Read in the atlantis dietcheck.txt file and perform some basic data transformations.

Read in the atlantis dietcheck.txt file and perform some basic data transformations.

load_dietcheck(
  dietcheck,
  fgs,
  prm_run,
  convert_names = FALSE,
  report = FALSE,
  version_flag = 2
)

Arguments

dietcheck	Character string giving the connection of the dietcheck file. The filename usually contains Dietcheck and ends in .txt".
fgs	Character string giving the connection to the functional groups file. The filename usually contains Groups and does end in .csv.
prm_run	Character string giving the connection of the run parameterfile. The filename usually contains run_fishing and ends in .prm".
convert_names	Logical indicating if group codes are transformed to LongNames (TRUE) or not (default = FALSE).
report	Logical indicating if incomplete DietCheck information shall be printed TRUE or not FALSE.
version_flag	The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. default is 2..

Value

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

See also

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

Examples

# Apply to bec-dev models.
d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
dietcheck <- file.path(d, "outputSETASDietCheck.txt")
fgs <- file.path(d, "SETasGroups.csv")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")

diet <- load_dietcheck(dietcheck, fgs, prm_run, version_flag = 1)
head(diet, n = 10)
#>    time pred habitat prey    atoutput
#> 1   0.2  CEP      WC  FPS 0.001538030
#> 4   0.4  CEP      WC  FPS 0.001944710
#> 7   0.6  CEP      WC  FPS 0.001812472
#> 10  0.8  CEP      WC  FPS 0.001615199
#> 13  1.0  CEP      WC  FPS 0.002414731
#> 16  1.2  CEP      WC  FPS 0.002694080
#> 19  1.4  CEP      WC  FPS 0.006028808
#> 22  1.6  CEP      WC  FPS 0.005396391
#> 25  1.8  CEP      WC  FPS 0.010229410
#> 28  2.0  CEP      WC  FPS 0.012357000

# Apply to trunk models.
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
dietcheck <- file.path(d, "outputSETASDietCheck.txt")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
diet <- load_dietcheck(dietcheck, fgs, prm_run)
head(diet, n = 10)
#>    time pred agecl prey     atoutput
#> 4     1  FPS     4  FPS 5.532030e-07
#> 5     1  FPS     5  FPS 5.532030e-07
#> 6     1  FPS     6  FPS 1.848350e-06
#> 7     1  FPS     7  FPS 1.840717e-06
#> 8     1  FPS     8  FPS 1.840717e-06
#> 9     1  FPS     9  FPS 1.832925e-06
#> 10    1  FPS    10  FPS 1.832925e-06
#> 11    1  FVS     1  FPS 4.424449e-04
#> 12    1  FVS     2  FPS 4.105409e-04
#> 13    1  FVS     3  FPS 7.037268e-05