ecostate_control {ecostate} | R Documentation |
Detailed control for ecostate structure
Description
Define a list of control parameters.
Usage
ecostate_control(
nlminb_loops = 1,
newton_loops = 0,
eval.max = 1000,
iter.max = 1000,
getsd = TRUE,
silent = getOption("ecostate.silent", TRUE),
trace = getOption("ecostate.trace", 0),
verbose = getOption("ecostate.verbose", FALSE),
profile = c("logF_ti", "log_winf_z", "s50_z", "srate_z"),
random = c("epsilon_ti", "alpha_ti", "nu_ti", "phi_tg2"),
tmb_par = NULL,
map = NULL,
getJointPrecision = FALSE,
integration_method = c("ABM", "RK4", "ode23", "rk4", "lsoda"),
process_error = c("epsilon", "alpha"),
n_steps = 10,
F_type = c("integrated", "averaged"),
derived_quantities = c("h_g2", "B_ti", "B0_i"),
scale_solver = c("joint", "simple"),
inverse_method = c("Standard", "Penrose_moore"),
tmbad.sparse_hessian_compress = 1,
start_tau = 0.001
)
Arguments
nlminb_loops |
Integer number of times to call |
newton_loops |
Integer number of Newton steps to do after running
|
eval.max |
Maximum number of evaluations of the objective function
allowed. Passed to |
iter.max |
Maximum number of iterations allowed. Passed to |
getsd |
Boolean indicating whether to call |
silent |
Disable terminal output for inner optimizer? |
trace |
Parameter values are printed every |
verbose |
Output additional messages about model steps during fitting? |
profile |
parameters that are profiled across,
passed to |
random |
parameters that are treated as random effects,
passed to |
tmb_par |
list of parameters for starting values, with shape identical
to |
map |
list of mapping values, passed to RTMB::MakeADFun |
getJointPrecision |
whether to get the joint precision matrix. Passed
to |
integration_method |
What numerical integration method to use. |
process_error |
Whether to include process error as a continuous rate
(i.e., an "innovation" parameterization, |
n_steps |
number of steps used in the ODE solver for biomass dynamics |
F_type |
whether to integrate catches along with biomass ( |
derived_quantities |
character-vector listing objects to ADREPORT |
scale_solver |
Whether to solve for ecotrophic efficiency EE given biomass B
( |
inverse_method |
whether to use pseudoinverse or standard inverse |
tmbad.sparse_hessian_compress |
passed to |
start_tau |
Starting value for the standard deviation of process errors |
Value
An S3 object of class "ecostate_control" that specifies detailed model settings, allowing user specification while also specifying default values