/gripeer-numerical-experiments

Primary LanguageMATLAB

griPEER - numerical experiments

This repository contains code scripts and data needed to reproduce results (figures) presented in the Numerical experiments section of manuscript: Damian Brzyski, Marta Karas, Beau M. Ances, Mario Dzemidzic, Joaquin Goni, Timothy W. Randolph, Jaroslaw Harezlak, "Connectivity-Informed Adaptive Regularization for Generalized Outcomes".

License

License of MATLAB code of griPEER method implementation is located at MATLAB/software/griPEER_license.txt.

Software usage notes

  • MATLAB toolbox penalized must be installed before using our software and running simulations code. To install the toolbox, visit corresponding article website and download the file linked next to "penalized.zip: MATLAB source code including replication materials". Next, unzip the zipped directory. Next, in MATLAB, change current folder to the unzipped toolbox directory and type: install_penalized.

Directory guide

data

Contains text files with pre-computed matrices used in simulation scenario.

  • sc_matrices_used_scenario_1a - directory with text files with pre-computed structural connectivity matrices used in simulation scenario 1 (part a).
  • sc_matrices_used_scenario_1b_p198 - directory with text files with pre-computed structural connectivity matrices used in simulation scenario 1 (part b).
  • sc_matrices_used_scenario_1c_p528 - directory with text files with pre-computed structural connectivity matrices used in simulation scenario 1 (part c).
  • sc_matrices_used_scenario_2 - directory with text files with pre-computed structural connectivity matrices used in simulation scenario 2.
  • sc_matrices_used_scenario_3 - directory with text files with pre-computed structural connectivity matrices used in simulation scenario 3.
  • Z_cov.txt - real data-based covariance matrix.

figures-manuscript

Contains directories named figure_2, ..., figure_9 with

  • R code to generate plot(s) building up a manuscript figure,
  • JPEG files of generated plot(s) building up a manucript figure,

for manuscripf figures named Figure 2, ..., Figure 9, respectively.

MATLAB

MATLAB/simulation-scripts

  • run_power_fdr.m - MATLAB code to run power/FDR simulation. The results of this file execution are saved at results/results_power_fdr.txt.
  • run_scenario_1a_p66.m - MATLAB code to run simulation scenario 1 (part a). The results of this file execution are saved at results/results_scenario_1a.txt.
  • run_scenario_1b_p198.m - MATLAB code to run simulation scenario 1 (part b). The results of this file execution are saved at results/results_scenario_1b.txt.
  • run_scenario_1c_p528_CLUSTER.m - MATLAB code to run simulation scenario 1 (part c). The results of this file execution are saved at results/results_scenario_1c.txt.
  • run_scenario_2.m - MATLAB code to run simulation scenario 2. The results of this file execution are saved at results/results_scenario_2.txt.
  • run_scenario_3.m - MATLAB code to run simulation scenario 3. The results of this file execution are saved at results/results_scenario_3.txt.
  • utils - directory with auxiliary functions used in code to run simulations.

MATLAB/software

  • griPEER.m - MATLAB code of griPEER method implementation.
  • griPEER_license.txt - license of MATLAB code of griPEER method implementation.

MATLAB/software-usage-examples

  • workingExample.m - a working example of griPEER method code usage.

results

Contains text files with simulation results.

  • results_power_fdr.txt - text file with power/FDR simulation results. The results were generated with the code MATLAB/simulation-scripts/run_power_fdr.m.
  • results_scenario_1a.txt - text file with simulation scenario 1 (part a) results. The results were generated with the code MATLAB/simulation-scripts/run_scenario_1a.m.
  • results_scenario_1b.txt - text file with simulation scenario 1 (part b) results. The results were generated with the code MATLAB/simulation-scripts/run_scenario_1b_p198.m.
  • results_scenario_1c.txt - text file with simulation scenario 1 (part c) results. The results were generated with the code MATLAB/simulation-scripts/run_scenario_1c_p528_CLUSTER.m executed on a computing cluster. The bash files which run that Maltab script are located at bash_scripts/.
  • results_scenario_2.txt - text file with simulation scenario 2 results. The results were generated with the code MATLAB/simulation-scripts/run_scenario_2.m.
  • results_scenario_3.txt -text file with simulation scenario 3 results. The results were generated with the code MATLAB/simulation-scripts/run_scenario_3.m.

bash_scripts

Contains directories with bash files that run Maltab scripts for executing numerical experiment parts in a computing cluster.

cluster_utils

Contains utility files for executing numerical experiment parts in a computing cluster.