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Load Atlantis outputfiles (netcdf)

Source: R/load-nc-physics.R
load_nc_physics.Rd

This function loads Atlantis outputfiles (netcdf) and converts them to a dataframe.

Usage

load_nc_physics(
  nc,
  select_physics,
  prm_run,
  bboxes,
  aggregate_layers = FALSE,
  warn_zeros = FALSE
)

Arguments

nc

Character string giving the connection of the netcdf file to read in. The filename usually contains output and ends in .nc".

select_physics

Character vector of physical variables which shall be read in. Names have to match the ones used in the ncdf file.

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.

aggregate_layers

Logical indicating if values for layers should be aggregated (TRUE) or not (FALSE). Default is FALSE.

warn_zeros

Logical indicating if check for actual zeros in the data shall be printed or not. Default is FALSE.

Value

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

Details

This functions converts the ATLANTIS output to a dataframe which can be processed in R.

See also

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

Examples


d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
nc <- file.path(d, "outputSETAS.nc")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
bboxes <- get_boundary(boxinfo = load_box(file.path(d, bgm = "VMPA_setas.bgm")))
select_physics = c("salt", "NO3", "NH3", "Temp", "Chl_a", "Denitrifiction")

test <- load_nc_physics(nc, select_physics, prm_run, bboxes)
head(test)
#>    variable polygon layer time     atoutput
#> 32    Chl_a       1     0    1 1.195206e+00
#> 33    Chl_a       1     1    1 9.336022e-01
#> 34    Chl_a       1     2    1 2.946814e-02
#> 35    Chl_a       1     3    1 2.166251e-03
#> 36    Chl_a       1     6    1 2.147856e+02
#> 37    Chl_a       2     0    1 1.590395e-01

test <- load_nc_physics(nc, select_physics = "nominal_dz", prm_run, bboxes)
head(test)
#>     variable polygon layer time atoutput
#> 1 nominal_dz       1     0    0       10
#> 2 nominal_dz       1     1    0       50
#> 3 nominal_dz       1     2    0       30
#> 4 nominal_dz       1     3    0       20
#> 5 nominal_dz       1     6    0        1
#> 6 nominal_dz       2     0    0      216