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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>mo_year()</code></p></li>
<li><p>An <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">ordered factor</a> in case of <code>mo_pathogenicity()</code></p></li>
<li><p>A <a href="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>
<li><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> in case of <code>mo_is_anaerobic()</code>, <code>mo_is_gram_negative()</code>, <code>mo_is_gram_positive()</code>, <code>mo_is_intrinsic_resistant()</code>, and <code>mo_is_yeast()</code></p></li>
<li><p>A named <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in case of <code>mo_synonyms()</code> and <code>mo_url()</code></p></li>
<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
</ul></div>
<p>- An [integer] in case of [mo_year()]
- An [ordered factor][factor] in case of [mo_pathogenicity()]
- A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()], and [mo_info()]
- A [logical] in case of [mo_is_anaerobic()], [mo_is_gram_negative()], [mo_is_gram_positive()], [mo_is_intrinsic_resistant()], and [mo_is_yeast()]
- A named [character] in case of [mo_synonyms()] and [mo_url()]
- A [character] in all other cases</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<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 about the renaming)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a once-per-session warning that the name is outdated)</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><a href="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, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a <a href="https://rdrr.io/pkg/data.table/man/fctr.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, <a href="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, <a href="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 yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, 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 <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). 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 antimicrobials).</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. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> will be used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on July 16th, 2024. See <em>Source</em> and the <a href="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 <a href="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>
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
<p>All functions will, at default, **not** keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example *Enterobacter aerogenes*, which was initially named in 1960 but renamed to *Klebsiella aerogenes* in 2017:
- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with a note about the renaming)
- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Enterobacter"` (with a once-per-session warning that the name is outdated)
- `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming)
- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated)</p>
<p>The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.</p>
<p>Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.</p>
<p>Determination of the Gram stain ([mo_gramstain()]) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` 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 `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).</p>
<p>Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials).</p>
<p>Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) will be based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria.</p>
<p>The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) will be used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise.</p>
<p>SNOMED codes ([mo_snomed()]) was last updated on `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()] (which will have the scientific reference as [name][base::names()]), the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names.</p>
<p>All output [will be translated][translate] where possible.</p>
</div>
<div class="section level2">
<h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>