update docs folder

docs/data-collection-and-processing.html

@@ -24,7 +24,7 @@
 <meta name="author" content="Rocío Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero and Mathieu Basille" />
 
 
-<meta name="date" content="2022-03-06" />
+<meta name="date" content="2022-05-10" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -240,8 +240,10 @@ <h1><span class="header-section-number">2</span> Data collection and processing<
 <div id="identification-of-movement-ecology-mov-eco-papers" class="section level2" number="2.1">
 <h2><span class="header-section-number">2.1</span> Identification of movement ecology (mov-eco) papers</h2>
 <center>
-<p><img src="posts/moveco-images/keywordsIIlow.png" style="width:50.0%" /></p>
-Fig. 2.1. Workflow to identify movement ecology papers.
+<div class="figure">
+<img src="posts/moveco-images/keywordsIIlow.png" title="Graphical representation of the algorithm to identify movement papers. First, define KEYWORDS for Web of Science and search. Get results on N papers. Then do quality control, consisting of selecting a random sample n (n = 100) from N, reading the abstracts, determining if they are from movement studies and computing a precision metric. If precision is greater than 0.8 and N is greater than 5000, we stop. Else, we edit keywords and do it all over again." style="width:50.0%" alt="" />
+<p class="caption">Fig. 2.1. Workflow to identify movement papers.</p>
+</div>
 </center>
 <p><br /></p>
 <div id="what-is-a-movement-ecology-paper" class="section level3" number="2.1.1">
@@ -358,8 +360,10 @@ <h3><span class="header-section-number">2.1.6</span> Differences with other appr
 <div id="downloading-whole-manuscripts" class="section level2" number="2.2">
 <h2><span class="header-section-number">2.2</span> Downloading whole manuscripts</h2>
 <center>
-<p><img src="posts/moveco-images/downloadpapers.png" style="width:40.0%" /></p>
-Fig. 2.2. Downloading movement ecology papers.
+<div class="figure">
+<img src="posts/moveco-images/downloadpapers.png" title="Graphical representation of the workflow to download whole manuscripts. We feed DOIs to the fulltext R package. Download access is subjected to Text and Data Mining agreements with publishers. So from N papers, N_1 papers are downloaded. Some of them are downloaded in xlm format and some others as pdfs." style="width:40.0%" alt="" />
+<p class="caption">Fig. 2.2. Downloading movement ecology papers.</p>
+</div>
 </center>
 <p><br /></p>
 <p>We used the <em>fulltext</em> package (<span class="citation"><a href="#ref-Rfulltext" role="doc-biblioref">Chamberlain</a> (<a href="#ref-Rfulltext" role="doc-biblioref">2019</a>)</span>) in R, using Elsevier,
@@ -375,8 +379,10 @@ <h2><span class="header-section-number">2.2</span> Downloading whole manuscripts
 <h2><span class="header-section-number">2.3</span> Extracting the Material and Methods (M&amp;M) sections</h2>
 <center>
 <!-- knitr::include_graphics("posts/moveco-images/MatMet.png"", out.width=33%) -->
-<p><img src="posts/moveco-images/MatMet_low.png" style="width:75.0%" /></p>
-Fig. 2.3. Summary of procedure to extract Material and Methods section from each paper.
+<div class="figure">
+<img src="posts/moveco-images/MatMet_low.png" title="Graphical representation of the workflow to extract the methods section of a paper. If it is in xml format, we use the xml2 R package, load the file in R, identify which type of journal group (we classified xml file structure in 3 journal groups) it corresponds to from the file name, then use children-parent relationships from the group to extract body text and identify sections. We then look for a subsection title containing the words &#39;method&#39;, &#39;model&#39;, &#39;case study&#39;, and &#39;data&#39;, in that order. If the subsection exists, we extract the text. If it&#39;s pdf, then we use the tm R package, load the file in R, identify which type of journal group (we classified pdf file structure in 7 journal groups) it corresponds to from the file name, then reconstruct the text as a one-column body text by identifying column and page breaks using group-specific rules. We then identify the first line of the methods section as containing &#39;MaterialandMethods&#39;, &#39;METHODS&#39;, &#39;StatisticalAnalys&#39;, or other expressions. If this first line exists, then we identify the end of the methods section as containing &#39;RESULTS&#39;, &#39;APPLICATION&#39;, &#39;Discussion&#39;, or other expressions. If the end exists, we extract the text between first and end." style="width:75.0%" alt="" />
+<p class="caption">Fig. 2.3. Summary of procedure to extract Material and Methods section from each paper.</p>
+</div>
 </center>
 <p><br /></p>
 <p>For some analyses (section <a href="analyses.html#analyses">3</a>), we needed the Material and methods
@@ -395,12 +401,14 @@ <h2><span class="header-section-number">2.3</span> Extracting the Material and M
 institutions we accessed them from.</p>
 <center>
 <!-- knitr::include_graphics("posts/moveco-images/MatMet.png"", out.width=33%) -->
-<p><img src="posts/moveco-images/journals.png" style="width:75.0%" /></p>
-Fig. 2.4. Number of articles about movement ecology of animals and human
+<div class="figure">
+<img src="posts/moveco-images/journals.png" title="Stacked bar plots of the number of movement articles identified by our algorithm and per journal, showing the number of articles that were downloaded (in blue) and how many of those had an identified (and extracted) methods section. Plos one had the number of articles (around 800) and almost all of them had an identified methods section. No other pattern can be seen from this plot." style="width:75.0%" alt="" />
+<p class="caption">Fig. 2.4. Number of articles about movement ecology of animals and human
 mobility identified by our algorithm and per journal. In blue, the number
 of articles that were downloaded and a methods section was identified.
 In yellow, the number of articles that were not downloaded. Only the journals
-with more than 20 identified articles are shown in the graphs.
+with more than 20 identified articles are shown in the graphs.</p>
+</div>
 </center>
 <p><br /></p>
 <!-- Wickham, Hadley, James Hester, and Jeroen Ooms. 2018. Xml2: Parse Xml. https://CRAN.R-project.org/package=xml2. -->

