R/parallel.R

In Cole-Monnahan-NOAA/adnuts: No-U-Turn MCMC Sampling for 'ADMB' Models

## #' Combine multiple fits as returned from \code{sample_tmb} or
## #' \code{sample_admb} run as a single chain.
## #'
## #' @param fits A list of fits, each having a single chain
## #' @return A merged fit across chains.
## combine_fits <- function(fits){
##   z <- list()
##   test <- lapply(fits, function(x) x$samples)
##   samples <- array(NA, dim=c(nrow(test[[1]]), length(test), ncol(test[[1]])))
##   dimnames(samples) <- dimnames(fits[[1]]$samples)
##   for(i in 1:length(test)) samples[,i,] <- test[[i]]
##   z$samples <- samples
##   sp <- sapply(fits, function(x) x$sampler_params)
##   z$sampler_params <- sp
##   z$time.warmup <- unlist(lapply(fits, function(x) x$time.warmup))
##   z$time.total <- unlist(lapply(fits, function(x) x$time.total))
##   z$algorithm <- fits[[1]]$algorithm
##   z$warmup <- fits[[1]]$warmup
##   z$model <- fits[[1]]$model
##   z$max_treedepth <- fits[[1]]$max_treedepth
##   return(z)
## }

## A wrapper for running ADMB models in parallel
sample_admb_parallel <- function(parallel_number, path, algorithm, ...){
  olddir <- getwd()
  on.exit(setwd(olddir))
  newdir <- paste0(path,"_chain_",parallel_number)
  if(dir.exists(newdir)){
    unlink(newdir, TRUE)
    if(dir.exists(newdir)) stop(paste("Could not remove folder:", newdir))
  }
  dir.create(newdir)
  if(!dir.exists(newdir)) stop(paste("Could not create parallel folder:", newdir))
  trash <- file.copy(from=list.files(path, full.names=TRUE), to=newdir)
  if(algorithm=="NUTS")
    fit <- sample_admb_nuts(path=newdir, chain=parallel_number, ...)
  if(algorithm=="RWM")
    fit <- sample_admb_rwm(path=newdir, chain=parallel_number, ...)
  unlink(newdir, TRUE)
  return(fit)
}

## A wrapper for running TMB models in parallel
sample_tmb_parallel <-  function(parallel_number, obj, init, path,
                                 algorithm, lower, upper, seed, laplace, ...){
  ## Each node starts in a random work directory. Rebuild TMB model obj so
  ## can link it in each session.
  setwd(path)
  dyn.load(TMB::dynlib(obj$env$DLL))
  ## Use 'shape' attribute to obtain full length of 'map'ped parameters.
  map.index <- which(names(obj$env$parameters) %in% names(obj$env$map))
  new.par <- obj$env$parameters
  new.par[map.index] <- lapply(obj$env$parameters[map.index], function(x) attr(x, "shape"))
  obj <- TMB::MakeADFun(data=obj$env$data, parameters=new.par, random=obj$env$random,
                   map=obj$env$map, DLL=obj$env$DLL, silent=TRUE)
  obj$env$beSilent()

  ## Ignore parameters declared as random? Borrowed from tmbstan.
  if(laplace){
    par <- obj$env$last.par.best[-obj$env$random]
    fn0 <- obj$fn
    gr0 <- obj$gr
  } else {
    par <- obj$env$last.par.best
    fn0 <- obj$env$f
    gr0 <- function(x) obj$env$f(x, order=1)
  }
  ## Parameter constraints, if provided, require the fn and gr functions to
  ## be modified to account for differents in volume. There are four cases:
  ## no constraints, bounded below, bounded above, or both (box
  ## constraint).
  bounded <- !(is.null(lower) & is.null(upper))
  if(bounded){
    if(is.null(lower)) lower <- rep(-Inf, len=length(upper))
    if(is.null(upper)) upper <- rep(Inf, len=length(lower))
    cases <- .transform.cases(lower, upper)
    fn <- function(y){
      x <- .transform(y, lower, upper, cases)
      scales <- .transform.grad(y, lower, upper, cases)
      -fn0(x) + sum(log(scales))
    }
    gr <- function(y){
      x <- .transform(y, lower, upper, cases)
      scales <- .transform.grad(y, lower, upper, cases)
      scales2 <- .transform.grad2(y, lower, upper, cases)
      -as.vector(gr0(x))*scales + scales2
    }
    ## Don't need to adjust this b/c init is already backtransformed in
    ## sample_tmb.
    ## init <- .transform.inv(x=unlist(init), a=lower, b=upper, cases=cases)
  } else {
    fn <- function(y) -fn0(y)
    gr <- function(y) -as.vector(gr0(y))
  }
  if(algorithm=="NUTS")
    fit <- sample_tmb_nuts(chain=parallel_number, fn=fn, gr=gr,
                         init=init, seed=seed, ...)
  if(algorithm=="RWM")
    fit <- sample_tmb_rwm(chain=parallel_number, fn=fn, init=init,
                        seed=seed, ...)
  return(fit)
}