skygrowth.map: 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 with a non-parametric growth model

Usage

skygrowth.map(
  tre,
  tau0 = 10,
  tau_logprior = "exponential",
  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
tau0	Initial guess of the precision parameter
tau_logprior	Prior for precision parameter (character string (gamma or exponential) or function)
res	Number of time intervals (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. If not provided, will use the median of root heights for input trees
...	Not implemented

Value

A fitted model including effective size through time

Examples

## Not run: 
require(skygrowth)
require(ape)
load( system.file( package='skygrowth', 'NY_flu.rda' , mustWork=TRUE) ) 
# NOTE branch lengths in weeks  / 13 years in all
fit <- skygrowth.map( NY_flu 
 , res = 24*13  # Ne changes every 2 weeks
 , tau0 = .1    # Smoothing parameter. If prior is not specified, 
                # this will also set the scale of the prior
)
plot( fit ) + scale_y_log10()

## End(Not run)

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