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@ -21,7 +21,7 @@ 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="">2.1.1.9135</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9136</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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@ -310,16 +310,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
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@ -530,198 +530,222 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<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">cipro</span><span class="op">:</span><span class="va">genta</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-msg co"><span class="r-pr">#></span> </span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
|
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<span class="r-msg co"><span class="r-pr">#></span> all the details of the breakpoint interpretations.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
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<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
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||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
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<span class="r-msg co"><span class="r-pr">#></span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
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||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
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||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism', EUCAST 2024...</span>
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||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
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<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX) 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> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (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 - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column '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> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column '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> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX) 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> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (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 - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX) 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> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (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 - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column '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> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for gentamicin (GEN) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX) 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> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (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 - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column '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> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'bacteria', CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'bacteria', CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 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: 'tobra' (TOB, tobramycin), CLSI 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: 'genta' (GEN, gentamicin), CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 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: 'tobra' (TOB, tobramycin), CLSI 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: 'genta' (GEN, gentamicin), CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> certain animal hosts, the CLSI guideline VET09 will be applied where</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> possible.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'bacteria', CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin) based on</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">column '</span><span style="color: #0000BB; font-weight: bold;">microorganism</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> certain animal hosts, the CLSI guideline VET09 will be applied where</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> possible.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'amoxicillin' (AMX), 'cipro' (CIP, ciprofloxacin),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'tobra' (TOB, tobramycin), and 'genta' (GEN, gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'bacteria', CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> certain animal hosts, the CLSI guideline VET09 will be applied where</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> possible.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • No CLSI 2024 MIC breakpoints available for test Antibiotic (TESTAB).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Please note that in the absence of specific veterinary breakpoints for</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> certain animal hosts, the CLSI guideline VET09 will be applied where</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> possible.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Please note that in the absence of specific veterinary breakpoints for</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> certain animal hosts, the CLSI guideline VET09 will be applied where</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> possible.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), and '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin) based on column</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">'</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">', </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Please note that in the absence of specific veterinary breakpoints for</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> certain animal hosts, the CLSI guideline VET09 will be applied where</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> possible.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic), </span><span style="color: #0000BB; font-weight: bold;">CLSI</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • No CLSI 2024 MIC breakpoints available for test Antibiotic (TESTAB).</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> The following animal host(s) could not be coerced: "animal_species"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming breakpoint_type = "animal", since host is set.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Please note that in the absence of specific veterinary breakpoints for</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> certain animal hosts, the CLSI guideline VET09 will be applied where</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> possible.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), CLSI 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: 'tobra' (TOB, tobramycin), CLSI 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: 'genta' (GEN, gentamicin), CLSI 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Please note that in the absence of specific veterinary breakpoints for</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> certain animal hosts, the CLSI guideline VET09 will be applied where</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> possible.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> The following animal host(s) could not be coerced: "animal_species"</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), 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 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> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), 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> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">nitrofuratoin</span><span style="color: #0000BB;">' (NIT,</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Assuming value "urine" in column '</span><span style="color: #0000BB; font-weight: bold;">specimen</span><span style="color: #0000BB;">' reflects a urinary tract</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> infection.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> Use </span><span style="color: #0000BB; background-color: #EEEEEE;">as.sir(uti = FALSE)</span><span style="color: #0000BB;"> to prevent this.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: 'cipro' (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: 'tobra' (TOB, tobramycin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 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: 'genta' (GEN, gentamicin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">nitrofuratoin</span><span style="color: #0000BB;">' (NIT,</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli 8 <NA> S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -730,25 +754,26 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'amoxicillin' (AMX), 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> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 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 - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">' (AMX), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for amoxicillin (AMX) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Intravenous'. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: column '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">' (TOB, tobramycin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for tobramycin (TOB) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">' (GEN, gentamicin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Breakpoints for UTI </span><span style="color: #080808; font-weight: bold;">and</span><span style="color: #080808;"> non-UTI available for gentamicin (GEN) in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming an unspecified body site. Use argument </span><span style="color: #080808; background-color: #EEEEEE;">uti</span><span style="color: #080808;"> to set which isolates are from urine. See </span><span style="color: #080808; background-color: #EEEEEE;">?as.sir</span><span style="color: #080808;">.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Assigning class 'sir' to already clean column '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">' (erythromycin)...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta 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>
|
||||
@ -757,16 +782,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-28 <span style="color: #949494;">14:23:05</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-28 <span style="color: #949494;">14:23:12</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-28 <span style="color: #949494;">14:23:12</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-28 <span style="color: #949494;">14:23:13</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-28 <span style="color: #949494;">14:23:13</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-28 <span style="color: #949494;">14:23:05</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-28 <span style="color: #949494;">14:23:12</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-28 <span style="color: #949494;">14:23:12</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-28 <span style="color: #949494;">14:23:13</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-28 <span style="color: #949494;">14:23:13</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-31 <span style="color: #949494;">15:06:42</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-31 <span style="color: #949494;">15:06:48</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-31 <span style="color: #949494;">15:06:49</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-31 <span style="color: #949494;">15:06:49</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-31 <span style="color: #949494;">15:06:50</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-31 <span style="color: #949494;">15:06:42</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-31 <span style="color: #949494;">15:06:48</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-31 <span style="color: #949494;">15:06:49</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-31 <span style="color: #949494;">15:06:49</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-31 <span style="color: #949494;">15:06:50</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
@ -780,11 +805,12 @@ 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">#></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.</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> NOTE </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus pneumoniae - assuming body site 'Non-meningitis'.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ampicillin (AMP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Streptococcus pneumoniae</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></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] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -795,10 +821,11 @@ 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">#></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.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: 'ampicillin' (AMP), 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> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">' (AMP), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></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] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -806,7 +833,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<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 '20' truncated (38%) that were invalid</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in column '20' 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-in"><span><span class="fu">as.sir</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>
|
||||
<span class="r-in"><span><span class="va">sir_data</span> <span class="op"><-</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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
@ -843,16 +870,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,990 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
|
||||
Reference in New Issue
Block a user