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Model Testing for Mode and Tempo

Model Testing for Mode and Tempo

Name: Stretching models

Start date: 3/1/2011

*Target Release: 0.4 (May 2011)

Status:  In Flight

Assignee:

Background

The Working Group identified a set of phylogenetic analyses to make available through the DE. One of this analyses involves the ability to stretch (i.e. increase the branch length of) a phylogenetic tree according to a given evolutionary model. A maximum likelihood framework is then used to estimate the models' parameters and to assess their likelihood. This project fulfills a requirement expressed by the Working Group as part of the iPToL Grand Challenge and belongs to the basic toolkit for post-tree analyses.

Project Description

The R package geiger provides a large number of stretching functions and the basic framework to run R scripts is already in place. A generic wrapper needs to be written around the functions to be integrated into the DE.

The functions to be integrated are, in order of priority:

  • fitContinuous
  • fitDiscrete
  • detaTree

deltaTree is necessary to display the modified tree, and therefore will be added to fitContinuous and fitDiscrete as a workflow.

In addition, the functions will be modified to handle large trees and run on HPC infrastructure.

Deliverables

Access through the DE to the functions specified above, exposing all components. The tools should also allow the user to perform different stretching operations (i.e. apply different models) to the same dataset at once. Additionally, the tool should warn the user when the parameter values are very close to the function bounds.

Milestones

Critical steps. Refer to project description and deliverables.

Milestone

ETA

Reached

Scoping of project

11W13

11W19

Define user personas

11W13

CANCELED

Use cases

11W13

CANCELED

Scripts written

11W21

 

Scripts tested

11W22

 

DE Integration

11W24

 

Team members (if applicable)

Name

Role

Contact

Naim

deltaTree integration

 

Jeremy

fitDiscrete integration

 

Barb

fitContinuous integration

 

Origin

TE110215

Dependencies/Related projects

DE