logLike.pars

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Description

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

Usage

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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

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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)