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README.md

Geocomputation with R

Launch Rstudio Binder Launch Rstudio Cloud Actions Docker DOI

Introduction

This repository hosts the code underlying Geocomputation with R, a book by Robin Lovelace, Jakub Nowosad, and Jannes Muenchow:

Lovelace, Robin, Jakub Nowosad and Jannes Muenchow (2019). Geocomputation with R. The R Series. CRC Press.

This book has been published by CRC Press in the R Series. The online version of this book is free to read at https://geocompr.robinlovelace.net/.

Contributing

We encourage contributions on any part of the book, including:

  • improvements to the text, e.g. clarifying unclear sentences, fixing typos (see guidance from Yihui Xie);
  • changes to the code, e.g. to do things in a more efficient way; and
  • suggestions on content (see the project’s issue tracker).

See our-style.md for the book’s style.

Many thanks to all contributors to the book so far via GitHub (this list will update automatically): prosoitos, florisvdh, katygregg, rsbivand, erstearns, eyesofbambi, nickbearman, tyluRp, giocomai, LaurieLBaker, mdsumner, pat-s, gisma, ateucher, annakrystalli, Darrellc1991, kant, gavinsimpson, Henrik-P, Himanshuteli, yutannihilation, jbixon13, yvkschaefer, katiejolly, KHwong12, layik, mtennekes, mvl22, ganes1410, richfitz, SymbolixAU, wdearden, yihui, chihinl, cshancock, gregor-d, jasongrahn, p-kono, pokyah, schuetzingit, sdesabbata, tim-salabim.

During the project we aim to contribute ‘upstream’ to the packages that make geocomputation with R possible. This impact is recorded in our-impact.csv.

Reproducing the book

To ease reproducibility, we created the geocompkg package. Installing it from GitHub will install all the R packages needed build the book (you will a computer with necessary system dependencies and the remotes package installed):

install.packages("remotes")
remotes::install_github("geocompr/geocompkg")

You need a recent version of the GDAL, GEOS, PROJ and UDUNITS libraries installed for this to work on Mac and Linux. See the sf package’s README for information on that.

Once the dependencies have been installed you should be able to build and view a local version the book with:

bookdown::render_book("index.Rmd") # to build the book
browseURL("_book/index.html") # to view it

Geocompr in binder

For many people the quickest way to get started with Geocomputation with R is in your web browser via Binder. To see an interactive RStudio Server instance click on the following button, which will open mybinder.org with an R installation that has all the dependencies needed to reproduce the book:

Launch Rstudio Binder

You can also have a play with the repo in RStudio Cloud by clicking on this link (requires log-in):

Launch Rstudio Cloud

Geocomputation with R in a Docker container

To ease reproducibility we have made Docker images available, at geocompr/geocompr on DockerHub. These images allow you to explore Geocomputation with R in a virtual machine that has up-to-date dependencies.

After you have installed docker and set-it up on your computer you can start RStudio Server without a password (see the Rocker project for info on how to add a password and other security steps for public-facing servers):

docker run -p 8787:8787 -e DISABLE_AUTH=TRUE geocompr/geocompr

If it worked you should be able to open-up RStudio server by opening a browser and navigating to http://localhost:8787/ resulting in an up-to-date version of R and RStudio running in a container.

Start a plain R session running:

docker run -it geocompr/geocompr R

See the geocompr/docker repo for details, including how to share volumes between your computer and the Docker image, for using geographic R packages on your own data and for information on available tags.

Reproducing this README

To reduce the book’s dependencies, scripts to be run infrequently to generate input for the book are run on creation of this README.

The additional packages required for this can be installed as follows:

source("code/extra-pkgs.R")

With these additional dependencies installed, you should be able to run the following scripts, which create content for the book, that we’ve removed from the main book build to reduce package dependencies and the book’s build time:

source("code/cranlogs.R")
source("code/sf-revdep.R")
source("code/08-urban-animation.R")
source("code/08-map-pkgs.R")

Note: the .Rproj file is configured to build a website not a single page. To reproduce this README use the following command:

rmarkdown::render("README.Rmd", output_format = "github_document", output_file = "README.md")

Citations

To cite packages used in this book we use code from Efficient R Programming:

# geocompkg:::generate_citations()

This generates .bib and .csv files containing the packages. The current of packages used can be read-in as follows:

pkg_df = readr::read_csv("extdata/package_list.csv")

Other citations are stored online using Zotero.

