Function reference • sdmgamindex

Get Data Format

get_bathy_grid(): Get bathymetric prediction grid corresponding to the area for a DATRASraw object using the 'marmap' package

get_datrasraw(): Data frame with one row per haul to DATRASraw alike object

get_effect(): Calculate confidence intervals for a named parameter in a survey index model.

get_grid(): Create a grid of haul positions from a DATRASraw object.

get_prediction_grid(): Prediction a grid for a specific year

get_surveyidx(): Calculate survey indices by age.

get_surveyidx_aic(): Akaike Information Criterion (or BIC) for survey index models

get_surveyidx_resid(): Randomized quantile residuals for class 'sdmgamindex'

get_surveyidx_sim(): Simulate data from a sdmgamindex model (experimental and subject to change)

get_surveyidx_stratmean(): Survey index using the stratified mean method using ICES statistical rectangles as strata.

Functions

anova_likelihood_ratio_test(): Likelihood ratio test for comparing two survey indices.

calc_distance(): Get distance (km) between two locations previously called gcd.hf

concentration_transform(): Concentration transform

consistency_external(): Calculate external consistencies between two survey indices.

consistency_internal(): Calculate internal consistency of a survey index.

convert_crs(): Change CRS of coordinates

convert_deg_rad(): Convert decimal degrees to radians Previously called deg2rad.

export_surveyidx(): Write survey index to file in standard XSA/SAM format

fix_age_group(): Helper function to "borrow" missing age groups from other years

qres_tweedie(): Randomized quantile residuals for Tweedie models

redo_surveyidx(): Re-compute standardized survey indices for an alternative grid from a previous fitted "surveyIdx" model.

Plot Functions

plot_simulation_list(): Plot survey index list (e.g. retrospective analysis)

plot_surveyidx(): Visualize results from a survey index model fitted with get_surveyidx().

plot_surveyidx_grid(): Plot a sdmgamindexGrid

Data

noaa_afsc_public_foss: Public data from FOSS for EBS walleye pollock, yellowfin sole, and red king crab from 1982 to present

noaa_afsc_biomass_estimates noaa_afsc_biomass_estimates: Biomass Estimates from AKFIN for EBS walleye pollock, yellowfin sole, and red king crab from 2015 to present

pred_grid_ebs: EBS Prediction Grid