<spanclass="r-err co"><spanclass="r-pr">#></span><spanclass="error">Error in as_sir_method(method_short = "disk", method_long = "disk diffusion zones", x = x, mo = mo, ab = ab, guideline = guideline, uti = uti, conserve_capped_values = FALSE, add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, include_screening = include_screening, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, host = NULL, ...):</span> object 'mo_var_found' not found</span>
<spanclass="r-in"><span></span></span>
<spanclass="r-in"><span><spanclass="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
<spanclass="r-in"><span><spanclass="fu"><ahref="as.sir.html">as.sir</a></span><spanclass="op">(</span><spanclass="va">df</span>, uti <spanclass="op">=</span><spanclass="cn">TRUE</span><spanclass="op">)</span></span></span>
@ -255,20 +252,7 @@
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-in"><span> x <spanclass="op">=</span><spanclass="fu">as.mic</span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="fl">0.01</span>, <spanclass="fl">2</span>, <spanclass="fl">4</span>, <spanclass="fl">8</span><spanclass="op">)</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> mo <spanclass="op">=</span><spanclass="fu"><ahref="as.mo.html">as.mo</a></span><spanclass="op">(</span><spanclass="st">"Streptococcus pneumoniae"</span><spanclass="op">)</span>,</span></span>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor.
These breakpoints are currently available:
For clinical microbiology from EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology from EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.3.1/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><linkhref="../deps/Lato-0.4.9/font.css"rel="stylesheet"><linkhref="../deps/Fira_Code-0.4.9/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js"integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js"integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw=="crossorigin="anonymous"referrerpolicy="no-referrer"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><metaproperty="og:description"content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor.
These breakpoints are currently available:
For clinical microbiology from EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology from EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@msberends"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
@ -175,9 +175,9 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<divclass="ref-description section level2">
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <ahref="https://rdrr.io/r/base/factor.html"class="external-link">factor</a>.</p>
<p>These breakpoints are currently available:</p><ul><li><p>For <strong>clinical microbiology</strong> from EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
<li><p>For <strong>veterinary microbiology</strong> from EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
</ul><p>All breakpoints used for interpretation are available in our <ahref="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
@ -292,7 +292,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt>uti</dt>
<dd><p>(Urinary Tract Infection) A vector with <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.sir()</code> on a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a>, this can also be a column containing <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dd><p>(Urinary Tract Infection) a vector (or column name) with <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.sir()</code> on a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a>, this can also be a column containing <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dt>conserve_capped_values</dt>
@ -347,19 +347,23 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>N</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <ahref="https://rdrr.io/r/base/regex.html"class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"<0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><ahref="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><ahref="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
<span><spanclass="va">your_data</span><spanclass="op"><ahref="https://magrittr.tidyverse.org/reference/pipe.html"class="external-link">%>%</a></span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html"class="external-link">mutate_if</a></span><spanclass="op">(</span><spanclass="va">is.mic</span>, <spanclass="va">as.sir</span>, ab <spanclass="op">=</span><spanclass="st">"column_with_antibiotics"</span>, mo <spanclass="op">=</span><spanclass="st">"column_with_microorganisms"</span><spanclass="op">)</span></span>
<span><spanclass="va">your_data</span><spanclass="op"><ahref="https://magrittr.tidyverse.org/reference/pipe.html"class="external-link">%>%</a></span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html"class="external-link">mutate_if</a></span><spanclass="op">(</span><spanclass="va">is.mic</span>, <spanclass="va">as.sir</span>, ab <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"cipro"</span>, <spanclass="st">"ampicillin"</span>, <spanclass="va">...</span><spanclass="op">)</span>, mo <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"E. coli"</span>, <spanclass="st">"K. pneumoniae"</span>, <spanclass="va">...</span><spanclass="op">)</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="co"># for veterinary breakpoints, also set `host`:</span></span>
<li><p>Operators like "<=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><ahref="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><ahref="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
<span><spanclass="va">your_data</span><spanclass="op"><ahref="https://magrittr.tidyverse.org/reference/pipe.html"class="external-link">%>%</a></span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html"class="external-link">mutate_if</a></span><spanclass="op">(</span><spanclass="va">is.disk</span>, <spanclass="va">as.sir</span>, ab <spanclass="op">=</span><spanclass="st">"column_with_antibiotics"</span>, mo <spanclass="op">=</span><spanclass="st">"column_with_microorganisms"</span><spanclass="op">)</span></span>
<span><spanclass="va">your_data</span><spanclass="op"><ahref="https://magrittr.tidyverse.org/reference/pipe.html"class="external-link">%>%</a></span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html"class="external-link">mutate_if</a></span><spanclass="op">(</span><spanclass="va">is.disk</span>, <spanclass="va">as.sir</span>, ab <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"cipro"</span>, <spanclass="st">"ampicillin"</span>, <spanclass="va">...</span><spanclass="op">)</span>, mo <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"E. coli"</span>, <spanclass="st">"K. pneumoniae"</span>, <spanclass="va">...</span><spanclass="op">)</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="co"># for veterinary breakpoints, also set `host`:</span></span>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.sir(your_data)</code>.</p></li>
</ol><p><strong>For points 2, 3 and 4: Use <code>sir_interpretation_history()</code></strong> to retrieve a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> (or <ahref="https://tibble.tidyverse.org/reference/tibble.html"class="external-link">tibble</a> if the <code>tibble</code> package is installed) with all results of the last <code>as.sir()</code> call.</p>
@ -576,50 +580,17 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-in"><span> x <spanclass="op">=</span><spanclass="fu"><ahref="as.disk.html">as.disk</a></span><spanclass="op">(</span><spanclass="fl">18</span><spanclass="op">)</span>,</span></span>
@ -651,10 +617,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanclass="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> The first warning was:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> In argument: `across(where(is.mic), as.sir)`.</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanclass="warning">Warning: </span>There were 4 warnings in `mutate()`.</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span>The first warning was:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> In argument: `across(AMP:TOB, as.sir)`.</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span> Caused by warning:</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<spanclass="r-wrn co"><spanclass="r-pr">#></span><spanstyle="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span>ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
<spanclass="r-msg co"><spanclass="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
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