<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><title>Get Properties of a Microorganism — mo_property • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.2.2/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.7/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js"integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Get Properties of a Microorganism — mo_property"><metaproperty="og:description"content="Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. See Examples."><metaproperty="og:image"content="https://msberends.g
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><ahref="as.mo.html">as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. See <em>Examples</em>.</p>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span><spanclass="fu">mo_current</span><spanclass="op">(</span><spanclass="va">x</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> open <spanclass="op">=</span><spanclass="cn">FALSE</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<dd><p>any <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> (vector) that can be coerced to a valid microorganism code with <code><ahref="as.mo.html">as.mo()</a></code>. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see <em>Examples</em>.</p></dd>
<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><ahref="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the <ahref="AMR-options.html">package option</a><code><ahref="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dd><p>other arguments passed on to <code><ahref="as.mo.html">as.mo()</a></code>, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'</p></dd>
<dd><p>one of the column names of the <ahref="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code></p></dd>
<li><p>A <ahref="https://rdrr.io/r/base/list.html"class="external-link">list</a> in case of <code>mo_taxonomy()</code>, <code>mo_synonyms()</code>, <code>mo_snomed()</code> and <code>mo_info()</code></p></li>
<p>All functions will, at default, <strong>not</strong> keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example <em>Enterobacter aerogenes</em>, which was initially named in 1960 but renamed to <em>Klebsiella aerogenes</em> in 2017:</p><ul><li><p><code>mo_genus("Enterobacter aerogenes")</code> will return <code>"Klebsiella"</code> (with a note about the renaming)</p></li>
<li><p><code>mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Enterobacter"</code> (with a once-per-session warning that the name is outdated)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes")</code> will return <code>"Tindall et al., 2017"</code> (with a note)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a warning)</p></li>
</ul><p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><ahref="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>Determination of human pathogenicity (<code>mo_pathogenicity()</code>) is strongly based on Bartlett <em>et al.</em> (2022, <ahref="https://doi.org/10.1099/mic.0.001269"class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a <ahref="https://rdrr.io/r/base/factor.html"class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <ahref="https://pubmed.ncbi.nlm.nih.gov/11837318/"class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <ahref="https://pubmed.ncbi.nlm.nih.gov/34694987/"class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> 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>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <ahref="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <ahref="https://www.eucast.org/expert_rules_and_expected_phenotypes"class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antibiotics).</p>
<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) are from the version of July 1st, 2021. See <em>Source</em> and the <ahref="microorganisms.html">microorganisms</a> data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <ahref="https://rdrr.io/r/base/names.html"class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
<h2id="matching-score-for-microorganisms">Matching Score for Microorganisms<aclass="anchor"aria-label="anchor"href="#matching-score-for-microorganisms"></a></h2>
<p>This function uses <code><ahref="as.mo.html">as.mo()</a></code> internally, which uses an advanced algorithm to translate arbitrary user input to valid taxonomy using a so-called matching score. You can read about this public algorithm on the <ahref="mo_matching_score.html">MO matching score page</a>.</p>
<ol><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <ahref="https://doi.org/10.18637/jss.v104.i03"class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
<li><p>Becker K <em>et al.</em> (2019). <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong><em>Clin Microbiol Infect</em>; <ahref="https://doi.org/10.1016/j.cmi.2019.02.028"class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci.</strong><em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <ahref="https://doi.org/10.1080/14787210.2020.1730813"class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong><em>J Exp Med.</em> 57(4): 571-95; <ahref="https://doi.org/10.1084/jem.57.4.571"class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong><em>Micro.rganisms</em> 10(9), 1801; <ahref="https://doi.org/10.3390/microorganisms10091801"class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
<li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <ahref="https://doi.org/10.1099/ijsem.0.004332"class="external-link">doi:10.1099/ijsem.0.004332</a>
. Accessed from <ahref="https://www.gbif.org"class="external-link">https://www.gbif.org</a> on December 11th, 2022.</p></li>
<li><p>Reimer, LC <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong> Nucleic Acids Res., 50(D1):D741-D74; <ahref="https://doi.org/10.1093/nar/gkab961"class="external-link">doi:10.1093/nar/gkab961</a>
. Accessed from <ahref="https://bacdive.dsmz.de"class="external-link">https://bacdive.dsmz.de</a> on May 12th, 2023.</p></li>
<li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <ahref="https://phinvads.cdc.gov"class="external-link">https://phinvads.cdc.gov</a></p></li>
<li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong><em>Microbiology</em> 168:001269; <ahref="https://doi.org/10.1099/mic.0.001269"class="external-link">doi:10.1099/mic.0.001269</a></p></li>
<h2id="reference-data-publicly-available">Reference Data Publicly Available<aclass="anchor"aria-label="anchor"href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <ahref="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <ahref="https://github.com/msberends/AMR/tree/main/data-raw"class="external-link">our GitHub repository</a>.</p>
<divclass="sourceCode"><preclass="sourceCode r"><code><spanclass="r-in"><span><spanclass="co"># taxonomic tree -----------------------------------------------------------</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_gramstain</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"de"</span><spanclass="op">)</span><spanclass="co"># German</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_gramstain</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"nl"</span><spanclass="op">)</span><spanclass="co"># Dutch</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_gramstain</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"es"</span><spanclass="op">)</span><spanclass="co"># Spanish</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_gramstain</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"el"</span><spanclass="op">)</span><spanclass="co"># Greek</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_gramstain</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"uk"</span><spanclass="op">)</span><spanclass="co"># Ukrainian</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-in"><span><spanclass="fu">mo_kingdom</span><spanclass="op">(</span><spanclass="st">"Klebsiella pneumoniae"</span>, language <spanclass="op">=</span><spanclass="st">"zh"</span><spanclass="op">)</span><spanclass="co"># Chinese, no effect</span></span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in filter(., mo_is_gram_positive()):</span><spanstyle="color: #00BBBB;">ℹ</span> In argument: `mo_is_gram_positive()`.</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanstyle="font-weight: bold;">Caused by error:</span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> in mo_is_gram_positive(): argument x is missing and no column with info</span>
<spanclass="r-err co"><spanclass="r-pr">#></span> about microorganisms could be found.</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in filter(., mo_is_intrinsic_resistant(ab = "vanco")):</span><spanstyle="color: #00BBBB;">ℹ</span> In argument: `mo_is_intrinsic_resistant(ab = "vanco")`.</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanstyle="font-weight: bold;">Caused by error:</span></span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> in mo_is_intrinsic_resistant(): argument x is missing and no column with</span>
<spanclass="r-err co"><spanclass="r-pr">#></span> info about microorganisms could be found.</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_blank"href="https://github.com/msberends/AMR/blob/main/LICENSE"class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
