├── .gitignore ├── README.md ├── docs ├── KalmanODE.rst ├── Makefile ├── car.rst ├── conf.py ├── figures │ ├── chkrebtiifigure.png │ └── fitzfigure.png ├── index.rst ├── make.bat └── utils.rst ├── examples ├── Graphs in Paper.ipynb ├── chkrebtii.py ├── euler_approx.py ├── fitz.py ├── inference.py ├── lorenz.py ├── lorenz_graph.py ├── mseir.py ├── readme_graph.py └── tutorial.ipynb ├── rodeo ├── __init__.py ├── car │ ├── __init__.py │ ├── car_cov.py │ ├── car_init.py │ ├── car_mou.py │ └── car_var.py ├── cython │ └── KalmanODE.pyx ├── eigen │ ├── KalmanODE.pyx │ ├── KalmanODE2.pyx │ ├── KalmanTV.h │ ├── KalmanTVODE.h │ └── KalmanTVODE.pxd ├── ibm │ ├── __init__.py │ └── ibm_init.py ├── numba │ ├── KalmanODE.py │ └── __init__.py └── utils │ ├── __init__.py │ └── utils.py ├── setup.py └── tests ├── KalmanODE_py.py ├── __init__.py ├── depreciated ├── general │ ├── Analytical vs Numerical Test.ipynb │ ├── Bayesian │ │ ├── README.md │ │ ├── __init__.py │ │ ├── bayes_ode.py │ │ ├── cov_exp.py │ │ ├── cov_rect.py │ │ └── cov_square_exp.py │ ├── README.md │ ├── Tuning.ipynb │ ├── ode_bayes_star.py │ ├── test_exp.py │ ├── test_exp_integrate.py │ ├── test_rect.py │ └── test_square_exp.py ├── kalman │ ├── CAR_Testing.ipynb │ ├── KalmanTV.pxd │ ├── KalmanTV.py │ ├── KalmanTest.h │ ├── KalmanTest.pxd │ ├── Kalman_Higher_Order_Solver.ipynb │ ├── Kalman_ODE_multi.ipynb │ ├── README.md │ ├── Reconstruction.ipynb │ ├── Statistical Inference.ipynb │ ├── V_euler.py │ ├── cython test timings.ipynb │ ├── filter_update_full.py │ ├── fitz.py │ ├── fitz_graph.py │ ├── higher_mvncond.py │ ├── inference speed test.ipynb │ ├── kalman_initial_draw.py │ ├── kalman_multi_solver.py │ ├── kalman_ode_chkrebtii.cpp │ ├── kalman_ode_higher.py │ ├── kalman_ode_higher.pyx │ ├── kalman_ode_offline_cy.pyx │ ├── kalman_ode_offline_py.py │ ├── kalman_ode_solve_cy.pyx │ ├── kalman_ode_solve_py.py │ ├── kalman_solver.py │ ├── kalmantest.pyx │ ├── kalmantv.pyx │ ├── mat_mult.pyx │ ├── multi_mvncond.py │ ├── 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