phylodyn (version 0.9.0)

smcp_sampling: SMC' sampler--inference from local genealogies

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