Package index • RHISEA

Main Analysis Functions

Core functions to run HISEA analyses

run_hisea_all(): Internal Main Function for HISEA Run

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

Functions to read, write, and prepare data for analysis

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

Estimators and Algorithms

Implementations of statistical estimators and algorithms

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 Tools

Functions for classification models and related utilities

classify_samples(): Classify Samples Using LDF Coefficients

compute_ldf_coefficients(): Compute Linear Discriminant Function (LDF) Coefficients

ordvec(): Generate Ordered Random Values (Order Statistics based)

Visualization and Output

Plotting and summary printing functions

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

Helper functions not usually called directly by users

.resample_baseline_data_helper(): Run HISEA Mixed Stock Analysis