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biblio.bib
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@misc{chatzilena2019contemporary,
title={Contemporary statistical inference for infectious disease models using Stan},
author={Anastasia Chatzilena and Edwin van Leeuwen and Oliver Ratmann and Marc Baguelin and Nikolaos Demiris},
year={2019},
eprint={1903.00423},
archivePrefix={arXiv},
primaryClass={stat.AP}
}
@article{kermack_contributions_1991,
title = {Contributions to the mathematical theory of epidemics{I}},
volume = {53},
issn = {1522-9602},
url = {https://doi.org/10.1007/BF02464423},
doi = {10.1007/BF02464423},
number = {1},
journal = {Bulletin of Mathematical Biology},
author = {Kermack, W. O. and McKendrick, A. G.},
month = mar,
year = {1991},
pages = {33--55}
}
@misc{carpenter2015stan,
title={The Stan Math Library: Reverse-Mode Automatic Differentiation in C++},
author={Bob Carpenter and Matthew D. Hoffman and Marcus Brubaker and Daniel Lee and Peter Li and Michael Betancourt},
year={2015},
eprint={1509.07164},
archivePrefix={arXiv},
primaryClass={cs.MS}
}
@article {PMID:12995455,
Title = {The analysis of equilibrium in malaria},
Author = {MACDONALD, G},
Number = {9},
Volume = {49},
Month = {September},
Year = {1952},
Journal = {Tropical diseases bulletin},
ISSN = {0041-3240},
Pages = {813—829},
URL = {http://europepmc.org/abstract/MED/12995455}
}
@conference{margossian_differential_2017,
Author = {Margossian, Charles C and Gillespie, William R},
Booktitle = {StanCon 2017},
Journal = {Journal of Pharmacokinetics and Pharmacodynamics},
Month = {January},
Title = {Differential Equation Based Models in Stan},
Year = {2017},
doi = {10.5281/zenodo.1284264}}
@misc{carpenter_predator-prey_2018,
title = {Predator-{Prey} {Population} {Dynamics}: the {Lotka}-{Volterra} model in {Stan}},
url = {https://mc-stan.org/users/documentation/case-studies/lotka-volterra-predator-prey.html},
author = {Carpenter, Bob},
year = {2018}
}
@misc{prior_choice,
title = {Prior Choice Recommendations},
url = {https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations},
author = {Stan Team},
year = {2020}
}
@article{hall_infectious_1992,
title = {Infectious {Diseases} of {Humans}. {R}. {M}. {Anderson} \& {R}. {M}. {May}. {Oxford} etc.: {Oxford} {University} {Press}, 1991. viii+757 pp. {Price} £50. {ISBN} 0-19-854599-1},
volume = {86},
issn = {0035-9203},
url = {https://doi.org/10.1016/0035-9203(92)90276-I},
doi = {10.1016/0035-9203(92)90276-I},
number = {4},
journal = {Transactions of The Royal Society of Tropical Medicine and Hygiene},
author = {Hall, A.J.},
year = {1992},
pages = {461--461}
}
@article{Riou_covid_2020,
Author = {Riou, Julien and Hauser, Anthony and Counotte, Michel J and Margossian, Charles C
and Konstantinoudis, Garyfallos and Low, Nicola and Althaus, Christian L},
Title = {Estimation of SARS-CoV-2 mortality during the early stages of an epidemic:
a modeling study in Hubei, China and northern Italy},
journal = {medRxiv:2020.03.04.20031104},
year = {2020}}
@article{Betancourt_hmc_2018,
Author = {Betancourt, Michael},
Journal = {arXiv:1701.02434v1},
Month = {January},
Title = {A Conceptual Introduction to Hamiltonian Monte Carlo},
Year = {2018}}
@article{Hoffman_nuts_2014,
Author = {Hoffman, Matthew D. and Gelman, Andrew},
Date-Added = {2016-10-07 17:06:45 +0000},
Date-Modified = {2017-08-17 09:27:44 +0000},
Journal = {Journal of Machine Learning Research},
Month = {April},
Pages = {1593-1623},
Title = {The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo},
Year = {2014}}
@techreport{Hindmarsh_ode_2020,
Author = {Hindmarsh, Alan and Serban, Radu},
Date-Modified = {2020-01-16 22:47:24 -0500},
