mcmc_nltt {nLTT}

function, using a Monte Carlo Markov Chain

Description

function, using a Monte Carlo Markov Chain

Usage

mcmc_nltt(
  phy,
  likelihood_function,
  parameters,
  logtransforms,
  iterations,
  burnin = round(iterations/3),
  thinning = 1,
  sigma = 1
)

Arguments

phy

phylo Vector of weights

likelihood_function

function Function that calculates the likelihood of our diversification model, given the tree. function should be of the format function(parameters, phy).

parameters

vector Initial parameters to start the chain.

logtransforms

scalar Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)

iterations

scalar Length of the chain

burnin

scalar Length of the burnin, default is 30% of iterations

thinning

scalar Size of thinning, default = 1

sigma

scalar Standard deviation of the jumping distribution, which is N(0, sigma).

Value

mcmc An MCMC object, as used by the package "coda".