Merge pull request #71 from trias-project/occurrence-indicators

Small improvements to occurrence indicator pipelines

.gitignore

@@ -34,6 +34,8 @@ vignettes/*.pdf
 src/*_cache/
 src/*_files/
 
+# knitr temp files (if failed to build website)
+src/*.html
 
 # Temporary files created by R markdown
 *.utf8.md

docs/get_data_input_checklist_indicators.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Damiano Oldoni" />
 
-<meta name="date" content="2019-12-09" />
+<meta name="date" content="2019-12-11" />
 
 <title>Get input data for checklist-based indicators</title>
 
@@ -418,7 +418,7 @@
 
 <h1 class="title toc-ignore">Get input data for checklist-based indicators</h1>
 <h4 class="author">Damiano Oldoni</h4>
-<h4 class="date">2019-12-09</h4>
+<h4 class="date">2019-12-11</h4>
 
 </div>
 

docs/index.html

@@ -369,15 +369,21 @@ <h2>Checklist-based indicators</h2>
 <h2>Occurrence-based indicators</h2>
 <p>In order to calculate an emergency index, we take into account:</p>
 <ol style="list-style-type: decimal">
-<li>number of occurrences per year</li>
-<li>area of occupancy (AOO)</li>
+<li>number of occurrences per year, or simply <em>occurrences</em></li>
+<li>area of occupancy (AOO), or simply <em>occupancy</em></li>
 </ol>
-<p>We work with GAM (Generalized Additive Models) and decision rules to assess the emerging status of a species. This is still work in progress. Still, if you want to get an idea about it, follow <a href="https://github.com/trias-project/indicators/issues/49">issue #49</a>.</p>
-<p>For the data manipulation of the taxonomic and occurrence information, see Appendix <a href="https://trias-project.github.io/indicators/occurrence_indicators_preprocessing.html">Preprocessing for occurrence-based indicators</a>.</p>
+<p>The workflow is divded in the following pipelines:</p>
+<ol style="list-style-type: decimal">
+<li><a href="https://trias-project.github.io/indicators/occurrence_indicators_appearing_taxa.html">Appearing or reappearing taxa in current year</a></li>
+<li><a href="https://trias-project.github.io/indicators/occurrence_indicators_modelling.html">Assessing partial emerging statuses of alien taxa</a></li>
+<li><a href="https://trias-project.github.io/indicators/ranking_emerging_status.html">Assessing emerging status and ranking</a></li>
+</ol>
+<p>We work with GAM (Generalized Additive Models) and decision rules to assess the emerging status of a species. This part is still work in progress, although all workflow steps are now completed. Follow <a href="https://github.com/trias-project/indicators/issues/49">issue #49</a> for more discussions about the different choices we took at every step of the workflow.</p>
+<p>For the data preparation of the taxonomic and occurrence information, see Appendix <a href="https://trias-project.github.io/indicators/occurrence_indicators_preprocessing.html">Preprocessing for occurrence-based indicators</a>. The output of this appendix is the starting point of the pipelines described above.</p>
 </div>
 <div id="repo-structure" class="section level2">
 <h2>Repo structure</h2>
-<p>The repository structure is based on <a href="http://drivendata.github.io/cookiecutter-data-science/">Cookiecutter Data Science</a>. Files indicated with <code>GENERATED</code> should not be edited manually.</p>
+<p>The repository structure is based on <a href="http://drivendata.github.io/cookiecutter-data-science/">Cookiecutter Data Science</a>. Files indicated with <code>GENERATED</code> should not be edited manually. This list can be not complete as the content of this repository is still in progress.</p>
 <pre><code>├── README.md              : Description of this repository
 ├── LICENSE                : Repository license
 ├── indicators.Rproj       : RStudio project file

docs/indicator_cumulative_number.html

@@ -15,7 +15,7 @@
 <meta name="author" content="Stijn Van Hoey" />
 <meta name="author" content="Tim Adriaens" />
 
-<meta name="date" content="2019-12-09" />
+<meta name="date" content="2019-12-11" />
 
 <title>Indicator: Cumulative number of alien species</title>
 
@@ -424,7 +424,7 @@ <h4 class="author">Damiano Oldoni</h4>
 <h4 class="author">Sander Devisscher</h4>
 <h4 class="author">Stijn Van Hoey</h4>
 <h4 class="author">Tim Adriaens</h4>
-<h4 class="date">2019-12-09</h4>
+<h4 class="date">2019-12-11</h4>
 
 </div>
 

docs/indicator_introductions_per_year.html

@@ -15,7 +15,7 @@
 <meta name="author" content="Stijn Van Hoey" />
 <meta name="author" content="Tim Adriaens" />
 
-<meta name="date" content="2019-12-09" />
+<meta name="date" content="2019-12-11" />
 
 <title>Indicator: Number of new introductions of alien species per year</title>
 
@@ -424,7 +424,7 @@ <h4 class="author">Damiano Oldoni</h4>
 <h4 class="author">Yasmine Verzelen</h4>
 <h4 class="author">Stijn Van Hoey</h4>
 <h4 class="author">Tim Adriaens</h4>
-<h4 class="date">2019-12-09</h4>
+<h4 class="date">2019-12-11</h4>
 
 </div>
 

docs/indicator_pathways.html

@@ -13,7 +13,7 @@
 <meta name="author" content="Damiano Oldoni" />
 <meta name="author" content="Stijn Van Hoey" />
 
-<meta name="date" content="2019-12-09" />
+<meta name="date" content="2019-12-11" />
 
 <title>Indicator: Pathways associated with alien species introductions</title>
 
@@ -421,7 +421,7 @@
 <h1 class="title toc-ignore">Indicator: Pathways associated with alien species introductions</h1>
 <h4 class="author">Damiano Oldoni</h4>
 <h4 class="author">Stijn Van Hoey</h4>
-<h4 class="date">2019-12-09</h4>
+<h4 class="date">2019-12-11</h4>
 
 </div>
 

docs/occurrence_indicators_appearing_taxa.html

@@ -14,7 +14,7 @@
 <meta name="author" content="Toon Van Daele" />
 <meta name="author" content="Tim Adriaens" />
 
-<meta name="date" content="2019-12-09" />
+<meta name="date" content="2019-12-11" />
 
 <title>Detect appearing and reappearing species</title>
 
@@ -422,7 +422,7 @@ <h1 class="title toc-ignore">Detect appearing and reappearing species</h1>
 <h4 class="author">Damiano Oldoni</h4>
 <h4 class="author">Toon Van Daele</h4>
 <h4 class="author">Tim Adriaens</h4>
-<h4 class="date">2019-12-09</h4>
+<h4 class="date">2019-12-11</h4>
 
 </div>