BMIM

Code to run simulations and analysis for "Bayesian Multiple Index Models for Environmental Mixtures"

Functions

bsmim2

Rcpp package to fit a BMIM in R

• bsmim2.R: contains main function bsmim2() for fitting BMIMs
• bsmim_predict2.R: contains functions for predicting response surface
• plot_univar_hnew2.R: contains functions for plotting exposure response curves (componentwise and indexwise)

Simulations

Code to replicate simulation scenarios

• NHANES_simA2.R: single index scenario
• NHANES_simB.R: 3-index scenario

as well as supplementary simulations:

• NHANES_simA1.R: linear single index scenario
• NHANES_simC.R: mis-specified index groupings
• NHANES_simD.R: generating under full BKMR

and Rmarkdown files to report results from main & supplementary simulations:

• report_NHANES_sims.Rmd
• report_NHANES_supp_sims.Rmd

Analysis

Code to replicate NHANES data analysis.

• NHANES_analysis.R: code to run NHANES analysis
• NHANES_analysis_CV.R: code to run 5-fold cross-validation on NHANES data (on cluster looping iter_no 1-5)
• report_NHANES_analysis.Rmd: code to report results of NHANES analysis