merging

.gitignore

@@ -49,3 +49,6 @@ examples
 .quarto/
 
 /.quarto/
+
+*.osm.pbf
+data_cambodia/geofabrik_cambodia-latest.gpkg

01-introduction.qmd

@@ -31,6 +31,29 @@ The packages `stars` [@stars] and `terra` [@terra] come to replace the package `
 Website of package `sf` : [Simple Features for R](https://r-spatial.github.io/sf/)
 :::
 
+Many of the spatial data available on the internet are in shapefile format, which can be opened in the following way
+
+```{r class.output="code-out"}
+library(sf)
+district <- st_read("data_cambodia/district.shp")
+```
+
+::: callout-important
+## Shapefile format limitations
+
+For the multiple limitations of this format (multi-file, limited number of records...) we advise you to prefer another format such as the geopackage `*.gpkg`. All the good reasons not to use the shapefile are [here](http://switchfromshapefile.org/).
+:::
+
+A geopackage is a database, to load a layer, you must know its name
+
+```{r class.output="code-out"}
+st_layers("data_cambodia/cambodia.gpkg")
+```
+
+```{r class.output="code-out"}
+road <- st_read("data_cambodia/cambodia.gpkg", layer = "road")
+```
+
 ### Format of spatial objects `sf`
 
 ![](img/sf.png){fig-align="center" width="600"}

02-data_acquisition.qmd

@@ -4,8 +4,35 @@ bibliography: references.bib
 
 # Data Acquisition
 
+All the data needed to complete this training can be retrieved at [this link](https://e1.pcloud.link/publink/show?code=XZQ60YZxwN09vWJ8bmuSivWezhuG8u94lCV).
+
 ## Online databases
 
+### On global scale
+
+Since the appearance of the `sf` package, which has greatly contributed to the popularization of spatial data manipulation with R, many packages for making geographic data (geometries and/or attributes) available have been developed. Most of them are API packages that allow to query data made available on the Web, directly with R. This chapter presents a non-exhaustive list of them.
+
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `rnaturalearth` [@R-rnaturalearth]: retrieves [Natural Earth map data](https://www.naturalearthdata.com/).\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `gadmr` [@R-gadmr]: retrieves data from the [GADM](https://gadm.org/index.html) (national and sub-national administrative divisions of all countries in the world).\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `rgeoboundaries` [@R-rgeoboundaries] : R client for the [geoBoundaries API](https://www.geoboundaries.org/index.html), providing political administrative boundaries of countries.
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `cshapes` [@R-cshapes]: makes available national boundaries, from 1886 to present.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `osmextract` [@R-osmextract]: allows importing [OpenStreetMap data](https://www.openstreetmap.org/).
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `osmdata` [@osmdata2017]: to download and use OpenStreetMap data.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `maptiles` [@R-maptiles] : This package downloads, composes and displays tiles from a large number of providers (*OpenStreetMap*, *Stamen*, *Esri*, *CARTO* or *Thunderforest*).\
+-   <img src="img/table.svg" alt="attribute data" width="20"/> `geonames` [@R-geonames] : allows you to query the [geonames DB](http://www.geonames.org/), which provides locations in particular.
+-   <img src="img/table.svg" alt="attribute data" width="20"/> `wbstats` [@wbstats2020] and `WDI` [@R-WDI]: provide access to World Bank data and statistics.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `sen2r` [@R-sen2r]: allows automatic download and preprocessing of Sentinel-2 satellite data.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `MODIStsp` [@MODIStsp2016]: find, download and process *MODIS* images.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `geodata` [@R-geodata]: provides access to [data](https://github.com/rspatial/geodata) on climate, elevation, soil, species occurrence and administrative boundaries.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `elevatr` [@R-elevatr]: provides access to elevation data made available by [*Amazon Web Services Terrain Tiles*](https://registry.opendata.aws/terrain-tiles/), the [*Open Topography Global Datasets API*](https://opentopography.org/developers/) and the [*USGS Elevation Point Query Service*](https://nationalmap.gov/epqs/).
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `rgee` [@R-rgee]: allows use of the [Google Earth Engine](https://www.google.com/intl/fr_in/earth/education/tools/google-earth-engine/) API, a public data catalog and computational infrastructure for satellite images.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `nasapower` [@nasapower2018]: *NASA* client API (global energy resource forecasting, meteorology, surface solar energy, and climatology).
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> `geoknife` [@geoknife2015]: allows processing (online) of large raster data from the *Geo Data Portal* of the *U.S. Geological Survey*.\
+-   <img src="img/table.svg" alt="attribute data" width="20"/> `wopr` [@R-wopr]: provides API access to the [*WorldPop Open Population Repository*](https://wopr.worldpop.org/) database.\
+-   <img src="img/geom.svg" alt="Geometries" width="20"/> <img src="img/table.svg" alt="attribute data" width="20"/> `rdhs` [@rdhs2019] : [Demographic and Health Survey (DHS) client API and data managements](https://dhsprogram.com/).
+
+Several data sets are referenced by the ESoR (Environnement, Societies and Health Risk) research group [here](https://www.netvibes.com/geohealth?page=geohealth#Online_databases)
+
 ## OpenStreetMap
 
