ecoffs

A dataset containing the epidemiological cut-off values (ECOFFs) for
different antibiotics and microorganisms. Currently, only the ECOFF values
for Escherichia coli are included.

datasets

Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data.
Validate the results of an MIC experiment by comparing observed MIC values to
a gold standard assay, in line with standards from the International Organization for
Standardization (2021) <https://www.iso.org/standard/79377.html>. Perform MIC prediction from
whole genome sequence data stored in the Pathosystems Resource Integration Center (2013)
<doi:10.1093/nar/gkt1099> database or locally.

Alessandro Gerada

Analysis of Antimicrobial Minimum Inhibitory Concentration Data

ecoffs function

<div class="section" id="ecoffs">
<h3><code>ecoffs</code></h3>
A data frame with 85 rows and 25 columns:<dl>
<dt>organism</dt>
<dd>Microorganism code in AMR::mo format</dd><dt>antibiotic</dt>
<dd>Antibiotic code in AMR::ab format</dd><dt><code>0.002</code>:<code>512</code></dt>
<dd>Counts of isolates in each concentration "bin"</dd><dt>Distributions</dt>
<dd>see EUCAST documentation below</dd><dt>Observations</dt>
<dd>Number of observations</dd><dt><code>(T)ECOFF</code></dt>
<dd>see EUCAST documentation below</dd><dt><code>Confidence interval</code></dt>
<dd>see EUCAST documentation below</dd>
</dl></div>

Format

ECOFF data — ecoffs

<div class='section' id='ecoffs'>
<h3><code>ecoffs</code></h3>


A data frame with 85 rows and 25 columns:<dl>
<dt>organism</dt>
<dd>Microorganism code in AMR::mo format</dd>

<dt>antibiotic</dt>
<dd>Antibiotic code in AMR::ab format</dd>

<dt><code>0.002</code>:<code>512</code></dt>
<dd>Counts of isolates in each concentration "bin"</dd>

<dt>Distributions</dt>
<dd>see EUCAST documentation below</dd>

<dt>Observations</dt>
<dd>Number of observations</dd>

<dt><code>(T)ECOFF</code></dt>
<dd>see EUCAST documentation below</dd>

<dt><code>Confidence interval</code></dt>
<dd>see EUCAST documentation below</dd>


</dl>

</div>

ecoffs: ECOFF data

Description

Usage

Arguments

Format

`ecoffs`