mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 20:06:11 +01:00
Compare commits
No commits in common. "74bb1abb0c900f4cc43906a6176aa641fdbe1323" and "c99168b4a661eb1491a81d291ddd5821255f699f" have entirely different histories.
74bb1abb0c
...
c99168b4a6
2
404.html
2
404.html
@ -30,7 +30,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
2456
AMRforRGPT.svg
2456
AMRforRGPT.svg
File diff suppressed because one or more lines are too long
|
Before Width: | Height: | Size: 327 KiB |
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
BIN
android-chrome-192x192.png
Normal file
BIN
android-chrome-192x192.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 32 KiB |
BIN
android-chrome-512x512.png
Normal file
BIN
android-chrome-512x512.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 128 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 16 KiB After Width: | Height: | Size: 17 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 22 KiB After Width: | Height: | Size: 23 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 28 KiB After Width: | Height: | Size: 29 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 6.6 KiB After Width: | Height: | Size: 6.5 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 9.1 KiB After Width: | Height: | Size: 9.1 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 28 KiB After Width: | Height: | Size: 9.8 KiB |
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -87,7 +87,7 @@
|
||||
website update since they are based on randomly created values and the
|
||||
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||||
Markdown</a>. However, the methodology remains unchanged. This page was
|
||||
generated on 02 October 2024.</p>
|
||||
generated on 30 September 2024.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2024-10-02</td>
|
||||
<td align="center">2024-09-30</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2024-10-02</td>
|
||||
<td align="center">2024-09-30</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2024-10-02</td>
|
||||
<td align="center">2024-09-30</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -270,12 +270,12 @@ taxonomic codes. Let’s check this:</p>
|
||||
<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
|
||||
<span><span class="co">#> </span></span>
|
||||
<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
||||
<span><span class="co">#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
|
||||
<span><span class="co">#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
|
||||
<span><span class="co">#> (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
|
||||
<span><span class="co">#> (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
|
||||
<span><span class="co">#> (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
|
||||
<span><span class="co">#> Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span></span>
|
||||
<span><span class="co">#> "E. coli" -> Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span></span>
|
||||
<span><span class="co">#> Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span></span>
|
||||
<span><span class="co">#> Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span></span>
|
||||
<span><span class="co">#> Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span></span>
|
||||
<span><span class="co">#> cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span></span>
|
||||
<span><span class="co">#> expressing (0.531), and Enterobacter cowanii (0.522)</span></span>
|
||||
<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
|
||||
<span><span class="co">#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
|
||||
<span><span class="co">#> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
|
||||
@ -333,15 +333,15 @@ dplyr:</p>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ESCHR_COLI R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ENTRC_CRTL R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ENTRC_CRTL R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ENTRC_CRTL S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 B_ENTRC_CRTL R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ENTRC_CRTL R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
|
||||
<p>This is basically it for the cleaning, time to start the data
|
||||
@ -396,9 +396,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
|
||||
<span><span class="co">#> ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
|
||||
<span><span class="co">#> ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
|
||||
<span><span class="co">#> of 2</span></span>
|
||||
<span><span class="co">#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a</span></span>
|
||||
<span><span class="co">#> => Found 2,764 'phenotype-based' first isolates (92.1% of total where a</span></span>
|
||||
<span><span class="co">#> microbial ID was available)</span></span></code></pre></div>
|
||||
<p>So only 91% is suitable for resistance analysis! We can now filter on
|
||||
<p>So only 92% is suitable for resistance analysis! We can now filter on
|
||||
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
|
||||
<code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
@ -408,24 +408,24 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>So we end up with 2 724 isolates for analysis. Now our data looks
|
||||
<p>So we end up with 2 764 isolates for analysis. Now our data looks
|
||||
like:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,764 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 B_ENTRC_CRTL R I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 B_ESCHR_COLI R S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P10 A 2015-12-10 B_ENTRC_CRTL S I S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B7 A 2015-03-02 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> M3 A 2015-10-25 B_ENTRC_CRTL R S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J3 A 2019-06-19 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> P4 A 2011-06-21 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> Z1 A 2014-09-05 B_ENTRC_CRTL S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span></code></pre></div>
|
||||
<p>Time for the analysis.</p>
|
||||
</div>
|
||||
</div>
|
||||
@ -438,44 +438,44 @@ impression, as it comes with support for the new <code>mo</code> and
|
||||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date </span></span>
|
||||
<span><span class="co">#> Length:2724 Length:2724 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-07 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-03 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-09 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-11 </span></span>
|
||||
<span><span class="co">#> Max. :2019-12-27 </span></span>
|
||||
<span><span class="co">#> Length:2764 Length:2764 Min. :2011-01-01 </span></span>
|
||||
<span><span class="co">#> Class :character Class :character 1st Qu.:2013-04-18 </span></span>
|
||||
<span><span class="co">#> Mode :character Mode :character Median :2015-06-07 </span></span>
|
||||
<span><span class="co">#> Mean :2015-06-16 </span></span>
|
||||
<span><span class="co">#> 3rd Qu.:2017-08-23 </span></span>
|
||||
<span><span class="co">#> Max. :2020-01-01 </span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> Class :mo Class:sir Class:sir </span></span>
|
||||
<span><span class="co">#> <NA> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) </span></span>
|
||||
<span><span class="co">#> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) </span></span>
|
||||
<span><span class="co">#> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> <NA> :0 %S :42.1% (n=1163) %S :53.0% (n=1464) </span></span>
|
||||
<span><span class="co">#> Unique:5 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> #1 :B_ESCHR_COLI %I :16.2% (n=447) %I :12.2% (n=337) </span></span>
|
||||
<span><span class="co">#> #2 :B_STPHY_AURS %R :41.8% (n=1154) %R :34.8% (n=963) </span></span>
|
||||
<span><span class="co">#> #3 :B_ENTRC_CRTL %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> CIP GEN first </span></span>
|
||||
<span><span class="co">#> Class:sir Class:sir Mode:logical </span></span>
|
||||
<span><span class="co">#> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 </span></span>
|
||||
<span><span class="co">#> %S :52.9% (n=1462) %S :61.5% (n=1699) TRUE:2764 </span></span>
|
||||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||||
<span><span class="co">#> %I : 6.5% (n=176) %I : 3.0% (n=82) </span></span>
|
||||
<span><span class="co">#> %R :41.0% (n=1117) %R :36.0% (n=981) </span></span>
|
||||
<span><span class="co">#> %I : 6.3% (n=174) %I : 3.0% (n=82) </span></span>
|
||||
<span><span class="co">#> %R :40.8% (n=1128) %R :35.6% (n=983) </span></span>
|
||||
<span><span class="co">#> %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> Rows: 2,724</span></span>
|
||||
<span><span class="co">#> Rows: 2,764</span></span>
|
||||
<span><span class="co">#> Columns: 9</span></span>
|
||||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "J3", "R7", "P3", "P10", "B7", "W3", "M3", "J3", "G6", "P4"…</span></span>
|
||||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…</span></span>
|
||||
<span><span class="co">#> $ hospital <span style="color: #949494; font-style: italic;"><chr></span> "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…</span></span>
|
||||
<span><span class="co">#> $ date <span style="color: #949494; font-style: italic;"><date></span> 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02…</span></span>
|
||||
<span><span class="co">#> $ bacteria <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_KLBSL_PNMN", "B_ESCHR_COLI", "B_ESCHR_COL…</span></span>
|
||||
<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> R, R, R, S, S, R, R, S, S, S, S, R, S, S, R, R, R, R, S, R,…</span></span>
|
||||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, S, I, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, S,…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ date <span style="color: #949494; font-style: italic;"><date></span> 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31…</span></span>
|
||||
<span><span class="co">#> $ bacteria <span style="color: #949494; font-style: italic;"><mo></span> "B_ENTRC_CRTL", "B_KLBSL_PNMN", "B_ENTRC_CRTL", "B_ENTRC_CRT…</span></span>
|
||||
<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, R, R, S, S, S, S, R, S, S, S, R, R, R, R, S, R,…</span></span>
|
||||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, I, S, S, S, S, S, S, S, S, S, I, S, S, S, S, R, S, S,…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S, S,…</span></span>
|
||||
<span><span class="co">#> $ first <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># number of unique values per column:</span></span>
|
||||
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||||
<span><span class="co">#> 260 3 1854 4 3 3 3 </span></span>
|
||||
<span><span class="co">#> 260 3 1877 5 3 3 3 </span></span>
|
||||
<span><span class="co">#> GEN first </span></span>
|
||||
<span><span class="co">#> 3 1</span></span></code></pre></div>
|
||||
<div class="section level3">
|
||||
@ -487,23 +487,25 @@ microorganisms:</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>024</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Enterococcus crotali 494</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 426</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae 326</span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 5 × 2</span></span></span>
|
||||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli 919</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 682</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 319</span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Enterococcus crotali 442</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Streptococcus pneumoniae 402</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">5</span> Klebsiella pneumoniae 319</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
|
||||
@ -515,113 +517,113 @@ in:</p>
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,764 × 2</span></span></span>
|
||||
<span><span class="co">#> date GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2012-11-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2018-04-03 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2014-09-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2015-12-10 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2015-03-02 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2018-03-31 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2015-10-25 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2015-12-10 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2015-03-02 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2018-03-31 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2015-10-25 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2019-06-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,764 × 3</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_CRTL R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S I </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ENTRC_CRTL S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</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.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,764 × 5</span></span></span>
|
||||
<span><span class="co">#> bacteria AMX AMC CIP GEN </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_CRTL R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> B_KLBSL_PNMN R I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ESCHR_COLI S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_STPHY_AURS R S R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CRTL S I S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B_STPHY_AURS R S R S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_CRTL R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ENTRC_CRTL S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,754 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 983 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B3 A 2016-07-24 B_ENTRC_CRTL S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 B_ENTRC_CRTL S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 B_ENTRC_CRTL S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 973 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 464 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ENTRC_CRTL R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ENTRC_CRTL R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 454 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># even works in base R (since R 3.0):</span></span>
|
||||
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
|
||||
<span><span class="co">#> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
|
||||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 464 × 9</span></span></span>
|
||||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||||
<span><span class="co">#> <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;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 B_ENTRC_CRTL R R R R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ENTRC_CRTL R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ENTRC_CRTL R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 454 more rows</span></span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
|
||||
@ -1220,7 +1222,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
|
||||
own:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> [1] 0.4203377</span></span></code></pre></div>
|
||||
<span><span class="co">#> [1] 0.4175109</span></span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
|
||||
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||||
@ -1230,9 +1232,9 @@ own:</p>
|
||||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
|
||||
<span><span class="co">#> hospital amoxicillin</span></span>
|
||||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.340</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.342</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.551</span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.362</span></span></code></pre></div>
|
||||
<hr>
|
||||
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
|
||||
</div>
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -91,14 +91,13 @@ antimicrobial resistance (AMR) data analysis, providing extensive
|
||||
functionality for working with microbial and antimicrobial properties.
