mirror of
https://github.com/msberends/AMR.git
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(v1.5.0.9006) major documentation update
This commit is contained in:
@ -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">1.5.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9006</span>
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</span>
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</div>
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@ -266,43 +266,43 @@
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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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<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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<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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<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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<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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<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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<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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<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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@ -326,25 +326,25 @@
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<td>
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<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
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</td>
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<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
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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="example_isolates_unclean.html">example_isolates_unclean</a></code> </p>
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</td>
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<td><p>Data set with unclean data</p></td>
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<td><p>Data Set with Unclean Data</p></td>
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</tr><tr>
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<td>
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<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
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</td>
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<td><p>Data set for R/SI interpretation</p></td>
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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="WHONET.html">WHONET</a></code> </p>
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</td>
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<td><p>Data set with 500 isolates - WHONET example</p></td>
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<td><p>Data Set with 500 Isolates - WHONET Example</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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@ -363,19 +363,19 @@
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<td>
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<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
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</td>
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<td><p>Transform input to a microorganism ID</p></td>
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<td><p>Transform Input to a Microorganism ID</p></td>
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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_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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<td><p>Get Properties of a Microorganism</p></td>
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</tr><tr>
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<td>
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<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
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</td>
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<td><p>User-defined reference data set for microorganisms</p></td>
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<td><p>User-Defined Reference Data Set for Microorganisms</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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@ -394,25 +394,25 @@
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<td>
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<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
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</td>
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<td><p>Transform input to an antibiotic ID</p></td>
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<td><p>Transform Input to an Antibiotic ID</p></td>
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</tr><tr>
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<td>
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<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
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</td>
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<td><p>Get properties of an antibiotic</p></td>
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<td><p>Get Properties of an Antibiotic</p></td>
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</tr><tr>
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<td>
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<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
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</td>
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<td><p>Retrieve antimicrobial drug names and doses from clinical text</p></td>
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<td><p>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</p></td>
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</tr><tr>
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<td>
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<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
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</td>
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<td><p>Get ATC properties from WHOCC website</p></td>
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<td><p>Get ATC Properties from WHOCC Website</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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@ -431,37 +431,37 @@
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<td>
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<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
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</td>
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<td><p>Interpret MIC and disk values, or clean raw R/SI data</p></td>
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<td><p>Interpret MIC and Disk Values, or Clean Raw R/SI Data</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
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</td>
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<td><p>Transform input to minimum inhibitory concentrations (MIC)</p></td>
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<td><p>Transform Input to Minimum Inhibitory Concentrations (MIC)</p></td>
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</tr><tr>
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<td>
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<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
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</td>
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<td><p>Transform input to disk diffusion diameters</p></td>
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<td><p>Transform Input to Disk Diffusion Diameters</p></td>
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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> <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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<td><p>Apply EUCAST Rules</p></td>
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</tr><tr>
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<td>
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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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<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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<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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@ -480,61 +480,61 @@
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<td>
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<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
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</td>
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<td><p>Calculate microbial resistance</p></td>
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<td><p>Calculate Microbial Resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
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</td>
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<td><p>Count available isolates</p></td>
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<td><p>Count Available Isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code> </p>
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</td>
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<td><p>Determine (new) episodes for patients</p></td>
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<td><p>Determine (New) Episodes for Patients</p></td>
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</tr><tr>
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<td>
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<p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
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</td>
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<td><p>Determine first (weighted) isolates</p></td>
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<td><p>Determine First (Weighted) Isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
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</td>
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<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
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<td><p>Key Antibiotics for First (Weighted) Isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">custom_mdro_guideline()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
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</td>
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<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
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<td><p>Determine Multidrug-Resistant Organisms (MDRO)</p></td>
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</tr><tr>
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<td>
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<p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p>
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</td>
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<td><p>AMR plots with <code>ggplot2</code></p></td>
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<td><p>AMR Plots with <code>ggplot2</code></p></td>
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</tr><tr>
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<td>
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<p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i><bug_drug_combinations></i>)</a></code> </p>
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</td>
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<td><p>Determine bug-drug combinations</p></td>
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<td><p>Determine Bug-Drug Combinations</p></td>
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</tr><tr>
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<td>
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<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
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</td>
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<td><p>Antibiotic class selectors</p></td>
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<td><p>Antibiotic Class Selectors</p></td>
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</tr><tr>
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<td>
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<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
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</td>
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<td><p>Filter isolates on result in antimicrobial class</p></td>
|
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<td><p>Filter Isolates on Result in Antimicrobial Class</p></td>
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</tr><tr>
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<td>
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@ -546,7 +546,7 @@
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<td>
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<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
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</td>
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<td><p>Guess antibiotic column</p></td>
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<td><p>Guess Antibiotic Column</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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@ -565,49 +565,49 @@
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<td>
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<p><code><a href="age_groups.html">age_groups()</a></code> </p>
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</td>
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<td><p>Split ages into age groups</p></td>
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<td><p>Split Ages into Age Groups</p></td>
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</tr><tr>
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<td>
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<p><code><a href="age.html">age()</a></code> </p>
|
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</td>
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<td><p>Age in years of individuals</p></td>
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<td><p>Age in Years of Individuals</p></td>
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</tr><tr>
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<td>
|
||||
<p><code><a href="availability.html">availability()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Check availability of columns</p></td>
|
||||
<td><p>Check Availability of Columns</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="translate.html">get_locale()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Translate strings from AMR package</p></td>
|
||||
<td><p>Translate Strings from AMR Package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="ggplot_pca.html">ggplot_pca()</a></code> </p>
|
||||
</td>
|
||||
<td><p>PCA biplot with <code>ggplot2</code></p></td>
|
||||
<td><p>PCA Biplot with <code>ggplot2</code></p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Join microorganisms to a data set</p></td>
|
||||
<td><p>Join microorganisms to a Data Set</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
|
||||
</td>
|
||||
<td><p>Pattern matching with keyboard shortcut</p></td>
|
||||
<td><p>Pattern Matching with Keyboard Shortcut</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_matching_score.html">mo_matching_score()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Calculate the matching score for microorganisms</p></td>
|
||||
<td><p>Calculate the Matching Score for Microorganisms</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -619,7 +619,7 @@
|
||||
<td>
|
||||
<p><code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_rsi()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Random MIC values/disk zones/RSI generation</p></td>
|
||||
<td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -644,13 +644,13 @@
|
||||
<td>
|
||||
<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Kurtosis of the sample</p></td>
|
||||
<td><p>Kurtosis of the Sample</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="skewness.html">skewness()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Skewness of the sample</p></td>
|
||||
<td><p>Skewness of the Sample</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -669,7 +669,7 @@
|
||||
<td>
|
||||
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Deprecated functions</p></td>
|
||||
<td><p>Deprecated Functions</p></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
Reference in New Issue
Block a user