mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 13:07:54 +02:00
Built site for AMR@3.0.0.9008: d94bdd2
This commit is contained in:
github-actions
@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
<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="">3.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -128,7 +128,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
|
||||
|
||||
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||||
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.sir()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
|
||||
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code>as.sir(df, penicillins())</code>.</p>
|
||||
<p>Otherwise: arguments passed on to methods.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
|
||||
@ -414,10 +415,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-07-17 <span style="color: #949494;">15:13:14</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-07-17 <span style="color: #949494;">15:13:15</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-07-17 <span style="color: #949494;">15:13:15</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-07-17 <span style="color: #949494;">15:13:16</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
@ -446,9 +447,12 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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 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">amoxicillin</span><span class="op">:</span><span class="va">tobra</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="antimicrobial_selectors.html">aminopenicillins</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># approaches that all work with additional arguments:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
|
||||
@ -544,6 +548,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">'</span></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>
|
||||
|
||||
Reference in New Issue
Block a user