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Built site for AMR: 2.0.0.9035@66eeeb4

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2023-07-11 12:37:00 +00:00
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@ -14,7 +14,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<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="">2.0.0.9034</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9035</small>
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@ -533,7 +533,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</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 ampicillin (AMP) in</span>
@ -565,19 +567,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo input</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-07-11 <span style="color: #949494;">07:55:27</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-07-11 <span style="color: #949494;">07:55:27</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-07-11 <span style="color: #949494;">07:55:27</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-07-11 <span style="color: #949494;">07:55:27</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-07-11 <span style="color: #949494;">07:55:21</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-07-11 <span style="color: #949494;">07:55:21</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-07-11 <span style="color: #949494;">07:55:21</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-07-11 <span style="color: #949494;">07:55:21</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-07-11 <span style="color: #949494;">07:55:20</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-07-11 <span style="color: #949494;">07:55:20</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2023-07-11 <span style="color: #949494;">07:55:20</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2023-07-11 <span style="color: #949494;">07:55:20</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2023-07-11 <span style="color: #949494;">07:55:19</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-07-11 <span style="color: #949494;">12:34:59</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-07-11 <span style="color: #949494;">12:34:59</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-07-11 <span style="color: #949494;">12:34:59</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-07-11 <span style="color: #949494;">12:34:59</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-07-11 <span style="color: #949494;">12:34:52</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-07-11 <span style="color: #949494;">12:34:52</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-07-11 <span style="color: #949494;">12:34:52</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-07-11 <span style="color: #949494;">12:34:52</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-07-11 <span style="color: #949494;">12:34:52</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-07-11 <span style="color: #949494;">12:34:51</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2023-07-11 <span style="color: #949494;">12:34:51</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2023-07-11 <span style="color: #949494;">12:34:51</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2023-07-11 <span style="color: #949494;">12:34:51</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-in"><span></span></span>
@ -589,7 +591,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</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> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
@ -604,7 +608,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</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> Class 'sir'</span>
@ -641,7 +647,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -654,7 +662,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -679,7 +689,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming an unspecified body site. Use argument uti to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -692,7 +704,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -717,7 +731,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming an unspecified body site. Use argument uti to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -742,7 +758,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming an unspecified body site. Use argument uti to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</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 ampicillin (AMP) in</span>
@ -763,18 +781,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming an unspecified body site. Use argument uti to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </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.sir(uti = FALSE) to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>