Difference between revisions of "R Hackathon 1/Trait Evolution SG"

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* Participants: Harmon, Hipp, Hunt
 
* Participants: Harmon, Hipp, Hunt
* Targets/Accomplishments
+
== Targets.==
** Evaluated the results of continuous character analyses in different packages, and corrected some errors
+
# Compare various implementations of the same methods (ape, geiger, OUCH, Mesquite)
 +
# Improve functionality of character fitting in r
 +
# Investigate statistical power of discriminating among various models
 +
# Identify gaps in current implementation
 +
Accomplishments
 +
# Evaluated the results of continuous character analyses in different packages
 +
#* Packages are mostly consistent
 +
#* Discrepancies come from two sources:
 +
#** Different approaches (e.g. marginal versus joint likelihood)
 +
#** Difficulties in finding the ML solution
 +
# Improve functionality or, at least, interpretability of output
 +
#* GEIGER was modified to give more reliable results by a more thorough search of the likelihood surface
 +
#* Some ape functions seem (to us) unreliable for large trees
 +
 
 
Test
 
Test
 
** Clarified why one sometimes gets different results from different programs
 
** Clarified why one sometimes gets different results from different programs

Revision as of 16:26, 24 January 2008

  • Participants: Harmon, Hipp, Hunt

Targets.

  1. Compare various implementations of the same methods (ape, geiger, OUCH, Mesquite)
  2. Improve functionality of character fitting in r
  3. Investigate statistical power of discriminating among various models
  4. Identify gaps in current implementation

Accomplishments

  1. Evaluated the results of continuous character analyses in different packages
    • Packages are mostly consistent
    • Discrepancies come from two sources:
      • Different approaches (e.g. marginal versus joint likelihood)
      • Difficulties in finding the ML solution
  2. Improve functionality or, at least, interpretability of output
    • GEIGER was modified to give more reliable results by a more thorough search of the likelihood surface
    • Some ape functions seem (to us) unreliable for large trees

Test

    • Clarified why one sometimes gets different results from different programs
    • Modified GEIGER package so that results for fitting models of character evolution are more robust
    • Modified functions to rescale trees and variance-covariance matrices for non-ultrametric trees