setup

QuickStart Software Installation Instructions

These are the QuickStart installation instructions. At points, they assume familiarity with the command line and with installation in general. As there are different operating systems and many different versions of operating systems and environments, these may not work on your computer. If an installation doesn’t work for you, please refer to the installation instructions for that software, listed in the table above.

R

Participants who do not already have R installed should download and install it.

Windows

To install R, Windows users should select “Download R for Windows” from RStudio and CRAN’s cloud download page, which will automatically detect a CRAN mirror for you to use. Select the base subdirectory after choosing the Windows download page. A .exe executable file containing the necessary components of base R can be downloaded by clicking on “Download R 3.x.x for Windows”.

macOS

To install R, macOS users should select “Download R for (Mac) OS X” from RStudio and CRAN’s cloud download page, which will automatically detect a CRAN mirror for you to use. A .pkg file containing the necessary components of base R can be downloaded by clicking on the first available link (this will be the most recent), which will read R-3.x.x.pkg.

Linux

To install R, Linux users should select “Download R for Linux” from RStudio and CRAN’s cloud download page, which will automatically detect a CRAN mirror for you to use. Instructions for a number of different Linux operating systems are available.

RStudio

RStudio is an GUI for using R that is available for Windows, macOS, and various Linux operating systems. It can be downloaded here. You will need the free Desktop version for your computer.

GDAL, GEOS, and PROJ.4

The installation of the geospatial libraries GDAL, GEOS, and PROJ.4 varies significantly based on operating system. These are all dependencies for sf, the R package that we will be using for spatial data operations throughout this workshop.

Windows

To install the geospatial libraries, install the latest version RTools

macOS

For participants who do not already have homebrew installed, and who may be less comfortable with the command line, the easiest was to obtain the geospatial libraries is to install the latest version of Kyng Chaos’s pre-built package for GDAL Complete. Be aware that several other libraries are also installed, including the UnixImageIO, SQLite3, and NumPy.

After downloading the package in the link above, you will need to double-click the cardbord box icon to complete the installation. Depending on your security settings, you may get an error message about “unidentified developers”. You can enable the installation by following these instructions for installing programs from unidentified developers.

Alternatively, participants who are comfortable with the command line can install the geospatial libraries individually using homebrew:

$ brew tap osgeo/osgeo4mac && brew tap --repair
$ brew install proj
$ brew install geos
$ brew install gdal2 --with-armadillo --with-complete --with-libkml --with-unsupported
$ brew link --force gdal2

Linux

Steps for installing the geospatial libraries will vary based on which form of Linux you are using. These instructions are adapted from the sf package’s README.

For Ubuntu:

$ sudo add-apt-repository ppa:ubuntugis
$ sudo apt-get update
$ sudo apt-get install libgdal-dev libgeos-dev libproj-dev

For Fedora:

$ sudo dnf install gdal-devel proj-devel proj-epsg proj-nad geos-devel

For Arch:

$ pacman -S gdal proj geos

For Debian: The rocker geospatial Dockerfiles may be helpful. Ubuntu Dockerfiles are found here.

UDUNITS

Linux users will have to install UDUNITS separately. Like the geospatial libraries discussed above, this is a dependency for the R package sf. Due to conflicts, it does not install properly on Linux machines when installed as part of the sf installation process. It is therefore necessary to install it using the command line ahead of time.

Linux

Steps for installing the geospatial will vary based on which form of Linux you are using. These instructions are adapted from the sf package’s README.

For Ubuntu:

$ sudo apt-get install libudunits2-dev

For Fedora:

$ sudo dnf install udunits2-devel

For Arch:

$ pacaur/yaourt/whatever -S udunits

For Debian:

$ sudo apt-get install -y libudunits2-dev

R Packages

The following R packages are used in the various geospatial lessons.

• dplyr
• ggplot2
• readr
• sf
• raster
• rgdal
• tmap
• rasterVis
• ggmap
• leaflet
• spData

To install these packages in RStudio, do the following:
1. Open RStudio by double-clicking the RStudio application icon. You should see something like this:

RStudio layout

2. Type (or even better, copy and paste) the following into the console and hit enter.

install.packages(c(
    #data science
    "dplyr", "ggplot2", "readr",
    #geospatial
    "sf", "raster", "rgdal", "geosphere",
    # mapping / plotting
    "tmap", "rasterVis", "ggmap", "leaflet",  
    #data
    "spData"))

You will need ggplot2 version >= 0.0.3

You should see a status message starting with:

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/dplyr_0.7.6.tgz'
Content type 'application/x-gzip' length 5686536 bytes (5.4 MB)
==================================================
downloaded 5.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/ggplot2_3.0.0.tgz'
Content type 'application/x-gzip' length 3577658 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

When the installation is complete, you will see a status message like:

The downloaded binary packages are in
/var/folders/7g/r8_n81y534z0vy5hxc6dx1t00000gn/T//RtmpJECKXM/downloaded_packages

You are now ready for the workshop!

Setup instructions modified from Data Carpentry Geospatial Workshop. June 2018: https://github.com/datacarpentry/geospatial-workshop