mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 11:51:59 +02:00
(v0.8.0.9033) antivirals data set, cleanup
This commit is contained in:
@ -84,7 +84,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9033</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -239,38 +239,6 @@
|
||||
</colgroup>
|
||||
|
||||
<tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
|
||||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||||
</td>
|
||||
<td><p>The <code>AMR</code> Package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
|
||||
</td>
|
||||
<td><p>The Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Version info of included Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
|
||||
</td>
|
||||
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
|
||||
@ -309,80 +277,50 @@
|
||||
<td><p>Class 'rsi'</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Use predefined reference data set</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
|
||||
</td>
|
||||
<td><p>EUCAST rules</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set for RSI interpretation</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Guess antibiotic column</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Use predefined reference data set</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Read data from 4D database</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set for RSI interpretation</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
|
||||
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||||
<h2 id="section-enhancing-your-data" class="hasAnchor"><a href="#section-enhancing-your-data" class="anchor"></a>Enhancing your data</h2>
|
||||
<p class="section-desc"><p>Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
</td>
|
||||
<td><p>Determine first (weighted) isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mdro.html">mdro()</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>
|
||||
</td>
|
||||
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</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>
|
||||
</td>
|
||||
<td><p>Property of a microorganism</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="age.html">age()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Age in years of individuals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
|
||||
</td>
|
||||
@ -390,9 +328,21 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="p_symbol.html">p_symbol()</a></code> </p>
|
||||
<p><code><a href="age.html">age()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Symbol of a p value</p></td>
|
||||
<td><p>Age in years of individuals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
</td>
|
||||
<td><p>Determine first (weighted) isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -402,9 +352,27 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
<td><p>Key antibiotics for first <em>weighted</em> isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mdro.html">mdro()</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>
|
||||
</td>
|
||||
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</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>
|
||||
</td>
|
||||
<td><p>Property of a microorganism</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="p_symbol.html">p_symbol()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Symbol of a p value</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -433,12 +401,6 @@
|
||||
<td><p>Count isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
</td>
|
||||
<td><p>Calculate microbial resistance</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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_tetracyclines()</a></code> </p>
|
||||
</td>
|
||||
@ -463,6 +425,12 @@
|
||||
<td><p>Kurtosis of the sample</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<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>
|
||||
</td>
|
||||
<td><p>Calculate microbial resistance</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
|
||||
</td>
|
||||
@ -478,7 +446,7 @@
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-included-data-sets" class="hasAnchor"><a href="#section-included-data-sets" class="anchor"></a>Included data sets</h2>
|
||||
<p class="section-desc"><p>References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.</p></p>
|
||||
<p class="section-desc"><p>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
@ -490,21 +458,15 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||||
<p><code><a href="antivirals.html">antivirals</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~70,000 microorganisms</p></td>
|
||||
<td><p>Data set with ~100 antivirals</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="example_isolates.html">example_isolates</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 2,000 blood culture isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||||
<td><p>Data set with 2,000 example isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -517,6 +479,50 @@
|
||||
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with previously accepted taxonomic names</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~70,000 microorganisms</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHONET.html">WHONET</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with 500 isolates - WHONET example</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-background-information" class="hasAnchor"><a href="#section-background-information" class="anchor"></a>Background information</h2>
|
||||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR.html">AMR</a></code> </p>
|
||||
</td>
|
||||
<td><p>The <code>AMR</code> Package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life.html">catalogue_of_life</a></code> </p>
|
||||
</td>
|
||||
<td><p>The Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Version info of included Catalogue of Life</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
|
||||
</td>
|
||||
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -551,12 +557,18 @@
|
||||
<p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Extended functions</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="reexports.html">reexports</a></code> </p>
|
||||
</td>
|
||||
<td><p>Objects exported from other packages</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>functions</h2>
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
@ -573,11 +585,11 @@
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#section-background-information">Background information</a></li>
|
||||
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
|
||||
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
|
||||
<li><a href="#section-enhancing-your-data">Enhancing your data</a></li>
|
||||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||||
<li><a href="#section-background-information">Background information</a></li>
|
||||
<li><a href="#section-other-functions">Other functions</a></li>
|
||||
<li><a href="#section-extended-functions">Extended functions</a></li>
|
||||
<li><a href="#section-functions">functions</a></li>
|
||||
|
||||
Reference in New Issue
Block a user