Introduction to Spatial data with R

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.title[
# Introduction to Spatial data with R
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.subtitle[
## Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology
]
.author[
### Andrea Sánchez-Tapia & Sara Mortara
]
.date[
### 26 July 2022
]

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## Introduction

+  __Geographic Information System (GIS)__ platforms. Powerful but point-and-click, some integrations. License needed!

+ __Free and open source software for geospatial (FOSS4G)__: R, Python, GRASS, QGIS

+ __Widely used__ external open source geo libraries written in C or C++: `GDAL`, `PROJ`, [`GEOS`](https://libgeos.org/)- Recent changes.

+ In R: supported for years, heterogeneous. Classic packages (`rgdal`, `rgeos` and `maptools`) will retire, lots of new packages (`stars`, `terra`, `leaflet`, `mapview`)

+ 📦 __Today (2022)__: `raster`, [`sf`](https://r-spatial.github.io/sf/), [`tmap`](https://github.com/mtennekes/tmap)

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## Vectorial and raster data

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## Vectorial data

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- __points__: (x, y) pairs and multipoints (e.g. all cities in a country)

- __lines__: several pairs (nodes), ordered. Polylines. Multiple (poly)lines (e.g.: a river and its tributaries, all the river systems in a region)

- __polygons__: Ordered polylines, _ending at the starting point_. They can have __holes__, they do not cross themselves. Multiple polygons (e.g.:an archipelago)

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## Types of vectorial data

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## File types: shapefiles

+ Vector data are usually stored as __shapefile__ formats

+ Three files: `.shp`, `.shx`, `.dbf` and a projection `.prj`

+ Other extensions also refered to as shapefiles: Geopackages

+ In R: package `sf`.

+ `sf::read_sf()`, `sf::write_sf()`

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## Raster data

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+ __Continuous space__ divided in a cell grid

+ __One value per cell__: can be the average inside the cell, a sample in the center, the result of an operation including contiguous cells

+ __Spatial extent__,  __resolution__ , (nrows, ncols, nlayers): 4716, 5388, 1
    
+ A __stack__ of rasters, or __multiband__ rasters

+ In R: `raster`, several filetypes: `.asc`, `.grd`, `.tif`
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## Where to find geospatial data?

- __Direct download__ in official country organizations (ex. the shapefile for a protected area)

- Spatial data __repositories__ (ex. Global Administrative Areas http://gadm.org, administrative information for all countries)

- Remote sensing data: Satellite (ex. MODIS, Sentinel, Landsat)

- Some R packages have map templates for quick mapping and options for downloading data (ex. `raster`)

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### https://rspatialdata.github.io

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## Coordinate reference systems, datums, projections

+ A __Coordinate Reference System__ is a standard to locate objects in the geographic space

+ The current default: __WGS84__ (World Geodetic System 1984).

+ Official CRS appropriate for regions and countries. Brazil: South America SAD69, Sirgass 2000, USA: NAD27, NAD83.

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## CRS are composed by

+ A __spheroid__, a model of the shape of the Earth

+ A __datum__, a reference for the coordinates, their origin and unit of measurement

+ A __projection__, how to transform 3-D system to 2-D,
Mercator, UTM, Robinson Lambert, Sinusoidal, Robinson, Albers
    
+ Lots of locally used CRS and one world standard: WGS84. Lots of deprecated/updated CRS. A repository with all the CRS: `https://spatialreference.org/`

WGS: https://spatialreference.org/ref/epsg/4326/

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## CRS are key for correct spatial analysis

+ When downloading data from official sources, check the __metadata__ available

+ When missing, usually assume __WGS84__ but triple check with the data sources and see __what makes sense in your context__. You an assign a CRS to an object with a missing CRS

###  Assigning a missing CRS does not make it correct and is not the same as re projecting

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### This is only the beginning

+ Spatial statistics
 
+ Movement ecology

+ Epidemiology

+ Biogeography

+ Geostatistics

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## Resources

+ Moraga, Paula. (2019). __Geospatial Health Data: Modeling and Visualization with R-INLA and Shiny.__ Chapman & Hall/CRC Biostatistics Series https://www.paulamoraga.com/book-geospatial/
+ __Spatial Data Science with R__ https://rspatial.org/
+ __Leaflet tutorial__ https://rstudio.github.io/leaflet/
+ Laurie Baker's tutorial with leaflet https://laurielbaker.github.io/DSCA_leaflet_mapping_in_r/slides/leaflet_slides2.html#66
+ __Geocomputation with R__ https://geocompr.robinlovelace.net/
+ RSpatial data: https://rspatialdata.github.io/
+ Fortin MJ, Dale MRT 2005. Spatial Analysis: A guide for Ecologists, Third Edit. ed. New York.

❤️

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# ¡Thanks!

<center>
<svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:#A70000;height:1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"></path></svg> [andreasancheztapia@gmail.com](mailto:andreasancheztapia@gmail.com) | [saramortara@gmail.com](mailto:saramortara@gmail.com)