Nothing
rtableICC.RxC.engine <-
function(R,C,T,M,p,N,cluster.size,theta){
if (max(cluster.size)>(length(theta))){
stop(c("Maximum number of individuals in one of the clusters is ", paste(max(cluster.size)),", which is greater than maximum allowed cluster size. (1) Re-run the function,
(2) increase maximum allowed cluster size by increasing the number of elements of theta,
(3) increase total number of clusters, or
(4) decrease total number of individuals!"))
}
rTable.raw=array(0,dim=c(R,C,N))
dat=array(0,dim=c(max(cluster.size),R,C,M))
rTable=array(0,dim=c(R,C))
g.t=array(0,dim=c(R,C,(T-1)))
g.tilde=array(0,dim=max((T-1)))
pp=as.vector(t(p))
bsl=1
say=1
selT=0
if (R==1){
p=t(as.matrix(p))
}else if (C==1){
p=as.matrix(p)
}
sumCounts=array(0,R*C)
for (r in 1:M){
if (cluster.size[r]>1){
counts=cbind(t(compositions(cluster.size[r],R*C,include.zero=TRUE)),0)
cl=ncol(counts)
for (j in 1:nrow(counts)){
if (sum(counts[j,]==0)==(R*C)){
for (i in 1:R){
for (k in 1:C){
if (counts[j,((i-1)*C+k)]>0){
counts[j,cl]=theta[cluster.size[r]]*p[i,k]+(1-theta[cluster.size[r]])*p[i,k]^theta[cluster.size[r]]
}
}
}
} else {
counts[j,cl]=(1-theta[cluster.size[r]])*prod(pp^counts[j,1:(R*C)])
}
}
counts[,cl]=counts[,cl]/sum(counts[,cl])
ind=rDiscrete(1,counts[,cl])$rDiscrete
sel=counts[ind,1:(R*C)]
sumCounts=sumCounts+sel
if (sum(sel==0)==((R*C)-1)){
for (i in 1:R){
for (k in 1:C){
if (sel[((i-1)*C+k)]>0){
g.t[i,k,(cluster.size[r]-1)]=g.t[i,k,(cluster.size[r]-1)]+1
rTable.raw[i,k,say:(say+sel[((i-1)*C+k)]-1)]=1
say=say+sel[((i-1)*C+k)]
}
}
}
} else {
g.tilde[(cluster.size[r]-1)]=g.tilde[(cluster.size[r]-1)]+1
for (i in 1:R){
for (k in 1:C){
if (sel[((i-1)*C+k)]>0){
rTable.raw[i,k,say:(say+sel[((i-1)*C+k)]-1)]=1
say=say+sel[((i-1)*C+k)]
}
}
}
}
} else if (cluster.size[r]==1){
ind=rDiscrete(1,pp)$rDiscrete
sumCounts[ind]=sumCounts[ind]+1
for (i in 1:R){
for (k in 1:C){
if (ind==((i-1)*C+k)){
rTable.raw[R,C,say]=1
say=say+1
}
}
}
}
}
rTable=sumCounts
list(rTable=rTable,rTable.raw=rTable.raw,g.t=g.t,g.tilde=g.tilde)
}
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