mirror of
https://github.com/msberends/AMR.git
synced 2025-07-12 17:01:57 +02:00
Built site for AMR@2.1.1.9152: 671d657
This commit is contained in:
github-actions
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
|
||||
<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="">2.1.1.9151</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9152</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">
|
||||
@ -332,25 +332,25 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic()"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) { lims[1] <- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() keeping all operators"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) { lims[1] <- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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">16</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'within' range"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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">0.032</span>, <span class="fl">256</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'outside' range"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using scale_y_mic() -----------------------------------------</span></span></span>
|
||||
@ -364,7 +364,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) { lims[1] <- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mic <span class="op">=</span> <span class="va">some_mic_values</span>,</span></span>
|
||||
<span class="r-in"><span> group <span class="op">=</span> <span class="va">some_groups</span><span class="op">)</span>,</span></span>
|
||||
@ -373,7 +373,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="cn">NA</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using scale_fill_mic() -----------------------------------------</span></span></span>
|
||||
@ -387,7 +387,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_fill_mic</span><span class="op">(</span>mic_range <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">0.5</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using scale_x_sir() -----------------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@ -397,7 +397,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_x_sir</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using scale_y_mic() and scale_colour_sir() ------------------</span></span></span>
|
||||
@ -421,36 +421,36 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<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;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
|
||||
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># and now with our MIC and SIR scale functions:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in if (!is.na(mic_range[1]) && mic_range[1] < lims[1]) { lims[1] <- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span>language <span class="op">=</span> <span class="st">"nl"</span>, eucast_I <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"In Dutch!"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using ggplot2's autoplot() ----------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Plotting using scale_y_percent() -------------------------------------</span></span></span>
|
||||
@ -471,9 +471,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
||||
<span class="r-in"><span> limits <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">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="plot-22.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-23.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-24.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user