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#####################################################################################
## Author: Isaac Gravestock [isaac *.* gravestock *a*t* uzh *.* ch]
## Project: BFPs for GLMs
##
## Description:
## Construct a Survival model formula based on a glmBfp object
##
## History:
## 14/07/2015 Copied from CoxTBFs project functions-funsel-2.bma.R
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{}
##' Construct a survival formula based on a glmBfp object with censInd not null.
##'
##' This is an internal function to construct a survival formula based on a glmBfp object
##' with censInd not null.
##'
##' @param models.listpart the glmBfp object for which to construct the survival formula
##' @param time.var the name of the time variable as character string
##' @param status.var the name of the censoring indicator variable as character string
##' @return The formula object based on the glmBfp object.
##'
##' @keywords internal utilities
writeFormula <- function(models.listpart, time.var, status.var){
surv.part <- paste("survival::Surv(", time.var, ", ", status.var, ") ~ ",sep="")
#extract linear terms
fix.parts <- models.listpart[[1]]$configuration$fixTerms
fix.names <- attributes(models.listpart)$termNames$fix
uc.parts <- models.listpart[[1]]$configuration$ucTerms
uc.names <- attributes(models.listpart)$termNames$uc
shift <- attributes(models.listpart)$shiftScaleMax[,1]
scale <- attributes(models.listpart)$shiftScaleMax[,2]
if(length(models.listpart[[1]]$configuration$powers)>0){
#extract powers for terms which should have transformations
powers <- models.listpart[[1]]$configuration$powers
bfp.trans <- vector("character")
for(i in 1:length(powers)){
this.term <- ""
if(length(powers[[i]])>0){
this.name <- names(powers[i])
this.power <- paste("c(",paste(powers[[i]],collapse=",", sep=""),")",sep="")
this.term <- paste("fpTrans(",this.name,",", this.power, sep="")
if(scale[i]!=0){
this.term <- paste(this.term,", ",scale[i],sep="")
}
if(shift[i]!=0){
this.term <- paste(this.term,", ",shift[i],sep="")
}
this.term <- paste(this.term, ")",sep="")
}
if(this.term != "") bfp.trans <- c(bfp.trans, this.term)
}
v <- paste(c(uc.names[uc.parts], bfp.trans, fix.names[fix.parts]), collapse=" + ")
return(formula(paste(surv.part,v)))
}
#when there are no transformed variables
v <- paste(c(uc.names[uc.parts], fix.names[fix.parts]), collapse=" + ")
return(formula(paste(surv.part,v)))
}
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