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Commit 3810e799 authored by Facundo Muñoz's avatar Facundo Muñoz :registered:
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Website. Update Readme.

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......@@ -3,7 +3,10 @@ output: github_document
---
<!-- badges: start -->
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mapMCDA)](https://cran.r-project.org/package=mapMCDA)
[![UMR ASTRE R-universe](https://cirad-astre.r-universe.dev/badges/:name)](https://cirad-astre.r-universe.dev)
[![mapMCDA R-universe status badge](https://cirad-astre.r-universe.dev/badges/mapMCDA)](https://cirad-astre.r-universe.dev/mapMCDA)
[![Build status](https://forgemia.inra.fr/umr-astre/mapMCDA/badges/master/pipeline.svg)](https://forgemia.inra.fr/umr-astre/mapMCDA/pipelines)
[![Appveyor Build status](https://ci.appveyor.com/api/projects/status/5p751lpceeiy18kp?svg=true)](https://ci.appveyor.com/project/famuvie/mapmcda)
<!-- badges: end -->
......@@ -72,7 +75,9 @@ remotes::install_gitlab("umr-astre/mapMCDA", host = "forgemia.inra.fr")
-->
```{r install-r-universe, eval = FALSE}
install.packages("mapMCDA", repos = "https://cirad-astre.r-universe.dev")
# Install mapMCDA in R:
install.packages('mapMCDA', repos = c('https://cirad-astre.r-universe.dev', 'https://cloud.r-project.org'))
```
......
<!-- badges: start -->
[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/mapMCDA)](https://cran.r-project.org/package=mapMCDA)
[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mapMCDA)](https://cran.r-project.org/package=mapMCDA)
[![UMR ASTRE
R-universe](https://cirad-astre.r-universe.dev/badges/:name)](https://cirad-astre.r-universe.dev)
[![mapMCDA R-universe status
badge](https://cirad-astre.r-universe.dev/badges/mapMCDA)](https://cirad-astre.r-universe.dev/mapMCDA)
[![Build
status](https://forgemia.inra.fr/umr-astre/mapMCDA/badges/master/pipeline.svg)](https://forgemia.inra.fr/umr-astre/mapMCDA/pipelines)
[![Appveyor Build
......@@ -50,8 +57,7 @@ r-universe as follows
<!-- ``` -->
<!-- To benefit from the latest features and bug fixes, install the development, version of the package using: -->
<!--
```r
&#10;```r
if (!require("remotes")) {
install.packages("remotes")
}
......@@ -60,7 +66,8 @@ remotes::install_gitlab("umr-astre/mapMCDA", host = "forgemia.inra.fr")
-->
``` r
install.packages("mapMCDA", repos = "https://cirad-astre.r-universe.dev")
# Install mapMCDA in R:
install.packages('mapMCDA', repos = c('https://cirad-astre.r-universe.dev', 'https://cloud.r-project.org'))
```
<!-- # Resources -->
......
<!-- badges: start -->
[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/mapMCDA)](https://cran.r-project.org/package=mapMCDA)
[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mapMCDA)](https://cran.r-project.org/package=mapMCDA)
[![UMR ASTRE
R-universe](https://cirad-astre.r-universe.dev/badges/:name)](https://cirad-astre.r-universe.dev)
[![mapMCDA R-universe status
badge](https://cirad-astre.r-universe.dev/badges/mapMCDA)](https://cirad-astre.r-universe.dev/mapMCDA)
[![Build
status](https://forgemia.inra.fr/umr-astre/mapMCDA/badges/master/pipeline.svg)](https://forgemia.inra.fr/umr-astre/mapMCDA/pipelines)
[![Appveyor Build
......@@ -21,7 +28,8 @@ factors** (e.g. animal density, proximity to border, proximity to water
courses, etc.).
In order to design a **stratified sampling** or a **surveillance
campaign**, a preliminar risk map based on expert judgement is required.
campaign**, a preliminary risk map based on expert judgement is
required.
This package (and method) provides a systematic and guided approach to
build such maps.
......@@ -40,39 +48,34 @@ mapMCDA_app()
## Installing the package
`mapMCDA` is on its way to CRAN. In the meanwhile, install from GitLab
as
follows.
`mapMCDA` is on its way to CRAN. In the meanwhile, install from our
r-universe 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, version of the package using: -->
``` r
<!--
&#10;```r
if (!require("remotes")) {
install.packages("remotes")
}
remotes::install_gitlab("umr-astre/mapMCDA", host = "forgemia.inra.fr")
