logLike.pars: logLike.pars

In SpeciesMix: Fit Mixtures of Archetype Species

Description

logLike.pars return loglike for give parameters. pi is on normal scale with G groups

Usage

logLike.pars(pi,coef,sp.form,sp.data,covar.data)

Arguments

pi	vector of pi returned from SpeciesMix
coef	matrix of coefficents returned from Species Mix
sp.form	an object of class "formula" (or one that can be coerced to that class):a symbolic description of the model to be fitted
sp.data	a data frame containing the species information. The frame is arranged so that each row is a site and each column is a species. Species names should be included as column names otherwise numbers from 1:S are assigned.
covar.data	a data frame containng the covariate data for each site. Names of columns must match that given in

Details

To Come

Value

logl	loglikelihood

Authors

Piers Dunstan and Scott Foster

Examples

G <-4
S <- 50
theta <- matrix(c(-9,35,-32,0,0.7,0,-16,23,-8.2,-3,-0.6,0.8),4,3,byrow=TRUE)
dat <- data.frame(y=rep(1,200),x=runif(200,0,2.5),z=rnorm(200,10,2))
dat <- data.frame(dat,x.sq=dat$x^2)
dat1 <- artificial.data(y~1+x+x.sq,dat,theta,S)
fm4 <- SpeciesMix(obs~1+x+x.sq,dat1$pa,dat,G=4,em.prefit=TRUE,em.refit=1,est.var=FALSE)
logLike.pars(fm4$pi,fm4$coef,obs~1+x+x.sq,dat1$pa,dat)

SpeciesMix documentation built on May 2, 2019, 4:22 a.m.