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(v1.4.0.9041) updates based on review
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9034</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9041</span>
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</span>
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</div>
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<ul class="nav navbar-nav">
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<li>
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<a href="../index.html">
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How to
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@ -106,77 +106,77 @@
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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<span class="fas fa-directions"></span>
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Conduct AMR analysis
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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<span class="fas fa-dice"></span>
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Predict antimicrobial resistance
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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<a href="../articles/EUCAST.html">
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Apply EUCAST rules
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<span class="fa fa-bug"></span>
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<span class="fas fa-bug"></span>
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Get properties of a microorganism
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<a href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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</a>
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@ -185,21 +185,21 @@
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<a href="../reference/index.html">
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Manual
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Changelog
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@ -208,14 +208,14 @@
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<ul class="nav navbar-nav navbar-right">
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<li>
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<a href="https://github.com/msberends/AMR">
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Source Code
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<a href="../survey.html">
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Survey
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</a>
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@ -344,7 +344,7 @@
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<li><p><code>mo_ref("Shimwellia blattae")</code> will return <code>"Priest et al., 2010"</code> (without a message)</p></li>
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</ul>
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<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (like <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like <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>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
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<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. 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>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
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<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>
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<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - 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> (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>
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<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> from 2020. The <code>mo_is_intrinsic_resistant()</code> can be vectorised over parameters <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
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