Commit 6342467b authored by Facundo Muñoz's avatar Facundo Muñoz ®️
Browse files

Migrate to Foregemia

parent 0980178e
Pipeline #4061 passed with stage
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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
pages:
stage: deploy
script:
- echo assuming pages are built in public
artifacts:
paths:
- public
only:
- master
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
......@@ -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).
......
destination: public
......@@ -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>
......
......@@ -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>
......
......@@ -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>
......
......@@ -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>
......
......@@ -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>
......@@ -79,7 +79,7 @@
<div class="page-header toc-ignore">
<h1>mapMCDA: aperçu du package</h1>
<h4 class="date">2019-06-12</h4>
<h4 class="date">2019-08-27</h4>
<div class="hidden name"><code>mapMCDA.Rmd</code></div>
......@@ -88,16 +88,16 @@
<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>(sp)</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>(sp)</code></pre></div>
<pre><code>## Loading required package: sp</code></pre>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(raster)</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)</code></pre></div>
<pre><code>## Loading required package: raster</code></pre>
<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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rasterVis)</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>(rasterVis)</code></pre></div>
<pre><code>## Loading required package: rasterVis</code></pre>
<pre><code>## Loading required package: lattice</code></pre>
<pre><code>## Loading required package: latticeExtra</code></pre>
<pre><code>## Loading required package: RColorBrewer</code></pre>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(mapMCDA)</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>(mapMCDA)</code></pre></div>
<pre><code>## Loading required package: mapMCDA</code></pre>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
......@@ -118,18 +118,18 @@
<p>L’objet <code>cmr</code> est une simple liste de cartes : objets de type <code>Spatial*</code> pour les cartes vectoriels et de type <code>RasterLayer</code> pour les cartes raster.</p>
<p>Pour utiliser d’autre cartographie, utiliser les fonctions <code><a href="https://www.rdocumentation.org/packages/rgdal/topics/readOGR">rgdal::readOGR()</a></code> et <code><a href="https://www.rdocumentation.org/packages/raster/topics/raster">raster::raster()</a></code> respectivement pour des cartes vectoriels ou raster.</p>
<p>On peut aussi bénéficier de la fonction <code><a href="../reference/layer_type.html">layer_type()</a></code> pour charger tout type des cartes automatiquement, comme démontré dans le code commenté.</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">cmr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mapMCDA_datasets.html">mapMCDA_datasets</a></span>()</a>
<a class="sourceLine" id="cb12-2" data-line-number="2"></a>
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="co"># layers &lt;- list.files(</span></a>
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co"># system.file("cartography/CMR", package = "mapMCDA"),</span></a>
<a class="sourceLine" id="cb12-5" data-line-number="5"><span class="co"># full.names = TRUE</span></a>
<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="co"># )</span></a>
<a class="sourceLine" id="cb12-7" data-line-number="7"><span class="co"># cmr &lt;- lapply(layers, load_layer)</span></a>
<a class="sourceLine" id="cb12-8" data-line-number="8"><span class="co"># names(cmr) &lt;- rmext(basename(layers)))</span></a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">cmr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mapMCDA_datasets.html">mapMCDA_datasets</a></span>()
<span class="co"># layers &lt;- list.files(</span>
<span class="co"># system.file("cartography/CMR", package = "mapMCDA"),</span>
<span class="co"># full.names = TRUE</span>
<span class="co"># )</span>
<span class="co"># cmr &lt;- lapply(layers, load_layer)</span>
<span class="co"># names(cmr) &lt;- rmext(basename(layers)))</span></code></pre></div>
<p>L’une de ces cartes est celle des unités épidémiologiques, utilisée pour établir le cadre de travail.</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">unites_epi &lt;-<span class="st"> </span>cmr<span class="op">$</span>cmr_admin3</a>
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">0</span>, <span class="dv">0</span>, <span class="dv">0</span>))</a>
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/plot">plot</a></span>(unites_epi)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">unites_epi &lt;-<span class="st"> </span>cmr$cmr_admin3
<span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">0</span>, <span class="dv">0</span>, <span class="dv">0</span>))
<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/plot">plot</a></span>(unites_epi)</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/unite-epidemiologique-1.png" alt="Unités épidémiologiques d'exemple pour le Cameroun." width="700"><p class="caption">
Unités épidémiologiques d’exemple pour le Cameroun.
