Description Usage Arguments Value See Also Examples
Loads Mort.txt file and partitions mortality based on fishing (F) and other mortality (M) Note: As the Atlantis manual states "This file is currenlty only useful for looking at relative M vs F values for a species, as it does not give accurate mortalities". Also if a species is set as isImpacted in the functional_group.csv, it will have some F value even if it is not explicity targeted by fishing.
1 | load_mort(mortFile, prm_run, fgs, convert_names = F)
|
mortFile |
Character string giving the path to the Mort.txt file.
The filename usually contains |
prm_run |
Character string giving the connection of the run parameterfile.
The filename usually contains |
fgs |
Character string giving the connection to the functional groups file.
The filename usually contains |
convert_names |
Logical indicating if group codes are transformed to LongNames ( |
Data frame with information about sources of mortality (M, F).
Other load functions:
load_box()
,
load_bps()
,
load_dietcheck()
,
load_fgs()
,
load_init_age()
,
load_init()
,
load_nc_physics()
,
load_nc()
,
load_rec()
,
load_spec_mort()
,
load_spec_pred_mort()
,
load_txt()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
mortFile <- file.path(d, "outputSETASMort.txt")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")
fgs <- file.path(d, "SETasGroups.csv")
df <- load_mort(mortFile, prm_run, fgs)
head(df)
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
mortFile <- file.path(d, "outputSETASMort.txt")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
df <- load_mort(mortFile, prm_run, fgs)
head(df)
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