GIS with R: examples from Slovakia

July 2019

Geospatial analysis. Why are we doing this?

  1. Most of our data we collect are a recording of some phenomena that happened at a specific place and time.
  2. Good visualisations and methods from spatio-temporal analysis field can help us understand our data.

This tutorial

  1. Spatial data and coordinate systems.
  2. Introduction to sf package.
  3. Visualisations.
  4. Example of analysis: spatial autocorrelation.

Extra resources

Recommended textbooks:

  • Geocomputation with R. Available online.
  • Gelfand, Alan E., ed. 2010. Handbook of Spatial Statistics. Chapman & Hall/CRC Handbooks of Modern Statistical Methods. Boca Raton: CRC Press.
  • Wikle, Christopher K., Andrew Zammit-Mangion, and Noel Cressie. 2019. Spatio-Temporal Statistics with R. 1st ed. Boca Raton, Florida : CRC Press, [2019]: Chapman and Hall/CRC. https://doi.org/10.1201/9781351769723.

Other sources:

  • r-spatial.org is a portal for people interested in spatial modelling.
  • Packages like sf, sp tend to be well-documented, and with worked examples.

Spatial data

  • Data frames, but now each row has a geometry associated with it (usually a point or an area).
  • We need to be careful with the coordinate systems:
    • If working at macro scale (at world level), we need to take into account curvature of the Earth.
    • We stick to coordinate systems where we can work with Euclidean geometry.
    • The cadaster office in Slovakia uses krovak system, which is the legally binding coordinate system (coded as EPSG:5513).
    • This website is useful for reading off the coordinates for a particular point.

Obtaining geometry (map) files

  • The map files come in different formats. One of the most common ones are shapefiles (.shp), geodatabase (.gdb), geopackage (.gpk), geoJSON (.geojson).
  • This page in the geoportal.sk has the necessary files in different formats. We stick to the shapefiles (.shp) format. The portal allows downloading the maps at different resolutions. In this guide, we will be working with the most precise one, which is referred to as ‘Základná úroveň/ ZBGIS - Administratívne hranice’.

sf package

Install the package using:

st_read() to load maps

st_read(dsn, layer)
  • dsn: file name of the map file.
  • layer: certain file formats allow saving multiple layers, we will work with single layer files (it does not mean we can’t have multiple indicators/statistic for each location).

Load the map of Slovakia at the municipality level:

Inspecting the map object - coordinates

To see what coordinate system it uses, st_crs() function can be used:

## Coordinate Reference System:
##   No EPSG code
##   proj4string: "+proj=krovak +lat_0=49.5 +lon_0=24.83333333333333 +alpha=30.28813975277778 +k=0.9999 +x_0=0 +y_0=0 +ellps=bessel +units=m +no_defs"

Due to the missing code, we do a transformation to the official code using st_transform() function.

Inspecting the map object - data

##       DOW                  AUT         ACH         SOI       FACC           IDN4              NM4            IDN3      
##  Min.   :2019-04-30   Min.   :1   Min.   :1   Min.   :9   FA004:2927   Min.   :500011   Lúčka   :   4   Min.   :101.0  
##  1st Qu.:2019-04-30   1st Qu.:1   1st Qu.:1   1st Qu.:9                1st Qu.:508989   Porúbka :   4   1st Qu.:402.0  
##  Median :2019-04-30   Median :1   Median :1   Median :9                Median :518204   Dúbrava :   3   Median :606.0  
##  Mean   :2019-04-30   Mean   :1   Mean   :1   Mean   :9                Mean   :521206   Lúčky   :   3   Mean   :547.7  
##  3rd Qu.:2019-04-30   3rd Qu.:1   3rd Qu.:1   3rd Qu.:9                3rd Qu.:526138   Petrovce:   3   3rd Qu.:708.0  
##  Max.   :2019-04-30   Max.   :1   Max.   :1   Max.   :9                Max.   :599972   Píla    :   3   Max.   :811.0  
##                                                                                         (Other) :2907                  
##               NM3            IDN2                    NM2          VYMERA            Shape_Leng       Shape_Area       
##  Košice - okolie: 114   Min.   :1.000   Prešovský      :665   Min.   :   361255   Min.   :  3211   Min.   :   354208  
##  Rimavská Sobota: 107   1st Qu.:4.000   Banskobystrický:516   1st Qu.:  7207245   1st Qu.: 14031   1st Qu.:  7207035  
##  Prešov         :  91   Median :6.000   Košický        :461   Median : 11655767   Median : 18582   Median : 11647728  
##  Levice         :  89   Mean   :5.415   Nitriansky     :354   Mean   : 16752332   Mean   : 21367   Mean   : 16747701  
##  Bardejov       :  86   3rd Qu.:7.000   Žilinský       :315   3rd Qu.: 19769322   3rd Qu.: 25503   3rd Qu.: 19794868  
##  Trebišov       :  82   Max.   :8.000   Trenčiansky    :276   Max.   :359784254   Max.   :204284   Max.   :359936992  
##  (Other)        :2358                   (Other)        :340                                                           
##           geometry   
##  MULTIPOLYGON :2927  
##  epsg:5513    :   0  
##  +proj=krov...:   0  
##                      
##                      
##                      
##

Inspecting the map object - data

From the columns included in the shapefiles, we see that:

  1. IDN4 is a unique identifier for each municipality.
  2. NM4 is the name of the municipality.
  3. IDN3 is the identifier for okres.
  4. NM3 is the name for okres.
  5. IDN2 is the identifier for kraj.
  6. NM2 is the name for kraj.
  7. Shape_Leng and Shape_Area are the perimeter and the area of a municipality.
  8. It’s not clear to me what VYMERA is given that the values slightly deviate from the Shape_Area.

The other columns are not relevant for this tutorial.

Data preparation

Before, we proceed, we rename the columns to more meaningful names:

Visualisation - options

Some of the most popular options are:

  1. default plot() method in the sf package,
  2. ggplot,
  3. tmap.

We will give examples of all throughout the rest of this tutorial.

Example: migration in Slovakia

  1. Load the migration and population data.
  2. Merge the data with the map files.
  3. Visualise the data: inflow / outflow.

Example: migration in Slovakia

Load migration and population data

Example: migration in Slovakia

Merge the data with maps

Example: migration in Slovakia

Plot using the default plot() method

Example: migration in Slovakia