docs/index.html

@@ -24,7 +24,7 @@
 <meta name="author" content="Rocío Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero and Mathieu Basille" />
 
 
-<meta name="date" content="2022-03-06" />
+<meta name="date" content="2022-05-10" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -238,12 +238,12 @@ <h1>
 <div id="header">
 <h1 class="title">Recent trends in movement ecology of animals and human mobility</h1>
 <p class="author"><em>Rocío Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero and Mathieu Basille</em></p>
-<p class="date" style="margin-top: 1.5em;"><em>2022-03-06</em></p>
+<p class="date" style="margin-top: 1.5em;"><em>2022-05-10</em></p>
 </div>
 <div id="introduction" class="section level1" number="1">
 <h1><span class="header-section-number">1</span> Introduction</h1>
 <center>
-<img src="posts/moveco-images/mov-logo.png" style="width:40.0%" />
+<img src="posts/moveco-images/mov-logo.png" title="Representation of a bird flying over a trajectory (series of points, each one characterized by location and time). Below there is a moving boat. On the right, the words MOV ECO." style="width:40.0%" />
 </center>
 <p>This is the companion website for the manuscript “Recent trends in movement ecology of animals and human mobility,”
 a quantitative review of animal and human movement literature in 2009-2018 from Joo et al., serving as the manuscript’s supplementary information page. The R codes for the analyses are available in <a href="https://github.com/rociojoo/mov-eco-review">this GitHub repository</a>.</p>
@@ -275,7 +275,7 @@ <h2><span class="header-section-number">1.1</span> Abstract of the manuscript</h
 exploration of key movement processes like navigation and the evolutionary,
 physiological, and life-history consequences of movement.</p>
 <center>
-<p><img src="posts/moveco-images/wordcloud_abstracts_low.png" style="width:50.0%" /></p>
+<p><img src="posts/moveco-images/wordcloud_abstracts_low.png" title="Word cloud with the most frequent words in movement abstracts. The most important ones are movement, behavior, study, individuals, time, data, animal, habitat, species, area, pattern, activity, result, model, species, more or less in that order." style="width:50.0%" /></p>
 </center>
 <p><br /></p>
 

docs/r-session-information.html

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 <meta name="author" content="Rocío Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero and Mathieu Basille" />
 
 
-<meta name="date" content="2022-03-06" />
+<meta name="date" content="2022-05-10" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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docs/references.html

@@ -24,7 +24,7 @@
 <meta name="author" content="Rocío Joo, Simona Picardi, Matthew E. Boone, Thomas A. Clay, Samantha C. Patrick, Vilma S. Romero-Romero and Mathieu Basille" />
 
 
-<meta name="date" content="2022-03-06" />
+<meta name="date" content="2022-05-10" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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