Package index • RHISEA

Main Analysis Functions

Core functions to run HISEA analyses

run_hisea_all(): Run HISEA Mixed Stock Analysis
run_hisea_estimates(): Run HISEA Estimations Only
simulate_mixture(): Simulate a Mixed Fishery Sample from Known Stock Proportions
create_hisea_summary_report(): Create HISEA Summary Report

Data Input and Output

Tools to prepare and process data

read_baseline(): Read HISEA Baseline File
read_mixture(): Read HISEA Mixture File
write_mix_from_dataframe(): Write Mixture Data to File
write_std_from_dataframe(): Write Standard Data to File
process_hisea_input(): Process HISEA Input Data
baseline: Baseline Data for RHISEA
mixture: Mixture dataset for RHISEA examples

Estimators and Algorithms

Statistical implementations

accel_em_algorithm(): Accelerated Expectation-Maximization (EM) Algorithm
em_algorithm(): Standard Expectation-Maximization (EM) Algorithm for Stock Proportions
compute_cook_estimators(): Compute Cook Estimators for Stock Proportions
estimate_millar_theta4(): Estimate Millar Theta4 Parameter
estimate_ml_theta5(): Estimate Stock Composition Using Direct Maximum Likelihood (Theta5)
get_phi(): Get Phi Matrix

Classification & Visualization

classify_samples(): Classify Samples Using LDF Coefficients
compute_ldf_coefficients(): Compute Linear Discriminant Function (LDF) Coefficients
ordvec(): Generate Ordered Random Values (Order Statistics based)
plot_hisea_theta(): Plot HISEA theta estimates with error bars utils::globalVariables(c("Stock", "Mean", "Estimator", "SD", "ActualValue"))
print_hisea_summary(): Print HISEA Summary Report to Console and/or File

Internal Helpers

.resample_baseline_data_helper(): Helper: resample baseline data per stock