BEAST v2.7.8 Documentation: beastclassic.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood

BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Distribution on a tree, typically a prior such as Coalescent or Yule
A likelihood function for a Gaussian Markov random field on a log population size trajectory
A generalization of the GMRF model that allows for the analysis of multilocus sequence data.

Reference:

Gill, M. S., Lemey, P., Faria, N. R., Rambaut, A., Shapiro, B., & Suchard, M. A. (2012). Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular biology and evolution, 30(3), 713-724.

doi:10.1093/molbev/mss265

Logable: yes, this can be used in a log.

Inputs:

trees, phi, ploidyFactors, numGridPoints, cutOff, groupSizes, populationSizes, precisionParameter, lambda, timeAwareSmoothing, rescaleByRootHeightInput, tree, treeIntervals