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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</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;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-09-01 <span style="color: #949494;">13:35:41</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-09-01 <span style="color: #949494;">13:35:42</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2022-10-05 <span style="color: #949494;">10:29:43</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2022-10-05 <span style="color: #949494;">10:29:44</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table <chr>, method <chr>,</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S <dbl>, breakpoint_R <dbl>, input <dbl>, interpretation <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
|
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@ -506,8 +506,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</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 Function `as.mo()` is uncertain about "S. pneumoniae" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Streptococcus pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
@ -554,7 +552,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="fu">as.rsi</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">NIT</span><span class="op">)</span>, <span class="va">as.rsi</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="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.rsi</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> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
@ -617,8 +615,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
@ -626,19 +622,29 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use `as.rsi(uti = FALSE)` to prevent this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in mutate_at(., vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE):</span> Can't subset columns that don't exist.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BB0000;">✖</span> Column `NIT` doesn't exist.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</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 of 'CIP' (ciprofloxacin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</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 of 'GEN' (gentamicin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</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 of 'TOB' (tobramycin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</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 I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For CLEANING existing R/SI values ------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</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">"I"</span>, <span class="st">"R"</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.rsi()`: 3 results truncated (50%) that were invalid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretations: "A", "B" and "C"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: 3 results in column '24' truncated (50%) 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 <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I R <NA> <NA> <NA></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
|
||||
@ -700,7 +706,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown-footer-right">
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Reference in New Issue
Block a user