P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:11:57 +02:00
Code Releases Activity

added boxplot for (grouped) freq()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-29 19:56:17 +02:00
parent 62e6f41961
commit 8b5e2b030b
20 changed files with 464 additions and 297 deletions
Download Patch File Download Diff File Expand all files Collapse all files

57
docs/reference/age_groups.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9042</span>
</span>
</div>
@ -273,7 +273,7 @@
<li><p>A numeric vector. A vector of e.g. <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
<li><p>A character:</p><ul>
<li><p><code>"children"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"children"</code> or <code>"kids"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(65, 75, 85)</a></code>. This will split on 0-64, 65-74, 75-84, 85+.</p></li>
<li><p><code>"fives"</code>, equivalent of: <code>1:20 * 5</code>. This will split on 0-4, 5-9, 10-14, ..., 90-94, 95-99, 100+.</p></li>
<li><p><code>"tens"</code>, equivalent of: <code>1:10 * 10</code>. This will split on 0-9, 10-19, 20-29, ... 80-89, 90-99, 100+.</p></li>
@ -291,39 +291,38 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>ages</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
<pre class="examples"># NOT RUN {
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
# split into 0-49 and 50+
age_groups(ages, 50)
<span class='co'># split into 0-19, 20-49 and 50+</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
# split into 0-19, 20-49 and 50+
age_groups(ages, c(20, 50))
<span class='co'># split into groups of ten years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
# split into groups of ten years
age_groups(ages, 1:10 * 10)
age_groups(ages, split_at = "tens")
<span class='co'># split into groups of five years</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
# split into groups of five years
age_groups(ages, 1:20 * 5)
age_groups(ages, split_at = "fives")
<span class='co'># split specifically for children</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
<span class='co'># same:</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
# split specifically for children
age_groups(ages, "children")
# same:
age_groups(ages, c(1, 2, 4, 6, 13, 17))
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># }</span></pre>
# resistance of ciprofloxacine per age group
library(dplyr)
septic_patients %>%
filter_first_isolate) %>%
filter(mo == as.mo("E. coli")) %>%
group_by(age_group = age_groups(age)) %>%
select(age_group, CIP) %>%
ggplot_rsi(x = "age_group")
# }
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>