Extract the dietmatrix from the biological parameterfile — load

Extracts the diet matrix as long dataframe from the biological paremeter file of any ATLANTIS simulation.

load_dietmatrix(
  prm_biol,
  fgs,
  transform = TRUE,
  convert_names = FALSE,
  version_flag = 2
)

write_diet(dietmatrix, prm_biol, save_to_disc = TRUE)

Arguments

prm_biol	Character string giving the connection to the biological parameterfile. The filename usually contains `biol_fishing` and does end in `.prm`.
fgs	Character string giving the connection to the functional groups file. The filename usually contains `Groups` and does end in `.csv`.
transform	Boolean indicating if the returned dataframe is displayed in "long" (`transform = TRUE, default`) or "wide" (`transform = FALSE`) format. You should use the "wide" format in case you aim to change your diet matrix entries.
convert_names	Logical indicating if group codes are transformed to LongNames (`TRUE`) or not (default = `FALSE`).
version_flag	The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. `default is 2.`.
dietmatrix	Dataframe of the ATLANTIS dietmatrix generated with `load_dietmatrix` using `transform = FALSE`.
save_to_disc	Logical indicating if the resulting prm file should be overwritten (`TRUE`) or not (`FALSE`). Defaults to `TRUE`.

Value

dataframe of the availability matrix in long format with columns pred, pred_stanza (1 = juvenile, 2 = adult), prey_stanza, prey, avail, code.

Examples

# Can be applied to trunk models.
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")

dm <- load_dietmatrix(prm_biol, fgs)
head(dm, n = 10)
#>    pred pred_stanza prey_stanza       code prey  avail prey_id
#> 1   FPS           1           1 pPREY1FPS1  FPS 0.0000       1
#> 2   FPS           2           1 pPREY1FPS2  FPS 0.0000       1
#> 3   FPS           1           2 pPREY2FPS1  FPS 0.0000       1
#> 4   FPS           2           2 pPREY2FPS2  FPS 0.0000       1
#> 5   FVS           1           1 pPREY1FVS1  FPS 0.1000       1
#> 6   FVS           2           1 pPREY1FVS2  FPS 0.1000       1
#> 7   FVS           1           2 pPREY2FVS1  FPS 0.1200       1
#> 8   FVS           2           2 pPREY2FVS2  FPS 0.1200       1
#> 9   CEP           1           1 pPREY1CEP1  FPS 0.0002       1
#> 10  CEP           2           1 pPREY1CEP2  FPS 0.0004       1

# Use write_diet to update your existing parameterfile.
dietmatrix <- load_dietmatrix(prm_biol, fgs, transform = FALSE)

# Write is set to FALSE here for technical reasons. Make sure to set it to TRUE in case you
# want to update your file.
new_diet <- write_diet(dietmatrix, prm_biol, save_to_disc = FALSE)

# And to bec-dev models.
d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_New.prm")
fgs <- file.path(d, "SETasGroups.csv")

dm <- load_dietmatrix(prm_biol, fgs, version_flag = 1)
head(dm, n = 10)
#>    pred pred_stanza prey_stanza       code prey avail prey_id
#> 1   FPL           1           1 pPREY1FPL1  FPL     0       1
#> 2   FPL           2           1 pPREY1FPL2  FPL     0       1
#> 3   FPL           1           2 pPREY2FPL1  FPL     0       1
#> 4   FPL           2           2 pPREY2FPL2  FPL     0       1
#> 5   FPO           1           1 pPREY1FPO1  FPL     0       1
#> 6   FPO           2           1 pPREY1FPO2  FPL     0       1
#> 7   FPO           1           2 pPREY2FPO1  FPL     0       1
#> 8   FPO           2           2 pPREY2FPO2  FPL     0       1
#> 9   FPS           1           1 pPREY1FPS1  FPL     0       1
#> 10  FPS           2           1 pPREY1FPS2  FPL     0       1