Load mortality information from specificMort.txt

Reads in the specificMort.txt file. Three values of instantaneous mortality for each functional group, age group, and stock. Predation (M2), other natural mortality (M1), Fishing (F)

load_spec_mort(mortFile, prm_run, fgs, convert_names = FALSE, removeZeros = T)

Arguments

mortFile	Character string giving the path to the specificMort.txt file. The filename usually contains SpecificMort 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).
removeZeros	Boolean. Remove all zeros from output. (Default = T)

Value

Data frame with information about sources of mortality (M1, M2, F).

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_pred_mort(), load_txt()

Examples

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

df <- load_spec_mort(specmort, prm_run, fgs)
head(df)
#> # A tibble: 6 × 5
#>    time code  agecl mort  atoutput
#>   <dbl> <chr> <dbl> <chr>    <dbl>
#> 1     1 FPS       1 M1    1.19e- 6
#> 2     2 FPS       1 M1    1.57e+18
#> 3     1 FPS       2 M1    9.92e- 7
#> 4     2 FPS       2 M1    2.27e- 6
#> 5     1 FPS       3 M1    9.51e- 7
#> 6     2 FPS       3 M1    1.83e- 6

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

df <- load_spec_mort(specmort, prm_run, fgs)
head(df)
#> # A tibble: 6 × 5
#>    time code  agecl mort     atoutput
#>   <dbl> <chr> <dbl> <chr>       <dbl>
#> 1     1 FPS       1 M1    0.000000992
#> 2     2 FPS       1 M1    0.00000150 
#> 3     1 FPS       2 M1    0.000000995
#> 4     2 FPS       2 M1    0.00000228 
#> 5     1 FPS       3 M1    0.000000954
#> 6     2 FPS       3 M1    0.00000185