Create a data frame of parameters you want to profile over. The default inputs for this function represent the typical parameters you would want to profile over but the data frame can actually accommodate any viable parameter in your Stock Synthesis model. Note that the defaults are, at a minimum, the profiles needed in your assessment document if you are presenting to the Pacific Fisheries Management Council.
A vector of character strings that specify the SS3 parameter names that you want to conduct profiles for.
A numeric vector specifying the low or high parameter bounds
you want to use for the profile of each parameter in parameters.
A numeric vector specifying the increments between the low
and high bounds for each parameter in parameters. These values will be
passed to seq(from = low, to = high, by = step_size).
A vector of character strings that specify the way in
which you want the parameter bounds to be translated. The available options
are, "real", "mulitplier", and "relative".
"real" indicates bounds in the parameter space,
"relative" indicates how far to go from the base parameter, and
"multiplier" indicates that low and high bounds are set at x\
and below the base parameter.
Deprecated: The use_prior_like input is no longer needed because r4ss now automatically plots the likelihood profile with and without any parameter prior likelihood contributions regardless of the setting in the user starter file.
A data frame with five columns,
parameters,
low,
high,
step_size, and
param_space. Where, there is one row for each parameter that will be profiled. The default settings provide users with a good template that they can add to or modify by giving some reasonable inputs for the default parameters that are requested in the Terms of Reference.
The param_space argument indicates where the range of of the profile
parameter should be interpreted as relative to the base model estimate vs.
across a pre-specified range. An example is for R0 where the default setting
below indicates that the param_space is relative where the low bound for the
profile is set = base model log(R0) - 2 and high = base model log(R0) + 2.
The default range for M is set as a multiplier to explore a range of (M -
0.40 * M) - (M + 0.40 * M) at a step size of 0.005. This range may be too
large (or small) with a step size too large (or too small) and should be
considered if the default settings are appropriate for your specific model.
The default setting for steepness is in 'real' space which means that the low
and high is in the same parameter space as the parameter. A user can select
any of the options for specifying a parameter range for any parameter.
if (FALSE) { # \dontrun{
# Define each parameter in real space
get_settings_profile(
parameters = c("NatM_uniform_Fem_GP_1", "SR_BH_steep", "SR_LN(R0)"),
low = c(0.02, 0.25, 8),
high = c(0.07, 1.0, 11),
step_size = c(0.005, 0.05, 0.25),
param_space = c("real", "real", "real")
)
# Example 2: Run a profile for natural mortality one with the prior likelihood and one without
get_settings_profile(
parameters = c("NatM_uniform_Fem_GP_1", "NatM_uniform_Fem_GP_1"),
low = c(0.40, 0.40),
high = c(0.40, 0.40),
step_size = c(0.005, 0.005),
param_space = c("multiplier", "multiplier")
)
} # }