├── .gitignore ├── LICENSE ├── README.md ├── data ├── counties │ ├── counties.pkl │ └── interaction_effects.npy ├── diseases │ ├── borreliosis.csv │ ├── borreliosis_notrend_hhh4.csv │ ├── campylobacter.csv │ ├── campylobacter_hhh4.csv │ ├── rotavirus.csv │ └── rotavirus_hhh4.csv └── raw │ ├── germany_county_shapes.json │ ├── germany_population_data.csv │ └── region_features.csv ├── figures ├── curves.pdf ├── curves_borreliosis_appendix.pdf ├── curves_campylobacter_appendix.pdf ├── curves_rotavirus_appendix.pdf ├── exogenous_components.pdf ├── forest_borreliosis.pdf ├── forest_campylobacter.pdf ├── forest_rotavirus.pdf ├── interaction_kernels.pdf ├── measures.pdf ├── rhat.pdf └── temporal_contribution.pdf ├── logs └── .keep ├── notebooks └── preprocess.ipynb └── src ├── BaseModel.py ├── config.py ├── evaluate.py ├── geo_utils.py ├── gridjob_sample_ia.sge ├── gridjob_sample_posterior.sge ├── model_selection.py ├── plot_curves.py ├── plot_curves_appendix.py ├── plot_exogenous_components.py ├── plot_forest.py ├── plot_interaction_contributions_appendix.py ├── plot_interaction_kernel.py ├── plot_interaction_weights_appendix.py ├── plot_kernels_appendix.py ├── plot_measures.py ├── plot_rhat.py ├── plot_schematic.py ├── plot_temporal_contribution.py ├── plot_utils.py ├── sample_ia_effects.py ├── sample_posterior.py ├── sample_predictions.py ├── sampling_utils.py └── shared_utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/README.md -------------------------------------------------------------------------------- /data/counties/counties.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/counties/counties.pkl -------------------------------------------------------------------------------- /data/counties/interaction_effects.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/counties/interaction_effects.npy -------------------------------------------------------------------------------- /data/diseases/borreliosis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/borreliosis.csv -------------------------------------------------------------------------------- /data/diseases/borreliosis_notrend_hhh4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/borreliosis_notrend_hhh4.csv -------------------------------------------------------------------------------- /data/diseases/campylobacter.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/campylobacter.csv -------------------------------------------------------------------------------- /data/diseases/campylobacter_hhh4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/campylobacter_hhh4.csv -------------------------------------------------------------------------------- /data/diseases/rotavirus.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/rotavirus.csv -------------------------------------------------------------------------------- /data/diseases/rotavirus_hhh4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/diseases/rotavirus_hhh4.csv -------------------------------------------------------------------------------- /data/raw/germany_county_shapes.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/raw/germany_county_shapes.json -------------------------------------------------------------------------------- /data/raw/germany_population_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/raw/germany_population_data.csv -------------------------------------------------------------------------------- /data/raw/region_features.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/data/raw/region_features.csv -------------------------------------------------------------------------------- /figures/curves.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/curves.pdf -------------------------------------------------------------------------------- /figures/curves_borreliosis_appendix.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/curves_borreliosis_appendix.pdf -------------------------------------------------------------------------------- /figures/curves_campylobacter_appendix.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/curves_campylobacter_appendix.pdf -------------------------------------------------------------------------------- /figures/curves_rotavirus_appendix.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/curves_rotavirus_appendix.pdf -------------------------------------------------------------------------------- /figures/exogenous_components.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/exogenous_components.pdf -------------------------------------------------------------------------------- /figures/forest_borreliosis.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/forest_borreliosis.pdf -------------------------------------------------------------------------------- /figures/forest_campylobacter.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/forest_campylobacter.pdf -------------------------------------------------------------------------------- /figures/forest_rotavirus.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/forest_rotavirus.pdf -------------------------------------------------------------------------------- /figures/interaction_kernels.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/interaction_kernels.pdf -------------------------------------------------------------------------------- /figures/measures.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/measures.pdf -------------------------------------------------------------------------------- /figures/rhat.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/rhat.pdf -------------------------------------------------------------------------------- /figures/temporal_contribution.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/figures/temporal_contribution.pdf -------------------------------------------------------------------------------- /logs/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /notebooks/preprocess.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/notebooks/preprocess.ipynb -------------------------------------------------------------------------------- /src/BaseModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/BaseModel.py -------------------------------------------------------------------------------- /src/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/config.py -------------------------------------------------------------------------------- /src/evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/evaluate.py -------------------------------------------------------------------------------- /src/geo_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/geo_utils.py -------------------------------------------------------------------------------- /src/gridjob_sample_ia.sge: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/gridjob_sample_ia.sge -------------------------------------------------------------------------------- /src/gridjob_sample_posterior.sge: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/gridjob_sample_posterior.sge -------------------------------------------------------------------------------- /src/model_selection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/model_selection.py -------------------------------------------------------------------------------- /src/plot_curves.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_curves.py -------------------------------------------------------------------------------- /src/plot_curves_appendix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_curves_appendix.py -------------------------------------------------------------------------------- /src/plot_exogenous_components.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_exogenous_components.py -------------------------------------------------------------------------------- /src/plot_forest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_forest.py -------------------------------------------------------------------------------- /src/plot_interaction_contributions_appendix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_interaction_contributions_appendix.py -------------------------------------------------------------------------------- /src/plot_interaction_kernel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_interaction_kernel.py -------------------------------------------------------------------------------- /src/plot_interaction_weights_appendix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_interaction_weights_appendix.py -------------------------------------------------------------------------------- /src/plot_kernels_appendix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_kernels_appendix.py -------------------------------------------------------------------------------- /src/plot_measures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_measures.py -------------------------------------------------------------------------------- /src/plot_rhat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_rhat.py -------------------------------------------------------------------------------- /src/plot_schematic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_schematic.py -------------------------------------------------------------------------------- /src/plot_temporal_contribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_temporal_contribution.py -------------------------------------------------------------------------------- /src/plot_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/plot_utils.py -------------------------------------------------------------------------------- /src/sample_ia_effects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/sample_ia_effects.py -------------------------------------------------------------------------------- /src/sample_posterior.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/sample_posterior.py -------------------------------------------------------------------------------- /src/sample_predictions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/sample_predictions.py -------------------------------------------------------------------------------- /src/sampling_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/sampling_utils.py -------------------------------------------------------------------------------- /src/shared_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ostojanovic/BSTIM/HEAD/src/shared_utils.py --------------------------------------------------------------------------------