......@@ -142,17 +142,17 @@ Unités épidémiologiques d’exemple pour le Cameroun.
<p>Chaque facteur de risque varie dans une échelle qui lui est propre. La densité animale, par exemple, varie entre 0 et presque 5500 têtes par <span class="math inline">\(km^2\)</span>.</p>
<p>Pour les cartes <em>vectorielles</em>, qui representent la localisation des entités spatiales telles que lacs ou forêts, on considère la <strong>distance</strong> à dites entités.</p>
<p>Ce package utilise pour l’instant une fonction linèaire pour la mise en échelle. Cependant, la rélation peut être directe ou inverse.</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/plot">plot</a></span>(</a>
<a class="sourceLine" id="cb14-2" data-line-number="2"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">x =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">100</span>), <span class="dt">y =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">100</span>)),</a>
<a class="sourceLine" id="cb14-3" data-line-number="3"> <span class="dt">type =</span> <span class="st">'l'</span>,</a>
<a class="sourceLine" id="cb14-4" data-line-number="4"> <span class="dt">xaxs =</span> <span class="st">"i"</span>,</a>
<a class="sourceLine" id="cb14-5" data-line-number="5"> <span class="dt">yaxs =</span> <span class="st">"i"</span>,</a>
<a class="sourceLine" id="cb14-6" data-line-number="6"> <span class="dt">xaxt =</span> <span class="st">"n"</span>,</a>
<a class="sourceLine" id="cb14-7" data-line-number="7"> <span class="dt">lab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">7</span>),</a>
<a class="sourceLine" id="cb14-8" data-line-number="8"> <span class="dt">xlab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Échelle originale"</span>),</a>
<a class="sourceLine" id="cb14-9" data-line-number="9"> <span class="dt">ylab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Échelle de risque"</span>)</a>
<a class="sourceLine" id="cb14-10" data-line-number="10">)</a>
<a class="sourceLine" id="cb14-11" data-line-number="11"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/abline">abline</a></span>(<span class="dv">100</span>, <span class="dv">-1</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/raster/topics/plot">plot</a></span>(
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">x =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">100</span>), <span class="dt">y =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">100</span>)),
<span class="dt">type =</span> <span class="st">'l'</span>,
<span class="dt">xaxs =</span> <span class="st">"i"</span>,
<span class="dt">yaxs =</span> <span class="st">"i"</span>,
<span class="dt">xaxt =</span> <span class="st">"n"</span>,
<span class="dt">lab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">7</span>),
<span class="dt">xlab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Échelle originale"</span>),
<span class="dt">ylab =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Échelle de risque"</span>)
)
<span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/abline">abline</a></span>(<span class="dv">100</span>, -<span class="dv">1</span>)</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/mise-echelle-1.png" alt="Mis en échelle directe ou inverse." width="384"><p class="caption">
Mis en échelle directe ou inverse.
......@@ -160,27 +160,27 @@ Mis en échelle directe ou inverse.
</div>
<p>La fonction <code><a href="../reference/risk_layer.html">risk_layer()</a></code> calcule la carte de risque associé à un facteur concret dans une échelle donnée. Par défault c’est entre 0 et 100. Pour inverser la rélation il suffit de passer les limits dans l’ordre inverse, e.g. <code><a href="https://www.rdocumentation.org/packages/base/topics/c">c(100, 0)</a></code>.</p>
<p>D’ailleurs, elle utilise la carte d’unités épidémiologiques pour établir les limits de calcul de risque.</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">risques &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(</a>
<a class="sourceLine" id="cb15-2" data-line-number="2"> <span class="dt">dens_animale =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(</a>
<a class="sourceLine" id="cb15-3" data-line-number="3"> cmr<span class="op">$</span>animal.density,</a>
<a class="sourceLine" id="cb15-4" data-line-number="4"> <span class="dt">boundaries =</span> unites_epi</a>
<a class="sourceLine" id="cb15-5" data-line-number="5"> <span class="co"># , scale_target = c(0, 100) # échelle directe par défault</span></a>
<a class="sourceLine" id="cb15-6" data-line-number="6"> ),</a>
<a class="sourceLine" id="cb15-7" data-line-number="7"> <span class="dt">points_eau =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(</a>
<a class="sourceLine" id="cb15-8" data-line-number="8"> cmr<span class="op">$</span>water_bodies,</a>
<a class="sourceLine" id="cb15-9" data-line-number="9"> <span class="dt">boundaries =</span> unites_epi,</a>
