skygrowth.map.covar: Maximum a posteriori estimate of effective size through time...

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

Description

Maximum a posteriori estimate of effective size through time using covariate data

Usage

skygrowth.map.covar(
  tre,
  formula,
  data,
  maxSampleTime,
  tau0 = 10,
  tau_logprior = "exponential",
  beta_logpriors = list(),
  res = 50,
  quiet = FALSE,
  maxiter = 20,
  abstol = 0.01,
  control = NULL,
  maxHeight = NULL,
  ...
)

Arguments

tre	A dated phylogeny in ape::phylo format (see documentation for ape) or a list of phylogenies or multi.phylo object
formula	An R formula with empty left-hand-side; the right-hand-side specifies relationship of covariates with growth rate of Ne
data	A data.frame, must include 'time' column
maxSampleTime	The scalar time that the most recent sample was collected
tau0	Initial guess of the precision parameter
tau_logprior	Prior for precision parameter (character string (gamma or exponential) or function)
beta_logpriors	Optional list of functions providing log density for coefficients (must correspond to data)
res	Number of time points (integer)
quiet	Provide verbose output?
maxiter	Maximum number of iterations
abstol	Criterion for convergence of likelihood
control	List of options passed to optim
maxHeight	The earliest time (furthest time in to the past) to estimate Ne
...	Not implemented

Value

A fitted model including effective size through time

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