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
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?
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.)
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