improve dataset part

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/07-basic_statistics.html

@@ -413,14 +413,14 @@ Statistical test
     Model used when sampling: Poisson 
     Number of simulations: 499 
     Statistic:  0.1566449 
-    p-value :  0.008 </code></pre>
+    p-value :  0.01 </code></pre>
 </div>
 <div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(m_test)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <p><img src="07-basic_statistics_files/figure-html/MoransI-1.png" class="img-fluid" width="768"></p>
 </div>
 </div>
-<p>The Moran’s statistics is here <span class="math inline">\(I =\)</span> 0.16. When comparing its value to the H0 distribution (built under 499 simulations), the probability of observing such a I value under the null hypothesis, i.e.&nbsp;the distribution of cases is spatially independent, is <span class="math inline">\(p_{value} =\)</span> 0.008. We therefore reject H0 with error risk of <span class="math inline">\(\alpha = 5\%\)</span>. The distribution of cases is therefore autocorrelated across districts in Cambodia.</p>
+<p>The Moran’s statistics is here <span class="math inline">\(I =\)</span> 0.16. When comparing its value to the H0 distribution (built under 499 simulations), the probability of observing such a I value under the null hypothesis, i.e.&nbsp;the distribution of cases is spatially independent, is <span class="math inline">\(p_{value} =\)</span> 0.01. We therefore reject H0 with error risk of <span class="math inline">\(\alpha = 5\%\)</span>. The distribution of cases is therefore autocorrelated across districts in Cambodia.</p>
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 <div class="callout-header d-flex align-content-center">
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@@ -541,7 +541,7 @@ Statistic distributions
 <span id="cb28-7"><a href="#cb28-7" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(df_secondary_clusters)</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>       SMR number.of.cases expected.cases p.value
-1 3.767698              16       4.246625    0.02</code></pre>
+1 3.767698              16       4.246625   0.012</code></pre>
 </div>
 </div>
 <p>We only have one secondary cluster composed of one district.</p>

public/img/geom.svg

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public/img/table.svg

+<svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="table" class="svg-inline--fa fa-table fa-w-16" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="currentColor" d="M464 32H48C21.49 32 0 53.49 0 80v352c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V80c0-26.51-21.49-48-48-48zM224 416H64v-96h160v96zm0-160H64v-96h160v96zm224 160H288v-96h160v96zm0-160H288v-96h160v96z"></path></svg>
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references.bib

@@ -405,3 +405,11 @@ Library},
 	year = {2022},
 	date = {2022}
 }
+
+@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}
+}