Load Atlantis outputfiles (netcdf)

This function loads Atlantis outputfiles (any netcdf file) and converts them to a data.frame.

load_nc(
  nc,
  fgs,
  bps,
  select_groups,
  select_variable,
  prm_run,
  bboxes,
  check_acronyms = TRUE,
  warn_zeros = FALSE,
  report = TRUE
)

Arguments

nc	Character string giving the connection of the netcdf file to read in. The filename usually contains output and ends in .nc".
fgs	Character string giving the connection to the functional groups file. The filename usually contains Groups and does end in .csv.
bps	Vector of character strings giving the complete list of epibenthic functional groups (Only present in the sediment layer). The names have to match the column 'Name' in the 'functionalGroups.csv' file. Can be created with load_bps.#'
select_groups	Character vector of funtional groups which shall be read in. Names have to match the ones used in the netcdf file. Check column "Name" in "functionalGroups.csv" for clarification.
select_variable	Character value specifying which variable to load. Only one variable of the options available (i.e., c( "N", "Nums", "ResN", "StructN", "Eat", "Growth", "Prodn", "Grazing") ) can be loaded at a time.
prm_run	Character string giving the connection of the run parameterfile. The filename usually contains run_fishing and ends in .prm".
bboxes	Integer vector giving the box-id of the boundary boxes. Can be created with get_boundary.
check_acronyms	Logical testing if functional-groups in select_groups are inactive in the current model run. They will be omitted in the output.
warn_zeros	Logical indicating if check for actual zeros in the data shall be printed or not. Default is FALSE.
report	Logical indicating if progress bars shall be printed (TRUE) or not (FALSE). Default is TRUE.

Value

A data.frame in long format with the following column names: species, timestep, polygon, agecl, and atoutput (i.e., variable).

See also

Other load functions: load_box(), load_bps(), load_dietcheck(), load_fgs(), load_init_age(), load_init(), load_mort(), load_nc_physics(), load_rec(), load_spec_mort(), load_spec_pred_mort(), load_txt()

Author

Alexander Keth

Examples

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")

nc <- file.path(d, "outputSETAS.nc")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
bps <- load_bps(init = file.path(d, "INIT_VMPA_Jan2015.nc"), fgs = fgs)
bboxes <- get_boundary(boxinfo = load_box(bgm = file.path(d, "VMPA_setas.bgm")))
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")

test <- load_nc(nc = nc, bps = bps, fgs = fgs, prm_run = prm_run, bboxes = bboxes,
  select_groups = c("Planktiv_S_Fish", "Cephalopod", "Diatom"),
  select_variable = "ResN")

test <- load_nc(nc = nc, bps = bps, fgs = fgs, prm_run = prm_run, bboxes = bboxes,
  select_groups = c("Planktiv_S_Fish", "Cephalopod", "Diatom"),
  select_variable = "Nums")