scenario_treatF1.R

#########treatment uptake 
treat.fun <- function(bl, history,t)
  {
  
  #identify the state we are in:
  m = gems:::auxcounter(ns) # matrix of all transitions (without the terminal states)
  if(all(history == 0)) {index_trans = 1} else {index_trans = max(which(history > 0))}
  index_state = which(m == index_trans, arr.ind = TRUE)[2] # to get the colum number(arrival state) that corresponds to the last transition
  
  #return in which fibrosis state is a certain state (which level of FIbrosis prog?)
  ref1 = cbind(rep(1:blocks_size, blocks_nb), 1:(ns - 22))
  ref2 = cbind(c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6), c(31,37,43,32,38,44,33,39,45,34,40,46,35,41,47,36,42,48))
  ref0 = rbind(ref1,ref2)
  
  index_fs.fun = function(state, ref=ref0)
    {
    ref[which(ref[,2] == state, arr.ind = TRUE),1]
  }
  index_fs=index_fs.fun(state = index_state, ref = ref0)
  # print(c("we are now in level/state", index_fs,index_state))
  
  if(index_fs>= 2&& (bl["BirthYear"] + bl["Age"] + sum(history) + t > 2014)) res <- rep(24/52, length(t)) # treat in F2
  
  else res <- rep(666, length(t)) 
  
}