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(v1.4.0.9000) more extensive unit tests
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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</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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</span>
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</div>
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@ -242,24 +242,24 @@
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<p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (like <code>"S. aureus"</code>), an abbreviation known in the field (like <code>"MRSA"</code>), or just a genus. Please see <em>Examples</em>.</p>
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</div>
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<pre class="usage"><span class='fu'>as.mo</span>(
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<span class='kw'>x</span>,
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Becker = <span class='fl'>FALSE</span>,
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Lancefield = <span class='fl'>FALSE</span>,
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allow_uncertain = <span class='fl'>TRUE</span>,
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reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
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ignore_pattern = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_ignore_pattern"</span>),
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language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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<span class='kw'>...</span>
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)
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<pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
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<span class='va'>x</span>,
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Becker <span class='op'>=</span> <span class='cn'>FALSE</span>,
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Lancefield <span class='op'>=</span> <span class='cn'>FALSE</span>,
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allow_uncertain <span class='op'>=</span> <span class='cn'>TRUE</span>,
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reference_df <span class='op'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span><span class='op'>(</span><span class='op'>)</span>,
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ignore_pattern <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_ignore_pattern"</span><span class='op'>)</span>,
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language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='fu'>is.mo</span>(<span class='kw'>x</span>)
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<span class='fu'>is.mo</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
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<span class='fu'>mo_failures</span>()
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<span class='fu'>mo_failures</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>mo_uncertainties</span>()
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<span class='fu'>mo_uncertainties</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>mo_renamed</span>()</pre>
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<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -306,7 +306,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<h3>General info</h3>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General info</h3>
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<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
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@ -334,7 +334,7 @@
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<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
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<h3>Coping with uncertain results</h3>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Coping with uncertain results</h3>
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<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
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@ -358,7 +358,7 @@
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</ul>
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<h3>Microbial prevalence of pathogens in humans</h3>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Microbial prevalence of pathogens in humans</h3>
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<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching score for microorganisms</em> below.</p>
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@ -423,39 +423,39 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># \donttest{</span>
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<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
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<span class='fu'>as.mo</span>(<span class='st'>"sau"</span>) <span class='co'># WHONET code</span>
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<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Zthafilokkoockus oureuz"</span>) <span class='co'># handles incorrect spelling</span>
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<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
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<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
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<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
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<span class='fu'>as.mo</span>(<span class='fl'>115329001</span>) <span class='co'># SNOMED CT code</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"sau"</span><span class='op'>)</span> <span class='co'># WHONET code</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"stau"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"STAU"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"staaur"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. aureus"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S aureus"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Staphylococcus aureus (MRSA)"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Zthafilokkoockus oureuz"</span><span class='op'>)</span> <span class='co'># handles incorrect spelling</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># Methicillin Resistant S. aureus</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># Vancomycin Intermediate S. aureus</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"VRSA"</span><span class='op'>)</span> <span class='co'># Vancomycin Resistant S. aureus</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='fl'>115329001</span><span class='op'>)</span> <span class='co'># SNOMED CT code</span>
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<span class='co'># Dyslexia is no problem - these all work:</span>
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<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticus"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasmium urealytica"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"Ureaplazma urealitycium"</span>)
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasma urealyticum"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasma urealyticus"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasmium urealytica"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplazma urealitycium"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
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<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
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<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Streptococcus group A"</span><span class='op'>)</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"GAS"</span><span class='op'>)</span> <span class='co'># Group A Streptococci</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"GBS"</span><span class='op'>)</span> <span class='co'># Group B Streptococci</span>
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<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
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<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. epidermidis"</span><span class='op'>)</span> <span class='co'># will remain species: B_STPHY_EPDR</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. epidermidis"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># will not remain species: B_STPHY_CONS</span>
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<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
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<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span><span class='op'>)</span> <span class='co'># will remain species: B_STRPT_PYGN</span>
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<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>, Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># will not remain species: B_STRPT_GRPA</span>
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<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
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<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
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<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
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<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Escherichia"</span>
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<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Gram negative"</span>
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<span class='co'># }</span>
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</pre>
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</div>
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@ -473,7 +473,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</div>
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</footer>
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