<li>Support for translation of disk diffusion and MIC values to RSI values (i.e.antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><ahref="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><ahref="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e.antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><ahref="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><ahref="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><ahref="../reference/mo_property.html">mo_name()</a></code> as alias of <code><ahref="../reference/mo_property.html">mo_fullname()</a></code>
<li>Function <code><ahref="../reference/mo_property.html">mo_name()</a></code> as alias of <code><ahref="../reference/mo_property.html">mo_fullname()</a></code>
@ -253,9 +270,9 @@
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><ahref="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <ahref="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><ahref="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <ahref="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
<li>Fixed a critical bug in <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a critical bug in <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixedd a bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Fixedd a bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li><p>Fix for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
<li><p>Fix for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
</ul>
</ul>
</div>
</div>
<divid="other" class="section level4">
<divid="other-1" class="section level4">
<h4class="hasAnchor">
<h4class="hasAnchor">
<ahref="#other" class="anchor"></a>Other</h4>
<ahref="#other-1" class="anchor"></a>Other</h4>
<ul>
<ul>
<li>Support for R 3.6.0 and later by providing support for <ahref="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
<li>Support for R 3.6.0 and later by providing support for <ahref="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
</ul>
<divid="new-1" class="section level4">
<divid="new-2" class="section level4">
<h4class="hasAnchor">
<h4class="hasAnchor">
<ahref="#new-1" class="anchor"></a>New</h4>
<ahref="#new-2" class="anchor"></a>New</h4>
<ul>
<ul>
<li>
<li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
@ -446,9 +463,9 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <ahref="https://msberends.gitlab.io/AMR"class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <ahref="https://msberends.gitlab.io/AMR"class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
<li>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code>
<li>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code>
</li>
</li>
@ -700,9 +717,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li><p>Percentages will now will rounded more logically (e.g.in <code>freq</code> function)</p></li>
<li><p>Percentages will now will rounded more logically (e.g.in <code>freq</code> function)</p></li>
</ul>
</ul>
</div>
</div>
<divid="other-2" class="section level4">
<divid="other-3" class="section level4">
<h4class="hasAnchor">
<h4class="hasAnchor">
<ahref="#other-2" class="anchor"></a>Other</h4>
<ahref="#other-3" class="anchor"></a>Other</h4>
<ul>
<ul>
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
@ -714,9 +731,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <ahref="https://itis.gov"class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <ahref="https://itis.gov"class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
<li>New functions based on the existing function <code>mo_property</code>:
<li>New functions based on the existing function <code>mo_property</code>:
@ -785,9 +802,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>
<li>
@ -837,9 +854,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</li>
</ul>
</ul>
</div>
</div>
<divid="other-3" class="section level4">
<divid="other-4" class="section level4">
<h4class="hasAnchor">
<h4class="hasAnchor">
<ahref="#other-3" class="anchor"></a>Other</h4>
<ahref="#other-4" class="anchor"></a>Other</h4>
<ul>
<ul>
<li>More unit tests to ensure better integrity of functions</li>
<li>More unit tests to ensure better integrity of functions</li>
</ul>
</ul>
@ -849,9 +866,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@ -922,9 +939,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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