https://github.com/cboettig/wrightscape
:package: Infer adaptive landscapes from phylogenetic trees
Science Score: 36.0%
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Low similarity (9.0%) to scientific vocabulary
Repository
:package: Infer adaptive landscapes from phylogenetic trees
Basic Info
- Host: GitHub
- Owner: cboettig
- License: cc0-1.0
- Language: R
- Default Branch: master
- Homepage: http://www.carlboettiger.info/archives/category/phylogenetics
- Size: 1 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
wrightscape
A fast C code implementation of maximum likelihood calculations for a multi-peak OU process with independent alpha, sigma, and theta parameters for each peak on phylogenetic trees (an extension of the ouch model). Includes R package wrapper as interface to C code. Likelihood calculation presented in http://www.carlboettiger.info/files/phylo-covariance.pdf, later the basis for: Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger and Brian O’Meara, (2012). Modeling Stabilizing Selection: Expanding the Ornstein-Uhlenbeck Model of Adaptive Evolution, Evolution 66 (8) 2369-2383. doi:10.1111/j.1558-5646.2012.01619.x
File overview
regimes.c:
Test the regimes data structure
Modify to handle a single regime
Implement a transition density calculation where transitions occur at nodes alone <<<
Pagel & Meade, Huelsenbeck papers -- what about transitions at nodes?
linear.c:
BM not really subset of OU, as alpha = 0 not acceptible OU calculation.
Modify the OU model to handle appropriately small alpha with Taylor Expansion or as BM
max likelihood:
Implement and test maximum likelihood searches over parameters against existing methods
mcmc.c:
Start implementing a basic MCMC solver!
matrix_method.c:
nonlinear transition densities?
Test the stationary distribution?
Error handling
This should probably be done mostly at the R level, enforcing the strict formats and conventions of the input (i.e. if not doing regimes, all states should be listed at 0. States must be numbered incrementally from 0 to n-1, where n is the number of regimes present.)
STEPPING STONES
- Recursive Joint Prob method using BM, compare to analyticals
- Bayesian OU vs BM in RJMCMC
- Use Pagel's BayesTraits run to "paint tree" with uncertainty, then repeat OUCH analysis with uncertainty in branch color
Owner
- Name: Carl Boettiger
- Login: cboettig
- Kind: user
- Company: UC Berkeley
- Website: http://carlboettiger.info
- Repositories: 173
- Profile: https://github.com/cboettig
GitHub Events
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Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carl Boettiger | c****g@g****m | 517 |
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 3
- Total pull requests: 0
- Average time to close issues: 8 months
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
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Top Authors
Issue Authors
- cboettig (3)