.coveragerc
.gitignore
CONTRIBUTING.md
LICENSE.txt
README.md
conda-env.yml
pyproject.toml
requirements.txt
setup.py
.github/pull_request_template.md
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debugging/stochastic parameter simulation.ipynb
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docs/md/intro.md
docs/md/module-documentation.md
docs/md/parameter_fitting.md
docs/md/solving.md
docs/md/unrollOde.md
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docs/notebooks/common_models/SEIR_Multiple.ipynb
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docs/notebooks/common_models/SIR_Birth_Death.ipynb
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docs/notebooks/common_models/vanDelPol.ipynb
docs/notebooks/paramfit/bvpSimple.ipynb
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docs/notebooks/paramfit/estimate2.ipynb
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docs/notebooks/paramfit/mle_ci_theory.ipynb
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docs/rst/autodoc-abc.rst
docs/rst/autodoc-loss.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
notebooks/sympy_bug_hunt.ipynb
notebooks/variable_store.ipynb
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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/simulate.py
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src/pygom/simulation/__init__.py
src/pygom/simulation/src/__init__.py
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src/pygom/simulation/src/simulation/deterministic/integrator.py
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src/pygom/simulation/src/simulation/stochastic/__init__.py
src/pygom/simulation/src/simulation/stochastic/config.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
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tests/test_model_multiple_origin.py
tests/test_model_vector.py
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tests/test_ode_func.py
tests/test_ode_simulate_jump.py
tests/test_ode_simulate_param.py
tests/test_package_basics.py
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tests/test_sir_discrete_estimate.py
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tests/test_sir_optimiser.ipynb
tests/test_unroll.ipynb
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