Migration to Forgemia: Readme and website installation instructions

DESCRIPTION

 Package: spreadrate
 Type: Package
 Title: Estimate the spread-rate of epidemics
-Version: 0.1.5
+Version: 0.1.6
 Date: 2019-07-17
 Authors@R: person("Facundo", "Muñoz", email = "facundo.munoz@cirad.fr",
         role = c("aut", "cre"), comment = c(ORCID =

README.Rmd

@@ -40,7 +40,7 @@ if (!require("remotes")) {
   install.packages("remotes")
 }
 install.packages("INLA", repos="https://inla.r-inla-download.org/R/testing")
-remotes::install_github("Cirad-ASTRE/mapMCDA")
+remotes::install_gitlab("umr-astre/spreadrate", host = "forgemia.inra.fr")
 ```
 
 

README.md

@@ -29,7 +29,7 @@ if (!require("remotes")) {
   install.packages("remotes")
 }
 install.packages("INLA", repos="https://inla.r-inla-download.org/R/testing")
-remotes::install_github("Cirad-ASTRE/mapMCDA")
+remotes::install_gitlab("umr-astre/spreadrate", host = "forgemia.inra.fr")
 ```
 
 ## Example
@@ -63,6 +63,16 @@ temporal variable. *Lon* and *Lat* are recognised automatically.
 
 ``` r
 library(spreadrate)
+#> Loading required package: raster
+#> Loading required package: sp
+#> 
+#> Attaching package: 'raster'
+#> The following object is masked from 'package:dplyr':
+#> 
+#>     select
+#> The following object is masked from 'package:tidyr':
+#> 
+#>     extract
 cases_sr <- sr_obs(cases, "date")
 ```
 
@@ -78,18 +88,13 @@ Everything is now set to perform a default estimation of spread-rate.
 
 ``` r
 sr_est <- sr(cases_sr)
-#> Warning: 
-#> Grid searches over lambda (nugget and sill variances) with  minima at the endpoints: 
-#>   (GCV) Generalized Cross-Validation 
-#>    minimum at  right endpoint  lambda  =  1.377511e-05 (eff. df= 41.79999 
-#> )
 ```
 
 Done\! Here is a quick plot of the estimated local spread-rate. The
 estimated velocity is practically constant, between 9 and 11 km / day.
 
 ``` r
-raster::plot(sr_est, col = hcl.colors(12))
+plot(sr_est, col = hcl.colors(12))
 ```
 
 <img src="man/figures/README-quick-plot-1.png" width="100%" />
@@ -100,7 +105,7 @@ the data.
 We can also retrieve the estimated surface of first-date of invasion:
 
 ``` r
-raster::plot(attr(sr_est, "fdoi"), col = hcl.colors(12))
+plot(attr(sr_est, "fdoi"), col = hcl.colors(12))
 ```
 
