R/calc_omdimensions.R

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

#'Internal calculations used in wrapper functions
#'
#'@NoRd
#'
  # This is the current script which needs to change into a set of functions
  # script only works with certain directory structure
  # #survey species inherited from omlist_ss
  # survspp <- omlist_ss$species_ss
  # # survey season and other time dimensioning parameters
  # # generalized timesteps all models
  # noutsteps <- omlist_ss$runpar$tstop/omlist_ss$runpar$outputstep
  # timeall <- c(0:noutsteps)
  # stepperyr <- if(omlist_ss$runpar$outputstepunit=="days") 365/omlist_ss$runpar$toutinc
  # midptyr <- round(median(seq(0,stepperyr)))
  #
  # # model areas, subset in surveyconfig
  # allboxes <- c(0:(omlist_ss$boxpars$nbox - 1))
  #
  # # fishery output: learned the hard way this can be different from ecosystem outputs
  # fstepperyr <- if(omlist_ss$runpar$outputstepunit=="days") 365/omlist_ss$runpar$toutfinc
  #
  # # survey selectivity (agecl based)
  # sp_age <- omlist_ss$funct.group_ss[, c("Name", "NumCohorts", "NumAgeClassSize")]
  #
  # # should return all age classes fully sampled (Atlantis output is 10 age groups per spp)
  # n_age_classes <- sp_age$NumCohorts
  # # changed below for multiple species NOTE survspp alphabetical; NOT in order of fgs!!
  # # this gives correct names
  # age_classes <- sapply(n_age_classes, seq)
  # names(age_classes)<-sp_age$Name
  #
  # n_annages <- sp_age$NumCohorts * sp_age$NumAgeClassSize
  # # changed below for multiple species
  # annages <- sapply(n_annages, seq)
  # names(annages)<-sp_age$Name