Load Atlantis outputfiles (netcdf)

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-becdev", package = "atlantistools")
nc <- file.path(d, "outputSETAS.nc")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")
bboxes <- get_boundary(boxinfo = load_box(file.path(d, bgm = "VMPA_setas.bgm")))
select_physics <- c("salt", "NO3", "volume")

test <- load_nc_physics(nc, select_physics, prm_run, bboxes)
str(test)
#> 'data.frame':	1488 obs. of  5 variables:
#>  $ variable: chr  "NO3" "NO3" "NO3" "NO3" ...
#>  $ polygon : int  1 1 1 1 1 2 2 2 2 2 ...
#>  $ layer   : num  0 1 2 3 6 0 1 2 3 4 ...
#>  $ time    : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ atoutput: num  14 12 6 6 15 25 14 12 6 6 ...

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")))

test <- load_nc_physics(nc, select_physics, prm_run, bboxes)
str(test)
#> 'data.frame':	453 obs. of  5 variables:
#>  $ variable: chr  "NO3" "NO3" "NO3" "NO3" ...
#>  $ polygon : int  1 1 1 1 1 2 2 2 2 2 ...
#>  $ layer   : num  0 1 2 3 6 0 1 2 3 4 ...
#>  $ time    : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ atoutput: num  14 12 6 6 15 25 14 12 6 6 ...

test <- load_nc_physics(nc, select_physics = "nominal_dz", prm_run, bboxes)