Extract the dietmatrix from the biological parameterfile

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

Usage

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)
#> # A tibble: 10 × 7
#>    pred  pred_stanza prey_stanza code       prey  avail prey_id
#>    <chr>       <dbl>       <dbl> <chr>      <chr> <dbl>   <int>
#>  1 FPS             1           1 pPREY1FPS1 FPS    0          1
#>  2 FPS             1           1 pPREY1FPS1 FVS    0          2
#>  3 FPS             1           1 pPREY1FPS1 CEP    0          3
#>  4 FPS             1           1 pPREY1FPS1 BML    0.01       4
#>  5 FPS             1           1 pPREY1FPS1 PL     0          5
#>  6 FPS             1           1 pPREY1FPS1 DL     0          6
#>  7 FPS             1           1 pPREY1FPS1 DR     0          7
#>  8 FPS             1           1 pPREY1FPS1 DC     0          8
#>  9 FPS             1           1 pPREY1FPS1 DLsed  0          9
#> 10 FPS             1           1 pPREY1FPS1 DRsed  0         10

# 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)
#> # A tibble: 10 × 7
#>    pred  pred_stanza prey_stanza code       prey  avail prey_id
#>    <chr>       <dbl>       <dbl> <chr>      <chr> <dbl>   <int>
#>  1 FPL             1           1 pPREY1FPL1 FPL   0           1
#>  2 FPL             1           1 pPREY1FPL1 FPO   0           2
#>  3 FPL             1           1 pPREY1FPL1 FPS   0.005       3
#>  4 FPL             1           1 pPREY1FPL1 FVD   0           4
#>  5 FPL             1           1 pPREY1FPL1 FVV   0           5
#>  6 FPL             1           1 pPREY1FPL1 FVS   0           6
#>  7 FPL             1           1 pPREY1FPL1 FVB   0           7
#>  8 FPL             1           1 pPREY1FPL1 FVT   0           8
#>  9 FPL             1           1 pPREY1FPL1 FVO   0           9
#> 10 FPL             1           1 pPREY1FPL1 FMM   0.01       10