mic_r_breakpoint

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

mic_r_breakpoint function

<dl><dt>mo</dt>
<dd>mo name (coerced using AMR::as.mo)</dd>
<dt>ab</dt>
<dd>ab name (coerced using AMR::as.ab)</dd>
<dt>accept_ecoff</dt>
<dd>if TRUE, ECOFFs will be used when no clinical breakpoints are available</dd>
<dt>...</dt>
<dd>additional arguments to pass to AMR::as.sir, which is used to
calculate the R breakpoint</dd></dl>

Arguments

R breakpoint for MIC — mic_r_breakpoint

<dl>

<dt>mo</dt>
<dd>mo name (coerced using AMR::as.mo)</dd>


<dt>ab</dt>
<dd>ab name (coerced using AMR::as.ab)</dd>


<dt>accept_ecoff</dt>
<dd>if TRUE, ECOFFs will be used when no clinical breakpoints are available</dd>


<dt>...</dt>
<dd>additional arguments to pass to AMR::as.sir, which is used to
calculate the R breakpoint</dd>

</dl>

mic_r_breakpoint: R breakpoint for MIC

Description

Usage

Value

Arguments

Examples