Commit 274c5027 authored by Facundo Muñoz's avatar Facundo Muñoz ®️
Browse files

update website

parent 760e7072
......@@ -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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</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">2019-04-13</h4>
<h4 class="date">2019-06-12</h4>
<div class="hidden name"><code>cmr_cartography-rmd.Rmd</code></div>
......@@ -90,60 +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"><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: 1.4-3, (SVN revision 828)</span>
<span class="co">#&gt; Geospatial Data Abstraction Library extensions to R successfully loaded</span>
<span class="co">#&gt; Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01</span>
<span class="co">#&gt; Path to GDAL shared files: /usr/share/gdal/2.1</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>
<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>))
<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>)
<span class="co">#&gt; Warning: replacing previous import 'gdalUtils::gdal_rasterize' by</span>
<span class="co">#&gt; 'sf::gdal_rasterize' when loading 'mapview'</span></code></pre></div>
<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 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"><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 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>
<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"><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 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>
</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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
This diff is collapsed.
......@@ -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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -35,7 +35,7 @@
</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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......@@ -89,22 +89,16 @@
<div class="page-header"><h1 class="hasAnchor">
<a href="#mapmcda" class="anchor"></a>mapMCDA <img src="reference/figures/logo.png" align="right">
</h1></div>
<div class="figure">
<img src="reference/figures/mapMCDA_overview.png">
</div>
<p><img src="reference/figures/mapMCDA_overview.png"></p>
<p><code>mapMCDA</code> helps producing <strong>risk maps</strong> by weighting <strong>risk factors</strong> using <strong>expert knowledge</strong>.</p>
<p>The typical use case is the lack of (reliable) data about the epidemics of a disease, but available information about well known <strong>risk factors</strong> (e.g. animal density, proximity to border, proximity to water courses, etc.).</p>
<p>In order to design a <strong>stratified sampling</strong> or a <strong>surveillance campaign</strong>, a preliminar risk map based on expert judgement is required.</p>
<p>This package (and method) provides a systematic and guided approach to build such maps.</p>
<div class="figure">
<img src="reference/figures/plot-risk-unit-1.png">
</div>
<p><img src="reference/figures/plot-risk-unit-1.png"></p>
<p>The package include a Graphical User Interface (Shiny) that helps in processing and weighting risk factors.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mapMCDA)
<span class="kw"><a href="reference/mapMCDA_app.html">mapMCDA_app</a></span>()</code></pre></div>
<div class="figure">
<img src="reference/figures/interface.png">
</div>
<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">library</a></span>(mapMCDA)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="reference/mapMCDA_app.html">mapMCDA_app</a></span>()</a></code></pre></div>
<p><img src="reference/figures/interface.png"></p>
<div id="installing-the-package" class="section level2">
<h2 class="hasAnchor">
<a href="#installing-the-package" class="anchor"></a>Installing the package</h2>
......@@ -114,10 +108,10 @@
<!-- install.packages("mapMCDA") -->
<!-- ``` -->
<!-- To benefit from the latest features and bug fixes, install the development, *github* version of the package using: -->
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><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>(<span class="st">"remotes"</span>)) {
<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"remotes"</span>)
}
remotes<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/remotes/topics/install_github">install_github</a></span>(<span class="st">"Cirad-ASTRE/mapMCDA"</span>)</code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><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>(<span class="st">"remotes"</span>)) {</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"remotes"</span>)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3">}</a>
<a class="sourceLine" id="cb2-4" data-line-number="4">remotes<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/remotes/topics/install_github">install_github</a></span>(<span class="st">"Cirad-ASTRE/mapMCDA"</span>)</a></code></pre></div>
<!-- # Resources -->
<!-- ## Vignettes -->
<!-- An overview and examples of *mapMCDA* are provided in the vignettes: -->
......
......@@ -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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
pandoc: 1.19.2.1
pandoc: 2.3.1
pkgdown: 1.3.0
pkgdown_sha: ~
articles:
......
......@@ -65,7 +65,7 @@
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -65,7 +65,7 @@
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -67,7 +67,7 @@ Pairwise Comparison Method (Saaty 1987, Saaty 1996, Malczewski 1999)" />
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -66,7 +66,7 @@ number of fields, or fails." />
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -65,7 +65,7 @@
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -66,7 +66,7 @@ within the limits of a given mask." />
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -65,7 +65,7 @@
</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">0.4.9</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
......@@ -65,7 +65,7 @@
</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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......@@ -160,11 +160,11 @@ the Basic Reproduction Number \(R_0\) of an epidemy to the
context of a network. It thus quantifies the potential for
transmission of an infection throughout the contact network. It is
computed in terms of the incoming-outgoing rates from the network's
nodes: $$R_0 = \beta \frac{\hat{k_\mathrm{in}
k_\mathrm{out}}}{\hat{k_\mathrm{in}}},$$
nodes: $$R_0 = \beta \frac{\overline{k_\mathrm{in}\cdot
k_\mathrm{out}}}{\overline{k_\mathrm{in}}},$$
where \(\beta\) is the transmission coefficient among animals,
\(k_\mathrm{in/out}\) are the in/out-degrees of a node
and the \(&lt;·&gt;\) symbol represents the average value
and the \(\overline{\cdot}\) symbol represents the average value
across all nodes in the graph.</p>
<p>The unweighted value computed above is most appropriate for a
highly infectious epidemy with high animal-prevalence on nodes, as
......@@ -175,7 +175,7 @@ is more appropriate for low-prevalence diseases, where the
transmission probability is assumed proportional to the number of
contacts.</p>
<p>The default value of 1 for the probability of transmission
<code>beta</code> implies that every infectious contact leads to
\(\beta\) implies that every infectious contact leads to
transmission.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
......
......@@ -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">0.4.10</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.13</span>
</span>
</div>
......
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