<a class="sourceLine" id="cb15-10" data-line-number="10"> <span class="dt">scale_target =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">0</span>) <span class="co"># échelle renversée</span></a>
<a class="sourceLine" id="cb15-11" data-line-number="11"> ),</a>
<a class="sourceLine" id="cb15-12" data-line-number="12"> <span class="dt">parcs =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(</a>
<a class="sourceLine" id="cb15-13" data-line-number="13"> cmr<span class="op">$</span>national_parks,</a>
<a class="sourceLine" id="cb15-14" data-line-number="14"> <span class="dt">boundaries =</span> unites_epi,</a>
<a class="sourceLine" id="cb15-15" data-line-number="15"> <span class="dt">scale_target =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">0</span>) <span class="co"># échelle renversée</span></a>
<a class="sourceLine" id="cb15-16" data-line-number="16"> )</a>
<a class="sourceLine" id="cb15-17" data-line-number="17">)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">risques &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(
<span class="dt">dens_animale =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(
cmr$animal.density,
<span class="dt">boundaries =</span> unites_epi
<span class="co"># , scale_target = c(0, 100) # échelle directe par défault</span>
),
<span class="dt">points_eau =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(
cmr$water_bodies,
<span class="dt">boundaries =</span> unites_epi,
<span class="dt">scale_target =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">0</span>) <span class="co"># échelle renversée</span>
),
<span class="dt">parcs =</span> <span class="kw"><a href="../reference/risk_layer.html">risk_layer</a></span>(
cmr$national_parks,
<span class="dt">boundaries =</span> unites_epi,
<span class="dt">scale_target =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="dv">0</span>) <span class="co"># échelle renversée</span>
)
)</code></pre></div>
<p>On voudrait examiner les cartes de risque ainsi calculées. Mais pour cela, il faut qu’elles soient <em>alignées</em>. C’est à dire, qu’elles aient les mêmes <em>extents</em>, <em>résolutions</em> et <em>projections</em>.</p>
<p>On peut se servir de la fonction <code><a href="../reference/align_layers.html">align_layers()</a></code> qui arrange tout ça pour nous. Noter que ce pas n’est pas nécessaire pour continuer, car cette fonction est automatiquement executée si besoin.</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">risques_alignes &lt;-<span class="st"> </span><span class="kw"><a href="../reference/align_layers.html">align_layers</a></span>(risques)</a>
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/rasterVis/topics/levelplot-methods">levelplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/stack">stack</a></span>(risques_alignes))</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">risques_alignes &lt;-<span class="st"> </span><span class="kw"><a href="../reference/align_layers.html">align_layers</a></span>(risques)
<span class="kw"><a href="https://www.rdocumentation.org/packages/rasterVis/topics/levelplot-methods">levelplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/stack">stack</a></span>(risques_alignes))</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/align-layers-1.png" alt="Niveaux de risque associé à chaque facteur." width="576"><p class="caption">
Niveaux de risque associé à chaque facteur.
......@@ -192,35 +192,35 @@ Niveaux de risque associé à chaque facteur.
<a href="#ponderation-des-facteurs-de-risque" class="anchor"></a>3. Pondération des facteurs de risque</h1>
<p>Il y a 3 facteurs à considérer. Il faut comparer 2-à-2 leurs importances relatives en une échelle de 1 à 9 et representer ces rélations en une matrice qui doit avoir des 1 dans son diagonale.</p>
<p>Noter que les élements symmetriques doivent être réciproques.</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">M &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(</a>
<a class="sourceLine" id="cb17-2" data-line-number="2"> <span class="dv">1</span>, <span class="dv">6</span>, <span class="dv">4</span>,</a>
<a class="sourceLine" id="cb17-3" data-line-number="3"> <span class="dv">1</span><span class="op">/</span><span class="dv">6</span>, <span class="dv">1</span>, <span class="dv">3</span>,</a>
<a class="sourceLine" id="cb17-4" data-line-number="4"> <span class="dv">1</span><span class="op">/</span><span class="dv">4</span>, <span class="dv">1</span><span class="op">/</span><span class="dv">3</span>, <span class="dv">1</span></a>
<a class="sourceLine" id="cb17-5" data-line-number="5">), <span class="dt">byrow =</span> <span class="ot">TRUE</span>, <span class="dv">3</span>, <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(M) &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">rownames</a></span>(M) &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/names">names</a></span>(risques)</a>