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />

public/LICENSE-text.html

@@ -60,7 +60,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/authors.html

@@ -60,7 +60,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/index.html

@@ -37,7 +37,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 
@@ -84,11 +84,11 @@
 <h2 class="hasAnchor">
 <a href="#installation" class="anchor"></a>Installation</h2>
 <p>To install the latest version of spreadrate, copy and paste the following in a R session.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if (!<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>)
-}
-<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"INLA"</span>, <span class="dt">repos=</span><span class="st">"https://inla.r-inla-download.org/R/testing"</span>)
-remotes::<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="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" 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="cb1-2" 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="cb1-3" data-line-number="3">}</a>
+<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"INLA"</span>, <span class="dt">repos=</span><span class="st">"https://inla.r-inla-download.org/R/testing"</span>)</a>
+<a class="sourceLine" id="cb1-5" data-line-number="5">remotes<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/remotes/topics/install_gitlab">install_gitlab</a></span>(<span class="st">"umr-astre/spreadrate"</span>, <span class="dt">host =</span> <span class="st">"forgemia.inra.fr"</span>)</a></code></pre></div>
 </div>
 <div id="example" class="section level2">
 <h2 class="hasAnchor">
@@ -111,28 +111,28 @@ remotes::<span class="kw"><a href="https://www.rdocumentation.org/packages/remot
 <p>Here is a visual representation of these observed cases.</p>
 <p><img src="reference/figures/README-map-obs-1.png" width="100%"></p>
 <p>First let <code>spreadrate</code> interpret the observational data appropriately with the function <code><a href="reference/sr_obs.html">sr_obs()</a></code>. You need to specify the name of the temporal variable. <em>Lon</em> and <em>Lat</em> are recognised automatically.</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>(spreadrate)
-<span class="co">#&gt; Loading required package: raster</span>
-<span class="co">#&gt; Loading required package: sp</span>
-<span class="co">#&gt; </span>
-<span class="co">#&gt; Attaching package: 'raster'</span>
-<span class="co">#&gt; The following object is masked from 'package:dplyr':</span>
-<span class="co">#&gt; </span>
-<span class="co">#&gt;     select</span>
-<span class="co">#&gt; The following object is masked from 'package:tidyr':</span>
-<span class="co">#&gt; </span>
-<span class="co">#&gt;     extract</span>
-cases_sr &lt;-<span class="st"> </span><span class="kw"><a href="reference/sr_obs.html">sr_obs</a></span>(cases, <span class="st">"date"</span>)</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"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(spreadrate)</a>
+<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co">#&gt; Loading required package: raster</span></a>
+<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co">#&gt; Loading required package: sp</span></a>
+<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#&gt; </span></a>
+<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#&gt; Attaching package: 'raster'</span></a>
+<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#&gt; The following object is masked from 'package:dplyr':</span></a>
+<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#&gt; </span></a>
+<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#&gt;     select</span></a>
+<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#&gt; The following object is masked from 'package:tidyr':</span></a>
+<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co">#&gt; </span></a>
+<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co">#&gt;     extract</span></a>
+<a class="sourceLine" id="cb3-12" data-line-number="12">cases_sr &lt;-<span class="st"> </span><span class="kw"><a href="reference/sr_obs.html">sr_obs</a></span>(cases, <span class="st">"date"</span>)</a></code></pre></div>
 <p>However, spread-rate calculations require projected (rather than geographic) coordinates. An appropriate projection for mainland France is EPSG:2154. See <a href="https://epsg.io/" class="uri">https://epsg.io/</a>.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">cases_sr &lt;-<span class="st"> </span><span class="kw">st_transform</span>(cases_sr, <span class="dt">crs =</span> <span class="dv">2154</span>)</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">cases_sr &lt;-<span class="st"> </span><span class="kw">st_transform</span>(cases_sr, <span class="dt">crs =</span> <span class="dv">2154</span>)</a></code></pre></div>
 <p>Everything is now set to perform a default estimation of spread-rate.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sr_est &lt;-<span class="st"> </span><span class="kw"><a href="reference/sr.html">sr</a></span>(cases_sr)</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">sr_est &lt;-<span class="st"> </span><span class="kw"><a href="reference/sr.html">sr</a></span>(cases_sr)</a></code></pre></div>
 <p>Done! Here is a quick plot of the estimated local spread-rate. The estimated velocity is practically constant, between 9 and 11 km / day.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(sr_est, <span class="dt">col =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/palettes">hcl.colors</a></span>(<span class="dv">12</span>))</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"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(sr_est, <span class="dt">col =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/palettes">hcl.colors</a></span>(<span class="dv">12</span>))</a></code></pre></div>
 <p><img src="reference/figures/README-quick-plot-1.png" width="100%"></p>
 <p>This is consistent with the value of 10^{4} m/day used for simulating the data.</p>
 <p>We can also retrieve the estimated surface of first-date of invasion:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attr">attr</a></span>(sr_est, <span class="st">"fdoi"</span>), <span class="dt">col =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/palettes">hcl.colors</a></span>(<span class="dv">12</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"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attr">attr</a></span>(sr_est, <span class="st">"fdoi"</span>), <span class="dt">col =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/palettes">hcl.colors</a></span>(<span class="dv">12</span>))</a></code></pre></div>
 <p><img src="reference/figures/README-unnamed-chunk-3-1.png" width="100%"></p>
 </div>
 <div id="references" class="section level2">

public/news/index.html

@@ -60,7 +60,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/pkgdown.yml

-pandoc: 1.16.0.2
+pandoc: 2.3.1
 pkgdown: 1.3.0
 pkgdown_sha: ~
 articles: []

public/reference/dist2arc.html

@@ -64,7 +64,7 @@ in both longitude and latitude." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/estimation_mask.html

@@ -63,7 +63,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/filter_earliest_neigh.html

@@ -65,7 +65,7 @@ earliest times observed in the neighbourhood to them." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/fit_surface.html

@@ -63,7 +63,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/get_lonlatvars.html

@@ -64,7 +64,7 @@ return the variable names." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/index.html

@@ -60,7 +60,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/invslope.html

@@ -64,7 +64,7 @@ first-date-of-invasion surface" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/mc_sample.html

@@ -63,7 +63,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/neigh_tol.html

@@ -64,7 +64,7 @@ of a sr_obs object." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/representative_points.html

@@ -64,7 +64,7 @@ each other." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 

public/reference/spreadrate-package.html

@@ -70,7 +70,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>
 
@@ -140,8 +140,8 @@ a dataset of observations prepared for spread-rate estimation, and
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>Useful links:</p><ul>
-<li><p><a href='https://Cirad-ASTRE.github.io/spreadrate'>https://Cirad-ASTRE.github.io/spreadrate</a></p></li>
-<li><p>Report bugs at <a href='https://github.com/Cirad-ASTRE/spreadrate/issues'>https://github.com/Cirad-ASTRE/spreadrate/issues</a></p></li>
+<li><p><a href='https://umr-astre.pages.mia.inra.fr/spreadrate'>https://umr-astre.pages.mia.inra.fr/spreadrate</a></p></li>
+<li><p>Report bugs at <a href='https://forgemia.inra.fr/umr-astre/spreadrate/issues'>https://forgemia.inra.fr/umr-astre/spreadrate/issues</a></p></li>
 </ul></div>
     
 

public/reference/sr.html

@@ -63,7 +63,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">spreadrate</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.5</span>
       </span>
     </div>