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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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="">3.0.1.9035</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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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@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
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<span class="r-out co"><span class="r-pr">#></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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-18 <span style="color: #949494;">09:41:20</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-18 <span style="color: #949494;">09:41:20</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-18 <span style="color: #949494;">09:41:21</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-18 <span style="color: #949494;">09:41:21</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-03-20 <span style="color: #949494;">16:07:38</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-03-20 <span style="color: #949494;">16:07:38</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-03-20 <span style="color: #949494;">16:07:39</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-03-20 <span style="color: #949494;">16:07:39</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
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@@ -435,17 +435,16 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co"># using parallel computing, which is available in base R:</span></span></span>
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<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Returning previously coerced values for various antimicrobials. Run</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> `ab_reset_session()` to reset this. This note will be shown once per</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> session.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Returning a previously coerced value for an antimicrobial. Run</span>
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<span class="r-msg co"><span class="r-pr">#></span> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note</span>
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<span class="r-msg co"><span class="r-pr">#></span> will be shown once per session.</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> <span style="color: #0000BB;">Running in parallel mode using 3 out of 4 cores, on columns '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">',</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;">cipro</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">tobra</span><span style="color: #0000BB;">', '</span><span style="color: #0000BB; font-weight: bold;">genta</span><span style="color: #0000BB;">', and '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">'...</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;"> DONE</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Running in parallel mode using 3 out of 4 cores, on columns '<span style="font-weight: bold;">amoxicillin</span>',</span>
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<span class="r-msg co"><span class="r-pr">#></span> '<span style="font-weight: bold;">cipro</span>', '<span style="font-weight: bold;">tobra</span>', '<span style="font-weight: bold;">genta</span>', and '<span style="font-weight: bold;">ERY</span>'...</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #5FD7AF;">DONE</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> </span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;"> of the breakpoint interpretations.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to</span>
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<span class="r-msg co"><span class="r-pr">#></span> retrieve a logbook with all details of the breakpoint interpretations.</span>
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<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
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<span class="r-in"><span></span></span>
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@@ -557,48 +556,47 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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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 style="color: #0000BB;">ℹ For `aminopenicillins()` using column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> For `aminopenicillins()` using column '<span style="font-weight: bold;">amoxicillin</span>'</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
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<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ...) ...`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</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> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</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;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic), </span><span style="color: #0000BB; font-weight: bold;">CLSI</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">2025</span><span style="color: #0000BB;">...</span></span>
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<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>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
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<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>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB; font-weight: bold;">CLSI 2025</span><span style="color: #0000BB;">...</span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Interpreting MIC values: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI 2025</span>...</span>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">2025</span>...</span>
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<span class="r-msg co"><span class="r-pr">#></span> Interpreting disk diffusion zones: '<span style="font-weight: bold;">antibiotic</span>' (TESTAB, test Antibiotic), <span style="font-weight: bold;">CLSI</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">2025</span>...</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
|
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<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
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<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</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> Some MICs were converted to the nearest higher log2 level, following the</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> CLSI interpretation guideline.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretation guideline.</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>
|
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<span class="r-in"><span></span></span>
|
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@@ -629,8 +627,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
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<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
|
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<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 truncated (38%) that were invalid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> interpretations: "A", "B", and "C"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.sir()` (`?AMR::as.sir()`): 3 results 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-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S SDD I R NI <NA> <NA> <NA></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>
|
||||
@@ -638,11 +636,13 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "I", and 3 as "R"</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] S I R</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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, S <span class="op">=</span> <span class="fl">3</span>, I <span class="op">=</span> <span class="fl">2</span>, R <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "I", and 3 as "S"</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 I S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user