="#section-cleaning-your-data">Cleaning your data</a></li> <li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li> <li><a href="#section-analysing-your-data">Analysing your data</a></li> <li><a href="#section-included-data-sets">Included data sets</a></li> <li><a href="#section-other-functions">Other functions</a></li> <li><a href="#section-deprecated-functions">Deprecated functions</a></li> </ul> </div> </div> <footer> <div class="copyright"> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> <script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script> <script> docsearch({ apiKey: 'f737050abfd4d726c63938e18f8c496e', indexName: 'amr', inputSelector: 'input#search-input.form-control', transformData: function(hits) { return hits.map(function (hit) { hit.url = updateHitURL(hit); return hit; }); } }); </script> </body> </html>