 ::: {style="float: right"}
@@ -111,7 +138,6 @@ The result contains a point layer and a polygon layer. The polygon layer contain
 sf_use_s2(FALSE)
 ```
 
-
 ```{r osmdata2, class.output="code-out", warning=FALSE, message=FALSE}
 hospital_point <- hospital$osm_points
 hospital_poly <- hospital$osm_polygons                                                             #Extracting centroids of polygons

public/01-introduction.html

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@@ -235,6 +298,65 @@ div.csl-indent {
 </div>
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 </div>
+<p>Many of the spatial data available on the internet are in shapefile format, which can be opened in the following way</p>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(sf)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.1; sf_use_s2() is TRUE</code></pre>
+</div>
+<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>district <span class="ot">&lt;-</span> <span class="fu">st_read</span>(<span class="st">"data_cambodia/district.shp"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stdout">
+<pre class="code-out"><code>Reading layer `district' from data source 
+  `/home/lucas/Documents/ForgeIRD/rspatial-for-onehealth/data_cambodia/district.shp' 
+  using driver `ESRI Shapefile'
+Simple feature collection with 197 features and 10 fields
+Geometry type: MULTIPOLYGON
+Dimension:     XY
+Bounding box:  xmin: 211534.7 ymin: 1149105 xmax: 784612.1 ymax: 1625495
+Projected CRS: WGS 84 / UTM zone 48N</code></pre>
+</div>
+</div>
+<div class="callout-important callout callout-style-default callout-captioned">
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+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-caption-container flex-fill">
+Shapefile format limitations
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>For the multiple limitations of this format (multi-file, limited number of records…) we advise you to prefer another format such as the geopackage <code>*.gpkg</code>. All the good reasons not to use the shapefile are <a href="http://switchfromshapefile.org/">here</a>.</p>
+</div>
+</div>
+<p>A geopackage is a database, to load a layer, you must know its name</p>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">st_layers</span>(<span class="st">"data_cambodia/cambodia.gpkg"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stdout">
+<pre class="code-out"><code>Driver: GPKG 
+Available layers:
+  layer_name     geometry_type features fields              crs_name
+1    country     Multi Polygon        1     10 WGS 84 / UTM zone 48N
+2   district     Multi Polygon      197     10 WGS 84 / UTM zone 48N
+3  education     Multi Polygon       25     19 WGS 84 / UTM zone 48N
+4   hospital             Point      956     13 WGS 84 / UTM zone 48N
+5      cases       Multi Point      972      2 WGS 84 / UTM zone 48N
+6       road Multi Line String        6      9 WGS 84 / UTM zone 48N</code></pre>
+</div>
+</div>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>road <span class="ot">&lt;-</span> <span class="fu">st_read</span>(<span class="st">"data_cambodia/cambodia.gpkg"</span>, <span class="at">layer =</span> <span class="st">"road"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stdout">
+<pre class="code-out"><code>Reading layer `road' from data source 
+  `/home/lucas/Documents/ForgeIRD/rspatial-for-onehealth/data_cambodia/cambodia.gpkg' 
+  using driver `GPKG'
+Simple feature collection with 6 features and 9 fields
+Geometry type: MULTILINESTRING
+Dimension:     XY
+Bounding box:  xmin: 212377 ymin: 1152214 xmax: 784654.7 ymax: 1625281
+Projected CRS: WGS 84 / UTM zone 48N</code></pre>
+</div>
+</div>
 <section id="format-of-spatial-objects-sf" class="level3" data-number="1.2.1">
 <h3 data-number="1.2.1" class="anchored" data-anchor-id="format-of-spatial-objects-sf"><span class="header-section-number">1.2.1</span> Format of spatial objects <code>sf</code></h3>
 <div class="quarto-figure quarto-figure-center">

public/07-basic_statistics.html

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references.bib

@@ -435,4 +435,12 @@ Library},
   number={25},
   pages={515},
   year={2018}
+}
+
+@article{rnaturalearth,
+	title = {rnaturalearth: World Map Data from Natural Earth},
+	author = {South, Andy},
+	year = {2017},
+	date = {2017},
+	url = {https://CRAN.R-project.org/package=rnaturalearth}
 }
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