Introduction GIS Tools /spatial epidemiology

This is the overview document on materials for the workshop: Introduction GIS Tools /spatial epidemiology at Global Health Academy.

Authors:

Session description: The workshop will introduce some fundamental concepts of how to work with spatial data by using Covid-19 data for Germany using R and RStudio as the analysis environment. We will cover different possibilities for spatial visualization, measures to identify spatial clusters and will sneak into the definition of spatial neighbourhood definitions and the consideration of spatial regression analysis in presence of spatial auto-correlation. Hands on exercise are part of the workshop. Experience in using R/RStudio will be beneficial but not mandatory as general concepts are transferable to other analysis environments.

See here the course details: Introduction GIS Tools /spatial epidemiology.

How to use these tutorials?

Code

The materials were created with R and the R package rmarkdown. The source are multiple R-markdown document that can be loaded in R, and executed there (just like a Jupyter notebook, but simpler). To do this, take the following steps:

  1. Go to the GitHub page of this course
  2. Click on the file of your interest ending with .Rmd
  3. Click on the “Raw” tab
  4. Right-click on that page, “save as”, and save it to a local copy of session.Rmd
  5. Click (or double-click) on this file, and RStudio should open it, showing the file
  6. In RStudio, click “knit” to recreate the entire rendered document, which runs all the R chunks
  7. For running individual R chunks, (notebook “cells”), use the arrows “Run all chunks above”, after which you can use “Run current chunk”

Data

Due to limited time, data acquisition and preprocessing will not be covered in the workshop. In order to be able to run the .Rmd files yourself, make sure you have copied the .Rdata files from this heiBOX folder in a data/ fodler next to your .Rmd files.

Alternatively you can run the acquisition and processing from scratch with the https://github.com/GIScience/global-health-academy/blob/main/00data_preparation.Rmd script.

Setup

pkgs <- c("rmdformats","tidyverse","ggplot2","lubridate","sf","zoo","spdep",
          "tmap","tidyquant","readODS","knitr","animation","cartogram",
          "kableExtra","pals","sf","ggpubr","GGally","MASS", "classInt", 
          "lattice", "latticeExtra", "grid", "gridExtra", "dbscan")

# on windows you might need to install the package directly from github
install.packages("devtools")
devtools::install_github("ge11232002/latticeExtra")

install.packages(pkgs)

The following version and setup was used to built this tutorials

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

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All contents are licensed under GNU General Public License v3.0