load_spec_pred_mort: Load mortality information from outputSpecificPredMort.txt

In alketh/atlantistools: Process and Visualise Output from Atlantis Models

Description

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_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)

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)

alketh/atlantistools documentation built on Oct. 30, 2021, 5:46 a.m.