R-SCB

2 hour workshop for UC Berkeley Society for Conservation Biology

Installations

Download R and RSTudio

Before the workshop be sure to download these three items:

1. Click here to download R version 3.6.1

2. Click here to download RStudio Desktop Open Source License Free

3. Click here to download workshop materials

• Git users can simply clone this repository

• Otherwise, click the green "Clone or download" button, click "Download ZIP", then extract the contents of this file someplace familiar such as your Desktop.

Package installation

Be sure to run lines 7 through 21 in the file "1-package-installation.Rmd" to install the packages to be used in this workshop.

Topics

1. Navigating RStudio

2. Variable assignment

3. The data

4. Data types

5. Data structures

6. Data visualization with ggplot2

7. Maps (ggplot2, ggmap, Google Maps Static API keys)

8. Going further (simple features, machine learning)

Resources

Basic statistics

Kerns GJ. 2010. Introduction to Probability and Statistics Using R

Everitt BS and T Hothorn. 2005. Handbook of Statistical Analyses Using R

Machine learning

James G, D Witten, T Hastie, R Tibshirani. 2000. An Introduction to Statistical Learning - with Applications in R. Amazon. Free PDF

Chollet F, JJ Allaire. 2018. Deep Learning with R

Community ecology

Lai J, CJ Lortie, RA Muenchen, J Yang, K Ma. 2019. Evaluating the popularity of R in ecology

Rózsa L, J Reiczigel, G Majoros. 2000. Quantifying parasites in samples of hosts

Bush AO, Lafferty KD, Lotz JM, Shostak AW. 1997. Parasitology meets ecology on its own terms: Margolis et al. revisited (broken link)

Komonen A, M Elo. 2017. Ecological response hides behind the species abundance distribution: Community response to low‐intensity disturbance in managed grasslands

Kindt R, R Coe. 2005. Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies

Oklahoma State University - Ordination Methods for Ecologists

Mensh B, K Kording. 2017. Ten simple rules for structuring papers

R resources

Oksanen J. 2019. Vegan: an introduction to ordination

Vegan functions

Zelený D. 2019. Analysis of community ecology data in R

Bates D, M Mächler, BM Bolker, SC Walker. 2015. Fitting Linear Mixed-Effects Models Using lme4

Paradis E and K Schliep. 2019. ape homepage

Paradis E. 2019. Moran's Autocorrelation Coefficient in Comparative Methods

BIOL 540 Montana State University R Labs for Community Ecologists

dkahle/ggmap. 2019

Simple features vignette. 2019.

D-Lab workshops

D-Lab workshops can be found on our calendar

• R-Fundamentals
• R Data Wrangling
• R Graphics
• Geospatial Fundamentals in R with sf
• Introduction to Machine Learning in R
• Introduction to Deep Learning in R

D-Lab consulting services

D-Lab offers FREE one-to-one coaching sessions for your individual research projects. Click here to learn more.