|
||||
But what if you’re working in Python and still want to benefit from the
|
||||
robust features of <code>AMR</code>?</p>
|
||||
<p>The best way is to access R directly from Python with the help of
|
||||
<code>rpy2</code>, a simple yet powerful Python package. You can easily
|
||||
call functions from the <code>AMR</code> package to process your own
|
||||
data in your own Python environment. This post will guide you through
|
||||
<p>Luckily, there is no need to port the package to Python! With the
|
||||
help of <code>rpy2</code>, a powerful Python package, you can easily
|
||||
access R from Python and call functions from the <code>AMR</code>
|
||||
package to process your own data. This post will guide you through
|
||||
setting up <code>rpy2</code> and show you how to use R functions from
|
||||
<code>AMR</code> in Python to supercharge your antimicrobial resistance
|
||||
analysis.</p>
|
||||
<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="../AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
|
||||
@ -128,44 +127,19 @@ environment.</li>
|
||||
<div class="section level3">
|
||||
<h3 id="step-1-install-r">Step 1: Install R<a class="anchor" aria-label="anchor" href="#step-1-install-r"></a>
|
||||
</h3>
|
||||
<p>Ensure that R is installed on your system. R has minimal dependencies
|
||||
and is very simple to install:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>Linux</strong>
|
||||
<ul>
|
||||
<li>Ubuntu / Debian:<br><code>sudo apt install r-base</code>
|
||||
</li>
|
||||
<li>Fedora:<br><code>sudo dnf install R</code>
|
||||
</li>
|
||||
<li>CentOS/RHEL:<br><code>sudo yum install R</code>
|
||||
</li>
|
||||
<li>Arch Linux:<br><code>sudo pacman -S r</code>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<strong>macOS</strong> (with Homebrew):<br><code>brew install r</code>
|
||||
</li>
|
||||
<li>
|
||||
<strong>Other Systems:</strong><br>
|
||||
Visit the <a href="https://cran.r-project.org" class="external-link">CRAN download
|
||||
page</a>.</li>
|
||||
</ul>
|
||||
<p>Ensure that you have R installed on your system. You can download R
|
||||
from <a href="https://cran.r-project.org/" class="external-link">CRAN</a>.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="step-2-install-the-amr-package-in-r">Step 2: Install the <code>AMR</code> package in R<a class="anchor" aria-label="anchor" href="#step-2-install-the-amr-package-in-r"></a>
|
||||
</h3>
|
||||
<p>On Linux and macOS, open Terminal and run:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">Rscript</span> <span class="at">-e</span> <span class="st">'install.packages("AMR")'</span></span></code></pre></div>
|
||||
<p>For other systems, open your R console and install the
|
||||
<code>AMR</code> package by running:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<p>Once you have R installed, open your R console and install the
|
||||
<code>AMR</code> package:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
|
||||
<p>On any system, you can also install the latest development version of
|
||||
the <code>AMR</code> package by setting <code>repos</code> to our beta
|
||||
channel:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<p>You can also install the latest development version of the
|
||||
<code>AMR</code> package if needed:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@ -173,53 +147,58 @@ channel:</p>
|
||||
</h3>
|
||||
<p>To install <code>rpy2</code>, simply run the following command in
|
||||
your terminal:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">pip</span> install rpy2</span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="step-4-test-rpy2-installation">Step 4: Test <code>rpy2</code> Installation<a class="anchor" aria-label="anchor" href="#step-4-test-rpy2-installation"></a>
|
||||
</h3>
|
||||
<p>To ensure everything is set up correctly, you can test your
|
||||
installation by running the following Python script, which essentially
|
||||
runs R in the background:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
|
||||
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
|
||||
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
|
||||
installation by running the following Python script:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a></span>
|
||||
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co"># Test a simple R function from Python</span></span>
|
||||
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>ro.r(<span class="st">'1 + 1'</span>)</span></code></pre></div>
|
||||
<p>If this returns <code>2</code>, you’re good to go!</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="working-with-amr-in-python">Working with <code>AMR</code> in Python<a class="anchor" aria-label="anchor" href="#working-with-amr-in-python"></a>
|
||||
<h2 id="working-with-amr-in-python-using-rpy2">Working with AMR in Python using <code>rpy2</code><a class="anchor" aria-label="anchor" href="#working-with-amr-in-python-using-rpy2"></a>
|
||||
</h2>
|
||||
<p>Now that we have <code>rpy2</code> set up, let’s walk through some
|
||||
practical examples of using the <code>AMR</code> package within
|
||||
Python.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="example-1-converting-taxonomic-data">Example 1: Converting Taxonomic Data<a class="anchor" aria-label="anchor" href="#example-1-converting-taxonomic-data"></a>
|
||||
<h3 id="example-1-loading-amr-and-example-data">Example 1: Loading <code>AMR</code> and Example Data<a class="anchor" aria-label="anchor" href="#example-1-loading-amr-and-example-data"></a>
|
||||
</h3>
|
||||
<p>Let’s start by converting taxonomic user input to valid taxonomy
|
||||
using the <code>AMR</code> package, from within Python:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
|
||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
|
||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a></span>
|
||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
|
||||
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
|
||||
<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a></span>
|
||||
<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
|
||||
<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
|
||||
<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a> <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
|
||||
<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a>})</span>
|
||||
<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a></span>
|
||||
<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
|
||||
<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> data</span>
|
||||
<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name <- mo_name(r_data$microorganism)'</span>)</span>
|
||||
<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a></span>
|
||||
<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
|
||||
<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'r_data'</span>)</span>
|
||||
<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
|
||||
<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
|
||||
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="im">import</span> rpy2.robjects <span class="im">as</span> ro</span>
|
||||
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="im">from</span> rpy2.robjects.packages <span class="im">import</span> importr</span>
|
||||
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="im">from</span> rpy2.robjects <span class="im">import</span> pandas2ri</span>
|
||||
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a></span>
|
||||
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="co"># Enable conversion between pandas and R data frames</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7" tabindex="-1"></a>pandas2ri.activate()</span>
|
||||
<span id="cb5-8"><a href="#cb5-8" tabindex="-1"></a></span>
|
||||
<span id="cb5-9"><a href="#cb5-9" tabindex="-1"></a><span class="co"># Load the AMR package from R</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10" tabindex="-1"></a>amr <span class="op">=</span> importr(<span class="st">'AMR'</span>)</span>
|
||||
<span id="cb5-11"><a href="#cb5-11" tabindex="-1"></a></span>
|
||||
<span id="cb5-12"><a href="#cb5-12" tabindex="-1"></a><span class="co"># Example user dataset in Python</span></span>
|
||||
<span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a>data <span class="op">=</span> pd.DataFrame({</span>
|
||||
<span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a> <span class="st">'microorganism'</span>: [<span class="st">'E. coli'</span>, <span class="st">'S. aureus'</span>, <span class="st">'P. aeruginosa'</span>, <span class="st">'K. pneumoniae'</span>]</span>
|
||||
<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a>})</span>
|
||||
<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a></span>
|
||||
<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co"># Convert the Python DataFrame to an R DataFrame</span></span>
|
||||
<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a>r_data <span class="op">=</span> pandas2ri.py2rpy(data)</span>
|
||||
<span id="cb5-19"><a href="#cb5-19" tabindex="-1"></a></span>
|
||||
<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co"># Apply mo_name() from the AMR package to the 'microorganism' column</span></span>
|
||||
<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a>ro.globalenv[<span class="st">'r_data'</span>] <span class="op">=</span> r_data</span>
|
||||
<span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a>ro.r(<span class="st">'r_data$mo_name <- mo_name(r_data$microorganism)'</span>)</span>
|
||||
<span id="cb5-23"><a href="#cb5-23" tabindex="-1"></a></span>
|
||||
<span id="cb5-24"><a href="#cb5-24" tabindex="-1"></a><span class="co"># Retrieve and print the modified R DataFrame in Python</span></span>
|
||||
<span id="cb5-25"><a href="#cb5-25" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(r_data)'</span>)</span>
|
||||
<span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a>result <span class="op">=</span> pandas2ri.rpy2py(result)</span>
|
||||
<span id="cb5-27"><a href="#cb5-27" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>In this example, a Python dataset with microorganism names like
|
||||
<em>E. coli</em> and <em>S. aureus</em> is passed to the R function
|
||||
<code><a href="../reference/mo_property.html">mo_name()</a></code>. The result is an updated <code>DataFrame</code>
|
||||
@ -233,12 +212,12 @@ that includes the standardised microorganism names based on the
|
||||
generating an antibiogram, a table that summarises the antimicrobial
|
||||
susceptibility of bacterial isolates. Here’s how you can generate an
|
||||
antibiogram from Python:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
|
||||
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
|
||||
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
|
||||
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># Run an antibiogram in R from Python</span></span>
|
||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))'</span>)</span>
|
||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a></span>
|
||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co"># Retrieve the result in Python</span></span>
|
||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>In this example, we generate an antibiogram by selecting
|
||||
aminoglycosides and carbapenems, two classes of antibiotics, and then
|
||||
convert the resulting R data frame into a Python-readable format.</p>
|
||||
@ -248,12 +227,12 @@ convert the resulting R data frame into a Python-readable format.</p>
|
||||
</h3>
|
||||
<p>Let’s say you want to filter the dataset for Gram-negative bacteria
|
||||
and display their resistance to certain antibiotics:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
|
||||
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
|
||||
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
|
||||
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
|
||||
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co"># Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>ro.r(<span class="st">'result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]'</span>)</span>
|
||||
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
|
||||
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co"># Retrieve the filtered result in Python</span></span>
|
||||
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>This example uses the AMR functions
|
||||
<code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and
|
||||
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to filter the dataset and
|
||||
@ -264,12 +243,12 @@ returns a subset of bacteria with resistance data.</p>
|
||||
</h3>
|
||||
<p>You can easily customise the antibiogram by passing different
|
||||
antibiotics or microorganism transformations, as shown below:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
|
||||
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
|
||||
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a></span>
|
||||
<span id="cb9-4"><a href="#cb9-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
|
||||
<span id="cb9-5"><a href="#cb9-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb9-6"><a href="#cb9-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co"># Customise the antibiogram with different settings</span></span>
|
||||
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a>ro.r(<span class="st">'result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")'</span>)</span>
|
||||
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a></span>
|
||||
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co"># Retrieve and print the result</span></span>
|
||||
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a>result <span class="op">=</span> ro.r(<span class="st">'as.data.frame(result)'</span>)</span>
|
||||
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="bu">print</span>(result)</span></code></pre></div>
|
||||
<p>Here, we use piperacillin/tazobactam (TZP) in combination with
|
||||
tobramycin (TOB) and gentamicin (GEN) to see how they perform against
|
||||
various Gram-negative bacteria.</p>
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -76,7 +76,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">02 October 2024</h4>
|
||||
<h4 data-toc-skip class="date">30 September 2024</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
@ -108,7 +108,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
|
||||
<em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 2 October 2024 08:20:05 UTC. Find more info
|
||||
<p>It was last updated on 30 September 2024 16:46:55 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@ -286,7 +286,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center">11158430</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.15</td>
|
||||
<td align="center">407310004, 407251000, 407281008, …</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@ -314,7 +314,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.15</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@ -342,7 +342,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">5427575</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.15</td>
|
||||
<td align="center">419388003</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@ -370,7 +370,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.50</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@ -398,7 +398,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">11286021</td>
|
||||
<td align="center"></td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.15</td>
|
||||
<td align="center">1095001000112106, 715307006, 737528008, …</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
@ -426,7 +426,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
|
||||
<td align="center">12233256</td>
|
||||
<td align="center">11286021</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">1</td>
|
||||
<td align="center">1.15</td>
|
||||
<td align="center"></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -29,7 +29,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
10
browserconfig.xml
Normal file
10
browserconfig.xml
Normal file
@ -0,0 +1,10 @@
|
||||
<?xml version="1.0" encoding="utf-8"?>
|
||||
<browserconfig>
|
||||
<msapplication>
|
||||
<tile>
|
||||
<square150x150logo src="/mstile-150x150.png?v=newlogo"/>
|
||||
<square310x310logo src="/mstile-310x310.png?v=newlogo"/>
|
||||
<TileColor>#128f76</TileColor>
|
||||
</tile>
|
||||
</msapplication>
|
||||
</browserconfig>
|
||||
25
extra.css
25
extra.css
@ -66,31 +66,8 @@
|
||||
--bs-dropdown-link-hover-color: var(--amr-green-light) !important;
|
||||
--bs-dropdown-link-hover-bg: var(--amr-green-dark) !important;
|
||||
--bs-dropdown-link-active-color: white !important;
|
||||
|
||||
}
|
||||
|
||||
/* Python page */
|
||||
body.amr-for-python * {
|
||||
--amr-green-light: #FFD43B; /* Python yellow */
|
||||
--amr-green-light-rgb: 255, 212, 59;
|
||||
--amr-green-dark: #306998; /* Python blue */
|
||||
--amr-green-dark-rgb: 48, 105, 152;
|
||||
--amr-green-middle: #b1bc5e; /* Adjusted middle yellow */
|
||||
--amr-green-middle-rgb: 177, 188, 94;
|
||||
--bs-success: var(--amr-green-dark) !important;
|
||||
--bs-light: var(--amr-green-light) !important;
|
||||
--bs-info: var(--amr-green-middle) !important;
|
||||
--bs-link-color: var(--amr-green-dark) !important;
|
||||
--bs-link-color-rgb: var(--amr-green-dark-rgb) !important;
|
||||
--bs-primary: var(--amr-green-dark) !important;
|
||||
--bs-primary-color: var(--amr-green-dark) !important;
|
||||
--bs-primary-rgb: var(--amr-green-dark-rgb) !important;
|
||||
--bs-secondary-color: var(--amr-green-dark) !important;
|
||||
--bs-navbar-active-color: var(--amr-green-light) !important;
|
||||
--bs-dropdown-bg: var(--amr-green-dark) !important;
|
||||
--bs-dropdown-link-hover-color: var(--amr-green-light) !important;
|
||||
--bs-dropdown-link-hover-bg: var(--amr-green-dark) !important;
|
||||
}
|
||||
|
||||
.nav-text.text-muted,
|
||||
.bg-primary .navbar-nav .show>.nav-link,
|
||||
.bg-primary .navbar-nav .nav-link.active,
|
||||
|
||||
2
extra.js
2
extra.js
@ -52,7 +52,7 @@ $(document).ready(function() {
|
||||
// make Python part more fancy - prepare for CSS
|
||||
if (window.location.href.includes('AMR_for_Python')) {
|
||||
$('body').addClass('amr-for-python');
|
||||
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg');
|
||||
$('img[src="logo.svg"]').attr('src', 'logo_python.svg');
|
||||
}
|
||||
|
||||
// add doctoral titles to authors
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 1.4 KiB After Width: | Height: | Size: 1.4 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 2.9 KiB After Width: | Height: | Size: 2.8 KiB |
BIN
favicon.ico
BIN
favicon.ico
Binary file not shown.
