R/move.HMM.pw2pn.R

In benaug/move.HMM: Fit HMM and HSMM animal movement models

#'Transform parameters back to real scale
#'
#'This function, modified from Langrock et al. (2012), transforms parameters
#'back to the real scale.  For internal use.
#'
#'@param parvect The vector of parameters to be estimated
#'@param inv.transforms A list of inverse transformations used to transform
#'parvect back to the original scale
#'@param nstates Number of hidden states
#'@param skeleton A list with the original parameter structure used to reassemble
#'parvect
#'@return A list of parameter values on the real scale with an element
#'for each distribution
#'@export
#'
move.HMM.pw2pn <- function(inv.transforms,parvect,skeleton,nstates){
  
  #back-transform gamma if nstates>1 and calculate stationary distribution
  if(nstates>1){
    gamma <- diag(nstates)
    gamma [! gamma] <- exp(parvect[1:(nstates*nstates-nstates)])
    gamma <- gamma/apply(gamma ,1,sum)
    delta <- solve(t(diag(nrow(gamma))-gamma+1),rep(1,nrow(gamma)))
  }else{
    delta=1
  }
  skeleton2 <- skeleton
  skeleton2[[1]] <- NULL
  if(nstates>1){
    params <- c(list(gamma),relist(parvect[(nstates*nstates-nstates+1):length(parvect)],skeleton2))
  }else{
    params <- c(list(1),relist(parvect[(nstates*nstates-nstates+1):length(parvect)],skeleton2))
  }
  
  #back-transform all other parameters
  ndist <- length(params)
  for(i in 2:ndist){
    #if not circular distribution
    if(inv.transforms$type[i-1]==1){
      #loop over parameter types
      for(j in 1:(max(ncol(params[[i]]),1))){
        params[[i]][,j] <- inv.transforms[[i-1]][[j]](params[[i]][,j])
      }
    }else{#if circular dist
      #loop over direction parameters that may require different transformations
      for(j in 1:(nrow(params[[i]]))){
        params[[i]][j,1] <- inv.transforms[[i-1]][[j]](params[[i]][j,1])
      }
      #concentration parameter
      params[[i]][,2] <- inv.transforms[[i-1]][[length(inv.transforms[[i-1]])]](params[[i]][,2])
    }
  }
  
  names(params) <- c("tmat",names(inv.transforms)[1:(length(names(inv.transforms))-1)])
  return(list(params=params,delta=delta))
}