smcp_sampling: SMC' sampler-inference from local genealogies

In phylodyn: Statistical Tools for Phylodynamics

Description

SMC' sampler–inference from local genealogies

Usage

smcp_sampling(data, nsamp, nburnin, grid, alpha = 0.001, beta = 0.001,
  stepsz = 0.1, Nleap = 15, rand_leap = TRUE, scaling = 10,
  tol = 1e-05)

Arguments

data	a list containing sufficient statistics
nsamp	integer specifying number of MCMC samples
nburnin	integer specifying the number of burnin samples
grid	a vector with the grid points
alpha	hyperparameter of precision of BM prior
beta	hyperparameter of precision of BM prior
stepsz	numeric tuning parameter for Split Hamiltonian Monte Carlo
Nleap	integer tuning parameter for Split Hamiltonian Monte Carlo
rand_leap	tuning parameter for Split Hamiltonian Monte Carlo
scaling	numeric re-scaling parameter
tol	tolerance to detect difference

Value

A matrix of sim rows. Entry x_i,j has the n-j+1-th coalescent time of the i-th tree

phylodyn documentation built on May 29, 2017, 1:28 p.m.