```
-->
<!-- # Resources -->
``` r
# Install mapMCDA in R:
install.packages('mapMCDA', repos = c('https://cirad-astre.r-universe.dev', 'https://cloud.r-project.org'))
```
<!-- # Resources -->
<!-- ## Vignettes -->
<!-- An overview and examples of *mapMCDA* are provided in the vignettes: -->
<!-- ... -->
<!-- ## Websites -->
<!-- The following websites are available: -->
<!-- ... -->
## Getting help online
......
......@@ -89,7 +89,7 @@ information for Cameroon</h1>
<h4 data-toc-skip class="author">Facundo
Muñoz</h4>
<h4 data-toc-skip class="date">2023-10-20</h4>
<h4 data-toc-skip class="date">2023-11-09</h4>
<div class="hidden name"><code>cmr_cartography-rmd.Rmd</code></div>
......
......@@ -86,7 +86,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Aperçu du package</h1>
<h4 data-toc-skip class="date">2023-10-20</h4>
<h4 data-toc-skip class="date">2023-11-09</h4>
<div class="hidden name"><code>mapMCDA.Rmd</code></div>
......
......@@ -95,7 +95,7 @@
<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>In order to design a <strong>stratified sampling</strong> or a <strong>surveillance campaign</strong>, a preliminary 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>
<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>
......@@ -106,17 +106,23 @@
<div class="section level2">
<h2 id="installing-the-package">Installing the package<a class="anchor" aria-label="anchor" href="#installing-the-package"></a>
</h2>
<p><code>mapMCDA</code> is on its way to CRAN. In the meanwhile, install from GitLab as follows.</p>
<p><code>mapMCDA</code> is on its way to CRAN. In the meanwhile, install from our r-universe as follows</p>
<!-- 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, version of the package using: -->
<!--
&#10;```r
if (!require("remotes")) {
install.packages("remotes")
}
remotes::install_gitlab("umr-astre/mapMCDA", host = "forgemia.inra.fr")
```
-->
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://remotes.r-lib.org" class="external-link">"remotes"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span></span>
<span><span class="op">}</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"umr-astre/mapMCDA"</span>, host <span class="op">=</span> <span class="st">"forgemia.inra.fr"</span><span class="op">)</span></span></code></pre></div>
<code class="sourceCode R"><span><span class="co"># Install mapMCDA in R:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">'mapMCDA'</span>, repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'https://cirad-astre.r-universe.dev'</span>, <span class="st">'https://cloud.r-project.org'</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<!-- # Resources -->
<!-- ## Vignettes -->
<!-- An overview and examples of *mapMCDA* are provided in the vignettes: -->
......@@ -174,7 +180,10 @@
<div class="dev-status">
<h2 data-toc-skip>Dev status</h2>
<ul class="list-unstyled">
<li><a href="https://www.repostatus.org/#active" class="external-link"><img src="https://www.repostatus.org/badges/latest/active.svg" alt="Project Status: Active – The project has reached a stable, usable state and is being actively developed."></a></li>
<li><a href="https://cran.r-project.org/package=mapMCDA" class="external-link"><img src="http://www.r-pkg.org/badges/version/mapMCDA" alt="CRAN_Status_Badge"></a></li>
<li><a href="https://cirad-astre.r-universe.dev" class="external-link"><img src="https://cirad-astre.r-universe.dev/badges/:name" alt="UMR ASTRE R-universe"></a></li>
<li><a href="https://cirad-astre.r-universe.dev/mapMCDA" class="external-link"><img src="https://cirad-astre.r-universe.dev/badges/mapMCDA" alt="mapMCDA R-universe status badge"></a></li>
<li><a href="https://forgemia.inra.fr/umr-astre/mapMCDA/pipelines" class="external-link"><img src="https://forgemia.inra.fr/umr-astre/mapMCDA/badges/master/pipeline.svg" alt="Build status"></a></li>
<li><a href="https://ci.appveyor.com/project/famuvie/mapmcda" class="external-link"><img src="https://ci.appveyor.com/api/projects/status/5p751lpceeiy18kp?svg=true" alt="Appveyor Build status"></a></li>
</ul>
......
public/man/figures/animal_mobility.png

