mirror of
https://github.com/msberends/AMR.git
synced 2025-07-13 01:12:08 +02:00
Built site for AMR@2.1.1.9133: 9520977
This commit is contained in:
github-actions
@ -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="">2.1.1.9125</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9133</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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@ -81,67 +81,38 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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<span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># Default S3 method</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
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<span> I <span class="op">=</span> <span class="st">"^(I)+$"</span>,</span>
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<span> R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
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<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>,</span>
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<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>, I <span class="op">=</span> <span class="st">"^(I)+$"</span>, R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
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<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>, SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for class 'mic'</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>, add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
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<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
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<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
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<span> host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for class 'disk'</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
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<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
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<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
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<span> host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="co"># S3 method for class 'data.frame'</span></span>
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<span><span class="fu">as.sir</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> <span class="va">...</span>,</span>
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<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
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<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>, uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
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||||
<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>, add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
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<span> include_screening <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
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||||
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>,</span>
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||||
<span> host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span></span>
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||||
<span><span class="op">)</span></span>
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<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, host <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
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</div>
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@ -786,16 +757,16 @@ 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> 2025-01-17 <span style="color: #949494;">11:16:11</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> 2025-01-17 <span style="color: #949494;">11:16:18</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> 2025-01-17 <span style="color: #949494;">11:16:18</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> 2025-01-17 <span style="color: #949494;">11:16:19</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> 2025-01-17 <span style="color: #949494;">11:16:19</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> 2025-01-17 <span style="color: #949494;">11:16:11</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> 2025-01-17 <span style="color: #949494;">11:16:18</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> 2025-01-17 <span style="color: #949494;">11:16:18</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> 2025-01-17 <span style="color: #949494;">11:16:19</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> 2025-01-17 <span style="color: #949494;">11:16:19</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> 2025-01-27 <span style="color: #949494;">21:13:26</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> 2025-01-27 <span style="color: #949494;">21:13:33</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> 2025-01-27 <span style="color: #949494;">21:13:34</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> 2025-01-27 <span style="color: #949494;">21:13:34</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> 2025-01-27 <span style="color: #949494;">21:13:34</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> 2025-01-27 <span style="color: #949494;">21:13:26</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> 2025-01-27 <span style="color: #949494;">21:13:33</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-27 <span style="color: #949494;">21:13:33</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-27 <span style="color: #949494;">21:13:34</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> 2025-01-27 <span style="color: #949494;">21:13:34</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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||||
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||||
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