If you would like to add to the references, please use Zotero, join the open group add your citation to the open geocompr library.

We use the following citation key format:

[auth:lower]_[veryshorttitle:lower]_[year]

This can be set from inside Zotero desktop with the Better Bibtex plugin installed (see github.com/retorquere/zotero-better-bibtex) by selecting the following menu options (with the shortcut Alt+E followed by N), and as illustrated in the figure below:

Edit > Preferences > Better Bibtex

Zotero settings: these are useful if you want to add references.

We use Zotero because it is a powerful open source reference manager that integrates well with the citr package. As described in the GitHub repo Robinlovelace/rmarkdown-citr-demo.

References

# remotes::install_github("gadenbuie/regexplain")
# regexplain::regexplain_file("extdata/package_list.csv")
pattern = " \\[[^\\}]*\\]" # perl=TRUE
pkg_df$Title = gsub(pattern = pattern, replacement = "", x = pkg_df$Title, perl = TRUE)
knitr::kable(pkg_df)
Name Title version
bookdown Authoring Books and Technical Documents with R Markdown 0.7
cartogram Create Cartograms with R 0.1.0
dismo Species Distribution Modeling 1.1.4
geosphere Spherical Trigonometry 1.5.7
ggmap Spatial Visualization with ggplot2 2.6.1
ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics 3.0.0.9000
gstat Spatial and Spatio-Temporal Geostatistical Modelling, Prediction 1.1.6
historydata Datasets for Historians 0.2.9001
htmlwidgets HTML Widgets for R 1.2
kableExtra Construct Complex Table with ‘kable’ and Pipe Syntax 0.9.0
kernlab Kernel-Based Machine Learning Lab 0.9.26
knitr A General-Purpose Package for Dynamic Report Generation in R 1.20
latticeExtra Extra Graphical Utilities Based on Lattice 0.6.28
leaflet Create Interactive Web Maps with the JavaScript ‘Leaflet’ 2.0.1
link2GI Linking Geographic Information Systems, Remote Sensing and Other 0.3.0
lwgeom Bindings to Selected ‘liblwgeom’ Functions for Simple Features 0.1.4
mapview Interactive Viewing of Spatial Data in R 2.4.0
microbenchmark Accurate Timing Functions 1.4.4
mlr Machine Learning in R 2.12.1
osmdata Import ‘OpenStreetMap’ Data as Simple Features or Spatial 0.0.7
pROC Display and Analyze ROC Curves 1.12.1
ranger A Fast Implementation of Random Forests 0.10.1
raster Geographic Data Analysis and Modeling 2.6.7
rcartocolor ‘CARTOColors’ Palettes 0.0.22
rgdal Bindings for the ‘Geospatial’ Data Abstraction Library 1.3.3
rgeos Interface to Geometry Engine - Open Source (‘GEOS’) 0.3.28
rgrass7 Interface Between GRASS 7 Geographical Information System and R 0.1.10
rmapshaper Client for ‘mapshaper’ for ‘Geospatial’ Operations 0.4.0
rmarkdown Dynamic Documents for R 1.10
rnaturalearth World Map Data from Natural Earth 0.2.0
rnaturalearthdata World Vector Map Data from Natural Earth Used in ‘rnaturalearth’ 0.1.0
RPostgreSQL R Interface to the ‘PostgreSQL’ Database System 0.6.2
RQGIS Integrating R with QGIS 1.0.3
RSAGA SAGA Geoprocessing and Terrain Analysis 1.1.0
sf Simple Features for R 0.6.3
sp Classes and Methods for Spatial Data 1.3.1
spData Datasets for Spatial Analysis 0.2.9.0
spDataLarge Large datasets for spatial analysis 0.2.7.0
stplanr Sustainable Transport Planning 0.2.4.9000
tabularaster Tidy Tools for ‘Raster’ Data 0.5.0
tidyverse Easily Install and Load the ‘Tidyverse’ 1.2.1
tmap Thematic Maps 2.0.1
tmaptools Thematic Map Tools 2.0.1
tree Classification and Regression Trees 1.0.39
vegan Community Ecology Package 2.5.2
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