Load mortality information from outputMort.txt

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.

Usage

load_mort(mortFile, prm_run, fgs, convert_names = F)

Arguments

mortFile

Character string giving the path to the Mort.txt file. The filename usually contains Mort 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).

Value

Data frame with information about sources of mortality (M, F).

See also

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

Examples

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)
#> # A tibble: 6 × 4
#>    time code  source atoutput
#>   <dbl> <chr> <chr>     <dbl>
#> 1     1 BB    F             0
#> 2     2 BB    F             0
#> 3     3 BB    F             0
#> 4     4 BB    F             0
#> 5     5 BB    F             0
#> 6     6 BB    F             0

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)
#> # A tibble: 6 × 4
#>    time code  source atoutput
#>   <dbl> <chr> <chr>     <dbl>
#> 1     1 BB    F             0
#> 2     2 BB    F             0
#> 3     3 BB    F             0
#> 4     4 BB    F             0
#> 5     5 BB    F             0
#> 6     6 BB    F             0