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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
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@ -81,7 +81,7 @@
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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">1.5.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9000</span>
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</span>
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</div>
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@ -263,6 +263,48 @@
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<td><p>The <code>AMR</code> Package</p></td>
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</tr><tr>
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<td>
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<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
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</td>
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<td><p>Data set with 2,000 example isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
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</td>
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<td><p>Data set with 67,151 microorganisms</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
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</td>
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<td><p>Data set with 5,580 common microorganism codes</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
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</td>
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<td><p>Data set with previously accepted taxonomic names</p></td>
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</tr><tr>
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<td>
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<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
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</td>
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<td><p>Data sets with 558 antimicrobials</p></td>
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</tr><tr>
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<td>
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<p><code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code> </p>
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</td>
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<td><p>Data set with bacterial intrinsic resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="dosage.html">dosage</a></code> </p>
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</td>
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<td><p>Data set with treatment dosages as defined by EUCAST</p></td>
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</tr><tr>
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<td>
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<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
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</td>
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@ -287,30 +329,6 @@
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<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
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</td>
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<td><p>Data set with 67,151 microorganisms</p></td>
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</tr><tr>
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<td>
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<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
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</td>
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<td><p>Data sets with 557 antimicrobials</p></td>
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</tr><tr>
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<td>
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<p><code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code> </p>
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</td>
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<td><p>Data set with bacterial intrinsic resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
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</td>
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<td><p>Data set with 2,000 example isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code> </p>
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</td>
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@ -323,18 +341,6 @@
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<td><p>Data set for R/SI interpretation</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
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</td>
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<td><p>Data set with 5,583 common microorganism codes</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
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</td>
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<td><p>Data set with previously accepted taxonomic names</p></td>
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</tr><tr>
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<td>
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<p><code><a href="WHONET.html">WHONET</a></code> </p>
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</td>
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@ -361,7 +367,7 @@
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</tr><tr>
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<td>
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<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_domain()</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_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</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_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
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<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_domain()</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_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</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_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
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</td>
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<td><p>Get properties of a microorganism</p></td>
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</tr><tr>
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@ -441,7 +447,7 @@
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</tr><tr>
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<td>
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<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
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<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code> </p>
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</td>
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<td><p>Apply EUCAST rules</p></td>
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</tr><tr>
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@ -450,6 +456,12 @@
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<p><code><a href="plot.html">plot(<i><disk></i>)</a></code> <code><a href="plot.html">plot(<i><mic></i>)</a></code> <code><a href="plot.html">barplot(<i><mic></i>)</a></code> <code><a href="plot.html">plot(<i><rsi></i>)</a></code> <code><a href="plot.html">barplot(<i><rsi></i>)</a></code> </p>
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</td>
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<td><p>Plotting for classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
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</tr><tr>
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<td>
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<p><code><a href="isolate_identifier.html">isolate_identifier()</a></code> </p>
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</td>
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<td><p>Create identifier of an isolate</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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