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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9200</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9201</small>
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@ -585,12 +585,6 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 2 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `amoxicillin = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> invalid microorganism code, NA generated</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
@ -603,13 +597,185 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in mutate(.tbl, !!!funs):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `tobra = (function (x, ...) ...`.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in function (x, ...) </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> {</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> UseMethod("as.sir")</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> }(): argument <span style="background-color: #EEEEEE;">capped_mic_handling</span> must be a text string, i.e. not be <span style="background-color: #EEEEEE;">TRUE</span> or</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">FALSE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #0000BB;"> infection.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli 8 &lt;NA&gt; S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
@ -620,35 +786,43 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>invalid microorganism code, NA generated</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>invalid microorganism code, NA generated</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in as.sir(): argument <span style="background-color: #EEEEEE;">capped_mic_handling</span> must be a text string, i.e. not be <span style="background-color: #EEEEEE;">TRUE</span> or</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">FALSE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 11 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-14 <span style="color: #949494;">16:07:42</span> 1 AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-14 <span style="color: #949494;">16:07:42</span> 1 AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-14 <span style="color: #949494;">16:07:42</span> 2 AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-03-14 <span style="color: #949494;">16:07:42</span> 3 AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-14 <span style="color: #949494;">16:07:42</span> 4 AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-14 <span style="color: #949494;">16:07:47</span> 1 amoxicillin <span style="color: #BB0000;"> NA</span> human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-14 <span style="color: #949494;">16:07:47</span> 1 cipro <span style="color: #BB0000;"> NA</span> human CIP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-14 <span style="color: #949494;">16:07:48</span> 1 amoxicillin <span style="color: #BB0000;"> NA</span> human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-14 <span style="color: #949494;">16:07:48</span> 1 cipro <span style="color: #BB0000;"> NA</span> human CIP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-14 <span style="color: #949494;">16:07:48</span> 1 amoxicillin <span style="color: #BB0000;"> NA</span> human AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2025-03-14 <span style="color: #949494;">16:07:49</span> 1 cipro <span style="color: #BB0000;"> NA</span> human CIP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 10 more variables: mo &lt;mo&gt;, host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-14 <span style="color: #949494;">16:16:25</span> 1 ampicillin Strep p… human AMP <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-14 <span style="color: #949494;">16:16:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-14 <span style="color: #949494;">16:16:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-14 <span style="color: #949494;">16:16:26</span> 1 GEN Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-14 <span style="color: #949494;">16:16:26</span> 1 TOB Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-14 <span style="color: #949494;">16:16:26</span> 1 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">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-14 <span style="color: #949494;">16:16:27</span> 1 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">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-14 <span style="color: #949494;">16:16:27</span> 2 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">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-14 <span style="color: #949494;">16:16:27</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">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># for single values</span></span></span>
@ -674,8 +848,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> in as.sir(): argument <span style="background-color: #EEEEEE;">capped_mic_handling</span> must be a text string, i.e. not be <span style="background-color: #EEEEEE;">TRUE</span> or</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">FALSE</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>