|
Before Width: | Height: | Size: 15 KiB After Width: | Height: | Size: 15 KiB |
@ -32,7 +32,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -91,7 +91,6 @@
|
||||
<li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
|
||||
</li>
|
||||
</ul>
|
||||
<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
|
||||
<div style="display: flex; font-size: 0.8em;">
|
||||
<p style="text-align:left; width: 50%;">
|
||||
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
|
||||
|
||||
591
logo_python.svg
591
logo_python.svg
File diff suppressed because one or more lines are too long
|
Before Width: | Height: | Size: 178 KiB |
BIN
mstile-150x150.png
Normal file
BIN
mstile-150x150.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 19 KiB |
BIN
mstile-310x310.png
Normal file
BIN
mstile-310x310.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 52 KiB |
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -47,18 +47,18 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9087" id="amr-2119087">AMR 2.1.1.9087<a class="anchor" aria-label="anchor" href="#amr-2119087"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.1.1.9084" id="amr-2119084">AMR 2.1.1.9084<a class="anchor" aria-label="anchor" href="#amr-2119084"></a></h2>
|
||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
||||
<div class="section level5">
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087"></a></h5>
|
||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9084">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9084"></a></h5>
|
||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="breaking-2-1-1-9087">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9087"></a></h3>
|
||||
<h3 id="breaking-2-1-1-9084">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9084"></a></h3>
|
||||
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="new-2-1-1-9087">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9087"></a></h3>
|
||||
<h3 id="new-2-1-1-9084">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9084"></a></h3>
|
||||
<ul><li>
|
||||
<strong>One Health implementation</strong>
|
||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||
@ -95,7 +95,7 @@
|
||||
</ul></li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="changed-2-1-1-9087">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9087"></a></h3>
|
||||
<h3 id="changed-2-1-1-9084">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9084"></a></h3>
|
||||
<ul><li>SIR interpretation
|
||||
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
||||
@ -146,13 +146,13 @@
|
||||
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="other-2-1-1-9087">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9087"></a></h3>
|
||||
<h3 id="other-2-1-1-9084">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9084"></a></h3>
|
||||
<ul><li>Greatly updated and expanded documentation</li>
|
||||
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
||||
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="older-versions-2-1-1-9087">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9087"></a></h3>
|
||||
<h3 id="older-versions-2-1-1-9084">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9084"></a></h3>
|
||||
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
|
||||
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
||||
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
||||
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
WHONET: WHONET.html
|
||||
last_built: 2024-10-02T08:36Z
|
||||
last_built: 2024-09-30T21:17Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -110,16 +110,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 58 58.82514 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.58743 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.91803 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.63115 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.61749 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.72678 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.09836 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.68306 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.29235 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.14481 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 58 58.81967 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.58197 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.91257 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.62568 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.61202 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.72131 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.09290 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.67760 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.28689 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.13934 13</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 34 KiB After Width: | Height: | Size: 34 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 51 KiB After Width: | Height: | Size: 47 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 49 KiB After Width: | Height: | Size: 45 KiB |
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -244,7 +244,7 @@
|
||||
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
|
||||
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.598\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
@ -316,7 +316,7 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterococcus"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"ESCO"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"ESCCOL"</span>, ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span></span></span>
|
||||
|
||||
@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -751,7 +751,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2024...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK </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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli 8 S <NA> <NA> R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
|
||||
@ -785,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-02 <span style="color: #949494;">08:37:04</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-02 <span style="color: #949494;">08:37:04</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-02 <span style="color: #949494;">08:37:11</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> 2024-10-02 <span style="color: #949494;">08:37:11</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> 2024-10-02 <span style="color: #949494;">08:37:12</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-09-30 <span style="color: #949494;">21:18:40</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-09-30 <span style="color: #949494;">21:18:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-09-30 <span style="color: #949494;">21:18:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-09-30 <span style="color: #949494;">21:18:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-09-30 <span style="color: #949494;">21:18:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-09-30 <span style="color: #949494;">21:18:40</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-09-30 <span style="color: #949494;">21:18:47</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> 2024-09-30 <span style="color: #949494;">21:18:47</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> 2024-09-30 <span style="color: #949494;">21:18:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-09-30 <span style="color: #949494;">21:18:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
||||
<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>
|
||||
<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>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -97,7 +97,7 @@
|
||||
