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<meta name="author" content="Alex Douglas" />
<title>Squid Analysis</title>
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<div id="header">
<h1 class="title toc-ignore">Squid Analysis</h1>
<h4 class="author">Alex Douglas</h4>
<h4 class="date">27/02/2020</h4>
</div>
<p> </p>
<div id="sampling-and-data-description" class="section level3">
<h3>Sampling and data description</h3>
<p>These data were originally collected as part of a study published in
Aquatic Living Resources (Smith <em>et al</em>., 2005). The aim of the
study was to investigate the seasonal patterns of investment in somatic
and reproductive tissues in the long finned squid <em>Loligo
forbesi</em> caught in Scottish waters. Squid were caught monthly from
December 1989 - July 1991 (<strong>month</strong> and <strong>year
variables</strong>). After capture, each squid was given a unique
specimen code (<strong>specimen variable</strong>) and the following
variables measured:</p>
<p> </p>
<ul>
<li><strong>weight variable</strong> - body weight (g)</li>
<li><strong>sex variable</strong> - sex (only female squid are included
here)</li>
<li><strong>DML variable</strong> - individual dorsal mantle length
(mm)</li>
<li><strong>eviscerate.weight variable</strong> - mantle weight measured
without internal organs (g)</li>
<li><strong>ovary.weight variable</strong> - gonad weight (g)</li>
<li><strong>nid.weight variable</strong> - nidamental gland weight
(g)</li>
<li><strong>nid.length variable</strong> - nidamental gland length
(g)</li>
<li><strong>dig.weight variable</strong> - digestive gland weight
(g)</li>
</ul>
<p> </p>
<p>Each individual was also assigned a categorical measure of maturity
(<strong>maturity.stage variable</strong>) ranging from 1 to 5 with 1 =
immature, 5 = mature.</p>
<p>Some interesting background information on squid morphology can be
found <a href="https://en.wikipedia.org/wiki/Loligo_forbesii">here</a>
and the following image provides a useful summary of squid anatomy.</p>
<div style="page-break-after: always;"></div>
<div class="float">
<img src="images/squid_anatomy.jpg" style="width:70.0%"
alt="squid anatomy" />
<div class="figcaption">squid anatomy</div>
</div>
<p> </p>
</div>
<div id="data-import-and-exploration" class="section level3">
<h3>Data import and exploration</h3>
<p> </p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>squid <span class="ot"><-</span> <span class="fu">read.table</span>(<span class="st">"./data/squid1.txt"</span>, <span class="at">header =</span> <span class="cn">TRUE</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">str</span>(squid, <span class="at">vec.len =</span> <span class="dv">2</span>)</span></code></pre></div>
<pre><code>## 'data.frame': 519 obs. of 13 variables:
