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
Jira link
Dependencies/Related projects
DE