Add the EM defined catch values for the next years.
Usage
update_OM(
OM_dir,
catch = NULL,
harvest_rate = NULL,
catch_basis = NULL,
F_limit = NULL,
EM_pars = NULL,
write_dat = TRUE,
impl_error = NULL,
verbose = FALSE,
seed = NULL,
n_F_search_loops = 20,
tolerance_F_search = 0.001
)Arguments
- OM_dir
The full path to the OM directory.
- catch
A dataframe of catch values and its associated information to add to the OM. The column names are the same as in an SS data file (e.g., year, season, fleet, catch, catch_se). Must input either a catch and/or a harvest rate data frame. If both are input the catch will override harvest rate as the management unit but harvest rate will be used as a starting guess for search.
- harvest_rate
A dataframe of harvest rate (F) values and associated information to add to the OM. The column names are as in an SS datafile. If harvest rate is input without a corresponding catch the OM will assume effort based management an use harvest rate directly with implementation error added.
- catch_basis
data frame with columns year, seas, fleet, basis that specifies if catch should reference retained biomass (1) or dead biomass (2). Any year/season/fleet not listed will assume a value of 1 referencing retained biomass. Entering -99 for any of year, season, or fleet will apply the basis across all values of that variable (i.e. a single row with -99, -99, -99, 1 would implement retained biomass for all cases)
- F_limit
data frame with columns year, fleet, season, limit that specifies a maximum F allowed in the OM or a negative value to specify a multiple of the historic maximum F. Any year/season/fleet not listed will assume a value of 1.5. Entering -99 for any of year, season, or fleet will apply the limit across all values of that variable (i.e. a single row with -99, -99, -99, -2 would implement a cap of twice the historic maximum F for all cases)
- EM_pars
a dataframe of parameter value updates to modify OM
- write_dat
Should the datafile be overwritten? Defaults to TRUE.
- impl_error
The implementation error
- verbose
Want verbose output? Defaults to FALSE.
- seed
A random seed so that reproducible results are possible.
- n_F_search_loops
Number of times to try to find an F that achieves the catches input in the OM. Defaults to 20.
- tolerance_F_search
How far apart the input catch and achieved catch can be in tried to find an F that achieves the catch input in the OM. Defaults to 0.001.