R for Community Ecologists

R Labs for Community Ecologists

This section of the Laboratory for Dynamic Synthetic Vegephenonenology (LabDSV) includes tutorials and lab exercises for a course in quantitative analysis and multivariate statistics in community ecology. Example data sets are included and may be downloaded to run the exercises if desired. Please understand, it is not my intention to teach community analysis in these labs. HTML is simply too limiting. My intention is to demonstrate the utility of R for ecological analysis, to teach the rudiments of R syntax, and to make routines and examples available to augment formal study in community ecology.

As a compromise to those more interested in ecology than R, I have written a number of functions that minimize the amount of S you have to learn to perform vegetation analysis. For those also interested in S, I have included annotated copies of the functions at the bottoms of the lab.

The web pages are undergoing a progressive transition to a CSS style sheet and may be in formatting flux for a little while.

The materials and exercises currently available include:

Introduction
- R for Ecologists, a primer on the S language and available software
Familiarization with Data
- Lab 1 Loading Community Data and Simple Graphical Data Summaries
- Lab 2 Loading Site/Environment Data and Simple Graphical Summaries
- Lab 3 Vegetation Tables and Summaries
Modeling Species Distributions
- Lab 4 Modeling Species Distributions with Generalized Linear Models
- Lab 5 Modeling Species Distributions with Generalized Additive Models
- Lab 6 Modeling Species Distributions with Classification Trees
Ordination
- Lab 7 Principal Components Analysis
- Lab 8 Principal Coordinates Analysis
- Lab 9 Nonmetric Multi-Dimensional Scaling
- Lab 10 Correspondence Analysis and Detrended Corresponence Analysis
- Lab 11 Fuzzy Set Ordination
- Lab 12 Canonical Correspondence Analysis
Cluster Analysis
- Lab 13 Cluster Analysis
- Lab 14 Discriminant Analysis with Tree Classifiers
Miscellaneous Scripts of Potential Interest
- Scripts

What About RStudio

Best Practices Using RStudio

The current versions of the LabDSV, optpart, fso, and coenoflex R packages are available for both linux/unix and Windows at https://cran.r-project.org.

For more information contact Dave Roberts at droberts@montana.edu

The syllabus for BIOL 540 - Analysis of Ecological Communities is available here:

BIOL 540 - Analysis of Ecological Communities

Portions of the work were conducted while a Sabbatical Fellow at the National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant #DEB-0072909), the University of California, and the Santa Barbara campus.