Institution = {Lawrence Livermore National Laboratory},
Month = {January},
Title = {User Documentation for CVODES v5.1.0},
Year = {2020}}
@book{Griewank_ad_2008,
Author = {Griewank, Andreas and Walther, Andrea},
Edition = {Second},
Publisher = {Society for Industrial and Applied Mathematics (SIAM), Philadelphia, PA},
Title = {Evaluating derivatives},
Year = {2008}}
@article{Margossian_ad_2019,
Author = {Charles C. Margossian},
Month = {3},
Title = {A Review of automatic differentiation and its efficient implementation},
journal = {Wiley interdisciplinary reviews: data mining and knowledge discovery},
volume = {9},
issue = {4},
doi = {10.1002/WIDM.1305},
Year = {2019}}
@article{margossian_mixed_solver_2017,
Author = {Margossian, Charles C and Gillespie, William R},
Booktitle = {American },
Journal = {Journal of Pharmacokinetics and Pharmacodynamics},
Month = {October},
Title = {Gaining Efficiency by Combining Analytical and Numerical Methods to Solve ODEs: Implementation in Stan and Application to Bayesian PK/PD },
Volume = {44},
Year = {2017}}
@article{Flaxman_covid_2020,
Author = {Seth Flaxman and Swapnil Mishra and Axel Gandy and H Juliette T Unwin and Helen Coupland and ... and Samir Bhatt},
title = {Report 13 - Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries},
journal = {arXiv:2004.11342},
year = {2020},
month = {April}}
@article{Carpenter_stan_2017,
Title = {Stan: A Probabilistic Programming Language},
Author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matt and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus A. and Guo, Jiqiang and Li, Peter and Riddel, Allen},
Journal = {Journal of Statistical Software},
volume = {76},
issue = {1},
pages = {1 --32},
Year = {2017},
doi = {10.18637/jss.v076.i01}}
@article{Chatzilena_tutorial_2019,
author = {Chatzilena, Anastasia and van Leeuwen, Edwin and Ratmann, Olivier
and Baguelin, Olivier and Demiris, Nikolaos},
title = {Contemporary statistical inference for infectious disease models using Stan},
journal = {Epidemics},
volume = {29},
year = {2019},
doi = {https://doi.org/10.1016/j.epidem.2019.100367}}
@article{Mihaljevic_tutorial_2016,
title = {Estimating transmission by fitting mechanistic models in Stan},
author = {Mihaljevic, Joseph},
year = {2016},
url = {https://jrmihalj.github.io/estimating-transmission-by-fitting-mechanistic-models-in-Stan/}
}
@article{Weber_ode_2018,
title = {Solving ODEs in the wild: Scalable pharmacometrics with Stan},
author = {Weber, Sebastian},
journal = {StanCon Helsinki 2018},
year = {2018}}
@article{Carpenter_predatory-prey_2018,
title = {Predator-Prey Population Dynamics: the Lotka-Volterra model in Stan},
author = {Carpenter, Bob},
url = {https://mc-stan.org/users/documentation/case-studies/lotka-volterra-predator-prey.html},
year = {2018}}
@article{Talts_sbc_2018,
author = {Talts, Sean and Betancourt, Michael and Simpson, Daniel and Vehtari, Aki and Gelman, Andrew},
title = {Validating Bayesian inference algorithms with simulation-based calibration},
journal = {arXiv:1804.06788v1},
year = {2018}}
@article{Roberts_mcmc_2004,
author = {Roberts, Gareth O and Rosenthal, Jeffrey S},
title = {General state space Markov chains and MCMC algorithms},
journal = {Probability survey},
volume = {1},
pages = {20 - 71},
doi = {10.1214/154957804100000024},
year = {2004}}
@misc{gelman2020bayesian,
title={Bayesian Workflow},
author={Andrew Gelman and Aki Vehtari and Daniel Simpson and Charles C. Margossian and Bob Carpenter and Yuling Yao and Lauren Kennedy and Jonah Gabry and Paul-Christian Bürkner and Martin Modrák},
year={2020},
eprint={2011.01808},
archivePrefix={arXiv},
primaryClass={stat.ME}
}