skygrowth.mcmc: A gibbs-metropolis algorithm for sampling Ne(t) with a...

In mrc-ide/skygrowth: Phylodynamic inference with nonparametric growth rate models

Description

A gibbs-metropolis algorithm for sampling Ne(t) with a non-parametric growth model

Usage

skygrowth.mcmc(
  tre,
  mhsteps = 1e+05,
  tau0 = 10,
  tau_logprior = "exponential",
  res = 50,
  quiet = F,
  control = NULL,
  gamma = NA,
  logRmean = NULL,
  logRsd = 1,
  maxHeight = NULL
)

Arguments

tre	A dated phylogeny in ape::phylo format (see documentation for ape)
mhsteps	Number of mcmc steps
tau0	Initial guess of the precision parameter
tau_logprior	Prior for precision parameter (character string (gamma or exponential) or function)
res	Number of time points (integer)
quiet	Provide verbose output?
control	List of options passed to optim
gamma	Death rate. If provided will compute R
logRmean	Mean of R in log space. Determines a lognormal prior on R(t). If used, _gamma_ must be provided
logRsd	SD of R in log space. Determines a lognormal prior on R(t). If used, _gamma_ must be provided
maxHeight	If supplied, will only compute Ne(t) estimates this far back in time. Otherwise will compute to the root of the tree.

Value

A fitted model including effective size through time

mrc-ide/skygrowth documentation built on May 19, 2020, 5:10 p.m.