R/ljrk.R

In ljr: Logistic Joinpoint Regression

ljrk <- function(k,y,n,tm,X=NULL,ofst=0)
{
 if (sum(duplicated(tm))>0){
  cat("Error: duplicated observation times\n")  
 }
 else{
  if ((is.null(X)==FALSE)&&(is.matrix(X)==FALSE))
   X=as.matrix(X)
  if (is.unsorted(tm)==TRUE){
   o=order(tm)
   y=y[o]
   n=n[o]
   tm=tm[o]
   if (is.null(X)==FALSE)
    X=as.matrix(X[o,])
   if ((length(ofst)>1)||(ofst[1]!=0))
    ofst=ofst[o]
  }
  N=length(y)
  m=ncol(X)
  or.ofst=ofst
  if (is.null(m))
    m=0
  if (k>N-2)
    k=N-2
   if (length(ofst)==1)
    ofst=as.double(rep(ofst,N))
   else 
    ofst=as.double(ofst)
   k=as.integer(k)
   out <- .C("ljrk",k,as.double(y),as.double(n),as.double(tm),as.double(X),ofst,beta=double(m+1),gamma=double(k+1),tau=double(k),N,m,ans=double(1),PACKAGE="ljr")
   cat('Model:\n')
   cat('y~Binom(n,p) where p=invlogit(eta)\n')
   if (m>0){
    if (is.null(dimnames(X)[[2]])==FALSE)
     m.variables=dimnames(X)[[2]]
    else
     m.variables=paste("X",1:ncol(X),sep="")
   }
   else
    m.variables=NULL
   m.variables=c('Intercept',m.variables)
   t.variables='t'
   if (length(out$tau)>0)
    for (i in 1:length(out$tau))
     t.variables=c(t.variables,paste('max(t-tau',i,',0)',sep=""))
   if ((or.ofst[1]==0)&(length(or.ofst)==1))
    cat('eta=b0')
   else
    cat('eta=ofst+b0')
  if (length(m.variables)>1)
   for (i in 2:length(m.variables))
    cat(paste(paste('+b',i-1,sep=""),'*',m.variables[i],sep=""))
  for (i in 0:(length(t.variables)-1))
   cat(paste(paste('+g',i,sep=""),'*',t.variables[i+1],sep=""))
  cat("\n\n")
  m.coef=c(out$beta,out$gamma)
  f1=data.frame(Variables=c(m.variables,t.variables),Coef=m.coef,row.names=c(paste('b',0:(length(m.variables)-1),sep=""),paste('g',0:(length(t.variables)-1),sep="")))
  j.labels=NULL
  if (length(out$tau)>0)
   for (i in 1:length(out$tau))
    j.labels=c(j.labels,paste('tau',i,'=',sep=""))
  f2=data.frame(j.labels,Joinpoints=out$tau)
  if (length(out$tau)>0)
   names(f2)=c(' ','  ')
  else
   names(f2)=NULL
  print(f1)
  cat('\nJoinpoints:\n')
  print(f2)
  ret1=m.coef
  names(ret1)=c(m.variables,t.variables)
  ret2=out$tau
  names(ret2)=j.labels
  return(list(Coef=ret1,Joinpoints=ret2,wlik=out$ans))
 }
}