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 (runRscript generate_data.R --help
to list all the options).run_methods.R
a script which generate the synthetic data (runRscript run_methods.R --help
to list all the options).evaluate.R
a script which evaluate the results (runRscript 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