#'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
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