Setup model objects for specifying recruitment module and associated processes
Setup_Mod_Rec.Rd
Setup model objects for specifying recruitment module and associated processes
Usage
Setup_Mod_Rec(
input_list,
rec_model,
rec_dd = NULL,
rec_lag = 1,
Use_h_prior = 0,
h_mu = NA,
h_sd = NA,
do_rec_bias_ramp = 0,
bias_year = NA,
max_bias_ramp_fct = 1,
sigmaR_switch = 1,
dont_est_recdev_last = 0,
sexratio = 1,
init_age_strc = 0,
equil_init_age_strc = 1,
init_F_prop = 0,
sigmaR_spec = NULL,
InitDevs_spec = NULL,
RecDevs_spec = NULL,
h_spec = NULL,
t_spawn = 0,
...
)
Arguments
- input_list
List containing data, parameters, and map lists used by the model.
- rec_model
Character string specifying the recruitment model. Options are:
"mean_rec"
: Recruitment is a fixed mean value."bh_rec"
: Beverton-Holt recruitment with steepness parameter.
- rec_dd
Character string specifying recruitment density dependence, options:
"local"
,"global"
, orNULL
.- rec_lag
Integer specifying the recruitment lag duration relative to spawning stock biomass (SSB).
- Use_h_prior
Integer flag (0 or 1) indicating whether to apply a prior on steepness
h
.- h_mu
Numeric vector (length
n_regions
) specifying the mean steepness prior values if used.- h_sd
Numeric vector (length
n_regions
) specifying the standard deviation for steepness priors if used.- do_rec_bias_ramp
Integer flag (0 or 1) indicating whether to apply a recruitment bias correction ramp.
- bias_year
Numeric vector of length 4 defining the recruitment bias ramp periods:
Element 1: End year of no bias correction period.
Element 2: End year of ascending bias ramp period.
Element 3: End year of full bias correction period.
Element 4: Start year of final no bias correction period.
For example, with 65 years total,
c(21, 31, 60, 64)
means:Years 1–21: No bias correction.
Years 22–31: Ascending bias correction.
Years 32–60: Full bias correction.
Years 61–63: Descending bias ramp.
Years 64–65: No bias correction.
- max_bias_ramp_fct
Numeric specifying the maximum bias correction to apply to the recruitment bias ramp (should be between 0 and 1)
- sigmaR_switch
Integer year indicating when
sigmaR
switches from early to late values (0 disables switching).- dont_est_recdev_last
Integer specifying how many of the most recent recruitment deviations to not estimate. Default is 0.
- sexratio
Numeric vector specifying recruitment sex ratio, dimensioned by number of sexes.
- init_age_strc
Integer flag specifying initialization of initial age structure:
0
: Initialize by iteration.1
: Initialize using a geometric series.
- equil_init_age_strc
Integer flag specifying how initial age structure deviations should be initialized. Default is stochastic for all ages except the recruitment age and the plus group.
0
: Equilibrium initial age structure.1
: Stochastic initial age structure for all ages, except for the plus group, which follows equilibrium calculations (geometric series)2
: Stochastic initial age structure for all ages
- init_F_prop
Numeric value specifying the initial fishing mortality proportion relative to mean fishing mortality for initializing age structure.
- sigmaR_spec
Character string specifying estimation of recruitment variability (
sigmaR
):NULL
: Estimate separatesigmaR
for early and late periods."est_shared"
: Estimate onesigmaR
shared across periods."fix"
: Fix bothsigmaR
values."fix_early_est_late"
: Fix earlysigmaR
, estimate latesigmaR
.
- InitDevs_spec
Character string specifying estimation of initial age deviations:
NULL
: Estimate deviations for all ages and regions."est_shared_r"
: Estimate deviations shared across regions."fix"
: Fix all deviations.
- RecDevs_spec
Character string specifying recruitment deviation estimation:
NULL
: Estimate deviations for all regions and years."est_shared_r"
: Estimate deviations shared across regions (global recruitment deviations)."fix"
: Fix all recruitment deviations.
- h_spec
Character string specifying steepness estimation:
NULL
: Estimate steepness for all regions ifrec_model == "bh_rec"
."est_shared_r"
: Estimate steepness shared across regions."fix"
: Fix steepness values.
If
rec_model == "mean_rec"
, steepness is fixed.- t_spawn
Numeric fraction specifying spawning timing within the year.
- ...
Additional arguments specifying starting values for recruitment parameters such as
ln_global_R0
,Rec_prop
,h
,ln_InitDevs
,ln_RecDevs
, andln_sigmaR
.