Function reference • bonsaiforest

Model Fit Functions

naivepop(): Naive Overall Population Model Estimation

naive(): Naive Model Estimation

elastic_net(): Elastic Net Penalization Model Estimation

horseshoe(): Bayesian Shrinkage Model Estimation

Data Folder

example_data: Example data

naivepop_fit_surv: Naivepop Fit Survival

naivepop_fit_bin: Naivepop Fit Binary

naive_fit_surv: Naive Fit Survival

naive_fit_bin: Naive Fit Binary

elastic_net_fit_surv: Elastic Net Fit Survival

elastic_net_fit_bin: Elastic Net Fit Binary

horseshoe_fit_surv: Horseshoe Fit Survival

horseshoe_fit_bin: Horseshoe Fit Binary

design_matrix1: Design Matrix Subgroup x_1a

design_dummy1: Design Dummy Subgroup x_1a

est_coef_bin1: Estimated coefficients elastic net Binary

elastic_net_surv: H0, Coefficients Elastic Net Survival Model and Matrices

Helper functions

generate_stacked_data(): Generation of Stacked Data by Subgroups

preprocess(): Data Preprocessing

lor_estimation(): Estimation of Log-Odds Ratio

survival_curves(): Average Survival Curves

ahr_estimation(): Average Hazard Ratio Estimation

ahr_from_km(): Average Hazard Estimation based on Kaplan-Meier Estimates

subgroups(): Subgroup Treatment Effect

trt_horseshoe(): Subgroup Treatment Effect Horseshoe

Summary

compare(): Compare Treatment Estimate Methods

summary(<naivepop>): Summary Naivepop Function

summary(<naive>): Summary Naive

summary(<elastic_net>): Summary Elastic Net Function

summary(<horseshoe>): Summary Horseshoe Function

Print

print(<summary.naivepop>): Print Function for Naivepop Summary

print(<summary.naive>): Print Function for Naive Summary

print(<summary.elastic_net>): Print Function for Elastic Net Summary

print(<summary.horseshoe>): Print Function for Horseshoe Summary

Plot

plot(<summary.naive>): Forest plot Summary Naive

plot(<summary.elastic_net>): Forest plot Summary Elastic Net

plot(<summary.horseshoe>): Forest plot Summary Horseshoe

plot(<compare.data>): Compare Forest Plots

Simulations

simul_covariates(): Generation of a Design Matrix for Simulations

simul_data(): Simulate Covariates and Progression Free Survival Data

simul_pfs(): Simulation of Progression Free Survival Times