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Infer adaptive landscapes from phylogenetic trees

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Octocat-spinner-32-eaf2f5

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Octocat-spinner-32 R
Octocat-spinner-32 data simulation.R autocommit December 01, 2011
Octocat-spinner-32 demo track legacy files November 21, 2012
Octocat-spinner-32 inst
Octocat-spinner-32 man
Octocat-spinner-32 src
Octocat-spinner-32 DESCRIPTION
Octocat-spinner-32 INSTALL
Octocat-spinner-32 LICENSE
Octocat-spinner-32 NAMESPACE
Octocat-spinner-32 README
Octocat-spinner-32 cleanup
Octocat-spinner-32 configure
Octocat-spinner-32 configure.ac
README
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? <<<<<


Handle the root node value... as a parameter?  Get better understanding of how existing software handles this!
R interface hands down tree and traits, but not model being tested.  


Generate some non-linear w(y|x) with pde  


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.)


########### Progress List ############




############# 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



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