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Migrate to Foregemia

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.Rbuildignore
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......@@ -8,9 +8,11 @@
^appveyor\.yml$
^codecov\.yml$
^cran-comments\.md$
^docs/
^public/
^R/pkg_deps.R
^CONDUCT\.md$
^inst/Example
^dev
^_pkgdown\.yml$
^\.gitlab-ci\.yml
.gitlab-ci.yml 0 → 100644
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pages:
stage: deploy
script:
- echo assuming pages are built in public
artifacts:
paths:
- public
only:
- master
DESCRIPTION
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Package: mapMCDA
Title: Produce an epidemiological risk map by weighting multiple risk
factors
Version: 0.4.14
Date: 2019-06-15
Version: 0.4.15
Date: 2019-08-27
Authors@R: c( person("Andrea", "Apolloni", email =
"andrea.apolloni@cirad.fr", role = c("ctb"), comment = "Animal
mobility algorithm"), person("Elena", "Arsevska", email =
......@@ -32,6 +32,6 @@ Imports: classInt, deldir, geojsonio, geojsonlint, geonetwork, igraph,
sp, stringr, utils
Suggests: devtools, knitr, mapview, rmarkdown, roxygen2, testthat
RoxygenNote: 6.1.1
URL: https://Cirad-ASTRE.github.io/mapMCDA
BugReports: https://github.com/Cirad-ASTRE/mapMCDA/issues
URL: https://umr-astre.pages.mia.inra.fr/mapMCDA
BugReports: https://forgemia.inra.fr/umr-astre/mapMCDA/issues
VignetteBuilder: knitr
README.Rmd
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......@@ -51,19 +51,19 @@ mapMCDA_app()
## Installing the package
`mapMCDA` is on its way to CRAN. In the meanwhile, install from
GitHub as follows.
GitLab as follows.
<!-- To install the current stable, CRAN version of the package, type: -->
<!-- ```{r install, eval = FALSE} -->
<!-- install.packages("mapMCDA") -->
<!-- ``` -->
<!-- To benefit from the latest features and bug fixes, install the development, *github* version of the package using: -->
```{r install-github, eval = FALSE}
<!-- To benefit from the latest features and bug fixes, install the development, version of the package using: -->
```{r install-gitlab, eval = FALSE}
if (!require("remotes")) {
install.packages("remotes")
}
remotes::install_github("Cirad-ASTRE/mapMCDA")
remotes::install_gitlab("umr-astre/mapMCDA", host = "forgemia.inra.fr")
```
......@@ -84,8 +84,8 @@ remotes::install_github("Cirad-ASTRE/mapMCDA")
## Getting help online
Bug reports and feature requests should be posted on *github* using
the [*issue*](http://github.com/Cirad-ASTRE/mapMCDA/issues) system.
Bug reports and feature requests should be posted on *GitLab* using
the [*issue*](http://forgemia.inra.fr/umr-astre/mapMCDA/issues) system.
For support, reach out in the
[mapMCDA mailing list](https://listes.cirad.fr/sympa/info/mapmcda).
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destination: public
docs/CONDUCT.html → public/CONDUCT.html
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......@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mapMCDA</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.14</span>
</span>
</div>
......
docs/LICENSE-text.html → public/LICENSE-text.html
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......@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mapMCDA</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.14</span>
</span>
</div>
......
