Specify model and parameter configuration for catchability

Specify model and parameter configuration for catchability

set_q(input, catchability = NULL)

Arguments

input

list containing data, parameters, map, and random elements (output from prepare_wham_input)

catchability

(optional) list specifying options for numbers-at-age random effects, initial parameter values, and recruitment model (see details)

catchability specifies options for catchability. If NULL and asap3 is not NULL, a single catchability parameter for each index is used with initial values specified in ASAP file. If both are NULL, initial catchabilities for all indices = 0.3. Otherwise, it is a list with the following optional entries:

$re

Time-varying (random effects) for each index. Vector with length = number of indices. Each entry of catchability$re must be one of the following options:

"none"

(default) are constant

"iid"

vary by year and age/par, but uncorrelated

"ar1"

correlated by year (AR1)

$initial_q

Initial catchabilities for each index. vector length = number of indices. Will override values provided in basic_info$q. If basic_info$q and asap3 are not provided, default q values are 0.3.

$q_lower

Lower bound for catchabilities for each index. vector length = number of indices. For indices with NULL components default lower values are 0.

$q_upper

Upper bound for catchabilities for each index. vector length = number of indices. For indices with NULL components default lower values are 1000.

$prior_sd

vector of NA and standard deviations to use for gaussian prior on logit transform of catchability parameter. Length = number of indices. Indices with non-NA values will have mean logit q as a random effect with mean determined by logit transform of catchability$initial_q and sigma as standard error.

$sigma_val

Vector of initial standard deviation values to use for annual random effects for each index. Values are not used if q$re = "none". Otherwise, a single value for all indices.

$sigma_map

Specify which sigma parameters to fix for the random effect deviations. Must be a vector with length = number of indices. Use NA to fix a parameter and integers to estimate. Use the same integer for multiple indices to share the same sigma parameter. Not used if re = 'none' for all indices.

$cor_vals

Vector of initial correlation values to use for annual random effects for each index. If unspecified all initial values are 0. Only used if q$re = "ar1"

$cor_map

Specify which ar1 correlation parameters to fix for the random effect deviations. Must be a vector with length = number of indices. If re = 'ar1', each element (index) must be a single value. Use NA to fix a parameter and integers to estimate. Use the same integer for multiple indices to share the same correlation parameter. Not used if re = 'none' or re = 'iid' for all indices.

Value

a named list with same elements as the input provided with catchability options modified.

See also

prepare_wham_input

Examples

if (FALSE) {
wham.dir <- find.package("wham")
path_to_examples <- system.file("extdata", package="wham")
asap3 <- read_asap3_dat(file.path(path_to_examples,"ex1_SNEMAYT.dat"))
input <- prepare_wham_input(asap3)
catchability = list(re = c("iid", "none"))
input <- set_q(input, catchability = catchability) #independent time-varying random effects on q for first survey.
}