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 = "Object generated by SS2Data function",
Common_Name = "", Species = "", Region = "", min_age_M = 1,
gender = 1, comp_fleet = "all", comp_season = "sum",
comp_partition = "all", comp_gender = "all", index_fleet = "SSB",
index_season = "mean", ...)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 which life history values are importing (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, characer 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 selecting the fleet of the index to put in the Data object. By default, "SSB"
will use the relative trend in spawning stock biomass as estimated in the model as the index.
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.
Arguments to pass to SS_output
An object of class Data.