docs/articles/cmr_cartography-rmd.html → public/articles/cmr_cartography-rmd.html
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......@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mapMCDA</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.14</span>
</span>
</div>
......@@ -80,7 +80,7 @@
<h1>Collection and pre-processing of cartographic information for Cameroon</h1>
<h4 class="author">Facundo Muñoz</h4>
<h4 class="date">2019-06-12</h4>
<h4 class="date">2019-08-27</h4>
<div class="hidden name"><code>cmr_cartography-rmd.Rmd</code></div>
......@@ -90,58 +90,58 @@
<p>Here we demonstrate how we have downloaded and pre-processed the cartographic information for Cameroon which is included in the package.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(raster)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">#&gt; Loading required package: raster</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co">#&gt; Loading required package: sp</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rgdal)</a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">#&gt; Loading required package: rgdal</span></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">#&gt; rgdal: version: 1.4-4, (SVN revision 833)</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co">#&gt; Geospatial Data Abstraction Library extensions to R successfully loaded</span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co">#&gt; Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15</span></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">#&gt; Path to GDAL shared files: /usr/share/gdal/2.2</span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co">#&gt; GDAL binary built with GEOS: TRUE </span></a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co">#&gt; Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="co">#&gt; Path to PROJ.4 shared files: (autodetected)</span></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">#&gt; Linking to sp version: 1.3-1</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14"></a>
<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="cf">if</span>(<span class="op">!</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(mapview, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)) </a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/cat">cat</a></span>(<span class="st">"We suggest installing the pacakge mapview for interactive visualisation"</span>,</a>
<a class="sourceLine" id="cb1-17" data-line-number="17"> <span class="st">"of cartography from within R"</span>)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(raster)
<span class="co">#&gt; Loading required package: raster</span>
<span class="co">#&gt; Loading required package: sp</span>
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rgdal)
<span class="co">#&gt; Loading required package: rgdal</span>
<span class="co">#&gt; rgdal: version: 1.4-4, (SVN revision 833)</span>
<span class="co">#&gt; Geospatial Data Abstraction Library extensions to R successfully loaded</span>
<span class="co">#&gt; Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15</span>
<span class="co">#&gt; Path to GDAL shared files: /usr/share/gdal/2.2</span>
<span class="co">#&gt; GDAL binary built with GEOS: TRUE </span>
<span class="co">#&gt; Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]</span>
<span class="co">#&gt; Path to PROJ.4 shared files: (autodetected)</span>
<span class="co">#&gt; Linking to sp version: 1.3-1</span>
if(!<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(mapview, <span class="dt">quietly =</span> <span class="ot">TRUE</span>))
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/cat">cat</a></span>(<span class="st">"We suggest installing the pacakge mapview for interactive visualisation"</span>,
<span class="st">"of cartography from within R"</span>)</code></pre></div>
<div id="administrative-borders" class="section level2">
<h2 class="hasAnchor">
<a href="#administrative-borders" class="anchor"></a>Administrative borders</h2>
<p>Download cartography from the Global Administrative Borders Database (GADM, <a href="https://gadm.org/" class="uri">https://gadm.org/</a>) directly from within R.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"></a>
<a class="sourceLine" id="cb2-2" data-line-number="2">cmr_admin3 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/getData">getData</a></span>(<span class="st">'GADM'</span>, <span class="dt">country =</span> <span class="st">"CMR"</span>, <span class="dt">level=</span><span class="dv">3</span>)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co"># mapview(cmr_admin3, zcol = "NAME_3")</span></a></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co">## This only works locally.</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3">prodel_path &lt;-<span class="st"> "/home/facu/CmisSync/Cirad/Sites/PRODEL/documentLibrary/carto"</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4">water_bodies &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/readOGR">readOGR</a></span>(prodel_path, <span class="dt">layer =</span> <span class="st">"wb_cam.shp"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">national_parks &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/readOGR">readOGR</a></span>(</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(prodel_path, <span class="st">"WDPA_Mar2018_CMR-shapefile"</span>),</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"> <span class="st">"WDPA_Mar2018_CMR-shapefile-polygons"</span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4">)</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Not using this for the moment</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2">ps_cam &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/raster">raster</a></span>(<span class="st">"ps_cam.tif"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">animal_density_world &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/raster">raster</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(prodel_path, <span class="st">"glw"</span>, <span class="st">"WdCt8k_vf_Mn_Rw_To.tif"</span>))</a>
<a class="sourceLine" id="cb6-2" data-line-number="2">animal_density &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/mask">mask</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/crop">crop</a></span>(animal_density_world, <span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/extent">extent</a></span>(cmr_admin3)), cmr_admin3)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># plot(animal_density)</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="co"># summary(animal_density$WdCt8k_vf_Mn_Rw_To)</span></a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">
cmr_admin3 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/getData">getData</a></span>(<span class="st">'GADM'</span>, <span class="dt">country =</span> <span class="st">"CMR"</span>, <span class="dt">level=</span><span class="dv">3</span>)
<span class="co"># mapview(cmr_admin3, zcol = "NAME_3")</span></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">
