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<h1 class="title toc-ignore">Expoloring the data from the CliRes database</h1>
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<div id="TOC">
<ul>
<li><a href="#packages">Packages</a></li>
<li><a href="#loading-the-data">Loading the data</a></li>
<li><a href="#numbers-of-farms-flocks-and-weeks">Numbers of farms, flocks and weeks</a></li>
<li><a href="#number-of-chicken">Number of chicken</a></li>
<li><a href="#feces-samplings">Feces samplings</a></li>
</ul>
</div>
<div id="packages" class="section level2">
<h2>Packages</h2>
<p>Installing the required packages:</p>
<pre class="r"><code>> required <- c("dplyr", "magrittr", "readr")
> to_install <- setdiff(required, row.names(installed.packages()))
> if (length(to_install)) install.packages(to_install)</code></pre>
<p>Loading <code>magrittr</code>:</p>
<pre class="r"><code>> library(magrittr)</code></pre>
</div>
<div id="loading-the-data" class="section level2">
<h2>Loading the data</h2>
<pre class="r"><code>> viparc <- readr::read_csv("https://raw.githubusercontent.com/viparc/clires_data/master/data/viparc.csv",
+ col_types = paste(c("cii", rep("l", 6), rep("d", 45), "lil"), collapse = ""))</code></pre>
</div>
<div id="numbers-of-farms-flocks-and-weeks" class="section level2">
<h2>Numbers of farms, flocks and weeks</h2>
<p>There are <strong>114 farms</strong> in the study:</p>
<pre class="r"><code>> length(unique(viparc$farm))
[1] 114</code></pre>
<p>And a total of <strong>315 flocks</strong>:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ nrow()
[1] 315</code></pre>
<p>Of which there are <strong>287 completed flocks</strong> :</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ nrow()
[1] 287</code></pre>
<p>This represents <strong>5391 weeks</strong> of observation:</p>
<pre class="r"><code>> nrow(viparc)
[1] 5391</code></pre>
<p>And <strong>5103 weeks</strong> for completed flocks:</p>
<pre class="r"><code>> nrow(dplyr::filter(viparc, completed))
[1] 5103</code></pre>
<p>The distribution of the number of flocks per farm:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ dplyr::group_by(farm) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ hist(n, 0:12, col = "grey", main = NA, xlab = "number of flocks", ylab = "number of farms")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-9-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<p>or:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ dplyr::group_by(farm) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ table(n)
n
1 2 3 4 5 6 7 8 12
46 22 10 13 10 6 3 3 1 </code></pre>
<p>The same thing, considering only completed flocks:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ dplyr::group_by(farm) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ hist(n, 0:12, col = "grey", main = NA, xlab = "number of completed flocks", ylab = "number of farms")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-11-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<p>or:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::select(farm, flock) %>%
+ unique() %>%
+ dplyr::group_by(farm) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ table(n)
n
1 2 3 4 5 6 7 8 10
37 23 12 14 12 2 2 2 1 </code></pre>
<p>The distribution of the number of weeks per flock:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ hist(n, 0:27, col = "grey", main = NA, xlab = "number of weeks", ylab = "number of flocks")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-13-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<pre class="r"><code>> viparc %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ table(n)
n
3 5 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 27
2 2 6 10 6 6 1 4 10 29 38 37 46 40 29 19 10 9 7 3 1 </code></pre>
<p>The same thing, considering only the completed flocks:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ hist(n, 0:27, col = "grey", main = NA, xlab = "number of weeks", ylab = "number of flocks")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-15-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ table(n)
