R/catch.R

In atlantistools: Process and Visualise Output from Atlantis Models

# setwd("c:/backup_z/Atlantis_models/Runs/dummy_02_ATLANTIS_NS/")
# catch <- load_nc(nc = "outputNorthSeaCATCH.nc", fgs = "functionalGroups.csv", bps = load_bps(fgs = "functionalGroups.csv", init = "init_NorthSea.nc"), select_groups = get_groups(fgs = "functionalGroups.csv"), select_variable = "Catch", bboxes = get_boundary(load_box(bgm = "NorthSea.bgm")))
#
# at_out <- RNetCDF::open.nc("outputNorthSeaCATCH.nc")
#
# var_names_ncdf <- sapply(seq_len(RNetCDF::file.inq.nc(at_out)$nvars - 1),
#                          function(x) RNetCDF::var.inq.nc(at_out, x)$name)
# #
# n_timesteps <- RNetCDF::dim.inq.nc(at_out, 0)$length
# n_boxes     <- RNetCDF::dim.inq.nc(at_out, 1)$length
# n_layers    <- RNetCDF::dim.inq.nc(at_out, 2)$length
#
# cod1 <- RNetCDF::var.get.nc(ncfile = at_out, variable = "cod1_Catch")
# cod2 <- RNetCDF::var.get.nc(ncfile = at_out, variable = "cod2_Catch")
#
# lapply(catch[, 1:ncol(catch)-1], unique)
#
#
# setwd("c:/backup_z/Atlantis_models/AEECmodel/output/")
# at_out <- RNetCDF::open.nc("AEECF_propDIS_survCATCH.nc")
#
# var_names_ncdf <- sapply(seq_len(RNetCDF::file.inq.nc(at_out)$nvars - 1),
#                          function(x) RNetCDF::var.inq.nc(at_out, x)$name)
#
# cod1 <- RNetCDF::var.get.nc(ncfile = at_out, variable = "Cod1_Catch")
# cod2 <- RNetCDF::var.get.nc(ncfile = at_out, variable = "Cod2_Catch")
#
#