Load mortality information from outputSpecificPredMort.txt

Source: R/load-spec-pred-mort.R

Load mortality information from outputSpecificPredMort.txt

load_spec_pred_mort(
  specmort,
  prm_run,
  fgs,
  convert_names = FALSE,
  version_flag = 2
)

Arguments

specmort

Character string giving the connection of the specific mortality file. The filename usually contains SpecificPredMort and ends in .txt".
prm_run

Character string giving the connection of the run parameterfile. The filename usually contains run_fishing and ends in .prm".
fgs

Character string giving the connection to the functional groups file. The filename usually contains Groups and does end in .csv.
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..

Value

Dataframe with information about ssb in tonnes and recruits in thousands.

See also

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

Examples

d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
specmort <- file.path(d, "outputSETASSpecificPredMort.txt")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")
fgs <- file.path(d, "SETasGroups.csv")

df <- load_spec_pred_mort(specmort, prm_run, fgs, version_flag = 1)
head(df)

#> # A tibble: 6 × 5
#>    time pred  agecl prey       atoutput
#>   <dbl> <chr> <dbl> <chr>         <dbl>
#> 1   0.2 CEP       1 CEP   0.00000000883
#> 2   0.2 FVS       1 FVS   0.00000962   
#> 3   0.4 CEP       1 CEP   0.0000000100 
#> 4   0.4 FVS       1 FVS   0.00000962   
#> 5   0.6 CEP       1 CEP   0.00000000898
#> 6   0.6 CEP       2 FPS   0.000161     

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
specmort <- file.path(d, "outputSETASSpecificPredMort.txt")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")

df <- load_spec_pred_mort(specmort, prm_run, fgs)
head(df)

#> # A tibble: 6 × 5
#>    time pred  agecl prey  atoutput
#>   <dbl> <chr> <dbl> <chr>    <dbl>
#> 1     1 CEP       1 CEP   4.73e+ 3
#> 2     1 CEP       1 FVS   6.80e+ 8
#> 3     1 CEP       2 CEP   3.92e-27
#> 4     1 CEP       2 FVS   9.74e- 5
#> 5     1 DC        1 BML   3.26e- 7
#> 6     1 DL        1 BML   3.23e- 9