Spatial Data Analysis with R
Society for Conservation GIS, July 2021

Introduction

About Me…

Some of My R Work

T-LoCoH

Home range constructor and spatial-temporal pattern analysis for wildlife tracking data

http://tlocoh.r-forge.r-project.org/

uasimg

Data management utilities for drone mapping.

https://ucanr-igis.github.io/uasimg/

Catalogs and manages drone images (sample)
Estimates footprints, computes overlap, explorts flight area to Shapefile
Creates World Files for single images

Bring climate data from Cal-Adapt into R using the API

https://ucanr-igis.github.io/caladaptr/

Shiny Apps

Chill Portions Under Climate Change Calculator
https://igis.shinyapps.io/chill/

Drone Mission Planner for Reforestation Monitoring Protocol
https://ucanr-igis.shinyapps.io/uav_stocking_survey/

Stock Pond Volume Calculator
https://ucanr-igis.shinyapps.io/PondCalc/

Calculator for Estimating Costs and Benefits of Medusahead Control
https://ucanr.shinyapps.io/medusahead_ipm/

About You…

https://forms.gle/pK5usnFz4Q5hu8WY9

Workshop Goals

Get better at:

Working with R and RStudio
Using the most common data classes and packages for spatial data
Importing spatial data from files and online sources
Fundamental spatial data processing and geoprocessing operations
Basic plotting
Finding resources to continue learning on your own

Wind up a little higher on the learning curve!

Strategy: Copy and Adapt

foundational concepts
+ code recipes
+ working examples
+ practice
+ a good search engine

functional pRoficiency!

Advice for Beginners

Try to get working code
Focus on adapting code rather than starting from scratch
Pay attention to syntax
Use meaningful variable names
Ask for help for cryptic error messages
Comment your code liberally

Workshop Materials

Slides

https://ucanr-igis.github.io/rspatial_scgis21/

Keyboard shortcuts for slides:

A: toggle display of current vs all slides
S: make fonts smaller
B: make fonts larger
F: toggle display of the footer
C: Show table of contents

Download slides here (Code button → Download zip → open Docs folder)

Practice

short exercises in slides (copy-paste starter code to RStudio)
R Notebooks

Community Forum

https://etherpad.wikimedia.org/p/rspatial-scgis2021

questions
code
resources

Virtual Environment

https://rstudio.cloud/project/2709500
Data and packages are pre-installed!

Data

RStudio Cloud: see ‘data’ directory in project
RStudio Desktop:

create a workshop folder
download data folder

usethis::use_course("bit.ly/rspatial-data", destdir = ".")

or download zip from https://bit.ly/rspatial-data and extract

Other Resources & Cheatsheets

see Resources.html

Getting Help

Office Hours

Sample Data

Yosemite National Park data

R & RStudio

a programming language to write scripts
software (“environment”) that interprets scripts written in R
inspired by ‘S’ (1976), first beta version ~2000
many user-contributed packages:
- CRAN: >20,200
- Bioconductor: >2,100
- R-Forge: >2,100
- GitHub: >70,400

a very popular tool (IDE) to work with both R software and R scripts
Version 1.0 came out in late 2016
RStudio needs R to run, but you can use R without RStudio
RStudio Cloud - run RStudio through a browser

RStudio Cloud

online version of RStudio
requires an account (free account gets you 15 hrs / month)
98% same as RStudio Desktop
have to upload your data to the cloud
everything gets saved between sessions
workspaces have projects
- workspaces are private by default
- projects can be private or shared

Workshop Project

RStudio Cloud project for this workshop: https://rstudio.cloud/project/2709500

RStudio Tour

Explore the interface
Change font size and colors
Execute code at the console
Getting help
Set your working directory
Start a new script
Execute commands in the script window

R Notebooks

R Notebooks are written in “R Markdown”, which combines text and R code.

We’ll be using R Notebooks for many of the workshop exercises.

When you’re in a R Notebook, the working directory is where the notebook Rmd file resides.

Download the Notebooks for today:

zip_url <- "https://github.com/ucanr-igis/rspatial_data/raw/master/scgis21_nb_sect01.zip"
temp_fn <- tempfile()
download.file(zip_url, destfile=temp_fn, mode="wb")
unzip(temp_fn, exdir = ".")
unlink(temp_fn)

Practice using R Notebook:

## Warning in if (is.na(nb_desc_chr)) {: the condition has length > 1 and only the first element will be used

nb_intro_scgis21.Rmd
Introduction to R Notebooks

nb_intro_scgis21.Rmd
NA

preview notebook | answer key

R Studio Shortcuts

Command history
- up/down arrows
- Ctrl-{up arrow} or Command-{up arrow}
Tab completion
Select a line or block for execution (source window)

Next: Syntax Review

Spatial Data Analysis with RSociety for Conservation GIS, July 2021