R/summary.TPidm.R

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

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