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# contribution of single cov group to likelihood
groupscontrib<-function(obj,lambda,X,nobj,ENV)
{
# set up design matrix by expanding basic matrix X with covariates
if (!is.null(names(obj$cov))) # only in case of covariates
X<-do.call("cbind", lapply(1:length(obj$cov), function(i) X *obj$cov[i])) # design matrix for covariates
if (! ENV$NItest) {
# add undecided if undec=TRUE
if(ENV$undec) X<-cbind(X,ENV$U)
# add dependencies if ia=TRUE
if(ENV$ia) X<-cbind(X,ENV$XI)
# add time dependencies for T models and iaT=TRUE
if(regexpr("T",ENV$resptype)>0 && ENV$iaT) X<-cbind(X,ENV$XIT)
######patprob was a function once
patt <- exp(X %*% lambda)
sumpatt<-sum(patt)
p.patt<-patt/sumpatt
####
# get likelihood contribution for single cov group
ll.bl<-lapply(obj[1:(length(obj)-1)],blcontrib,p.patt) # last element of obj is covariate structure
} else { # for testing ignorable missing
## first complete cases
NIcovs<-c(1,0)
XM<-do.call("cbind", lapply(1:2, function(i) X * NIcovs[i])) # design matrix for ign missings
# add undecided if undec=TRUE
if(ENV$undec) XM<-cbind(XM,ENV$U)
# add dependencies if ia=TRUE
if(ENV$ia) XM<-cbind(XM,ENV$XI)
patt <- exp(XM %*% lambda)
sumpatt<-sum(patt)
p.patt<-patt/sumpatt
ll.bl<-lapply(obj[1],blcontrib,p.patt)
## now incompletes
NIcovs<-c(1,1)
XM<-do.call("cbind", lapply(1:2, function(i) X * NIcovs[i])) # design matrix for ign missings
# add undecided if undec=TRUE
if(ENV$undec) XM<-cbind(XM,ENV$U)
# add dependencies if ia=TRUE
if(ENV$ia) XM<-cbind(XM,ENV$XI)
patt <- exp(XM %*% lambda)
sumpatt<-sum(patt)
p.patt<-patt/sumpatt
ll.mbl<-lapply(obj[2:(length(obj)-1)],blcontrib,p.patt) # last element of obj is covariate structure
ll.bl<-c(ll.bl,ll.mbl)
}
ll.bl
}
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