/confound_it

Primary LanguageJupyter NotebookBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Recovering latent confounders from high-dimensional proxy variables

This repository contains the code to replicate the experiments and examples from Recovering latent confounders from high-dimensional proxy variables

requirements

The scripts need R (for the simualtion experiments) and pyhton (for the real-world examples) installed.

The following R packages need to be installed:

  • ggplot2
  • reshape2
  • pbapply
  • optparse
  • fastICA
  • mdatools

The following python libraries need to be available:

TODO

reproduce the simulation experiments

To run the simulation experiments and produce the results we provide in the simulations/ folder:

  • generate_data.R a script which generate the synthetic data (run Rscript generate_data.R --help to list all the options).
  • run_methods.R a script which generate the synthetic data (run Rscript run_methods.R --help to list all the options).
  • evaluate.R a script which evaluate the results (run Rscript evaluate.R --help to list all the options).
  • get_plots.R a script to produce the final plots.

The exact simualtion and experiments can be reproduced with the commands in the experiments.sh file.

reproduce the examples

TODO