Reproducing the MultiAddGPs analyses

R scripts for reproducing figures in the MultiAddGPs manuscript.

Gut analyses

Human gut: Main Figure 3 and Web Figures 9–12.

Artificial gut: Main Figure 4 and Web Figures 6–8.

Rscript --vanilla Human_gut_analysis.R
Rscript --vanilla Artificial_gut_analysis.R

Simulation 1

Generate Main Figures 1–2 (comparison and runtime plots) from the supplied summary tables:

Rscript --vanilla scripts/create_final_plots.R

To rerun the fits, prepare manifests from config/seeds.csv, then generate datasets and fit models (task 1 shown):

Rscript --vanilla scripts/prepare_experiment.R
Rscript --vanilla scripts/generate_dataset_task.R manifests/datasets.csv 1
Rscript --vanilla scripts/run_model_task.R manifests/multiadd.csv 1

After all fits finish:

Rscript --vanilla scripts/aggregate_experiment_results.R
Rscript --vanilla scripts/create_final_plots.R

Simulation 2

Redraw Web Figures 3–5 from the saved data and fitted results:

Rscript --vanilla simulation2.R

To rerun hyperparameter optimization and model fitting for NAddGP and MultiAddGP:

Rscript --vanilla simulation2_fit.R