## This only works locally.
prodel_path &lt;-<span class="st"> "/home/facu/CmisSync/Cirad/Sites/PRODEL/documentLibrary/carto"</span>
water_bodies &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/readOGR">readOGR</a></span>(prodel_path, <span class="dt">layer =</span> <span class="st">"wb_cam.shp"</span>)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">national_parks &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/readOGR">readOGR</a></span>(
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(prodel_path, <span class="st">"WDPA_Mar2018_CMR-shapefile"</span>),
<span class="st">"WDPA_Mar2018_CMR-shapefile-polygons"</span>
)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Not using this for the moment</span>
ps_cam &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/raster">raster</a></span>(<span class="st">"ps_cam.tif"</span>)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">animal_density_world &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/raster">raster</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(prodel_path, <span class="st">"glw"</span>, <span class="st">"WdCt8k_vf_Mn_Rw_To.tif"</span>))
animal_density &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/mask">mask</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/crop">crop</a></span>(animal_density_world, <span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/extent">extent</a></span>(cmr_admin3)), cmr_admin3)
<span class="co"># plot(animal_density)</span>
<span class="co"># summary(animal_density$WdCt8k_vf_Mn_Rw_To)</span></code></pre></div>
</div>
<div id="save-pre-processed-cartography-for-use-within-the-package" class="section level2">
<h2 class="hasAnchor">
<a href="#save-pre-processed-cartography-for-use-within-the-package" class="anchor"></a>Save pre-processed cartography for use within the package</h2>
<p>Prefer standard and modern Open Geospatial Consortium (<a href="http://www.opengeospatial.org/">OGC</a>) formats: GeoPackage for vector maps and GeoTiff for raster images.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">cmr_dir &lt;-<span class="st"> "./inst/cartography/CMR"</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/files2">dir.create</a></span>(cmr_dir, <span class="dt">recursive =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb7-3" data-line-number="3"></a>
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(cmr_admin3, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"cmr_admin3.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"cmr_admin3"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)</a>
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(water_bodies, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"water_bodies.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"water_bodies"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)</a>
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(national_parks, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"national_parks.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"national_parks"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)</a>
<a class="sourceLine" id="cb7-7" data-line-number="7"></a>
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/writeRaster">writeRaster</a></span>(animal_density, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"animal.density.tif"</span>))</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">cmr_dir &lt;-<span class="st"> "./inst/cartography/CMR"</span>
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/files2">dir.create</a></span>(cmr_dir, <span class="dt">recursive =</span> <span class="ot">TRUE</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(cmr_admin3, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"cmr_admin3.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"cmr_admin3"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(water_bodies, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"water_bodies.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"water_bodies"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/rgdal/topics/writeOGR">writeOGR</a></span>(national_parks, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"national_parks.gpkg"</span>), <span class="dt">layer =</span> <span class="st">"national_parks"</span>, <span class="dt">driver =</span> <span class="st">"GPKG"</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/writeRaster">writeRaster</a></span>(animal_density, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/file.path">file.path</a></span>(cmr_dir, <span class="st">"animal.density.tif"</span>))</code></pre></div>
</div>
</div>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mapMCDA</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.14</span>
</span>
</div>
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......@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mapMCDA</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.14</span>
</span>
</div>
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