X003.5 Geostatistics and Interpolation in R

This course is designed for those who are interested in collecting, creating, processing, and interpolating geostatistical data. Through this course, you will learn variogram analysis and kriging methods to model and analyze spatial data based on information collected from sampled locations. You will have the opportunity to immediately practice your new skills via hands-on exercises focused on agri-food applications throughout the 2.5-hour course.

The course will be delivered via a Jupyter Notebook hosted on the GEMS Informatics Platform. You do not need to have R or RStudio installed on your machine to participate.

Prerequisites:

• Access to the internet
• A GEMS Platform user account
• GEMSx003.0

Initial Setup

1. Login to GEMS Platform at https://gems.agroinformatics.org/

   • GEMS Platform uses Globus to authenticate your account, so if your institution is already linked to Globus (for example, University of Minnesota and many other universities), you can search and select your institution from the list and use your institutional account to log into GEMS Platform. Alternatively, you can log in using Google or ORCID iD, or create your own Globus account to log in.

2. Once logged in, click Analyze > RStudio from the homepage (top right corner). If you do not have an Analyze option next to Data Products and My Workspace please let your TA know immediately. They will need to assign you permissions using their administrator account.

3. Install packages needed for course. If you have any issues please reference the R Troubleshooting document on Canvas and/or let your TA know immediately.

   # the `stars` and `tmaptools` packages are explicitly installed to enable
   #   installation of `tmap` on the GEMS Platform
   #   if you want to install `tmap` on your own machine, you can do so directly  
   library(devtools)
   install_version("stars", version="0.5-5") 
   install.packages('tmaptools')
   
   packages_to_install <- c("tmap", "spData")
   
   for ( package in packages_to_install ) {
       if (!require(package, character.only=T, quietly=T, warn.conflicts=F)) {
           install.packages(package)
       }
   }

4. While your packages are installing, reclick on your GEMS Informatics Platform tab and click Analyze > JupyterLab from the homepage

5. Open a bash terminal by clicking 'Terminal' icon in the Launcher OR by clicking File > New > Terminal

6. If the directories classes\GEMSX003 were not created before, create directories for this class in the bash terminal using the following four commands

   mkdir classes  
   cd classes  
   mkdir GEMSX003  
   cd GEMSX003

   If these directories already exist, use the following commands to change to this directory

   cd classes
   cd GEMSX003

Lecture: Geostatistics and Interpolation

1. Navigate to your GEMSX003 directory using the following commands:

   cd classes
   cd GEMSX003

2. Clone the git repository for this week's lecture

   git clone https://github.com/abjoglekar/GEMS-X003-Geostatistics-Interpolation-R.git

3. In your JupyterLab environment, open the GEMS-X003-Geostatistics-Interpolation-R directory and then open the x003_Module5_Geostats.ipynb Jupyter Notebook to follow along throughout the class