## $ sample.no : int 105128901 105128901 105128901 105128901 105128901 ...
## $ specimen : int 1002 1003 1005 1007 1008 ...
## $ year : int 1989 1989 1989 1989 1989 ...
## $ month : int 12 12 12 12 12 ...
## $ weight : num 152 106 ...
## $ sex : int 2 2 2 2 2 ...
## $ maturity.stage : int 3 1 2 2 3 ...
## $ DML : int 174 153 169 175 169 ...
## $ eviscerate.weight: num 87.5 62.6 79.4 83.1 72.2 ...
## $ dig.weight : num 4.65 3.14 ...
## $ nid.length : num 39.4 24.1 39 41.4 39.8 ...
## $ nid.weight : num 2.46 0.319 ...
## $ ovary.weight : num 1.68 0.103 0.289 0.252 0.86 ...</code></pre>
<p>In this dataset 519 squid were caught and 13 variables were measured
for each squid. Details are shown above.</p>
<p> </p>
<p>The variables <code>maturity.stage</code>, <code>month</code> and
<code>year</code> were converted from integers to factors in the
dataframe <code>squid</code>. These recoded variables were named
<code>Fmaturity</code>, <code>Fmonth</code> and <code>Fyear</code>.</p>
<p> </p>
<p>Next, let’s take a look at the number of observations across years
and months.</p>
<p> </p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="fu">kable</span>(<span class="fu">table</span>(squid<span class="sc">$</span>Fmonth, squid<span class="sc">$</span>Fyear), <span class="at">row.names =</span> <span class="cn">TRUE</span>, <span class="at">format =</span> <span class="st">"markdown"</span>)</span></code></pre></div>
<table>
<thead>
<tr class="header">
<th align="left"></th>
<th align="right">1989</th>
<th align="right">1990</th>
<th align="right">1991</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="right">0</td>
<td align="right">3</td>
<td align="right">37</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">30</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="right">0</td>
<td align="right">40</td>
<td align="right">29</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="right">0</td>
<td align="right">10</td>
<td align="right">33</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">30</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">14</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="right">0</td>
<td align="right">42</td>
<td align="right">1</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="right">0</td>
<td align="right">29</td>
<td align="right">0</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="right">0</td>
<td align="right">82</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="right">0</td>
<td align="right">19</td>
<td align="right">0</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="right">0</td>
<td align="right">76</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="right">12</td>
<td align="right">31</td>
<td align="right">0</td>
</tr>
</tbody>
</table>
<p> </p>
<p>In 1989 data were only collected during December and in 1991 data
collection stopped in August. During 1990, no data were collected in
either February or June. There are also some months that have very few
observations (May 1990 and July 1991 for example) so care must be taken
when modelling these data.</p>
<p> </p>
<!-- If you want a fancy table with the variable names (month and year) then use the pander function from the pander package. You will also have to provide the dimnames to the table and use the ftable function to 'flatten' the table. I have hidden this code and output in the final document but all you need to do is remove include=FALSE argument from the code chunk. -->
<p> </p>
<p>Number of observations in each month for each of the squid maturity
stages are given in the table below.</p>
<p> </p>
<table>
<thead>
<tr class="header">
<th align="left"></th>
<th align="right">1</th>
<th align="right">2</th>
<th align="right">3</th>
<th align="right">4</th>
<th align="right">5</th>
<th align="right">6</th>
<th align="right">7</th>
<th align="right">8</th>
<th align="right">9</th>
<th align="right">10</th>
<th align="right">11</th>
<th align="right">12</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">2</td>
<td align="right">0</td>
<td align="right">4</td>
<td align="right">8</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">1</td>
<td align="right">1</td>
<td align="right">4</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="right">1</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">6</td>
<td align="right">22</td>
<td align="right">21</td>
<td align="right">76</td>
<td align="right">17</td>
<td align="right">31</td>
<td align="right">7</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="right">2</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">5</td>
<td align="right">5</td>
<td align="right">1</td>
<td align="right">31</td>
<td align="right">11</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="right">18</td>
<td align="right">8</td>
<td align="right">21</td>
<td align="right">20</td>
<td align="right">6</td>
<td align="right">1</td>
<td align="right">5</td>
<td align="right">3</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">10</td>
<td align="right">15</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="right">19</td>
<td align="right">21</td>
<td align="right">48</td>
<td align="right">19</td>
<td align="right">24</td>
<td align="right">3</td>
<td align="right">8</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">3</td>
<td align="right">6</td>
</tr>
</tbody>
</table>
<p> </p>
<p>Not all maturity stages were observed in all months. Very few squid
of maturity stage 1, 2 or 3 were caught in the months January to May
whereas maturity stages 4 and 5 were predominantly caught during these
months.</p>
<p> </p>
<p>Now let’s check for any unusual observations in the variables;
<code>DML</code>, <code>weight</code>, <code>nid.length</code> and
<code>ovary.weight</code>.</p>
<p> </p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">par</span>(<span class="at">mfrow =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">2</span>))</span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">dotchart</span>(squid<span class="sc">$</span>DML, <span class="at">main =</span> <span class="st">"DML"</span>)</span>
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="fu">dotchart</span>(squid<span class="sc">$</span>weight, <span class="at">main =</span> <span class="st">"weight"</span>)</span>
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a><span class="fu">dotchart</span>(squid<span class="sc">$</span>nid.length, <span class="at">main =</span> <span class="st">"nid length"</span>)</span>
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="fu">dotchart</span>(squid<span class="sc">$</span>ovary.weight, <span class="at">main =</span> <span class="st">"ovary weight"</span>)</span></code></pre></div>
<p><img src="squid_analysis_files/figure-html/dotplot-1.png" width="672" /></p>
<p> </p>
<p>It looks like the variable <code>nid.length</code> contains an
<strong>unusually large</strong> value. Actually, this value is
biologically implausible and clearly an error. I went back and checked
my field notebook and sure enough it’s a typo. I was knackered at the
time and accidentally inserted a zero by mistake when transcribing these
data. <strong>Doh!</strong> This squid was identified as 11 with a
sample number 105128901. This observation was subsequently removed from
the data set.</p>
<p> </p>
<p>Let’s take a look at whether DML changes with maturity stage.</p>
<p> </p>
<p><img src="squid_analysis_files/figure-html/maturity-dml-1.png" width="480" style="display: block; margin: auto;" /></p>
<p>DML was lowest for maturity stage 1 with a mean length of 139.14 mm.
