Add new data to an existing EM dataset — add_new

This should be used for the feedback loops when an EM is used.

Usage

add_new_dat(
  OM_dat,
  EM_datfile,
  sample_struct,
  EM_dir,
  nyrs_assess,
  do_checks = TRUE,
  new_datfile_name = NULL,
  verbose = FALSE
)

OM_dat: An valid SS data file read in using r4ss. In particular, this should be sampled data.
EM_datfile: Datafile name run in previous iterations with the EM. Assumed to exist in EM_dir.
sample_struct: A optional list including which years, seasons, and fleets should be added from the OM into the EM for different types of data. If NULL, the data structure will try to be inferred from the pattern found for each of the datatypes within the EM datafiles. Include this structure for the number of years to extend the model out. Note that the data should be specified using the list component names and column names as in would be used in r4ss::SS_readdat(). The run_SSMSE_iter function examples give an example of what this structure should be. Running the function create_sample_struct() will also produce a sample_struct object in the correct form. Can be NULL only when MS is not EM.
EM_dir: Absolute or relative path to the Estimation model directory.
nyrs_assess: The number of years between assessments. E.g., if an assessment is conducted every 3 years, put 3 here. A single integer value.
do_checks: Should checks on the data be performed? Defaults to TRUE.
new_datfile_name: An optional name of a file to write the new datafile to. If NULL, a new datafile will not be written.
verbose: Want verbose output? Defaults to FALSE.

A new SS datafile containing the data in EM_datfile with new data from OM_dat appended

Kathryn Doering