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Actinomucor</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Arthroderma</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Bipolaris</em>, <em>Blastobotrys</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chilomastix</em>, <em>Chrysonilia</em>, <em>Chrysosporium</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Clavispora</em>, <em>Coccidioides</em>, <em>Cokeromyces</em>, <em>Conidiobolus</em>, <em>Coniochaeta</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Cryptosporidium</em>, <em>Cunninghamella</em>, <em>Curvularia</em>, <em>Cyberlindnera</em>, <em>Debaryozyma</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Epidermophyton</em>, <em>Exidia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Geotrichum</em>, <em>Giardia</em>, <em>Graphium</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hansenula</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hortaea</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Kloeckera</em>, <em>Kluyveromyces</em>, <em>Kodamaea</em>, <em>Lacazia</em>, <em>Leishmania</em>, <em>Lichtheimia</em>, <em>Lodderomyces</em>, <em>Lomentospora</em>, <em>Madurella</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Millerozyma</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Nannizzia</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Paecilomyces</em>, <em>Paracoccidioides</em>, <em>Pediculus</em>, <em>Penicillium</em>, <em>Phaeoacremonium</em>, <em>Phaeomoniella</em>, <em>Phialophora</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoscopulariopsis</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Purpureocillium</em>, <em>Quambalaria</em>, <em>Rhinocladiella</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Saksenaea</em>, <em>Saprochaete</em>, <em>Sarcoptes</em>, <em>Scedosporium</em>, <em>Schistosoma</em>, <em>Schizosaccharomyces</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Sporopachydermia</em>, <em>Sporothrix</em>, <em>Sporotrichum</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syncephalastrum</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Talaromyces</em>, <em>Teleomorph</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, <em>Ulocladium</em>, <em>Ustilago</em>, <em>Verticillium</em>, <em>Wallemia</em>, <em>Wangiella</em>, <em>Wickerhamomyces</em>, <em>Wuchereria</em>, <em>Yarrowia</em>, or <em>Zygosaccharomyces</em>;</p></li>
|
||||
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
|
||||
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.598\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.381\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
@ -113,18 +113,18 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_ENTRC_CRTL</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Matching scores are based on the resemblance between the input and the full</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Enterococcus crotali (B_ENTRC_CRTL, 0.650)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Escherichia coli (0.598), Enterococcus columbae (0.595),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Enterococcus camelliae (0.591), Enterococcus casseliflavus (0.577),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Escherichia coli coli (0.559), Enterococcus canis (0.556), Enterococcus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> cecorum (0.550), Enterococcus canintestini (0.540), Escherichia coli</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> expressing (0.531), and Enterobacter cowanii (0.522)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Only the first 10 other matches of each record are shown. Run</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
|
||||
@ -134,7 +134,7 @@
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> n <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">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.6875000 0.3809524</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5978261 0.3809524</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 71 KiB |
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
@ -263,7 +263,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data</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">data</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="resistance_predict-4.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in resistance_predict(): the data provided in argument x must contain rows and columns (current</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> dimensions: 0x46)</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
|
||||
<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="">2.1.1.9087</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
|
||||
|
||||
512
safari-pinned-tab.svg
Normal file
512
safari-pinned-tab.svg
Normal file
@ -0,0 +1,512 @@
|
||||
<?xml version="1.0" standalone="no"?>
|
||||
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN"
|
||||
"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
|
||||
<svg version="1.0" xmlns="http://www.w3.org/2000/svg"
|
||||
width="714.000000pt" height="714.000000pt" viewBox="0 0 714.000000 714.000000"
|
||||
preserveAspectRatio="xMidYMid meet">
|
||||
<metadata>
|
||||
Created by potrace 1.14, written by Peter Selinger 2001-2017
|
||||
</metadata>
|
||||
<g transform="translate(0.000000,714.000000) scale(0.100000,-0.100000)"
|
||||
fill="#000000" stroke="none">
|
||||
<path d="M2048 6354 l-1528 -764 0 -2020 0 -2020 1530 -765 1530 -765 1530
|
||||
765 1530 765 0 2020 0 2020 -1530 765 c-841 421 -1531 765 -1532 764 -2 0
|
||||
-690 -344 -1530 -765z m2275 290 c402 -201 734 -368 737 -371 3 -2 -11 -17
|
||||
-30 -33 l-35 -29 48 -48 c26 -27 47 -54 47 -61 0 -9 -54 -12 -220 -12 l-220 0
|
||||
0 -25 c0 -16 6 -25 15 -25 13 0 15 -31 15 -223 l0 -223 -82 -33 c-333 -135
|
||||
-514 -281 -534 -433 -11 -81 -60 -130 -198 -200 -65 -32 -226 -98 -242 -98 -2
|
||||
0 -4 53 -4 118 0 96 4 125 21 162 27 60 37 70 148 144 94 62 203 159 252 223
|
||||
24 31 25 32 74 21 179 -38 330 171 271 373 -19 66 -65 133 -109 159 -23 14
|
||||
-37 34 -50 71 -13 35 -37 71 -76 110 -52 54 -58 65 -68 123 -13 74 -32 118
|
||||
-73 168 -57 68 -165 97 -244 64 -34 -14 -34 -14 -65 24 -63 78 -181 106 -268
|
||||
62 -51 -26 -110 -94 -124 -143 l-12 -37 -41 19 c-199 90 -402 -144 -328 -378
|
||||
l19 -61 -48 -32 c-109 -70 -169 -220 -148 -368 29 -206 210 -345 373 -287 l39
|
||||
14 102 -102 c139 -139 148 -159 153 -350 2 -82 0 -152 -4 -157 -32 -30 -947
|
||||
-200 -1075 -200 l-22 0 21 23 c12 13 26 46 32 75 18 97 52 124 126 98 71 -24
|
||||
89 -21 113 18 12 18 21 43 21 54 0 12 -27 51 -59 88 l-59 68 24 29 c32 38 33
|
||||
99 2 121 -19 13 -25 14 -43 2 -11 -7 -22 -26 -25 -42 -5 -27 -8 -29 -50 -29
|
||||
-42 0 -45 2 -50 29 -13 74 -90 61 -90 -15 l0 -39 -360 0 c-367 0 -403 -3 -415
|
||||
-39 -2 -9 -19 -22 -36 -30 -50 -22 -59 -58 -59 -239 0 -176 6 -199 53 -190 25
|
||||
5 27 3 27 -28 0 -32 -1 -33 -52 -38 -29 -3 -116 -8 -193 -12 -127 -6 -138 -5
|
||||
-126 10 8 9 28 16 48 16 63 0 102 33 103 88 0 24 -6 35 -23 43 -13 6 -27 18
|
||||
-32 28 -31 56 -59 91 -72 91 -8 0 -38 -24 -66 -53 -115 -117 -131 -127 -195
|
||||
-127 -49 0 -62 4 -82 25 -23 25 -44 30 -74 19 -23 -9 -20 -57 4 -79 11 -10 20
|
||||
-31 20 -47 l0 -28 -70 0 -70 0 0 538 0 537 1473 737 c809 405 1480 737 1490
|
||||
737 9 1 347 -164 750 -365z m806 -403 c12 -8 11 -13 -10 -30 -28 -23 -35 -25
|
||||
-44 -10 -4 5 1 19 11 30 19 22 23 22 43 10z m206 -103 c80 -40 145 -78 145
|
||||
-85 0 -7 11 -13 25 -13 14 0 75 -25 135 -55 97 -48 110 -58 110 -81 0 -24 3
|
||||
-25 48 -23 26 1 57 -3 70 -10 22 -12 22 -15 22 -206 l0 -195 -245 0 -244 0 -3
|
||||
108 -3 107 -87 3 -88 3 0 -111 0 -110 -245 0 -245 0 0 285 0 285 205 0 205 0
|
||||
0 62 c0 50 4 66 22 85 12 13 23 23 25 23 1 0 68 -33 148 -72z m945 -473 l270
|
||||
-135 0 -1201 0 -1202 -20 26 c-24 31 -70 43 -102 27 -13 -7 -46 -35 -74 -62
|
||||
l-52 -50 -69 51 c-38 28 -81 54 -94 59 -18 7 -64 -2 -189 -38 -91 -26 -178
|
||||
-50 -194 -54 -17 -4 -63 -40 -106 -82 l-76 -74 -98 0 c-90 0 -99 -2 -121 -25
|
||||
-35 -34 -35 -96 0 -130 23 -24 29 -25 155 -25 77 0 140 5 153 11 12 6 47 36
|
||||
78 66 l56 55 45 -132 45 -131 -121 -82 c-75 -51 -126 -93 -134 -110 -11 -23
|
||||
-9 -54 13 -210 29 -206 37 -232 76 -252 49 -26 94 -13 123 35 16 28 15 37 -4
|
||||
172 -11 79 -23 150 -26 159 -3 11 17 30 67 63 50 33 70 42 64 30 -4 -11 -12
|
||||
-30 -18 -45 -13 -32 37 -403 59 -437 39 -60 138 -46 164 24 5 12 -2 92 -16
|
||||
195 l-24 173 56 126 c32 71 58 145 61 170 3 31 -7 86 -31 175 -19 71 -33 131
|
||||
-31 134 2 2 27 -15 56 -38 41 -33 60 -41 92 -41 38 0 47 6 139 98 l98 98 0
|
||||
-723 0 -723 -148 -74 -147 -74 -172 -11 c-94 -6 -272 -11 -395 -11 -184 0
|
||||
-244 4 -334 21 -329 61 -575 89 -793 89 -136 0 -374 -22 -496 -46 -353 -69
|
||||
-624 -204 -801 -398 -107 -118 -161 -246 -184 -441 -16 -133 -30 -206 -46
|
||||
-237 l-14 -28 -1205 603 -1205 602 0 1407 0 1408 73 0 73 0 -4 -35 c-3 -21 2
|
||||
-45 11 -59 13 -20 24 -23 74 -23 69 -1 83 8 83 53 0 19 5 34 10 34 6 0 10 -13
|
||||
10 -29 0 -47 55 -83 76 -50 4 8 9 8 17 0 16 -16 43 -14 61 5 10 10 16 33 16
|
||||
65 0 49 0 49 33 49 17 0 61 3 97 6 62 6 66 5 66 -14 0 -16 -3 -18 -13 -10 -17
|
||||
14 -43 3 -43 -20 0 -10 -21 -38 -46 -62 -45 -45 -78 -93 -68 -102 2 -3 -2 -11
|
||||