DML increased until maturity stage 3 (mean 222.35 mm) after which it
remained reasonably consistent for maturity stages 4 (mean 238.6 mm) and
5 (mean 233.99 mm).</p>
<p> </p>
</div>
<div id="session-information" class="section level3">
<h3>Session Information</h3>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
<!-- But i prefere to use the pander package as it wraps long lines nicely when rendering to PDF. I have hidden this code and output in the final document but all you need to do is remove echo=FALSE argument from the code chunk. -->
<p><strong>R version 4.4.1 (2024-06-14)</strong></p>
<p><strong>Platform:</strong> aarch64-apple-darwin20</p>
<p><strong>locale:</strong>
en_US.UTF-8||en_US.UTF-8||en_US.UTF-8||C||en_US.UTF-8||en_US.UTF-8</p>
<p><strong>attached base packages:</strong> <em>stats</em>,
<em>graphics</em>, <em>grDevices</em>, <em>utils</em>,
<em>datasets</em>, <em>methods</em> and <em>base</em></p>
<p><strong>other attached packages:</strong> <em>pander(v.0.6.5)</em>,
<em>kableExtra(v.1.4.0)</em>, <em>ggplot2(v.3.5.1)</em>,
<em>htmltools(v.0.5.8.1)</em>, <em>stringr(v.1.5.1)</em>,
<em>dplyr(v.1.1.4)</em> and <em>knitr(v.1.49)</em></p>
<p><strong>loaded via a namespace (and not attached):</strong>
<em>gtable(v.0.3.6)</em>, <em>jsonlite(v.1.8.9)</em>,
<em>compiler(v.4.4.1)</em>, <em>Rcpp(v.1.0.13-1)</em>,
<em>tidyselect(v.1.2.1)</em>, <em>tinytex(v.0.54)</em>,
<em>xml2(v.1.3.6)</em>, <em>jquerylib(v.0.1.4)</em>,
<em>systemfonts(v.1.1.0)</em>, <em>scales(v.1.3.0)</em>,
<em>yaml(v.2.3.10)</em>, <em>fastmap(v.1.2.0)</em>,
<em>R6(v.2.5.1)</em>, <em>labeling(v.0.4.3)</em>,
<em>generics(v.0.1.3)</em>, <em>tibble(v.3.2.1)</em>,
<em>munsell(v.0.5.1)</em>, <em>svglite(v.2.1.3)</em>,
<em>bslib(v.0.8.0)</em>, <em>pillar(v.1.9.0)</em>,
<em>rlang(v.1.1.4)</em>, <em>utf8(v.1.2.4)</em>,
<em>cachem(v.1.1.0)</em>, <em>stringi(v.1.8.4)</em>,
<em>xfun(v.0.49)</em>, <em>sass(v.0.4.9)</em>,
<em>viridisLite(v.0.4.2)</em>, <em>cli(v.3.6.3)</em>,
<em>withr(v.3.0.2)</em>, <em>magrittr(v.2.0.3)</em>,
<em>formatR(v.1.14)</em>, <em>digest(v.0.6.37)</em>,
<em>grid(v.4.4.1)</em>, <em>rstudioapi(v.0.17.1)</em>,
<em>fontawesome(v.0.5.2)</em>, <em>lifecycle(v.1.0.4)</em>,
<em>vctrs(v.0.6.5)</em>, <em>evaluate(v.1.0.1)</em>,
<em>glue(v.1.8.0)</em>, <em>farver(v.2.1.2)</em>,
<em>fansi(v.1.0.6)</em>, <em>colorspace(v.2.1-1)</em>,
<em>rmarkdown(v.2.29)</em>, <em>tools(v.4.4.1)</em> and
<em>pkgconfig(v.2.0.3)</em></p>
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