R/tef_getTermsWeibull.R

In akcochrane/TEfits: Time-evolving model fits

#' Define the terms for a Weibull change function
#'
#' \code{\link{TEfit}} internal.
#'
#' @param modList TEfit modList
#' @param pPrefix prefix for parameters
#'
#' @export
#'
#' @noRd
#'

tef_getTermsWeibull <- function(modList,pPrefix){

  datTerms <- list()
  if(dim(modList$varIn)[2] >2){
    if(!exists(paste0(pPrefix,'Asym'),where=modList$covarTerms)){
      curFitAsym <- rep(T,length(modList$covars))}else{
        curFitAsym <- modList$covarTerms[[paste0(pPrefix,'Asym')]]
      }

    if(!exists(paste0(pPrefix,'Start'),where=modList$covarTerms)){
      curFitStart <- rep(T,length(modList$covars))}else{
        curFitStart <- modList$covarTerms[[paste0(pPrefix,'Start')]]
      }

    if(!exists(paste0(pPrefix,'Rate'),where=modList$covarTerms)){
      curFitRate <- rep(T,length(modList$covars))}else{
        curFitRate <- modList$covarTerms[[paste0(pPrefix,'Rate')]]
      }
    # # default to no shape covars
    if(!exists(paste0(pPrefix,'Shape'),where=modList$covarTerms)){
      curFitShape <- rep(F,length(modList$covars))}else{
        curFitShape <- modList$covarTerms[[paste0(pPrefix,'Shape')]]
      }

    if(any(curFitAsym)){
      datTerms$pA <- paste0(paste0(pPrefix,'Asym_'),
                            c('0',
                              paste0(paste0(modList$covars[curFitAsym],'*'),
                                     modList$covars[curFitAsym])
                            ),collapse='+')}else{datTerms$pA <- paste0(pPrefix,'Asym')}

    if(any(curFitStart)){
      datTerms$pS <- paste0(paste0(pPrefix,'Start_'),
                            c('0',paste0(paste0(modList$covars[curFitStart],'*'),
                                         modList$covars[curFitStart])
                            ),collapse='+')}else{datTerms$pS <- paste0(pPrefix,'Start')}

    if(any(curFitRate)){
      datTerms$pR <- paste0(paste0(pPrefix,'Rate_'),
                            c('0',paste0(paste0(modList$covars[curFitRate],'*'),
                                         modList$covars[curFitRate])
                            ),collapse='+')}else{datTerms$pR <- paste0(pPrefix,'Rate')}
    if(any(curFitShape)){
      datTerms$pShape <- paste0(paste0(pPrefix,'Shape_'),
                                c('0',paste0(paste0(modList$covars[curFitShape],'*'),
                                             modList$covars[curFitShape])
                                ),collapse='+')}else{datTerms$pShape <- paste0(pPrefix,'Shape')}
  }else{
    datTerms$pA <- paste0(pPrefix,'Asym')
    datTerms$pS <- paste0(pPrefix,'Start')
    datTerms$pR <- paste0(pPrefix,'Rate')
    datTerms$pShape <- paste0(pPrefix,'Shape')
  }

  ## ##
  ## replace the parameter with a constant number, if input
  ## ##
  # if(pPrefix=='p'){ ## ## only if this is the parameter of interest why?
    # for(curFix in modList$pFix){ # what is this loop??
      if(any(grep('Asym',names(modList$pFix)))){datTerms$pA <- modList$pFix[[grep('Asym',names(modList$pFix))]]}
      if(any(grep('Start',names(modList$pFix)))){datTerms$pS <- modList$pFix[[grep('Start',names(modList$pFix))]]}
      if(any(grep('Rate',names(modList$pFix)))){datTerms$pR <- modList$pFix[[grep('Rate',names(modList$pFix))]]}
      if(any(grep('Shape',names(modList$pFix)))){datTerms$pShape <- modList$pFix[[grep('Shape',names(modList$pFix))]]}
    # }
  # }

  return(datTerms)

}