pou_logl_fast: Fast Phylogenetic Likelihood

In jpmeagher/sdsBAT:

Description

Using the inline and RcppEigen packages performs a fast calculation of the Phylogenetic Ornsetin-Uhelenbeck Process negative log likelihood, given the process hyperparameters, a phylogenetic tree, and some data. The C++ code was taken from code accompanying Hajipantelis et al.

Usage

pou_logl_fast(ln_hyperparameters, phylogenetic_tree, observations)

Arguments

ln_hyperparameters	Vector of the natural logarithm of hyperparameters for an Ornstein-Uhlenbeck kernel in order log(phylogenetic noise, phylogenetic length-scale, non-phylogenetic noise)
phylogenetic_tree	Phylogenetic tree of relationships between observations
observations	Observations from the tips of the phylogenetic tree

Value

A positive value which is the negative log likelihood for the data.

Source

P. Z. Hadjipantelis, N. S. Jones, J. Moriarty, D. A. Springate, and C. G. Knight, Function-valued traits in evolution, Journal of The Royal Society Interface. 10(82), 20121032 (2013). https://github.com/fpgpr

jpmeagher/sdsBAT documentation built on May 5, 2019, 3:50 a.m.