.coveragerc
.gitignore
.travis.yml
LICENSE.txt
MANIFEST.in
README.rst
conda-env.yml
requirements.txt
setup.py
.github/workflows/main.yml
.github/workflows/python.yml
doc/Makefile
doc/README.rst
doc/make.bat
doc/requirements.txt
doc/source/bvpSimple.rst
doc/source/common_models.rst
doc/source/conf.py
doc/source/epi.rst
doc/source/epijson.rst
doc/source/estimate1.rst
doc/source/estimate2.rst
doc/source/faq.rst
doc/source/fh.rst
doc/source/getting_started.rst
doc/source/gradient.rst
doc/source/index.rst
doc/source/initialGuess.rst
doc/source/profile.rst
doc/source/ref.rst
doc/source/sir.rst
doc/source/stochastic.rst
doc/source/transition.rst
doc/source/unrollOde.rst
doc/source/_static/.gitignore
doc/source/common_models/FitzHugh.rst
doc/source/common_models/Legrand_Ebola_SEIHFR.rst
doc/source/common_models/Lorenz.rst
doc/source/common_models/Lotka_Volterra.rst
doc/source/common_models/Lotka_Volterra_4State.rst
doc/source/common_models/Robertson.rst
doc/source/common_models/SEIR.rst
doc/source/common_models/SEIR_Birth_Death.rst
doc/source/common_models/SEIR_Birth_Death_Periodic.rst
doc/source/common_models/SEIR_Multiple.rst
doc/source/common_models/SIR.rst
doc/source/common_models/SIR_Birth_Death.rst
doc/source/common_models/SIS.rst
doc/source/common_models/SIS_Periodic.rst
doc/source/common_models/vanDelPol.rst
doc/source/mod/common_models.rst
doc/source/mod/confidence_interval.rst
doc/source/mod/deterministic.rst
doc/source/mod/epi_analysis.rst
doc/source/mod/get_init.rst
doc/source/mod/index.rst
doc/source/mod/losstype.rst
doc/source/mod/odeloss.rst
doc/source/mod/odeutils.rst
doc/source/mod/simulate.rst
doc/source/mod/transition.rst
doc/source/unroll/unrollBD.rst
doc/source/unroll/unrollHard.rst
doc/source/unroll/unrollSimple.rst
notebooks/.gitignore
notebooks/Demo parallel stochastic simulation.ipynb
notebooks/ParameterEstimation.ipynb
notebooks/PyGOM_Ebola.ipynb
notebooks/PyGOM_SEIRsetup.ipynb
notebooks/Stochasticity.ipynb
pygom/__init__.py
pygom.egg-info/PKG-INFO
pygom.egg-info/SOURCES.txt
pygom.egg-info/dependency_links.txt
pygom.egg-info/requires.txt
pygom.egg-info/top_level.txt
pygom/approximate_bayesian_computation/__init__.py
pygom/approximate_bayesian_computation/approximate_bayesian_computation.py
pygom/data/eg1.json
pygom/loss/.gitignore
pygom/loss/__init__.py
pygom/loss/base_loss.py
pygom/loss/confidence_interval.py
pygom/loss/epijson_loss.py
pygom/loss/get_init.py
pygom/loss/loss_type.py
pygom/loss/ode_loss.py
pygom/loss/read_epijson.py
pygom/model/__init__.py
pygom/model/_model_errors.py
pygom/model/_model_verification.py
pygom/model/_ode_composition.py
pygom/model/_tau_leap.c
pygom/model/_tau_leap.pyx
pygom/model/base_ode_model.py
pygom/model/common_models.py
pygom/model/deterministic.py
pygom/model/epi_analysis.py
pygom/model/ode_variable.py
pygom/model/simulate.py
pygom/model/stochastic_simulation.py
pygom/model/transition.py
pygom/model/ode_utils/__init__.py
pygom/model/ode_utils/checks_and_conversions.py
pygom/model/ode_utils/compile_canary.py
pygom/model/ode_utils/plot_det.py
pygom/model/ode_utils/plot_stoc.py
pygom/utilR/__init__.py
pygom/utilR/distn.py
tests/__init__.py
tests/simple_jump_process.py
tests/test_abc.py
tests/test_adding_to_parameterlist.py
tests/test_compile_canary.py
tests/test_epi_analysis.py
tests/test_epijson.py
tests/test_fh_estimate.py
tests/test_input_symbols.py
tests/test_loss_types.py
tests/test_model_existing.py
tests/test_model_multiple_origin.py
tests/test_model_vector.py
tests/test_ode_decomposition.py
tests/test_ode_func.py
tests/test_ode_simulate_jump.py
tests/test_ode_simulate_param.py
tests/test_package_basics.py
tests/test_pickle.py
tests/test_sir_discrete_estimate.py
tests/test_sir_estimate.py