-11 -18 -8 -7 -15 -17 -15 -22 0 -5 -16 -25 -35 -45 -20 -20 -34 -41 -32 -47
|
||||
7 -21 25 -15 60 19 20 19 40 35 45 35 4 0 13 5 20 12 6 6 22 13 34 15 13 2 48
|
||||
28 78 58 31 30 63 55 73 55 22 0 33 26 18 44 -9 11 -8 14 6 12 28 -2 27 34 -2
|
||||
64 l-26 27 47 7 c94 12 94 12 94 -44 0 -62 34 -106 73 -95 35 11 47 35 47 97
|
||||
0 32 4 58 10 58 6 0 10 -28 10 -64 0 -56 3 -67 22 -80 31 -22 45 -20 73 9 21
|
||||
20 25 34 25 85 0 55 2 60 23 61 12 0 77 6 145 13 l122 12 0 -83 c0 -77 2 -84
|
||||
24 -99 22 -13 29 -14 53 -2 27 13 28 15 31 106 3 115 22 123 22 9 0 -54 5 -90
|
||||
14 -102 15 -21 70 -25 89 -6 7 7 14 53 17 109 l5 97 95 13 c527 71 952 159
|
||||
1259 262 291 97 450 209 451 317 1 126 177 271 484 398 46 19 87 35 90 35 3 0
|
||||
6 -29 6 -65 l0 -65 630 0 630 0 0 190 0 190 35 0 c25 0 112 -39 305 -135z
|
||||
m-930 -110 l0 -85 -40 0 -40 0 0 85 0 85 40 0 40 0 0 -85z m-1540 18 c25 -12
|
||||
54 -24 64 -28 18 -5 16 -9 -15 -41 -31 -33 -190 -137 -197 -129 -4 3 61 174
|
||||
78 205 6 12 14 20 18 18 4 -2 27 -13 52 -25z m-434 -89 c6 -22 14 -54 17 -72
|
||||
l7 -33 -59 52 -59 52 20 34 c19 31 22 33 42 20 11 -8 26 -32 32 -53z m-1036
|
||||
-388 c0 -38 25 -56 80 -56 55 0 80 18 80 56 0 15 6 24 15 24 28 0 18 -59 -16
|
||||
-91 l-31 -29 66 -77 c36 -42 66 -84 66 -93 0 -9 -9 -26 -20 -38 -19 -20 -23
|
||||
-21 -48 -8 -79 40 -140 24 -173 -47 -10 -23 -19 -54 -19 -68 0 -31 -32 -75
|
||||
-60 -84 -18 -6 -20 -16 -20 -119 0 -89 -3 -116 -15 -126 -12 -10 -18 -10 -30
|
||||
0 -12 10 -15 37 -15 127 l0 114 -37 -3 -38 -3 -3 -117 c-2 -84 -6 -117 -16
|
||||
-121 -29 -11 -35 10 -38 123 l-3 115 -147 3 c-142 2 -148 2 -148 -17 0 -30
|
||||
-30 -41 -114 -41 l-76 0 0 -89 c0 -73 -3 -90 -16 -95 -41 -16 -44 3 -44 305 0
|
||||
247 -2 289 -15 289 -28 0 -35 -39 -35 -195 0 -121 -3 -156 -12 -153 -10 4 -14
|
||||
48 -16 165 -2 149 -1 161 18 186 12 15 30 27 41 27 10 0 19 6 19 14 0 8 10 22
|
||||
22 30 19 14 75 16 411 16 l388 0 -15 22 c-21 29 -21 78 -1 78 9 0 15 -9 15
|
||||
-24z m-1190 -401 c0 -8 9 -19 20 -25 11 -6 22 -21 26 -34 3 -13 14 -26 25 -29
|
||||
24 -6 25 -39 2 -59 -10 -9 -39 -18 -65 -20 -44 -5 -49 -3 -88 37 l-41 41 51
|
||||
47 c27 25 50 51 50 57 0 6 5 8 10 5 6 -3 10 -13 10 -20z m-360 -130 c20 -22
|
||||
32 -25 87 -25 36 0 76 6 92 14 27 14 29 14 70 -28 l42 -43 -3 -74 c-2 -58 -6
|
||||
-74 -18 -74 -10 0 -16 13 -18 43 -2 28 -8 42 -17 42 -9 0 -15 -14 -17 -42 -2
|
||||
-30 -8 -43 -18 -43 -10 0 -16 13 -18 43 l-3 42 -74 0 -74 0 -3 -42 c-2 -30 -8
|
||||
-43 -18 -43 -12 0 -16 19 -18 95 -3 85 -5 97 -28 121 -23 24 -23 39 1 39 6 0
|
||||
22 -11 35 -25z m1250 -24 c0 -5 -35 -12 -77 -15 -43 -4 -102 -9 -132 -13 -52
|
||||
-5 -53 -5 -42 16 11 20 20 21 131 21 66 0 120 -4 120 -9z m-320 -130 c0 -61
|
||||
-16 -89 -45 -77 -11 4 -15 22 -15 71 l0 65 30 0 c30 0 30 0 30 -59z m-352 -40
|
||||
c-33 -10 -39 -23 -21 -44 15 -17 16 -20 2 -15 -11 4 -35 -13 -75 -53 -32 -32
|
||||
-64 -59 -72 -59 -7 0 -24 -7 -38 -16 -31 -21 -41 -12 -20 18 9 12 16 29 16 38
|
||||
0 9 27 42 59 74 40 40 57 64 53 75 -4 13 -1 12 17 -4 19 -16 24 -17 31 -5 6 8
|
||||
10 21 10 29 0 10 8 7 26 -10 17 -16 21 -25 12 -28z m-478 -16 c0 -16 -6 -25
|
||||
-15 -25 -9 0 -15 9 -15 25 0 16 6 25 15 25 9 0 15 -9 15 -25z m5334 -1267 l79
|
||||
-57 69 64 c38 36 76 65 86 65 33 0 62 -29 62 -63 0 -27 -14 -46 -88 -120 -110
|
||||
-110 -117 -111 -231 -26 -45 34 -83 60 -85 58 -2 -2 16 -78 40 -169 24 -91 44
|
||||
-179 44 -197 0 -18 -27 -94 -60 -169 l-60 -136 23 -171 c15 -104 21 -181 16
|
||||
-194 -17 -45 -87 -55 -108 -15 -5 10 -22 104 -36 208 l-27 189 36 79 c20 44
|
||||
30 76 23 73 -18 -7 -216 -137 -221 -145 -2 -4 7 -79 20 -167 23 -156 24 -161
|
||||
6 -185 -25 -34 -62 -37 -89 -8 -17 19 -26 58 -47 211 -25 170 -26 191 -12 212
|
||||
8 12 69 57 135 100 67 43 121 80 121 84 1 13 -103 306 -112 316 -5 5 -39 -21
|
||||
-86 -68 l-77 -77 -122 0 c-67 0 -129 3 -138 6 -37 15 -38 82 -1 106 6 4 54 8
|
||||
106 8 l95 0 75 74 75 74 190 55 c105 30 197 52 205 49 8 -3 51 -32 94 -64z
|
||||
m-1499 -1578 c205 -12 346 -30 565 -72 152 -29 182 -32 375 -32 116 0 275 3
|
||||
355 7 l145 7 -1144 -573 -1144 -573 -51 25 c-28 13 -67 33 -87 42 -19 10 -54
|
||||
21 -76 25 l-41 6 -4 67 c-2 37 1 69 7 73 5 4 12 3 13 -3 6 -17 60 -39 97 -39
|
||||
97 0 165 92 165 224 0 45 -1 48 -22 42 -13 -4 -57 -10 -98 -15 -41 -4 -89 -15
|
||||
-106 -24 -37 -19 -68 -78 -62 -118 3 -16 1 -29 -2 -29 -4 0 -13 34 -19 76 -13
|
||||
75 -8 162 11 197 11 21 38 23 38 3 0 -21 40 -46 72 -46 28 0 98 53 98 74 -1
|
||||
14 -88 56 -117 56 -12 0 -28 -7 -37 -15 -15 -15 -41 -21 -34 -7 32 66 44 82
|
||||
63 82 35 0 64 28 70 68 3 20 8 48 11 61 5 23 4 24 -47 19 -69 -7 -104 -43 -96
|
||||
-97 4 -22 1 -46 -8 -61 l-14 -25 -1 26 c0 42 -23 61 -86 74 -32 7 -63 9 -67 5
|
||||
-15 -13 11 -94 38 -117 29 -25 64 -30 83 -11 17 17 16 -1 -4 -70 -9 -30 -17
|
||||
-85 -18 -122 0 -42 -5 -66 -11 -63 -6 2 -9 18 -7 36 4 38 -30 95 -68 113 -14
|
||||
7 -61 17 -105 22 -44 6 -88 14 -97 17 -16 6 -18 0 -18 -48 0 -30 7 -74 15 -98
|
||||
40 -112 158 -160 229 -94 55 51 95 -27 96 -186 0 -64 -1 -67 -27 -75 -16 -4
|
||||
-55 -8 -88 -9 -63 -1 -136 -30 -153 -61 -7 -13 -26 -7 -133 47 l-125 62 18 54
|
||||
c10 30 23 91 29 136 38 309 73 395 218 542 234 237 630 375 1141 398 36 2 72
|
||||
4 80 5 8 1 92 -3 185 -8z m-996 -1210 c20 -10 52 -25 71 -33 l35 -14 -130 -65
|
||||
-130 -66 -119 60 c-119 60 -119 60 -99 80 28 27 89 40 136 27 32 -8 42 -7 57
|
||||
6 42 38 112 40 179 5z"/>
|
||||
<path d="M2570 6435 c0 -25 74 -165 87 -165 23 0 24 19 3 60 -11 22 -18 45
|
||||
-15 50 13 21 33 8 50 -30 12 -26 25 -40 37 -40 22 0 23 12 2 53 -33 66 -66 83
|
||||
-97 53 -12 -13 -16 -12 -25 10 -13 26 -42 33 -42 9z"/>
|
||||
<path d="M2509 6398 c0 -2 -2 -20 -4 -40 -3 -28 0 -38 10 -38 8 0 24 -18 35
|
||||
-40 21 -41 45 -51 68 -28 20 20 15 41 -8 35 -15 -4 -24 2 -35 23 -14 26 -13
|
||||
30 1 38 22 12 8 35 -17 27 -13 -4 -19 -2 -19 9 0 12 -28 25 -31 14z"/>
|
||||
<path d="M2441 6381 c-9 -6 -2 -29 31 -95 23 -47 46 -86 51 -86 21 0 15 35
|
||||
-17 103 -38 81 -45 90 -65 78z"/>
|
||||
<path d="M2371 6279 c-26 -28 -27 -39 -1 -39 11 0 20 5 20 10 0 6 7 10 15 10
|
||||
21 0 19 -13 -5 -28 -24 -14 -26 -54 -5 -72 13 -11 23 -9 55 6 46 22 48 34 17
|
||||
89 -28 49 -64 58 -96 24z m69 -74 c0 -8 -7 -15 -16 -15 -14 0 -14 3 -4 15 7 8
|
||||
14 15 16 15 2 0 4 -7 4 -15z"/>
|
||||
<path d="M2282 6239 c-64 -24 -37 -131 33 -131 28 0 65 27 65 49 0 18 -20 16
|
||||
-41 -3 -11 -10 -25 -14 -36 -9 -15 5 -12 10 20 26 38 20 47 39 25 56 -22 17
|
||||
-42 21 -66 12z m28 -39 c-20 -13 -33 -13 -25 0 3 6 14 10 23 10 15 0 15 -2 2
|
||||
-10z"/>
|
||||
<path d="M2163 6218 c2 -13 8 -31 12 -40 5 -12 -1 -21 -24 -32 -39 -21 -37
|
||||
-21 -50 14 -10 29 -34 40 -46 20 -7 -12 72 -170 85 -170 20 0 23 32 7 59 -16
|
||||
27 -16 28 18 44 l35 17 15 -31 c10 -18 23 -29 32 -27 21 4 20 9 -19 95 -24 52
|
||||
-38 72 -52 73 -14 0 -17 -5 -13 -22z"/>
|
||||
<path d="M1952 6074 c-15 -10 -22 -26 -22 -47 -1 -27 -2 -29 -11 -14 -12 21
|
||||
-62 23 -79 2 -7 -8 -19 -15 -26 -15 -20 0 -18 -14 11 -70 23 -46 42 -60 58
|
||||
-44 3 4 -3 24 -13 45 -24 46 -25 55 -5 63 11 4 22 -8 37 -39 21 -43 40 -56 53
|
||||
-35 3 5 -2 24 -11 42 l-16 33 21 -22 c28 -30 71 -30 99 0 27 29 28 37 2 37
|
||||
-11 0 -20 -4 -20 -9 0 -14 -32 -23 -43 -12 -7 7 3 16 27 27 42 20 43 27 16 54
|
||||
-24 24 -48 25 -78 4z m38 -34 c-20 -13 -33 -13 -25 0 3 6 14 10 23 10 15 0 15
|
||||
-2 2 -10z"/>
|
||||
<path d="M1656 5979 c-36 -28 -37 -95 -2 -136 32 -37 93 -39 130 -4 36 34 37
|
||||
101 1 136 -31 32 -91 34 -129 4z m92 -26 c32 -28 36 -59 13 -82 -12 -12 -29
|
||||
-21 -39 -21 -46 0 -73 80 -36 107 24 17 38 16 62 -4z"/>
|
||||
<path d="M1043 5650 c-6 -24 -26 -26 -43 -5 -18 22 -32 18 -28 -7 3 -20 -1
|
||||
-23 -29 -22 -28 2 -32 -1 -30 -20 2 -17 -3 -21 -25 -19 -28 2 -40 -21 -16 -29
|
||||
19 -7 1 -38 -22 -38 -11 0 -20 -4 -20 -10 0 -5 7 -10 15 -10 22 0 18 -37 -5
|
||||
-43 -25 -7 -26 -27 -1 -27 24 0 36 -29 16 -36 -25 -10 -17 -27 9 -20 35 9 55
|
||||
-2 49 -25 -7 -27 5 -24 36 9 22 23 26 24 29 10 2 -10 10 -18 18 -18 16 0 19
|
||||
26 4 35 -16 10 11 43 32 37 22 -5 25 16 3 24 -19 8 -19 23 0 31 9 3 25 -3 35
|
||||
-12 20 -18 22 -17 24 20 1 16 7 19 29 17 26 -3 37 11 17 23 -17 10 -11 32 10
|
||||
38 26 7 26 27 1 27 -26 0 -36 17 -20 36 16 19 6 28 -18 16 -24 -13 -43 -5 -43
|
||||
19 0 25 -20 25 -27 -1z"/>
|
||||
<path d="M5280 6095 c0 -33 -2 -35 -35 -35 -32 0 -35 -2 -35 -30 0 -28 3 -30
|
||||
35 -30 33 0 35 -2 35 -35 0 -32 2 -35 30 -35 28 0 30 3 30 34 0 32 3 35 33 38
|
||||
27 2 32 7 32 28 0 21 -5 26 -32 28 -30 3 -33 6 -33 38 0 31 -2 34 -30 34 -28
|
||||
0 -30 -3 -30 -35z"/>
|
||||
<path d="M4790 5920 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M4934 5946 c-3 -8 -4 -25 -2 -38 2 -19 10 -24 41 -26 l37 -3 0 40 c0
