A function that uses the file location of a fitted SS3 model including input files to population the various slots of an Data object.
SS2Data(
SSdir,
Name = "Imported by SS2Data",
Common_Name = "",
Species = "",
Region = "",
min_age_M = 1,
gender = 1,
comp_fleet = "all",
comp_season = "sum",
comp_partition = "all",
comp_gender = "all",
index_season = "mean",
silent = FALSE,
...
)An object of class Data.
A folder with Stock Synthesis input and output files in it
The name for the Data object
Character string for the common name of the stock.
Scientific name of the species
Geographic region of the stock or fishery.
Currently, the Data object supports a single value of M for all ages. The argument selects the minimum age for calculating the mean of age-dependent M from the SS assessment.
An integer index for the sex for importing biological parameters (1 = female, 2 = male).
A vector of indices corresponding to fleets in the assessment over which to aggregate the composition
(catch-at-length and catch-at-age) data. By default, character string "all" will aggregate across all fleets.
Integer, for seasonal models, the season for which the value of the index will be used. By default, "mean"
will take the average across seasons.
Integer vector for selecting length/age observations that are retained (2), discarded (1), or both (0). By default, "all"
sums over all available partitions.
Integer vector for selecting length/age observations that are female (1), male (2), or both (0), or both scaled to sum to one (3).
By default, "all" sums over all gender codes.
Integer, for seasonal models, the season for which the value of the index will be used. By default, "mean"
will take the average across seasons.
Logical. Suppress all messages?
Arguments to pass to SS_output
T. Carruthers and Q. Huynh
SS2OM