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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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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="">3.0.1.9050</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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@@ -187,7 +187,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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<dt id="arg-reference-data">reference_data<a class="anchor" aria-label="anchor" href="#arg-reference-data"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
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<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must have the same column names as the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Column types are coerced automatically where possible: the <code>mo</code> column is passed through <code><a href="as.mo.html">as.mo()</a></code>, the <code>ab</code> column through <code><a href="as.ab.html">as.ab()</a></code>, and plain character, numeric, or logical columns are cast to the expected type. When <code>reference_data</code> is manually set, the <code>guideline</code> argument is optional: if omitted (or if its value does not match any row in the custom data), all rows in <code>reference_data</code> are considered. If <code>guideline</code> is set to a value that exists in the <code>guideline</code> column of the custom data, only matching rows are used — useful when a single custom table contains multiple guidelines. For the R classification, the EUCAST convention is used by default: MIC values <code>> breakpoint_R</code> and disk diffusion values <code>< breakpoint_R</code> are classified as R, with values between <code>breakpoint_S</code> and <code>breakpoint_R</code> classified as I (or SDD). Only when using the standard <a href="clinical_breakpoints.html">clinical_breakpoints</a> with a CLSI guideline are the closed-interval rules (<code>>= breakpoint_R</code> for MIC, <code><= breakpoint_R</code> for disk) applied; custom <code>reference_data</code> always uses the open-interval (EUCAST) convention regardless of the guideline name.</p></dd>
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<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
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@@ -227,7 +227,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. The <code>parallel</code> package is part of base <span style="R">R</span> and no additional packages are required. On Unix/macOS with <span style="R">R</span> >= 4.0.0, <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> (fork-based) is used; on Windows and <span style="R">R</span> < 4.0.0, <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> with a PSOCK cluster is used (requires the AMR package to be installed, not just loaded via <code>devtools::load_all()</code>). Parallelism distributes columns across cores; it is most beneficial when there are many antibiotic columns and a large number of rows.</p></dd>
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<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
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@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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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> 2026-04-25 <span style="color: #949494;">12:45:43</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> 2026-04-25 <span style="color: #949494;">12:45:43</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> 2026-04-25 <span style="color: #949494;">12:45:44</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> 2026-04-25 <span style="color: #949494;">12:45:44</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> 2026-04-25 <span style="color: #949494;">14:25:30</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> 2026-04-25 <span style="color: #949494;">14:25:30</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> 2026-04-25 <span style="color: #949494;">14:25:31</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> 2026-04-25 <span style="color: #949494;">14:25:31</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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