This function loads Atlantis outputfiles (netcdf) and converts them to a dataframe.
load_nc_physics( nc, select_physics, prm_run, bboxes, aggregate_layers = FALSE, warn_zeros = FALSE )
| nc | Character string giving the connection of the netcdf file to read in.
The filename usually contains |
|---|---|
| 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 |
| bboxes | Integer vector giving the box-id of the boundary boxes.
Can be created with |
| aggregate_layers | Logical indicating if values for layers should be
aggregated ( |
| warn_zeros | Logical indicating if check for actual zeros in the
data shall be printed or not. Default is |
A data.frame in long format with the following column names:
variable, time, polygon, layer, and atoutput (i.e., variable).
This functions converts the ATLANTIS output to a dataframe which can be processed in R.
Other load functions:
load_box(),
load_bps(),
load_dietcheck(),
load_fgs(),
load_init_age(),
load_init(),
load_mort(),
load_nc(),
load_rec(),
load_spec_mort(),
load_spec_pred_mort(),
load_txt()
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)