R/ts.getdata.r

In AtlanticR/bio.groundfish: Core utilities to operate with groundfish data bases within Ecomod and associated projects.

ts.getdata = function (set=NULL, from.file=T, variables=NULL, plottimes=NULL, regions=NULL, do.parallel=F, fname="all", custom="normal", clusters=NULL, libs=NULL, cltype="SOCK" ) {

  outfile1 = paste( "byyear", fname, "rdata", sep=".")
  outfile2 = paste( "bystrata", fname, "rdata", sep=".")

  if (custom != "normal" ) {
    outfile1 = paste( "byyear", custom, fname, "rdata", sep=".")
    outfile2 = paste( "bystrata", custom, fname, "rdata", sep=".")
  }


  R.gs = file.path( project.datadirectory("bio.groundfish"), "R" )
  if (from.file) {
    load ( file.path(R.gs, outfile1 ) )
  } else {

    bystrata = byyear = ts.yr = NULL
    nid = length(regions)

    if (!do.parallel) {
      res = get.ts.core( set=set, do.parallel=F, regions=regions, plottimes=plottimes, variables=variables, custom=custom , libs=libs)
      byyear = res$byyear
      bystrata = res$bystrata
    } else {
      cl = makeCluster( spec=clusters, type=cltype)
      ssplt = lapply( clusterSplit(cl, 1:nid), function(i) i )   # subset data into lists
      ts.snow = clusterApplyLB( cl, ssplt, get.ts.core, set=set, do.parallel=T, regions=regions, plottimes=plottimes, variables=variables, custom=custom, libs=libs   )
      stopCluster(cl)
      byyear = bystrata = NULL
      for (m in 1:length(ts.snow)) {
        byyear = rbind( byyear, ts.snow[[m]]$byyear)
        bystrata = rbind( bystrata, ts.snow[[m]]$bystrata)
      }
    } # end parallel

    save(byyear, file=file.path(R.gs, outfile1), compress=T )
    save(bystrata, file=file.path(R.gs, outfile2), compress=T )

  } # end if from file

  return(byyear)
}