|
||||
40 -1 41 -35 41 -22 0 -38 -6 -41 -14z"/>
|
||||
<path d="M5080 5920 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M5460 5920 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M5600 5920 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M4790 5810 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M4934 5836 c-3 -8 -4 -25 -2 -38 2 -19 10 -24 41 -26 l37 -3 0 40 c0
|
||||
40 -1 41 -35 41 -22 0 -38 -6 -41 -14z"/>
|
||||
<path d="M5080 5810 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M5460 5810 l0 -40 40 0 40 0 0 40 0 40 -40 0 -40 0 0 -40z"/>
|
||||
<path d="M5607 5843 c-4 -3 -7 -21 -7 -40 0 -32 1 -33 40 -33 l40 0 0 40 c0
|
||||
39 -1 40 -33 40 -19 0 -37 -3 -40 -7z"/>
|
||||
<path d="M5750 5811 l0 -41 41 0 40 0 -3 38 c-3 35 -5 37 -40 40 l-38 3 0 -40z"/>
|
||||
<path d="M4794 5726 c-3 -8 -4 -27 -2 -43 3 -25 7 -28 38 -28 34 0 35 1 35 40
|
||||
0 38 -2 40 -33 43 -21 2 -34 -2 -38 -12z"/>
|
||||
<path d="M4937 5733 c-9 -8 -9 -46 -1 -67 4 -10 18 -16 40 -16 34 0 34 1 34
|
||||
45 0 44 0 45 -33 45 -19 0 -37 -3 -40 -7z"/>
|
||||
<path d="M5082 5698 c3 -42 4 -43 38 -43 34 0 35 1 35 40 0 39 -1 40 -38 43
|
||||
l-38 3 3 -43z"/>
|
||||
<path d="M5464 5726 c-3 -8 -4 -27 -2 -43 3 -25 7 -28 38 -28 34 0 35 1 35 40
|
||||
0 38 -2 40 -33 43 -21 2 -34 -2 -38 -12z"/>
|
||||
<path d="M5604 5726 c-3 -8 -4 -27 -2 -43 3 -24 8 -28 41 -31 l37 -3 0 45 c0
|
||||
46 0 46 -35 46 -22 0 -38 -6 -41 -14z"/>
|
||||
<path d="M5750 5695 l0 -46 38 3 c36 3 37 4 37 43 0 39 -1 40 -37 43 l-38 3 0
|
||||
-46z"/>
|
||||
<path d="M4792 5583 c3 -36 5 -38 38 -38 33 0 35 2 38 38 l3 37 -41 0 -41 0 3
|
||||
-37z"/>
|
||||
<path d="M4937 5613 c-4 -3 -7 -19 -7 -34 0 -22 6 -30 25 -35 40 -10 55 1 55
|
||||
41 0 33 -2 35 -33 35 -19 0 -37 -3 -40 -7z"/>
|
||||
<path d="M5082 5583 c3 -36 5 -38 38 -38 33 0 35 2 38 38 l3 37 -41 0 -41 0 3
|
||||
-37z"/>
|
||||
<path d="M5462 5583 c3 -36 5 -38 38 -38 33 0 35 2 38 38 l3 37 -41 0 -41 0 3
|
||||
-37z"/>
|
||||
<path d="M5602 5583 c3 -36 5 -38 38 -38 33 0 35 2 38 38 l3 37 -41 0 -41 0 3
|
||||
-37z"/>
|
||||
<path d="M5750 5585 c0 -40 15 -51 55 -41 21 5 25 12 25 41 0 34 -1 35 -40 35
|
||||
-39 0 -40 -1 -40 -35z"/>
|
||||
<path d="M6214 5625 c-3 -8 -3 -19 1 -25 3 -5 0 -10 -9 -10 -8 0 -22 -3 -31
|
||||
-6 -11 -5 -18 0 -22 15 -8 31 -34 27 -31 -5 3 -29 -30 -60 -39 -36 -5 14 -33
|
||||
17 -33 3 0 -5 7 -16 15 -25 8 -8 15 -26 15 -40 0 -21 -5 -26 -26 -26 -32 0
|
||||
-27 -24 6 -28 35 -6 52 -33 34 -53 -8 -8 -14 -19 -14 -22 0 -12 27 -7 39 6 6
|
||||
8 23 12 41 9 26 -4 29 -7 24 -28 -5 -18 -2 -24 10 -24 8 0 18 11 22 25 7 28
|
||||
25 32 44 10 10 -12 10 -21 0 -45 -15 -36 -4 -53 16 -26 11 16 16 17 29 6 8 -7
|
||||
15 -25 15 -41 0 -19 5 -29 15 -29 8 0 15 9 15 20 0 15 7 20 25 20 14 0 30 -9
|
||||
37 -20 7 -11 16 -20 20 -20 12 0 9 38 -3 45 -6 5 -3 13 11 22 16 11 24 12 35
|
||||
3 25 -21 39 0 16 24 -24 26 -18 66 10 66 11 0 19 7 19 16 0 12 -7 15 -26 11
|
||||
-33 -6 -49 27 -28 60 18 28 18 33 -1 33 -9 0 -18 -7 -22 -15 -5 -14 -8 -14
|
||||
-25 2 -15 13 -18 25 -13 50 6 35 -7 45 -23 17 -15 -27 -52 -8 -52 27 0 19 -5
|
||||
29 -15 29 -8 0 -15 -9 -15 -20 0 -11 -5 -20 -11 -20 -23 0 -49 22 -49 40 0 23
|
||||
-18 27 -26 5z"/>
|
||||
<path d="M4925 5019 c-4 -5 -4 -21 -1 -33 5 -20 1 -24 -25 -30 -55 -11 -67 -7
|
||||
-78 24 -15 45 -35 39 -27 -8 5 -34 2 -41 -23 -60 -29 -21 -29 -21 -46 -1 -20
|
||||
21 -45 25 -45 7 0 -7 11 -23 24 -37 18 -21 22 -34 19 -63 -5 -36 -7 -38 -39
|
||||
-38 -52 0 -45 -27 9 -35 33 -5 46 -13 59 -36 16 -28 16 -30 -2 -42 -11 -6 -20
|
||||
-17 -20 -24 0 -24 20 -24 44 0 22 22 27 23 70 13 48 -11 49 -14 31 -58 -5 -13
|
||||
-2 -18 9 -18 18 0 36 30 36 59 0 25 26 28 58 5 26 -18 30 -68 7 -101 -24 -34
|
||||
3 -42 30 -9 l21 26 28 -29 c24 -25 28 -36 23 -66 -5 -30 -3 -36 11 -33 11 2
|
||||
18 14 20 33 3 27 6 30 39 29 28 -1 42 -8 63 -34 31 -38 49 -26 26 17 -14 26
|
||||
-13 30 11 55 l26 27 28 -20 c39 -28 51 -4 14 28 -25 22 -27 28 -19 61 7 30 14
|
||||
38 37 40 15 2 27 10 27 17 0 21 -15 26 -44 15 -24 -9 -27 -7 -41 27 -14 33
|
||||
-14 38 5 70 11 19 20 36 20 39 0 12 -29 2 -45 -16 -18 -20 -19 -20 -47 7 -29
|
||||
28 -32 46 -13 96 11 28 -24 21 -37 -8 -6 -14 -14 -24 -17 -22 -3 1 -18 9 -33
|
||||
16 -24 12 -28 20 -28 58 0 30 -4 43 -14 43 -15 0 -26 -21 -26 -51 0 -20 -8
|
||||
-20 -71 -3 -10 3 -20 20 -23 39 -7 35 -19 44 -31 24z"/>
|
||||
<path d="M3113 4581 c5 -37 3 -39 -32 -50 -31 -9 -40 -8 -63 9 -15 11 -32 20
|
||||
-38 20 -18 0 -11 -28 11 -43 20 -15 20 -15 -16 -43 -33 -25 -39 -26 -69 -16
|
||||
-41 15 -46 15 -46 -1 0 -8 12 -19 26 -26 l26 -11 -21 -33 c-17 -27 -26 -32
|
||||
-60 -32 -21 0 -43 -4 -47 -8 -11 -11 15 -27 44 -27 26 0 26 0 10 -51 -10 -35
|
||||
-14 -39 -45 -39 -27 0 -33 -4 -33 -21 0 -19 4 -21 33 -16 l32 5 2 -49 c3 -46
|
||||
1 -49 -25 -55 -39 -10 -44 -14 -32 -29 8 -9 20 -11 39 -5 25 7 32 4 51 -23
|
||||
l23 -30 -21 -18 c-24 -19 -29 -39 -10 -39 6 0 21 8 32 18 16 14 32 18 64 14
|
||||
l43 -4 -6 -39 c-5 -31 -4 -39 8 -39 17 0 27 21 27 55 0 16 11 30 35 44 l36 21
|
||||
11 -25 c6 -14 17 -25 25 -25 19 0 16 34 -6 54 -17 16 -18 20 -5 44 8 15 14 35
|
||||
14 45 0 20 13 22 40 5 10 -7 23 -9 27 -5 13 13 -13 41 -46 51 -26 7 -30 13
|
||||
-25 30 4 12 11 27 16 34 15 17 65 15 99 -5 38 -23 51 -7 17 22 l-26 23 28 27
|
||||
c25 24 33 26 69 20 33 -5 41 -4 41 8 0 16 -21 27 -52 27 -14 0 -18 5 -14 16 3
|
||||
9 6 27 6 41 0 18 8 28 30 36 17 6 30 17 30 24 0 16 -42 17 -57 2 -18 -18 -64
|
||||
40 -52 63 5 9 14 20 19 23 16 10 11 25 -8 25 -9 0 -23 -9 -30 -21 -11 -18 -19
|
||||
-20 -50 -14 -41 8 -52 19 -52 53 0 14 -6 22 -16 22 -13 0 -16 -7 -11 -39z"/>
|
||||
<path d="M4160 4574 c-331 -38 -532 -114 -656 -247 -77 -83 -84 -113 -84 -377
|
||||
0 -276 5 -298 98 -390 135 -133 344 -207 653 -231 470 -38 909 103 1010 324
|
||||
17 38 19 68 19 298 0 255 0 255 -26 307 -67 135 -279 248 -559 297 -86 15
|
||||
-382 28 -455 19z m410 -79 c196 -29 389 -103 482 -185 50 -43 88 -110 88 -153
|
||||
0 -40 -27 -97 -62 -134 l-31 -32 -37 24 c-106 67 -307 127 -492 146 -138 15
|
||||
-413 7 -528 -15 -149 -29 -310 -87 -383 -138 l-28 -20 -25 23 c-58 54 -79 149
|
||||
-48 214 24 50 102 119 182 159 234 118 556 158 882 111z m570 -545 c0 -38 -1
|
||||
-39 -18 -22 -17 16 -17 19 -3 39 9 12 17 23 19 23 1 0 2 -18 2 -40z m-1633
|
||||
-17 c-16 -16 -17 -15 -17 17 0 32 1 33 17 17 16 -16 16 -18 0 -34z"/>
|
||||
<path d="M1349 4091 c-82 -76 -100 -102 -113 -162 -3 -15 -29 -45 -67 -75
|
||||
-105 -84 -149 -154 -173 -275 -14 -72 -14 -73 -17 -29 -5 77 0 102 36 186 38
|
||||
89 43 130 20 174 -22 43 -50 55 -81 35 -25 -16 -33 -58 -14 -70 17 -10 12 -34
|
||||
-25 -115 -19 -43 -38 -98 -41 -123 -8 -56 11 -168 36 -217 19 -37 82 -100 101
|
||||
-100 6 0 22 -13 36 -30 24 -29 28 -30 110 -30 46 0 93 5 103 10 13 7 21 7 25
|
||||
0 8 -13 52 -13 59 -1 4 5 19 4 36 -2 22 -8 35 -9 48 -1 15 10 18 39 24 235 5
|
||||
152 4 239 -3 272 -13 54 -10 60 43 77 44 14 78 52 78 89 0 15 -21 57 -47 96
|
||||
-25 38 -49 83 -53 100 -3 16 -12 31 -20 33 -8 1 -54 -34 -101 -77z m146 -68
|
||||
c25 -35 45 -73 45 -83 0 -27 -34 -59 -70 -66 -16 -4 -37 -15 -46 -25 -15 -17
|
||||
-16 -26 -6 -67 7 -32 9 -123 5 -270 -5 -197 -8 -223 -22 -220 -13 3 -17 20
|
||||
-19 93 l-3 89 -19 -29 c-13 -20 -20 -47 -20 -80 0 -59 -11 -81 -35 -71 -15 5
|
||||
-16 14 -10 64 4 31 8 96 9 144 1 86 1 87 -33 122 -37 38 -68 46 -78 20 -4 -10
|
||||
5 -26 25 -44 55 -49 55 -155 2 -222 -17 -20 -30 -39 -30 -42 0 -2 12 -6 28 -8
|
||||
16 -2 27 -9 27 -18 0 -12 -17 -16 -82 -18 -80 -3 -81 -2 -103 28 -12 16 -27
|
||||
30 -35 30 -26 0 -73 50 -95 102 -17 39 -23 74 -24 133 -1 73 3 88 39 168 36
|
||||
82 38 90 26 123 -17 47 -2 65 28 33 31 -33 26 -80 -16 -173 -33 -72 -37 -89
|
||||
-35 -154 2 -80 24 -144 61 -176 l22 -20 -7 80 c-12 152 37 262 161 364 73 58
|
||||
85 75 85 117 0 22 17 44 82 105 76 71 83 76 91 56 4 -11 28 -50 52 -85z"/>
|
||||
<path d="M745 4030 c-98 -40 -98 -56 2 -97 43 -17 81 -29 86 -26 9 5 -10 43
|
||||
-22 43 -5 0 -26 7 -47 16 l-39 16 50 20 c50 20 68 35 59 50 -7 11 -10 10 -89
|
||||
-22z"/>
|
||||
<path d="M5505 4039 c-4 -5 -4 -21 -1 -35 5 -17 0 -33 -12 -49 -17 -22 -21
|
||||
-23 -38 -10 -11 8 -22 15 -26 15 -15 0 -8 -28 11 -41 10 -8 21 -31 24 -52 6
|
||||
-37 5 -38 -21 -35 -19 2 -27 -2 -27 -12 0 -10 12 -16 38 -18 28 -2 37 -8 37
|
||||
-22 0 -34 -29 -53 -72 -46 -30 5 -38 3 -38 -9 0 -8 6 -15 14 -15 24 0 29 -19
|
||||
12 -45 -10 -16 -26 -25 -41 -25 -16 0 -25 -6 -25 -16 0 -12 7 -15 29 -12 26 4
|
||||
30 1 35 -26 5 -22 1 -35 -14 -51 -11 -12 -20 -24 -20 -28 0 -12 23 -7 40 8 14
|
||||
13 22 14 43 4 22 -10 24 -15 16 -36 -12 -32 -12 -33 6 -33 9 0 20 11 25 25 12
|
||||
33 69 36 77 5 3 -11 12 -20 19 -20 16 0 18 14 4 39 -16 31 20 54 69 46 47 -8