n
3 5 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 27
1 2 1 2 2 4 1 3 10 27 37 36 43 40 29 19 10 9 7 3 1 </code></pre>
</div>
<div id="number-of-chicken" class="section level2">
<h2>Number of chicken</h2>
<p>The distribution of the flocks sizes:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(week < 2) %$%
+ hist(nb_chicken, nclass = 30, col = "grey", main = NA, xlab = "number of chicken", ylab = "number of flocks")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-17-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<p>Or:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(week < 2) %$%
+ head(sort(nb_chicken), 15)
[1] 50 72 93 96 96 97 97 97 98 98 99 99 100 100 100</code></pre>
<p>The distribution of the farms sizes:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(week < 2) %>%
+ dplyr::group_by(farm) %>%
+ dplyr::summarise(size = mean(nb_chicken)) %>%
+ dplyr::ungroup() %$%
+ hist(size, col = "grey", main = NA, xlab = "number of chicken", ylab = "number of farms")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-19-1.png" width="407.736" style="display: block; margin: auto;" /></p>
<p>Or:</p>
<pre class="r"><code>> viparc %>%
+ dplyr::filter(week < 2) %>%
+ dplyr::group_by(farm) %>%
+ dplyr::summarise(size = mean(nb_chicken)) %>%
+ dplyr::ungroup() %$%
+ head(round(sort(size)), 15)
[1] 72 83 98 100 101 101 102 102 108 112 122 124 126 139 145</code></pre>
</div>
<div id="feces-samplings" class="section level2">
<h2>Feces samplings</h2>
<p>Not all the flocks are sampled 3 times:</p>
<pre class="r"><code>> (samplings <- viparc %>%
+ dplyr::select(farm, flock, completed, sampling) %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::summarise(completed = mean(completed), sampling = sum(sampling, na.rm = TRUE)) %>%
+ dplyr::ungroup() %>%
+ dplyr::mutate(completed = completed > 0))
# A tibble: 315 x 4
farm flock completed sampling
<chr> <int> <lgl> <int>
1 75-001 1 TRUE 3
2 75-001 2 TRUE 3
3 75-001 3 TRUE 3
4 75-001 4 TRUE 3
5 75-001 5 TRUE 3
6 75-001 6 TRUE 3
7 75-002 1 TRUE 3
8 75-002 2 TRUE 3
9 75-002 3 TRUE 3
10 75-002 4 TRUE 3
# … with 305 more rows</code></pre>
<pre class="r"><code>> with(samplings, table(completed, sampling))
sampling
completed 0 1 2 3
FALSE 0 6 17 5
TRUE 3 7 21 255</code></pre>
<p>The reasons for less than 3 samplings seems to be</p>
<ul>
<li>the flock is uncomplete</li>
<li>the flock died prematuraly</li>
<li>some samplings were missed</li>
</ul>
<p>Let’s explore a bit more by focusing on the completed flocks and see whether the flocks with less than 3 samplings tend to be short ones (i.e. suggesting premature death of the flock):</p>
<pre class="r"><code>> hist2 <- function(x, ...) hist(x, breaks = 0:30, ...)
>
> # Let's plot the durations of the completed flocks:
>
> viparc %>%
+ dplyr::filter(completed) %>%
+ dplyr::group_by(farm, flock) %>%
+ dplyr::tally() %>%
+ dplyr::ungroup() %$%
+ hist2(n, col = "grey", xlab = "duration (weeks)", ylab = "number of flocks", main = NA)
>
> # Let's now plot the durations of the completed flocks with 1 sample only:
>
> samplings %>%
+ dplyr::filter(completed, sampling == 1) %$%
+ purrr::map2(farm, flock, function(x, y) nrow(dplyr::filter(viparc, farm == x, flock == y))) %>%
+ unlist() %>%
+ hist2(col = adjustcolor("red", .5), add = TRUE)
>
> # And the durations of the completed flocks with 2 samples only:
>
> samplings %>%
+ dplyr::filter(completed, sampling == 2) %$%
+ purrr::map2(farm, flock, function(x, y) nrow(dplyr::filter(viparc, farm == x, flock == y))) %>%
+ unlist() %>%
+ hist2(col = adjustcolor("blue", .5), add = TRUE)
>
> legend("left", c("1 sampling only", "2 samplings only"), fill = adjustcolor(c("red", "blue"), .5), bty = "n")</code></pre>
<p><img src="explore_data_files/figure-html/unnamed-chunk-23-1.png" width="407.736" style="display: block; margin: auto;" /></p>
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