Load mortality information from outputSpecificPredMort.txt

Load mortality information from outputSpecificPredMort.txt

Usage

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(), load_init_age(), load_mort(), load_nc(), load_nc_physics(), load_rec(), load_spec_mort(), load_txt()

Examples

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)
#> Error in dplyr::arrange(tidyr::pivot_longer(data, cols = dplyr::setdiff(names(data),     id_col), names_to = "code", values_to = "atoutput"), id_col,     code): ℹ In argument: `..1 = id_col`.
#> Caused by error:
#> ! `..1` must be size 1512 or 1, not 4.
head(df)
#>                                               
#> 1 function (x, df1, df2, ncp, log = FALSE)    
#> 2 {                                           
#> 3     if (missing(ncp))                       
#> 4         .Call(C_df, x, df1, df2, log)       
#> 5     else .Call(C_dnf, x, df1, df2, ncp, log)
#> 6 }