R/util-cens2pseudo.R

In aursiber/fitdistrplus: Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

#############################################################################
#   Copyright (c) 2024 Christophe Dutang, Marie Laure Delignette-Muller                                                                                                  
#                                                                                                                                                                        
#   This program is free software; you can redistribute it and/or modify                                               
#   it under the terms of the GNU General Public License as published by                                         
#   the Free Software Foundation; either version 2 of the License, or                                                   
#   (at your option) any later version.                                                                                                            
#                                                                                                                                                                         
#   This program is distributed in the hope that it will be useful,                                                             
#   but WITHOUT ANY WARRANTY; without even the implied warranty of                                          
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                                 
#   GNU General Public License for more details.                                                                                    
#                                                                                                                                                                         
#   You should have received a copy of the GNU General Public License                                           
#   along with this program; if not, write to the                                                                                           
#   Free Software Foundation, Inc.,                                                                                                              
#   59 Temple Place, Suite 330, Boston, MA 02111-1307, USA                                                             
#                                                                                                                                                                         
#############################################################################
# compute pseudo data from a censored dataset

# INPUTS 
# censdata : a two-column matrix with left, right and/or interval censored data

# OUTPUTS 
# a vector of pseudo data (needed to compute starting values)
# a vector of right censored data
# a vector of left censored data
# a vector of non censored data
# a vector of interval censored data

cens2pseudo <- function(censdata)
{
  # Definition of datasets lcens (left censored)=vector, rcens (right censored)= vector, 
  #   icens (interval censored) = dataframe with left and right 
  #  ncens (not censored) = vector and 
  # pseudo (data transformed in non censored pseudo data by taking the
  # mean of bounds for interval censored data and the left or right bound for the other 
  # censored data) = vector
  
  irow.lcens <- is.na(censdata$left) # rows corresponding to lcens data
  lcens <- censdata[irow.lcens, ]$right
  irow.rcens <- is.na(censdata$right)  # rows corresponding to rcens data
  rcens <- censdata[irow.rcens, ]$left
  if (any(is.na(lcens)) )
    stop("An observation cannot be both right and left censored, coded with two NA values")
  
  irow.ncens <- censdata$left==censdata$right & !is.na(censdata$left) & 
    !is.na(censdata$right)  # rows corresponding to ncens data
  ncens<-censdata[irow.ncens, ]$left
  irow.icens <- censdata$left!=censdata$right & !is.na(censdata$left) & 
    !is.na(censdata$right)  # rows corresponding to icens data
  icens<-censdata[irow.icens, ]
  
  pseudo <- c(rcens, lcens, ncens, (icens$left+icens$right)/2)
  list(pseudo=pseudo, rcens=rcens, lcens=lcens, ncens=ncens, icens=icens)
}

# compute row indexes from a censored dataset
cens2idxrow <- function(censdata)
{
  # Definition of datasets lcens (left censored)=vector, rcens (right censored)= vector, 
  #   icens (interval censored) = dataframe with left and right 
  # and ncens (not censored) = vector
  
  irow.lcens <- is.na(censdata$left) # rows corresponding to lcens data
  irow.rcens <- is.na(censdata$right)  # rows corresponding to rcens data
  irow.ncens <- censdata$left==censdata$right & !is.na(censdata$left) & 
    !is.na(censdata$right)  # rows corresponding to ncens data
  irow.icens <- censdata$left!=censdata$right & !is.na(censdata$left) & 
    !is.na(censdata$right)  # rows corresponding to icens data
  list(lcens=irow.lcens, rcens=irow.rcens, ncens=irow.ncens, icens=irow.icens)
}