set_indices: Specify index selectivity blocks and aggregate and age...

In timjmiller/wham: Woods Hole Assessment Model (WHAM)

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

Description

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

Usage

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.

timjmiller/wham documentation built on Feb. 4, 2025, 10:31 p.m.