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Compute OSA residuals for composition data

get_osa.Rd

Formats observed and expected composition data and calculates one-step-ahead (OSA) residuals using multinomial, Dirichlet-multinomial, or logistic-normal likelihoods. This function is the main interface for residual diagnostics, internally calling [run_osa()] to perform the residual calculations.

Usage

get_osa(
  obs_mat,
  exp_mat,
  N = NULL,
  DM_theta = NULL,
  LN_Sigma = NULL,
  years,
  fleet,
  bins,
  comp_type,
  bin_label,
  comp_like = 0
)

Arguments

obs_mat

Array of observed compositions, dimensioned by [region, year, bin, sex, fleet]. May contain NAs, which are removed when filtering by years.

exp_mat

Array of expected compositions, dimensioned the same as obs_mat. May contain NAs, which are removed when filtering by years.

N

Input (or effective if Multinomial) sample size. Dimensions depend on comp_type:

  • comp_type = 0 (aggregated): vector of length n_years.

  • comp_type = 1 (split by region and sex): array [n_regions, n_years, n_sexes].

  • comp_type = 2 (split by region, joint by sex): matrix [n_regions, n_years].

DM_theta

Dirichlet-multinomial overdispersion parameter(s). Dimensions must match N:

  • aggregated: scalar

  • split by sex: matrix [n_regions, n_sexes]

  • joint by sex: vector of length n_regions

LN_Sigma

Logistic-normal covariance matrix. Dimensions depend on comp_type:

  • aggregated: matrix [n_bins, n_bins]

  • split by region and sex: array [n_regions, n_bins, n_bins, n_sexes]

  • joint by sex: array [n_regions, n_bins, n_bins]

Use [get_logistN_Sigma()] to help construct this input.

years

Vector of years to filter to. Must match dimensions of obs_mat and exp_mat.

fleet

Fleet identifier (character or numeric) to filter to.

bins

Vector of age or length bin labels corresponding to the composition categories.

comp_type

Integer specifying how compositions are structured:

  • 0 = aggregated across regions and sexes

  • 1 = split by region and sex

  • 2 = split by region, joint by sex

bin_label

Character label describing whether bins represent ages or lengths.

comp_like

Integer specifying the likelihood type (defaults to 0):

  • 0 = multinomial

  • 1 = Dirichlet-multinomial

  • 2–4 = logistic-normal variants

Value

A list with one element:

res

Data frame of OSA residuals. Columns include: fleet, index_label, year, index, resid, region, sex, and comp_type.

See also

Other Model Diagnostics: do_jitter(), do_likelihood_profile(), do_retrospective(), do_runs_test(), get_catch_fits_plot(), get_comp_prop(), get_idx_fits(), get_idx_fits_plot(), get_model_rep_from_mcmc(), get_nLL_plot(), get_retrospective_plot(), get_retrospective_relative_difference(), plot_resids()