581 KiB

......@@ -5,5 +5,5 @@ articles:
animal_mobility: animal_mobility.html
cmr_cartography-rmd: cmr_cartography-rmd.html
mapMCDA: mapMCDA.html
last_built: 2023-10-20T14:12Z
last_built: 2023-11-09T13:40Z
public/reference/Rplot001.png

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public/reference/Rplot001.png

2.72 KiB | W: | H:

public/reference/Rplot001.png
public/reference/Rplot001.png
public/reference/Rplot001.png
public/reference/Rplot001.png
  • 2-up
  • Swipe
  • Onion skin
public/reference/borders0-1.png

35.2 KiB

public/reference/borders0-2.png

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<a href="../articles/animal_mobility.html">Cheatsheet: Animal Mobility File Format</a>
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<h1>Outer boundaries of a vector map</h1>
<div class="hidden name"><code>borders0.Rd</code></div>
</div>
<div class="ref-description">
<p>Outer boundaries of a vector map</p>
</div>
<pre class="usage"><span class='fu'>borders0</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>A SpatialPolygons* object</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A single polygon with the outermost boundary.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='no'>cmr</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mapMCDA_datasets.html'>mapMCDA_datasets</a></span>()
<span class='kw pkg'>sp</span><span class='kw ns'>::</span><span class='fu'>plot</span>(<span class='no'>cmr</span>$<span class='no'>cmr_admin3</span>)</div><div class='img'><img src='borders0-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='kw pkg'>sp</span><span class='kw ns'>::</span><span class='fu'>plot</span>(<span class='fu'>borders0</span>(<span class='no'>cmr</span>$<span class='no'>cmr_admin3</span>))</div><div class='img'><img src='borders0-2.png' alt='' width='700' height='433' /></div></pre>
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<h2 data-toc-skip>Contents</h2>
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<p>Developed by Sylvain Falala, Facundo Muñoz.</p>
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......@@ -90,11 +90,11 @@ appropriate read function.</p>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"cartography/CMR"</span>, package <span class="op">=</span> <span class="st">"mapMCDA"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> full.names <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "/tmp/Rtmp8LwVPB/temp_libpath8cca221a5c1e/mapMCDA/cartography/CMR/animal.density.tif" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [2] "/tmp/Rtmp8LwVPB/temp_libpath8cca221a5c1e/mapMCDA/cartography/CMR/cmr_admin3.gpkg" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "/tmp/Rtmp8LwVPB/temp_libpath8cca221a5c1e/mapMCDA/cartography/CMR/mobility.csv" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "/tmp/Rtmp8LwVPB/temp_libpath8cca221a5c1e/mapMCDA/cartography/CMR/national_parks.gpkg"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "/tmp/Rtmp8LwVPB/temp_libpath8cca221a5c1e/mapMCDA/cartography/CMR/water_bodies.gpkg" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "/tmp/RtmpeyrFpy/temp_libpath687537d2985d/mapMCDA/cartography/CMR/animal.density.tif" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [2] "/tmp/RtmpeyrFpy/temp_libpath687537d2985d/mapMCDA/cartography/CMR/cmr_admin3.gpkg" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "/tmp/RtmpeyrFpy/temp_libpath687537d2985d/mapMCDA/cartography/CMR/mobility.csv" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "/tmp/RtmpeyrFpy/temp_libpath687537d2985d/mapMCDA/cartography/CMR/national_parks.gpkg"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "/tmp/RtmpeyrFpy/temp_libpath687537d2985d/mapMCDA/cartography/CMR/water_bodies.gpkg" </span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="va">epiunits</span> <span class="op">&lt;-</span> <span class="fu">load_layer</span><span class="op">(</span><span class="va">pkg_layers</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span>
</code></pre></div>
......
......@@ -114,9 +114,9 @@ either source or destination.</p>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>All the links are unidirectional which seems implausible.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Note that mapMCDA works only with directed networks.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> If you are sure that the network is directed, you can proceed.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IGRAPH 2ec3040 DN-- 2 1 -- </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> IGRAPH 2c03393 DN-- 2 1 -- </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> + attr: name (v/c)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> + edge from 2ec3040 (vertex names):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> + edge from 2c03393 (vertex names):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] A-&gt;B</span>
</code></pre></div>
</div>
......
public/reference/voronoi-1.png

11.5 KiB | W: | H:

public/reference/voronoi-1.png

8.75 KiB | W: | H:

public/reference/voronoi-1.png
public/reference/voronoi-1.png
public/reference/voronoi-1.png
public/reference/voronoi-1.png
  • 2-up
  • Swipe
  • Onion skin
......@@ -97,10 +97,9 @@
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">pts</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, <span class="fl">2</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">region</span> <span class="op">&lt;-</span> <span class="fu">terra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/terra/man/ext.html" class="external-link">ext</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3</span>, <span class="fl">0</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">st_geometry</span><span class="op">(</span><span class="fu">voronoi</span><span class="op">(</span><span class="va">pts</span>, <span class="va">region</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': could not find function "st_geometry"</span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">sf</span><span class="fu">::</span><span class="fu"><a href="https://r-spatial.github.io/sf/reference/st_geometry.html" class="external-link">st_geometry</a></span><span class="op">(</span><span class="fu">voronoi</span><span class="op">(</span><span class="va">pts</span>, <span class="va">region</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/points.html" class="external-link">points</a></span><span class="op">(</span><span class="va">pts</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in plot.xy(xy.coords(x, y), type = type, ...):</span> plot.new has not been called yet</span>
<span class="r-plt img"><img src="voronoi-1.png" alt="" width="700" height="433"></span>
</code></pre></div>
</div>
</div>
......
......@@ -33,9 +33,6 @@
<url>
<loc>/reference/align_layers.html</loc>
</url>
<url>
<loc>/reference/borders0.html</loc>
</url>
<url>
<loc>/reference/compute_weights.html</loc>
</url>
......
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