Extract parameters from the biological parameter file and transform them to a dataframe.

prm_to_df(prm_biol, fgs, group, parameter)

prm_to_df_ages(prm_biol, fgs, group, parameter)

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`.
group	Character vector giving the functional Groups to extract.
parameter	Character vector giving the parameters to extract.

Value

Dataframe with columns 'species' and as many columns as parameters.

Examples

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")
group <- c("FPS", "FVS")
parameter <- c("mum", "C")

prm_to_df_ages(prm_biol, fgs, group, parameter)
#>                     species agecl       c     mum
#> 1  Small planktivorous fish     1 2.0e-04   0.003
#> 2  Small planktivorous fish     2 3.0e-01   0.500
#> 3  Small planktivorous fish     3 6.0e-01   0.500
#> 4  Small planktivorous fish     4 6.0e-01   0.500
#> 5  Small planktivorous fish     5 6.0e-01   0.500
#> 6  Small planktivorous fish     6 6.0e-01   0.500
#> 7  Small planktivorous fish     7 5.0e-01   0.500
#> 8  Small planktivorous fish     8 5.0e-01   0.500
#> 9  Small planktivorous fish     9 4.0e-01   0.500
#> 10 Small planktivorous fish    10 4.0e-01   0.500
#> 11 Shallow piscivorous fish     1 4.0e+01 150.000
#> 12 Shallow piscivorous fish     2 4.0e+01 150.000
#> 13 Shallow piscivorous fish     3 4.0e+01 150.000
#> 14 Shallow piscivorous fish     4 1.2e+02 250.000
#> 15 Shallow piscivorous fish     5 1.5e+02 250.000
#> 16 Shallow piscivorous fish     6 2.5e+02 250.000
#> 17 Shallow piscivorous fish     7 2.5e+02 250.000
#> 18 Shallow piscivorous fish     8 3.0e+02 250.000
#> 19 Shallow piscivorous fish     9 3.0e+02 250.000
#> 20 Shallow piscivorous fish    10 3.0e+02 250.000
prm_to_df(prm_biol, fgs, group, parameter)
#>                    species  c mum
#> 1 Small planktivorous fish 10  10
#> 2 Shallow piscivorous fish 10  10