.coveragerc
.gitignore
CONTRIBUTING.md
LICENSE.txt
README.md
conda-env.yml
pyproject.toml
requirements.txt
setup.py
.github/pull_request_template.md
.github/workflows/book.yml
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.github/workflows/test_package.yml
docs/_config.yml
docs/_toc.yml
docs/requirements.txt
docs/rst_to_md.sh
docs/bib/ref.bib
docs/images/download.png
docs/images/logo_pygom.jpg
docs/md/bib.md
docs/md/building_doc.md
docs/md/common_models.md
docs/md/faq.md
docs/md/installation.md
docs/md/intro.md
docs/md/module-documentation.md
docs/md/parameter_fitting.md
docs/md/solving.md
docs/md/unrollOde.md
docs/notebooks/epi.ipynb
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docs/notebooks/common_models/Robertson.ipynb
docs/notebooks/common_models/SEIR.ipynb
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docs/notebooks/common_models/SIR.ipynb
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docs/rst/autodoc-abc.rst
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docs/rst/autodoc-utilR.rst
notebooks/.gitignore
notebooks/ABC loss function tests.ipynb
notebooks/Demo parallel stochastic simulation.ipynb
notebooks/Loss function Calculations.ipynb
notebooks/ParameterEstimation.ipynb
notebooks/PyGOM_Ebola.ipynb
notebooks/PyGOM_SEIRsetup.ipynb
notebooks/Stochasticity.ipynb
notebooks/Testing loss functions fitted to simulated data.ipynb
notebooks/abc_eg.ipynb
notebooks/debug_tau_leap.ipynb
src/pygom/__init__.py
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src/pygom/approximate_bayesian_computation/approximate_bayesian_computation.py
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src/pygom/loss/.gitignore
src/pygom/loss/__init__.py
src/pygom/loss/base_loss.py
src/pygom/loss/confidence_interval.py
src/pygom/loss/epijson_loss.py
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src/pygom/model/__init__.py
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src/pygom/model/_transition_graph.py
src/pygom/model/base_ode_model.py
src/pygom/model/common_models.py
src/pygom/model/deterministic.py
src/pygom/model/epi_analysis.py
src/pygom/model/ode_variable.py
src/pygom/model/simulate.py
src/pygom/model/stochastic_simulation.py
src/pygom/model/transition.py
src/pygom/model/ode_utils/__init__.py
src/pygom/model/ode_utils/checks_and_conversions.py
src/pygom/model/ode_utils/compile_canary.py
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src/pygom/utilR/__init__.py
src/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
tests/test_unroll.ipynb