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cli-147-2043
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@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9050</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -567,6 +567,52 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co">## Using dplyr -------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="co"># approaches that all work without additional arguments:</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> </span></span>
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||||
<span class="r-in"><span> <span class="co"># approaches that all work with additional arguments:</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
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<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> </span></span>
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<span class="r-in"><span> <span class="co"># for veterinary breakpoints, add 'host':</span></span></span>
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<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"horse"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span></span>
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||||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span>, host <span class="op">=</span> <span class="st">"species_column"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>,</span></span>
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||||
<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="st">"column1"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> </span></span>
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<span class="r-in"><span> <span class="co"># to include information about urinary tract infections (UTI)</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
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||||
<span class="r-in"><span> nitrofuratoin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
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||||
<span class="r-in"><span> from_the_bladder <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span>uti <span class="op">=</span> <span class="st">"from_the_bladder"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
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||||
<span class="r-in"><span> nitrofuratoin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
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||||
<span class="r-in"><span> specimen <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in UseMethod("tbl_vars"):</span> no applicable method for 'tbl_vars' applied to an object of class "function"</span>
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<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
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<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span><span class="co"># a whole data set, even with combined MIC values and disk zones</span></span></span>
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<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
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@ -600,24 +646,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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||||
<span class="r-in"><span></span></span>
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||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
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||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 7 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, host <chr>, ref_table <chr>, uti <lgl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 15</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo method</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-06-15 <span style="color: #949494;">13:38:22</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-06-15 <span style="color: #949494;">13:38:18</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN MIC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2024-06-15 <span style="color: #949494;">13:38:17</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN DISK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 8 more variables: input <dbl>, outcome <sir>, host <chr>, notes <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, ref_table <chr>, uti <lgl>, breakpoint_S_R <chr></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># for single values</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||||
@ -652,172 +698,11 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"microorganism"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># to include information about urinary tract infections (UTI)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> from_the_bladder <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span>uti <span class="op">=</span> <span class="st">"from_the_bladder"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> specimen <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">as.sir</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use as.sir(uti = FALSE) to prevent this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> thus assuming uti = TRUE. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations. Note that some</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S <NA> S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '24' truncated (38%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '28' truncated (38%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B", and "C"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></span>
|
||||
|
||||
Reference in New Issue
Block a user