HowTo/HelpWiki
Beginners HowTo (draft)
These pages are intended to be eventually moved to a more permanent location...
Contents
- Getting Started - Smith
- Downloading R (for Mac & PC)
- Packages (for comparative methods) - w/ pointers to relevant R documents
- Which ones - pointer to task view?
- How to install
- Checking for updates
- Basics of Using R
- Setting up your workspace - eg using library(package)
- How to Access Help
- help.search("x")
- ?x
- Changing your working directory
- Saving your work
- Saving the workspace
- Saving a script
- CRAN Task View Comparative Phylogenetic Methods - Price & Vision
- Using Vignettes - Vision
- Inputting Trees - Sidlauskas
- Inputting trees
- Taxon names without spaces or quotes
- Nexus (translation table or names)
- Newick (names only)
- Exporting trees
- Working with multi tree files
- Example files
- Inputting trees
- Inputting and Exporting Data - Sidlauskas
- Tab-delimited tables
- Taxon names should appear in first column for translation to rownames
- Basic Tree and Data Manipulation - Sidlauskas
- Rooting
- Resolving polytomies
- Setting branch lengths
- Identifying subgroups
- Identifying most recent common ancestors
- Culling taxa
- Calculating patristic distances
- Plotting trees
- Modeling Discrete Character Evolution in R - Smith
- Formatting discrete data for analysis
- Model fitting
- Comparisons with the likelihood ratio test
- How to do I run Phylogenetic Independent Contrasts in R? - Price
- Calculating contrasts
- Plotting contrasts
- Calculating and plotting correlated trait evolution
- Testing for Correlated Evolution among Continuous Characters with PGLS in R - Smith
- Assuming a Brownian Motion correlation structure
- Assuming an Ornstein-Uhlenbeck correlation structure
- How do I Reconstruct Ancestral States in R? - Sidlauskas
- Continuous Data
- Discrete Data