<a class="sourceLine" id="cb17-7" data-line-number="7">knitr<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(M, <span class="dt">digits =</span> <span class="dv">2</span>)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">M &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(
<span class="dv">1</span>, <span class="dv">6</span>, <span class="dv">4</span>,
<span class="dv">1</span>/<span class="dv">6</span>, <span class="dv">1</span>, <span class="dv">3</span>,
<span class="dv">1</span>/<span class="dv">4</span>, <span class="dv">1</span>/<span class="dv">3</span>, <span class="dv">1</span>
), <span class="dt">byrow =</span> <span class="ot">TRUE</span>, <span class="dv">3</span>, <span class="dv">3</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(M) &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">rownames</a></span>(M) &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/raster/topics/names">names</a></span>(risques)
knitr::<span class="kw">kable</span>(M, <span class="dt">digits =</span> <span class="dv">2</span>)</code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="left"></th>
<th align="right">dens_animale</th>
<th align="right">points_eau</th>
<th align="right">parcs</th>
</tr></thead>
<tbody>
<tr class="odd">
<td>dens_animale</td>
<td align="left">dens_animale</td>
<td align="right">1.00</td>
<td align="right">6.00</td>
<td align="right">4</td>
</tr>
<tr class="even">
<td>points_eau</td>
<td align="left">points_eau</td>
<td align="right">0.17</td>
<td align="right">1.00</td>
<td align="right">3</td>
</tr>
<tr class="odd">
<td>parcs</td>
<td align="left">parcs</td>
<td align="right">0.25</td>
<td align="right">0.33</td>
<td align="right">1</td>
......@@ -229,7 +229,7 @@ Niveaux de risque associé à chaque facteur.
</table>
<p>Dans cette exemple, on considère que la densité animale est 6 fois plus importante que la distance aux points d’eau, et 4 fois plus importante que la distance aux parcs. Au même temps, que la distance aux points d’eau est 3 fois plus importante que celle aux parcs.</p>
<p>Le système calcule les coefficients de pondération les plus consistents avec ces valorations par paires, avec la fonction <code><a href="../reference/compute_weights.html">compute_weights()</a></code>.</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">w &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compute_weights.html">compute_weights</a></span>(M)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">w &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compute_weights.html">compute_weights</a></span>(M)</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/compute-weights-1.png" alt="Pondération des facteurs de risque." width="384"><p class="caption">
Pondération des facteurs de risque.
......@@ -240,15 +240,15 @@ Pondération des facteurs de risque.
<h1 class="hasAnchor">
<a href="#calcul-de-la-carte-de-risque" class="anchor"></a>4. Calcul de la carte de risque</h1>
<p>La fonction <code><a href="../reference/wlc.html">wlc()</a></code> (pour weighted linear combination) combine tous les facteurs de risque en utilisant les poids calculés précedament, et produise une carte de risque qui couvre toute la région.</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">risque_combine &lt;-<span class="st"> </span><span class="kw"><a href="../reference/wlc.html">wlc</a></span>(risques, w)</a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/rasterVis/topics/levelplot-methods">levelplot</a></span>(risque_combine)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">risque_combine &lt;-<span class="st"> </span><span class="kw"><a href="../reference/wlc.html">wlc</a></span>(risques, w)
<span class="kw"><a href="https://www.rdocumentation.org/packages/rasterVis/topics/levelplot-methods">levelplot</a></span>(risque_combine)</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/wlc-1.png" alt="Carte de risque combiné." width="576"><p class="caption">
Carte de risque combiné.
</p>
</div>
<p>Enfin, on peut produîre una carte par unité épidémiologique et dans une échelle de quelques niveaux de risque.</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw"><a href="../reference/risk_plot.html">risk_plot</a></span>(unites_epi, <span class="kw"><a href="../reference/risk_unit.html">risk_unit</a></span>(risque_combine, unites_epi), <span class="dt">n =</span> <span class="dv">5</span>)</a></code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/risk_plot.html">risk_plot</a></span>(unites_epi, <span class="kw"><a href="../reference/risk_unit.html">risk_unit</a></span>(risque_combine, unites_epi), <span class="dt">n =</span> <span class="dv">5</span>)</code></pre></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/risk-plot-1.png" alt="Carte de niveaux de risque par unité épidémiologique." width="576"><p class="caption">
Carte de niveaux de risque par unité épidémiologique.
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