|
||||
57 9 16 25 l-26 10 23 30 c16 23 30 30 55 30 41 0 43 17 4 27 -29 8 -29 9 -16
|
||||
41 11 24 20 32 40 32 16 0 25 6 25 16 0 12 -7 15 -30 12 -29 -4 -30 -3 -30 34
|
||||
0 32 4 39 25 44 14 3 25 12 25 20 0 16 -14 18 -39 5 -14 -8 -20 -4 -31 27 -12
|
||||
33 -11 37 9 50 11 8 21 18 21 23 0 13 -34 11 -47 -2 -8 -8 -18 -6 -36 6 -23
|
||||
14 -24 20 -15 41 16 35 0 43 -25 12 -13 -15 -34 -28 -52 -30 -26 -3 -30 0 -33
|
||||
25 -3 28 -16 35 -27 16z"/>
|
||||
<path d="M6392 3988 c-6 -6 -12 -29 -12 -50 l0 -39 63 3 c72 3 83 21 17 28
|
||||
-31 3 -45 10 -45 20 0 10 14 17 45 20 25 3 45 10 45 15 0 15 -98 18 -113 3z"/>
|
||||
<path d="M694 3902 c-24 -15 -34 -50 -24 -77 14 -36 36 -27 32 13 -2 18 1 32
|
||||
7 32 6 0 11 -16 11 -35 0 -28 4 -35 20 -35 11 0 20 -4 20 -10 0 -5 -20 -10
|
||||
-44 -10 -30 0 -46 -5 -50 -15 -8 -21 3 -45 20 -45 8 0 14 7 14 15 0 10 10 15
|
||||
30 15 20 0 30 -5 30 -15 0 -8 7 -15 15 -15 8 0 15 7 15 15 0 8 9 15 20 15 25
|
||||
0 26 18 3 27 -27 10 -45 31 -33 38 17 10 11 61 -8 78 -19 18 -59 22 -78 9z
|
||||
m63 -54 c-3 -8 -6 -5 -6 6 -1 11 2 17 5 13 3 -3 4 -12 1 -19z"/>
|
||||
<path d="M6408 3883 c-34 -9 -35 -93 -2 -93 12 0 14 7 9 30 -4 19 -3 30 4 30
|
||||
6 0 11 -9 11 -19 0 -11 7 -27 16 -35 14 -15 13 -16 -6 -16 -50 0 -59 -15 -57
|
||||
-93 l2 -72 60 0 c47 0 60 3 60 15 0 11 -13 16 -47 18 -33 2 -48 8 -48 17 0 9
|
||||
15 15 48 17 59 4 61 21 3 28 -61 7 -67 30 -7 30 48 0 69 16 44 34 -13 9 -13
|
||||
13 -2 24 8 7 12 27 10 49 -3 36 -5 38 -42 40 -22 0 -47 -1 -56 -4z m66 -48 c3
|
||||
-8 1 -15 -4 -15 -6 0 -10 7 -10 15 0 8 2 15 4 15 2 0 6 -7 10 -15z"/>
|
||||
<path d="M698 3709 c-29 -16 -39 -44 -28 -74 14 -36 36 -27 32 13 -2 18 1 32
|
||||
7 32 6 0 11 -16 11 -35 0 -30 3 -35 23 -35 31 0 47 18 47 51 0 45 -52 72 -92
|
||||
48z m59 -61 c-3 -7 -5 -2 -5 12 0 14 2 19 5 13 2 -7 2 -19 0 -25z"/>
|
||||
<path d="M667 3594 c-16 -16 8 -34 45 -34 31 0 41 -4 45 -20 10 -37 32 -23 31
|
||||
20 l0 40 -58 0 c-31 0 -59 -3 -63 -6z"/>
|
||||
<path d="M6382 3583 c2 -13 14 -19 46 -21 28 -2 42 -8 42 -18 0 -10 -12 -14
|
||||
-45 -14 -38 0 -45 -3 -45 -20 0 -17 7 -20 48 -20 60 0 81 20 77 70 l-2 35 -63
|
||||
3 c-55 3 -61 1 -58 -15z"/>
|
||||
<path d="M667 3504 c-15 -15 8 -24 64 -24 46 0 59 3 59 15 0 12 -13 15 -58 15
|
||||
-32 0 -62 -3 -65 -6z"/>
|
||||
<path d="M800 3490 c0 -15 5 -20 18 -18 9 2 17 10 17 18 0 8 -8 16 -17 18 -13
|
||||
2 -18 -3 -18 -18z"/>
|
||||
<path d="M6340 3460 c0 -16 6 -20 30 -20 28 0 30 -3 30 -36 0 -33 -2 -35 -27
|
||||
-32 -20 2 -29 -2 -31 -15 -3 -16 4 -18 79 -15 52 2 84 7 86 15 3 7 -10 13 -34
|
||||
15 -35 3 -38 6 -41 35 -3 30 -1 32 35 35 26 2 38 8 38 18 0 12 -17 16 -82 18
|
||||
-78 3 -83 2 -83 -18z"/>
|
||||
<path d="M670 3440 c0 -17 7 -20 45 -20 33 0 45 -4 45 -15 0 -11 -12 -15 -45
|
||||
-15 -38 0 -45 -3 -45 -20 0 -17 7 -20 49 -20 58 0 70 12 69 68 l0 42 -59 0
|
||||
c-52 0 -59 -2 -59 -20z"/>
|
||||
<path d="M5760 3453 c-68 -26 -117 -107 -106 -176 24 -145 196 -198 289 -88
|
||||
93 111 19 273 -125 270 -23 0 -50 -3 -58 -6z m145 -54 c64 -57 66 -151 4 -203
|
||||
-75 -64 -177 -39 -215 51 -18 42 -18 67 3 110 22 47 66 73 125 73 39 0 54 -6
|
||||
83 -31z"/>
|
||||
<path d="M3340 3426 c0 -31 -28 -42 -45 -19 -17 23 -33 8 -18 -16 18 -28 5
|
||||
-61 -23 -61 -29 0 -32 -20 -5 -27 30 -8 34 -33 11 -58 -22 -24 -15 -40 10 -25
|
||||
25 15 42 -28 23 -57 -14 -21 -14 -23 0 -23 9 0 19 5 22 10 13 21 37 -12 31
|
||||
-42 -6 -31 10 -38 28 -12 18 24 46 7 46 -27 0 -33 16 -39 25 -9 9 28 53 27 57
|
||||
-2 4 -31 28 -35 28 -5 0 30 30 45 46 23 18 -25 27 -19 21 14 -9 44 0 61 30 54
|
||||
32 -8 28 16 -5 31 -25 11 -36 44 -16 52 22 8 16 25 -8 22 -46 -5 -85 19 -58
|
||||
36 15 9 12 25 -4 25 -7 0 -20 -10 -28 -22 -8 -12 -19 -18 -26 -14 -17 10 -15
|
||||
42 3 60 16 16 20 36 7 36 -4 0 -14 -6 -20 -12 -18 -18 -34 9 -28 45 6 30 -10
|
||||
37 -28 11 -14 -19 -42 -10 -49 17 -7 27 -27 24 -27 -5z"/>
|
||||
<path d="M667 3326 c-3 -8 -3 -31 0 -50 5 -34 8 -36 45 -36 54 0 78 15 78 48
|
||||
0 15 -4 33 -9 41 -13 21 -32 3 -25 -25 4 -14 2 -24 -5 -24 -6 0 -11 8 -11 18
|
||||
0 10 -5 23 -12 30 -17 17 -55 15 -61 -2z m40 -38 c-3 -8 -6 -5 -6 6 -1 11 2
|
||||
17 5 13 3 -3 4 -12 1 -19z"/>
|
||||
<path d="M666 3222 c-10 -16 11 -31 49 -34 28 -2 41 -8 43 -20 5 -25 -52 -51
|
||||
-95 -43 -29 5 -34 3 -31 -10 3 -15 123 -75 149 -75 22 0 6 29 -23 41 l-31 13
|
||||
31 15 c30 14 32 17 31 68 l-2 53 -58 0 c-32 0 -60 -4 -63 -8z"/>
|
||||
<path d="M4959 3187 c-19 -12 -45 -43 -58 -70 -32 -64 -24 -123 25 -177 67
|
||||
-74 163 -78 233 -12 82 78 71 203 -24 262 -46 29 -131 27 -176 -3z m164 -26
|
||||
c40 -23 70 -90 61 -138 -13 -72 -98 -127 -168 -109 -38 9 -83 53 -96 92 -24
|
||||
71 13 144 85 169 43 15 74 11 118 -14z"/>
|
||||
<path d="M4354 2928 c-12 -5 -27 -21 -33 -34 -23 -52 -14 -77 73 -193 96 -127
|
||||
109 -140 149 -141 38 0 63 14 121 69 27 25 46 38 43 29 -31 -87 -78 -298 -74
|
||||
-328 3 -20 37 -87 81 -157 42 -67 76 -130 76 -138 0 -9 -18 -79 -40 -156 -50
|
||||
-174 -51 -208 -9 -243 38 -32 80 -33 113 -3 19 17 36 63 75 204 28 99 51 196
|
||||
51 215 0 19 -11 49 -25 71 -14 20 -23 37 -19 37 3 0 30 -15 60 -32 l54 -33 0
|
||||
-187 c0 -184 0 -187 25 -216 46 -54 108 -50 145 10 18 30 20 51 20 243 0 258
|
||||
4 247 -144 337 -59 34 -105 67 -103 73 2 5 19 61 38 122 19 62 37 113 41 113
|
||||
3 0 27 -36 53 -80 51 -86 66 -100 114 -100 32 0 258 107 278 132 34 42 22 102
|
||||
-26 131 -41 24 -63 21 -141 -18 l-70 -35 -26 42 c-112 182 -81 160 -336 233
|
||||
-115 32 -176 45 -194 41 -15 -4 -60 -39 -100 -77 l-72 -71 -49 65 c-62 84 -96
|
||||
101 -149 75z m122 -90 c31 -40 61 -77 65 -82 5 -6 44 24 93 72 46 45 92 82
|
||||
102 82 35 0 379 -102 396 -118 10 -8 30 -36 45 -61 15 -25 42 -70 60 -98 l34
|
||||
-53 81 41 c89 45 117 46 144 3 30 -45 9 -68 -128 -134 -87 -42 -130 -58 -146
|
||||
-54 -15 4 -44 42 -88 115 -36 60 -68 109 -72 109 -14 0 -105 -321 -94 -332 5
|
||||
-5 56 -38 113 -72 59 -35 109 -73 116 -87 16 -30 18 -405 3 -444 -14 -38 -57
|
||||
-51 -89 -27 l-26 19 -5 198 -5 199 -98 59 c-55 33 -102 56 -107 51 -5 -5 13
|
||||
-44 40 -87 55 -89 57 -59 -15 -310 -42 -145 -52 -170 -73 -180 -36 -16 -76 9
|
||||
-80 50 -2 18 15 99 38 180 23 81 42 155 42 163 1 8 -36 74 -80 146 -52 83 -82
|
||||
141 -82 159 0 15 23 113 51 218 28 104 48 192 44 195 -3 3 -45 -33 -93 -81
|
||||
-64 -63 -94 -87 -113 -87 -30 0 -63 33 -148 148 -64 88 -74 121 -44 154 32 35
|
||||
58 23 119 -54z"/>
|
||||
<path d="M1287 2783 c-3 -4 -66 -163 -140 -353 -112 -286 -274 -698 -294 -747
|
||||
-4 -10 20 -13 99 -13 91 0 107 3 122 19 10 11 36 70 59 133 l42 113 225 3 225
|
||||
2 38 -109 c21 -61 47 -122 58 -136 20 -24 25 -25 126 -25 80 0 104 3 100 13
|
||||
-5 13 -376 955 -412 1047 l-21 55 -111 3 c-61 1 -114 -1 -116 -5z m196 -459
|
||||
c43 -116 77 -214 77 -217 0 -4 -72 -7 -160 -7 -88 0 -160 3 -160 7 0 4 34 98
|
||||
75 210 41 111 75 210 75 220 0 35 19 -7 93 -213z"/>
|
||||
<path d="M2050 2230 l0 -560 100 0 101 0 -3 384 c-2 211 -2 384 -1 383 0 -1
|
||||
74 -137 162 -302 89 -165 171 -308 182 -317 31 -26 101 -24 134 5 14 12 98
|
||||
157 185 322 l160 300 0 -387 0 -388 95 0 95 0 0 560 0 560 -98 0 c-63 0 -104
|
||||
-4 -115 -12 -15 -12 -342 -613 -373 -688 l-15 -35 -41 80 c-77 154 -331 620
|
||||
-346 638 -13 14 -33 17 -119 17 l-103 0 0 -560z"/>
|
||||
<path d="M3480 2230 l0 -560 110 0 110 0 0 215 0 215 54 0 c43 0 60 -5 80 -22
|
||||
14 -13 75 -99 137 -193 61 -93 121 -180 132 -192 19 -21 29 -23 139 -23 65 0
|
||||
118 3 118 6 0 11 -288 429 -308 448 -21 18 -21 18 27 43 233 116 243 465 16
|
||||
572 -89 42 -157 51 -392 51 l-223 0 0 -560z m416 377 c113 -24 149 -67 142
|
||||
-173 -7 -117 -73 -164 -239 -172 l-99 -5 0 182 0 181 68 0 c37 0 95 -6 128
|
||||
-13z"/>
|
||||
<path d="M780 2716 c0 -27 -38 -44 -47 -20 -3 8 -11 14 -19 14 -16 0 -18 -9
|
||||
-5 -29 14 -22 -6 -51 -34 -51 -30 0 -33 -16 -5 -25 27 -9 26 -51 -1 -66 -15
|
||||
-8 -18 -14 -10 -22 7 -7 15 -7 25 2 13 11 16 8 22 -15 4 -16 2 -35 -5 -46 -15
|
||||
-25 -7 -35 14 -18 23 19 47 -15 32 -47 -13 -30 -2 -41 20 -20 26 23 57 4 49
|
||||
-29 -7 -28 10 -33 29 -8 15 22 55 10 55 -17 0 -25 20 -25 27 0 7 26 34 36 45
|
||||
16 14 -24 31 -18 24 10 -9 36 12 66 35 52 30 -19 35 2 6 29 -30 27 -36 54 -12
|
||||
54 8 0 15 7 15 16 0 12 -6 15 -22 11 -27 -7 -78 26 -59 37 16 10 14 26 -4 26
|
||||
-7 0 -18 -7 -23 -17 -12 -21 -42 -10 -42 17 0 11 9 25 20 32 11 7 20 18 20 25
|
||||
0 16 -6 16 -30 3 -15 -8 -19 -5 -25 17 -3 14 -1 31 4 36 16 16 13 27 -4 27 -9
|
||||
0 -18 -6 -21 -14 -8 -21 -43 -7 -50 20 -8 31 -24 31 -24 0z"/>
|
||||
<path d="M6237 2214 c-4 -4 -7 -19 -7 -34 0 -14 -5 -31 -10 -36 -7 -7 -10 -56
|
||||
-8 -125 l3 -114 39 -3 c22 -2 51 -12 64 -23 34 -26 105 -26 132 1 26 26 25 36
