Convert SS3 data into format required by FIMS

Uses output from r4ss::SS_read() and does filtering, simplifying, and reformatting.

Usage

ss3_data_to_fims(
  ss3_dir = NULL,
  ss_new = TRUE,
  ss3_inputs = NULL,
  ss3_output = NULL,
  fleets = NULL,
  maxage = NULL,
  lengths = NULL
)

ss3_dir: Directory containing the SS3 input and output model files. Alternatively the SS3 input and output lists can be input directly using ss3_inputs and ss3_output
ss_new: Logical indicating whether to read in the .ss_new files instead of the original input files. Beneficial for dealing with negative years in the wtatage file which can't yet be processed by this function.
ss3_inputs: A list containing dat and wtatage such as that created by r4ss::SS_read(). Only required if ss3_dir is not provided.
ss3_output: A list created by r4ss::SS_output(). Only required if ss3_dir is not provided.
fleets: Which fleets to include in the processed output. Note that the only start year population weight-at-age is read from the wtatage element (fleet = 0). NULL will default to including all fleets from the SS3 model.
maxage: Max age to include in the processed output. NULL will default to using age 0 up to the maximum age data bin in the SS3 model.
lengths: Vector of lengths to include in the processed output. Needs to be a subset of the length bins in the SS3 model. NULL will default to using all length data bins from the SS3 model.

A data frame that can be passed to FIMS::FIMSFrame()

Ian G. Taylor, Megumi Oshima, Kelli F. Johnson