Specify index selectivity blocks and aggregate and age composition observations for indices

Source: R/set_indices.R

Specify index selectivity blocks and aggregate and age composition observations for indices

set_indices(input, index_info = NULL)

Arguments

input

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

index_info

(optional) list specifying various aspects about catch by indices (see details)

index_info specifies observations, and various configuration options for index-specific catch observations and will overwrite attributes specified in the ASAP data file. If NULL, all settings from the ASAP data file or basic_info are used. index_info is a list with any of the following entries:

$n_indices

number of indices

$index_regions

vector (n_indices) of regions where each fleet operates.

$index_seasons

vector (n_indices) of 0/1 values flagging which seasons each index occurs.

$index_names

character vector (n_indices) of names for indices Used for naming results in plots and tables.

$agg_indices

matrix (n_years_model x n_indices) of annual aggregate index catches.

$agg_index_cv

matrix (n_years_model x n_indices) of CVs for annual aggregate index catches.

$fracyr_indices

matrix (n_years_model x n_indices) of fractions of year at which index occurs within the season (difference between time of survey and time at start of season).

$use_indices

matrix (n_years_model x n_indices) of 0/1 values flagging whether to use aggregate observations.

$units_indices

matrix (n_years_model x n_indices) of 1/2 values flagging whether aggregate observations are biomass (1) or numbers (2).

$index_paa

array (n_indices x n_years_model x n_ages) of annual catch proportions at age by index.

$use_index_paa

matrix (n_years_model x n_indices) of 0/1 values flagging whether to use proportions at age observations.

$units_index_paa

matrix (n_years_model x n_indices) of 1/2 values flagging whether composition observations are biomass (1) or numbers (2).

$index_Neff

matrix (n_years_model x n_indices) of effective sample sizes for proportions at age observations.

$waa_pointer_indices

vector (n_indices) of itegers indicated waa to use for each index.

$selblock_pointer_indices

matrix (n_years_model x n_indices) of itegers indicated selblocks to use.

$initial_index_sd_scale

vector (n_indices) of scalar multipliers of annual log-observation standard deviation. Default = 1.

$map_index_sd_scale

integer vector (n_indices) specifying which sd scalar parameters to fix. Use NA to fix a parameter and integers to estimate. Use the same integer for multiple indices to estimate a shared scalar parameter.