R Hackathon 1/HelpWiki

From Phyloinformatics
Jump to: navigation, search

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
  • 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
  • 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