run: Run model fits

Description Usage Arguments

View source: R/sampling.R

Description

This function fit a hierarchical or a fixed-effect model, using Bayeisan sampling. We use pMCMC, with a suite of DE-MCMC, DGMC, and simply, crossover (i.e., DE-MC), mutation, or migration operators. Note that the latter two operators essentially are random-walk Metroplolis, so they will be very inefficient, if been applied alone, even with our fast C++ implementation.

Usage

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run(samples, report = 100, ncore = 1, pm = 0, qm = 0, hpm = 0,
  hqm = 0, gammamult = 2.38, ngroup = 5, force = FALSE,
  sampler = "DE-MCMC", slice = FALSE)

CheckConverged(samples)

Arguments

samples

a sample list generated by calling DMC's samples.dmc.

report

how many iterations to return a report

ncore

parallel core for run_many

pm

probability of migration

qm

probability of mutation

hpm

probability of migration at the hyper level

hqm

probability of mutation at the hyper level

gammamult

a tuning parameter, affecting the size of jump

ngroup

number of distributed groups

force

set force to FALSE for turning off recalculation of PDA. Set it as an integer between 1 and 10, forcing to re-calculate new likelihood, every e.g., 1, 2, 3 step.

sampler

which sampler to run MCMC, "DE-MCMC" or "DGMC"

slice

use for debugging blocked sampling


ggdmc documentation built on Sept. 2, 2018, 1:03 a.m.