├── .gitignore ├── LICENSE ├── README.md ├── notebooks ├── Figure1.ipynb ├── Figure2.ipynb ├── Figure3.ipynb ├── Figure4.ipynb ├── Figure5.ipynb ├── Figure6.ipynb ├── Figure7.ipynb ├── FigureS1a-c.ipynb ├── FigureS1d-g.ipynb ├── FigureS1h-j.ipynb ├── FigureS1k-m.ipynb ├── FigureS2.ipynb ├── FigureS3.ipynb ├── FigureS4.ipynb ├── FigureS5.ipynb ├── FigureS6.ipynb └── FigureS7.ipynb ├── poetry.lock ├── pyproject.toml ├── replay_structure ├── __init__.py ├── config.py ├── descriptive_stats.py ├── deviance_models.py ├── diffusion_constant.py ├── forward_backward.py ├── highsynchronyevents.py ├── marginals.py ├── metadata.py ├── model_comparison.py ├── model_recovery.py ├── pf_analysis.py ├── predictive_analysis.py ├── ratday_preprocessing.py ├── read_write.py ├── ripple_preprocessing.py ├── run_snippet_preprocessing.py ├── simulated_neural_data.py ├── simulated_trajectories.py ├── structure_analysis_input.py ├── structure_models.py ├── structure_models_gridsearch.py ├── structure_trajectory.py ├── utils.py └── viterbi.py └── scripts ├── __init__.py ├── local ├── generate_model_recovery_data.py ├── get_descriptive_stats.py ├── get_marginals.py ├── get_trajectories.py ├── preprocess_ratday_data.py ├── preprocess_spikemat_data.py ├── reformat_data_for_structure_analysis.py ├── run_deviance_explained.py ├── run_diffusion_constant.py ├── run_factorial_model_comparison.py ├── run_model.py ├── run_model_comparison.py ├── run_pf_analysis.py └── run_predictive_analysis.py └── o2 ├── __init__.py ├── diffusion_gridsearch.py ├── diffusion_gridsearch.sh ├── momentum_gridsearch.sh ├── momentum_gridsearch_ratdayripple.py ├── momentum_gridsearch_ratdayripple.sh ├── o2_lib.py ├── sg_gridsearch.py ├── sg_gridsearch.sh ├── viterbi_trajectories.py └── viterbi_trajectories.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugowitschLab/HippocampalSWRDynamics/HEAD/.gitignore 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