R/residuals.smoothSurvReg.R

In smoothSurv: Survival Regression with Smoothed Error Distribution

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#### AUTHOR:    Arnost Komarek             ####
####            02/05/2004                 ####
####                                       ####
#### FILE:      residuals.smoothSurvReg.R  ####
####                                       ####
#### FUNCTIONS: residuals.smoothSurvReg    ####
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### =================================================================================
### residuals.smoothSurvReg: Compute residuals for objects of class 'smoothSurvReg'
### =================================================================================
## object .......... object of class 'smoothSurvReg'
## ... ........ other arguments passed to 'residuals' function 
##              (it's here only for compatibility with a generic function)
residuals.smoothSurvReg <- function(object, ...){
   ny <- ncol(object$y)
   nx <- ncol(object$x)
   nz <- ncol(object$z)

   est.scale <- object$estimated["Scale"]
   common.logscale <- object$estimated["common.logscale"]
   regres <- object$regres[, "Value"]
   names(regres) <- rownames(object$regres)
   beta <- regres[1:nx]
   if (common.logscale){
     if (est.scale) scale <- regres["Scale"]
     else           scale <- object$init.regres["Scale", "Value"]
   }
   else{
     parscale <- matrix(regres[(nx+1):(nx+nz)], ncol = 1)
     logscale <- (object$z %*% parscale)
     scale <- exp(logscale)
   }
   eta <- object$x %*% beta

   y1 <- (object$y[,1] - eta)/scale
   if (ny > 2){
      y2 <- (object$y[,2] - eta)/scale
      y2[object$y[,3] == 2] <- 0
      y2[object$y[,3] == 0] <- 0
   }

   if (ny <= 2){
      out <- cbind(y1, object$y[,2])
      colnames(out) <- c("res", "censor")
   }
   else{
      out <- cbind(y1, y2, object$y[,3])
      colnames(out) <- c("res", "res2", "censor")
   }

   return(out)
}