pmc (version 0.0-8)

pmc_fit: Fit any model used in PMC

Description

The fitting function used by pmc to generalize fitting to any model

Usage

pmc_fit(tree, data, model, options = list())

Arguments

tree

a phylogenetic tree. can be ouch or ape format

data

trait data in ape or ouch format

model

the name of the model to fit, see details for a list of currently supported types

options

whatever additional options would be provided to the model fit, see details

Value

• a pmc_model object, anything that has methods "simulate", "update", getParameters, and getLikelihood

Details

options should include all parameters required by the fit method Currently methods avialable are fitContinuous (see geiger package) and hansen (see the ouch package).

Examples

## a geiger example
require(geiger) # just to load the data
data(geospiza)
attach(geospiza)
lambdaFit<-pmc_fit(geospiza.tree, geospiza.data, model="lambda")
## Or a single trait at a time:
lambdaFit<-pmc_fit(geospiza.tree, geospiza.data[1], model="lambda")
## an ouch example
require(ouch) # just for the data,
data(bimac)
tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species))
ou.3 <- pmc_fit(data=log(bimac['size']),tree, model="hansen",
                list(regimes=bimac['OU.3'],sqrt.alpha=1,sigma=1))