|
||||
-5 64 -23 21 -25 31 -25 108 0 46 -4 88 -9 94 -5 5 -11 23 -13 39 l-3 30 -75
|
||||
3 c-42 1 -79 0 -83 -4z m139 -44 c-4 -22 -1 -32 9 -36 8 -4 15 -12 15 -20 0
|
||||
-9 -20 -14 -72 -16 l-73 -3 -3 -52 -3 -53 75 0 c44 0 76 -4 76 -10 0 -5 -16
|
||||
-10 -35 -10 -25 0 -43 -7 -59 -25 -14 -14 -34 -25 -50 -25 l-26 0 0 104 c0 83
|
||||
3 105 15 110 10 4 13 14 9 36 l-6 30 67 0 68 0 -7 -30z m24 -125 c0 -24 -3
|
||||
-25 -60 -25 -57 0 -60 1 -60 25 0 24 3 25 60 25 57 0 60 -1 60 -25z m41 -121
|
||||
c11 -14 10 -18 -6 -30 -30 -22 -45 -17 -45 16 0 23 5 30 19 30 10 0 25 -7 32
|
||||
-16z"/>
|
||||
<path d="M2132 1614 c-28 -19 -44 -49 -51 -94 -5 -29 -11 -36 -34 -38 -35 -4
|
||||
-34 -35 1 -40 21 -3 23 -7 18 -40 -11 -64 -36 -276 -36 -300 0 -17 5 -23 18
|
||||
-20 21 4 36 71 53 240 l12 117 46 3 c34 2 47 7 49 21 3 14 -4 17 -44 17 l-46
|
||||
0 6 32 c11 55 32 78 71 78 28 0 35 4 35 20 0 16 -7 20 -38 20 -21 0 -48 -7
|
||||
-60 -16z"/>
|
||||
<path d="M2954 1623 c-6 -4 -20 -93 -32 -198 -13 -104 -25 -207 -28 -227 -5
|
||||
-35 -4 -38 19 -38 24 0 25 4 37 100 l12 100 32 0 c29 0 35 -7 90 -100 49 -85
|
||||
61 -100 83 -100 31 0 29 5 -39 119 -28 46 -47 86 -42 88 27 9 75 45 89 66 40
|
||||
62 26 145 -28 174 -33 17 -176 29 -193 16z m176 -63 c24 -24 26 -77 4 -109
|
||||
-21 -30 -73 -51 -125 -51 l-41 0 6 58 c16 130 11 122 77 122 46 0 64 -5 79
|
||||
-20z"/>
|
||||
<path d="M2335 1493 c-68 -18 -125 -105 -125 -192 0 -70 22 -115 67 -136 103
|
||||
-49 213 51 213 193 0 56 -3 66 -32 97 -33 36 -79 50 -123 38z m89 -63 c24 -23
|
||||
26 -109 3 -162 -28 -67 -106 -93 -150 -50 -49 49 -16 189 54 224 37 19 64 16
|
||||
93 -12z"/>
|
||||
<path d="M2685 1492 c-11 -2 -32 -16 -47 -30 l-28 -26 0 27 c0 20 -5 27 -19
|
||||
27 -23 0 -26 -12 -41 -155 -6 -55 -13 -117 -17 -137 -5 -35 -4 -38 19 -38 24
|
||||
0 26 4 32 68 10 100 24 146 58 186 22 26 37 36 59 36 16 0 29 2 29 4 0 2 3 11
|
||||
6 19 6 16 -19 25 -51 19z"/>
|
||||
<path d="M1240 4315 c-42 -43 -43 -46 -27 -62 16 -17 20 -15 64 29 40 40 45
|
||||
49 34 62 -19 22 -22 21 -71 -29z"/>
|
||||
<path d="M4156 1397 c-13 -13 -40 -34 -60 -46 -43 -27 -60 -55 -52 -86 7 -26
|
||||
46 -58 86 -70 14 -4 36 -16 49 -26 31 -24 56 -24 74 1 11 16 21 19 45 14 37
|
||||
-7 62 8 62 38 0 14 5 18 16 14 9 -3 25 -6 35 -6 28 0 15 -17 -32 -40 -49 -26
|
||||
-73 -61 -65 -96 9 -34 49 -70 94 -85 21 -6 46 -20 57 -29 31 -28 69 -34 89
|
||||
-15 9 9 16 21 16 26 0 5 20 6 45 2 51 -7 75 7 75 42 0 19 5 22 42 21 36 -1 44
|
||||
3 57 27 15 24 15 30 0 55 -13 23 -22 27 -56 26 -37 -1 -42 2 -47 27 -6 34 -45
|
||||
48 -88 31 -24 -9 -28 -8 -28 8 0 30 -26 43 -75 38 -44 -5 -45 -5 -45 23 0 36
|
||||
-32 56 -66 41 -20 -10 -23 -8 -26 16 -3 25 -7 27 -48 27 -35 0 -47 4 -55 20
|
||||
-16 31 -69 32 -99 2z m82 -14 c2 -9 -9 -13 -40 -13 -40 1 -42 2 -23 16 23 17
|
||||
56 15 63 -3z m1 -37 c7 -9 11 -38 9 -73 l-3 -58 -44 -3 c-37 -3 -43 -1 -37 13
|
||||
15 40 17 67 8 94 -10 28 -9 30 16 34 15 2 30 5 33 6 4 0 12 -5 18 -13z m96 4
|
||||
c8 -13 -5 -13 -25 0 -13 8 -13 10 2 10 9 0 20 -4 23 -10z m0 -65 c0 -17 -8
|
||||
-33 -20 -41 -20 -13 -21 -12 -21 42 -1 53 -1 54 20 41 13 -9 21 -25 21 -42z
|
||||
m-197 16 c5 -32 -6 -71 -20 -71 -17 0 -48 31 -48 48 0 22 31 53 49 50 9 -2 17
|
||||
-14 19 -27z m287 -30 c-9 -29 -39 -23 -43 8 -2 13 2 27 10 32 19 12 41 -14 33
|
||||
-40z m-148 -8 c-3 -10 -5 -2 -5 17 0 19 2 27 5 18 2 -10 2 -26 0 -35z m258
|
||||
-24 c9 -14 7 -16 -44 -24 -32 -5 -42 -4 -36 5 15 24 69 37 80 19z m-195 -19
|
||||
c0 -13 -28 -25 -38 -16 -3 4 0 11 8 16 20 13 30 12 30 0z m215 -40 c8 -26 8
|
||||
-137 0 -150 -3 -6 -29 -10 -57 -10 -48 0 -50 1 -43 23 11 29 11 108 1 129 -8
|
||||
18 7 25 61 27 24 1 33 -4 38 -19z m110 9 c12 -19 -2 -21 -32 -5 l-28 15 27 1
|
||||
c15 0 30 -5 33 -11z m-432 -10 c-8 -8 -16 -8 -30 0 -16 9 -14 10 12 11 21 0
|
||||
26 -3 18 -11z m432 -49 c9 -28 -3 -58 -27 -71 -11 -6 -21 -9 -23 -7 -1 2 -5
|
||||
31 -7 65 l-4 62 27 -15 c15 -7 30 -23 34 -34z m-241 9 c9 -27 4 -62 -13 -89
|
||||
-9 -13 -14 -12 -38 6 -37 27 -41 60 -12 90 28 30 51 27 63 -7z m163 -66 c-2
|
||||
-21 -4 -6 -4 32 0 39 2 55 4 38 2 -18 2 -50 0 -70z m181 43 c4 -35 -9 -50 -37
|
||||
-41 -15 4 -21 15 -21 35 0 48 53 54 58 6z m-98 -75 c0 -16 -27 -31 -45 -25
|
||||
-15 6 -15 9 6 20 28 16 39 17 39 5z m-130 -51 c0 -13 -30 -13 -50 0 -11 7 -7
|
||||
10 18 10 17 0 32 -4 32 -10z"/>
|
||||
<path d="M4100 1300 c0 -5 7 -10 15 -10 8 0 15 5 15 10 0 6 -7 10 -15 10 -8 0
|
||||
-15 -4 -15 -10z"/>
|
||||
<path d="M4380 1124 c0 -9 5 -14 12 -12 18 6 21 28 4 28 -9 0 -16 -7 -16 -16z"/>
|
||||
<path d="M5483 1275 c1 -19 6 -35 11 -35 6 0 18 -15 26 -33 12 -26 21 -32 45
|
||||
-32 21 0 31 5 33 19 3 15 0 18 -16 14 -15 -4 -23 1 -32 20 -8 19 -8 28 -1 30
|
||||
20 7 12 35 -8 29 -12 -3 -22 1 -25 9 -11 29 -34 15 -33 -21z"/>
|
||||
<path d="M5415 1232 c-16 -9 -31 -18 -33 -18 -2 -1 9 -27 25 -58 22 -43 31
|
||||
-53 43 -46 12 8 12 14 -3 45 -16 34 -16 55 2 55 4 0 15 -16 24 -35 17 -35 47
|
||||
-48 47 -20 0 25 -28 73 -49 85 -24 12 -20 13 -56 -8z"/>
|
||||
<path d="M5307 1172 c-10 -10 -17 -27 -17 -37 0 -15 -3 -16 -12 -7 -17 17 -57
|
||||
15 -64 -3 -4 -8 -16 -15 -28 -15 -22 -1 -56 -22 -56 -35 0 -5 9 -28 21 -52 14
|
||||
-28 27 -43 40 -43 24 0 24 2 -1 49 -18 35 -18 51 0 51 4 0 15 -18 25 -40 10
|
||||
-22 22 -40 27 -40 17 0 19 29 4 59 -18 35 -20 51 -6 51 5 0 19 -18 30 -40 11
|
||||
-22 25 -40 30 -40 16 0 21 19 10 41 -11 20 -11 20 13 4 29 -19 70 -8 86 24 15
|
||||
27 -4 38 -28 17 -19 -17 -41 -21 -41 -7 0 5 14 14 30 21 34 14 37 22 14 44
|
||||
-21 21 -57 20 -77 -2z m53 -16 c0 -2 -7 -6 -15 -10 -8 -3 -15 -1 -15 4 0 6 7
|
||||
10 15 10 8 0 15 -2 15 -4z"/>
|
||||
<path d="M3990 1159 c-14 -5 -38 -23 -55 -40 -16 -17 -45 -40 -64 -52 -19 -12
|
||||
-43 -34 -54 -49 -37 -50 1 -110 91 -145 26 -9 54 -25 64 -35 39 -39 96 -36
|
||||
116 5 11 22 16 25 32 17 28 -15 76 -12 94 6 9 8 16 27 16 41 0 20 4 24 18 18
|
||||
58 -25 102 -2 102 53 0 59 -49 89 -101 62 -16 -9 -19 -7 -19 15 0 14 -9 34
|
||||
-21 46 -21 21 -40 22 -96 4 -19 -6 -23 -4 -23 13 0 23 -35 52 -60 51 -8 0 -26
|
||||
-5 -40 -10z m68 -31 c22 -22 12 -28 -45 -28 l-58 1 24 19 c26 23 61 26 79 8z
|
||||
m140 -61 c4 -17 2 -18 -27 -2 -38 19 -39 27 -4 23 17 -2 29 -10 31 -21z m-114
|
||||
-39 c6 -29 6 -67 0 -95 l-9 -48 -62 -3 c-35 -2 -63 -1 -63 1 0 3 7 22 16 43
|
||||
15 37 15 76 -2 132 -6 22 -5 23 52 20 l59 -3 9 -47z m30 11 c8 -43 6 -110 -4
|
||||
-134 -6 -13 -7 -1 -3 35 3 31 1 72 -5 93 -6 20 -7 37 -2 37 4 0 10 -14 14 -31z
|
||||
m-185 -25 c8 -28 6 -45 -6 -75 -8 -21 -19 -39 -23 -39 -15 0 -70 58 -70 75 0
|
||||
27 19 54 48 69 33 18 39 14 51 -30z m19 21 c-3 -3 -9 2 -12 12 -6 14 -5 15 5
|
||||
6 7 -7 10 -15 7 -18z m222 8 c49 -29 49 -87 0 -116 -15 -9 -30 -17 -32 -17 -1
|
||||
0 -3 34 -3 75 0 41 1 75 3 75 2 0 17 -8 32 -17z m134 -19 c18 -7 22 -69 5 -79
|
||||
-5 -4 -21 -4 -35 -1 -19 5 -24 13 -24 40 0 25 5 36 18 39 9 3 18 5 19 6 1 0 8
|
||||
-2 17 -5z m-347 -26 c-3 -8 -6 -5 -6 6 -1 11 2 17 5 13 3 -3 4 -12 1 -19z
|
||||
m243 -97 c0 -21 -32 -37 -51 -25 -7 4 0 14 18 25 34 23 33 23 33 0z m-143 -53
|
||||
c-5 -15 -46 -13 -61 2 -7 7 3 10 28 10 26 0 36 -4 33 -12z"/>
|
||||
<path d="M3880 1005 c0 -8 7 -15 15 -15 8 0 15 7 15 15 0 8 -7 15 -15 15 -8 0
|
||||
-15 -7 -15 -15z"/>
|
||||
<path d="M5043 1046 c-26 -12 -28 -19 -12 -47 10 -20 10 -20 -14 -4 -33 21
|
||||
-73 11 -92 -24 -8 -14 -14 -20 -15 -13 0 17 -21 15 -50 -7 l-24 -19 24 -52
|
||||
c16 -34 29 -50 39 -47 18 4 18 7 -1 55 -11 28 -10 34 2 42 11 7 21 1 38 -20
|
||||
40 -51 105 -32 105 30 l0 32 14 -26 c7 -14 18 -26 23 -26 18 0 20 20 5 51 -16
|
||||
30 -14 59 3 59 4 0 17 -18 28 -40 15 -30 22 -37 34 -30 12 8 11 15 -8 54 -18
|
||||
39 -26 46 -49 45 -16 -1 -38 -6 -50 -13z m-38 -97 c9 -28 -9 -46 -30 -29 -8 7
|
||||
-15 21 -15 31 0 26 37 25 45 -2z"/>
|
||||
<path d="M4773 954 c-3 -8 -1 -20 6 -27 13 -13 15 -28 4 -26 -31 5 -35 -2 -29
|
||||
-43 l7 -43 -31 30 c-24 23 -33 26 -43 16 -10 -10 -3 -20 33 -52 62 -54 76 -49
|
||||
73 26 l-3 60 22 -42 c14 -27 29 -43 40 -43 10 0 18 4 18 9 0 17 -51 106 -60
|
||||
104 -4 -1 -6 6 -3 16 6 23 -25 37 -34 15z"/>
|
||||
<path d="M4498 819 c-21 -11 -38 -24 -38 -29 0 -17 64 -140 73 -140 20 0 87
|
||||
42 87 55 0 16 -25 21 -34 6 -3 -5 -14 -11 -25 -14 -30 -8 -35 22 -6 35 28 12
|
||||
34 38 9 38 -8 0 -24 -4 -34 -10 -13 -7 -19 -6 -24 5 -3 10 5 20 24 30 30 15
|
||||
41 45 18 45 -7 -1 -30 -10 -50 -21z"/>
|
||||
<path d="M4608 824 l-27 -15 26 -54 c15 -30 31 -55 35 -55 17 0 19 29 3 59
|
||||
-15 31 -13 51 5 51 5 0 19 -18 30 -40 14 -27 25 -38 35 -34 19 8 19 11 -8 59
|
||||
-25 45 -54 53 -99 29z"/>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 34 KiB |
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue
Block a user