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Built site for AMR: 1.8.2.9041@d20caae

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2022-10-31 12:32:32 +00:00
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9041</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -476,16 +476,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / gentamicin (GEN) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / tobramycin (TOB) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Assigning class 'rsi' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
@ -496,16 +496,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-31 <span style="color: #949494;">10:24:50</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-31 <span style="color: #949494;">10:24:51</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-31 <span style="color: #949494;">10:24:51</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-31 <span style="color: #949494;">10:24:51</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-31 <span style="color: #949494;">10:24:52</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-31 <span style="color: #949494;">10:24:53</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-31 <span style="color: #949494;">10:24:53</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-31 <span style="color: #949494;">10:24:53</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-31 <span style="color: #949494;">10:24:54</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-31 <span style="color: #949494;">10:24:54</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-31 <span style="color: #949494;">12:29:44</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-31 <span style="color: #949494;">12:29:45</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-31 <span style="color: #949494;">12:29:45</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-31 <span style="color: #949494;">12:29:45</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-31 <span style="color: #949494;">12:29:45</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-31 <span style="color: #949494;">12:29:46</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-31 <span style="color: #949494;">12:29:46</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-31 <span style="color: #949494;">12:29:46</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-31 <span style="color: #949494;">12:29:47</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-31 <span style="color: #949494;">12:29:47</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>
@ -520,9 +520,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints available for S. pneumoniae / ampicillin -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> assuming body site 'Non-meningitis'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints available for S. pneumoniae / ampicillin - assuming body site</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'Non-meningitis'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
@ -582,16 +582,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / gentamicin (GEN) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / tobramycin (TOB) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -606,16 +606,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / gentamicin (GEN) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / tobramycin (TOB) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -624,16 +624,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / gentamicin (GEN) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / tobramycin (TOB) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -642,23 +642,23 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / gentamicin (GEN) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: breakpoints for UTI and non-UTI available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Enterobacterales / tobramycin (TOB) - assuming non-UTI. Use argument `uti`</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to set which isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming `uti = TRUE`. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use `as.rsi(uti = FALSE)` to prevent this.</span>
@ -668,7 +668,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming `uti = TRUE`. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>