phylandml: Maximum likelihood inference of migration rates and effective...

In emvolz-phylodynamics/phyland: Phylogeographic analysis using structured coalescent models

Description

Maximum likelihood inference of migration rates and effective population size between demes

Usage

phylandml(tree, delimiter = "_", index = NULL, regex = NULL,
  design = NULL, method = "BFGS", quiet = FALSE, start_migrate = NA,
  start_Ne = NA, Ne_logprior = function(x) 0,
  migrate_logprior = function(x) 0, nstarts = 1, ncpu = 1, minBL = 0,
  ...)

Arguments

tree	A time-scaled phylogeny in ape::phylo format
delimiter	A character string which will be used to infer the deme of sampling from tip labels
index	The integer position within tip labels of the sample deme information. If not provided will use the last position, e.g. <accession number>_locationOfSampling
regex	As an alternative to delimiter/index, the location of sampling can be inferred by matching a regular expression string
design	A matrix describing which migration rates to estimate and which migration rates are assumed to be equal. Row and column names should correspond to names of demes. Unique integers should specify rates to estimate. If not provided, all rates will be estimated
method	Optimisation method to be used by optim
quiet	If TRUE, will suppress likelihood printing to stdout
start_migrate	Optional starting value for optimisation of migration rates
start_Ne	Optional starting value for optimisation of Ne
Ne_logprior	Optional log prior density for Ne
migrate_logprior	Optional log prior density for migration rate
nstarts	integer number of starting conditions to generate for optimisation
ncpu	On multi-cpu computers, will conduct optimisation from different starting conditions in parallel on this many cpu's
minBL	Any short branch lengths will be rounded up to this value
...	Additional parameters passed to optim

Value

A fitted model with summary and coef methods.

emvolz-phylodynamics/phyland documentation built on May 4, 2019, 3:21 p.m.