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 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

• Testing for Correlated Evolution among Discrete Characters in R

• Modeling Continuous Character Evolution in R - Hunt

• How to do I run Phylogenetic Independent Contrasts in R? - Price
  • Calculating contrasts
  • Plotting contrasts
  • Calculating and plotting correlated trait evolution

• How do I run analyses of diversification in R? - Price

• 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

• How do I estimate divergence times in R? - Bell

• Using Mesquite in R