Collection of tutorials to analyze community data in R
Here are some tutorials that I have come across and have found helpful. I'll also post some code I've been working on. When possible, I've added R scripts and links. Feel free to suggest edits and additions.
vegan-centric
Multivariate analyses of ecological communities in R: vegan tutorial
- Author: Jari Oksanen
- Type: pdf
- Source: http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf
Multivariate Statistics
- Author: Jeff Powell
- Type: pdf from a Western Sydney HIE course
- Source: http://www.hiercourse.com/docs/Rnotes_multivariate.pdf
Variation Partitioning
- Author: Jeff Powell
- Type: R markdown
- Source: http://www.hiercourse.com/docs/variationPartitioning.html
#source("code/variationPartitioning.Rmd")Use distance-based redundancy analysis (vegan::capscale) and model selection (ordistep) to determine which wood traits best explain variation in OTU composition
- Author: Marissa Lee
- Type: modified project code
- Source: https://github.com/Zanne-Lab/woodEndophytes
#source("code/modelselection_capscale.R")mvabund-centric
mvabund: an R package for model-based analysis of multivariate abundance data
- Author: Yi Wang, Ulrike Naumann, Stephen T. Wright, David I. Warton
- Type: Article in MEE
- Source: http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00190.x/full
MVABUND package, 2014 updates prepared for Eco-Stats lab
- Author: David Warton
- Type: R script from a course
- Source: http://eco-stats.blogspot.com.au/2014/09/september-eco-stats-lab-mvabund-package.html
#source("code/mvabundTute.R")Introduction to mvabund
- Author: Rachel V. Blakey & Andrew Letten
- Type: Blog post
- Source: http://environmentalcomputing.net/introduction-to-mvabund/
Use mvabund and model selection to determine which wood traits best explain variation in OTU abundances
- Author: Marissa Lee
- Type: modified project code
- Source: https://github.com/Zanne-Lab/woodEndophytes
#source("code/modelselection_mvabund.R")boral-centric
boral – Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in R
- Author: Francis K.C. Hui
- Type: Article in MEE
- Source: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12514/abstract
- Video: https://www.youtube.com/watch?v=vyMsgyytcUI
So Many Variables: Joint Modeling in Community Ecology
- Author: David I.Warton. F. Guillaume Blanchet, Robert B.O’Hara, Otso Ovaskainen, Sara Taskinen, Steven C.Walker, Francis K.C.Hui
- Type: Article in TREE
- Source: http://www.sciencedirect.com/science/article/pii/S0169534715002402?via%3Dihub
#source("code/startercode.R")
#source("code/speciesrichness-analysis.R")
#source("code/fourthcorner-analysis.R")
#which use...
#source("code/fourthcorner-analysis-auxilaryfunctions.R")
#source("code/speciesrichness-auxilaryfunctions.R")Boral example particularly designed for studies with very diverse communities, e.g. OTU data
- Author: Marissa Lee
- Type: modified project code
- Source: https://github.com/Zanne-Lab/woodEndophytes
#source("code/boral_withOTUs.R")
#which uses...
#source("code/boral_withOTUs_auxilaryfunctions.R")