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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="">2.1.1.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9095</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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@ -727,8 +727,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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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>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
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<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024...</span>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
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<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), EUCAST 2024...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK </span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
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<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
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@ -736,8 +736,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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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>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
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<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2024...</span>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: column 'nitrofuratoin' (NIT,</span>
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<span class="r-msg co"><span class="r-pr">#></span> nitrofurantoin), EUCAST 2024...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK </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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@ -785,16 +785,16 @@ 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: 57 × 16</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-15 <span style="color: #949494;">15:21:30</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-15 <span style="color: #949494;">15:21:37</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-15 <span style="color: #949494;">15:21:37</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-15 <span style="color: #949494;">15:21:38</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-15 <span style="color: #949494;">15:21:38</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-15 <span style="color: #949494;">15:21:30</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-15 <span style="color: #949494;">15:21:37</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-15 <span style="color: #949494;">15:21:37</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-15 <span style="color: #949494;">15:21:38</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-15 <span style="color: #949494;">15:21:38</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
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<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>
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<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>
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