R/print.TPidm.R

In TP.idm: Estimation of Transition Probabilities for the Illness-Death Model

print.TPidm <-
function(x, ...){
    if(!inherits(x,"TPidm")) stop("'x' must be of class 'TPidm'.")
    
    cat("Call:\n")
    print(x$call)
    cat("\n")
    
    if(is.null(x$cov)){
      cat("Parameters:","\n")
      cat("s=", x$s, "\n")
      cat("t=", x$t, "\n")
      cat("Method=", x$method, "\n")
      cat("CI=", x$CI, "\n")
      cat("CI transformation=", x$ci.transformation, "\n")
      cat(paste("Possible transitions:\n", sep=""))
      print(x$p.trans, row.names = FALSE)
      
      
      cat("\n")
      if(x$CI==TRUE){
        if(x$s==0){
          cat("Occupation probabilities at time t:", "\n", "\n")
          
          idm.info<-data.frame(transition=rownames(x$probs),
                               probs=x$probs[,1],
                               lower=x$probs[,2],
                               upper=x$probs[,3],
                               variance=x$probs[,4])
          
        }else{
          cat("Transition probabilities at time t:", "\n", "\n")
          
          idm.info<-data.frame(transition=rownames(x$probs),
                               probs=x$probs[,1],
                               lower=x$probs[,2],
                               upper=x$probs[,3],
                               variance=x$probs[,4])
          
        }
      }else{
        if(x$s==0){
          cat("Occupation probabilities at time t:", "\n", "\n")
          
          estimations<-c()
          for(j in 1:length(x$p.trans)){
            idx<-unlist(strsplit(x$p.trans[j], " "))
            estimations[j]<-x$all.probs[length(x$times),,j]
          }
          
          idm.info<-data.frame(transition=x$p.trans,
                               probs=estimations)
          
        }else{
          cat("Transition probabilities at time t:", "\n", "\n")
          
          estimations<-c()
          for(j in 1:length(x$p.trans)){
            idx<-unlist(strsplit(x$p.trans[j], " "))
            estimations[j]<-x$all.probs[length(x$times),,j]
          }
          
          idm.info<-data.frame(transition=x$p.trans,
                               probs=estimations)
          
        }
      }
    } else{
      
      cat("Parameters:","\n")
      cat("s=", x$s, "\n")
      cat(paste("t:\n", sep=""))
      print(x$t, row.names = FALSE)
      cat("\n")
      cat("Covariate=", x$cov, "\n")
      cat("Method=", x$method, "\n")
      cat("CI=", x$CI, "\n")
      cat("CI transformation=", x$ci.transformation, "\n")
      cat(paste("Possible transitions:\n", sep=""))
      print(x$p.trans, row.names = FALSE)
      
      cat("\n")
      if(x$CI==TRUE){
        if(x$s==0){
          cat("Occupation probabilities at time t:", "\n", "\n")
          names(x$probs)<-x$names.cov
          idm.info<-list(probs=x$probs)
          
        }else{
          cat("Transition probabilities at time t:", "\n", "\n")
          names(x$probs)<-x$names.cov
          idm.info<-list(probs=x$probs)
          
        }
      }else{
        if(x$s==0){
          cat("Occupation probabilities at time t:", "\n", "\n")
          names(x$probs)<-x$names.cov
          idm.info<-list(probs=x$probs)
          
        }else{
          cat("Transition probabilities at time t:", "\n", "\n")
          names(x$probs)<-x$names.cov
          idm.info<-list(probs=x$probs)
          
        }
      }
      
      
    }
    
    cat("\n")
    print(idm.info, row.names=FALSE)
    
    
  }