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supplement.bib
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@Article{pomp2016,
title = {Statistical Inference for Partially Observed {Markov}
Processes via the {R} Package {pomp}},
author = {Aaron A. King and Dao Nguyen and Edward L. Ionides},
journal = {Journal of Statistical Software},
year = {2016},
volume = {69},
number = {12},
pages = {1--43},
doi = {10.18637/jss.v069.i12},
}
@Manual{,
title = {{pomp}: {Statistical} Inference for Partially Observed
{Markov} Processes},
author = {Aaron A. King and Edward L. Ionides and Carles Martinez
Bret\'o and Stephen P. Ellner and Matthew J. Ferrari and Bruce E.
Kendall and Michael Lavine and Dao Nguyen and Daniel C. Reuman
and Helen Wearing and Simon N. Wood},
year = {2020},
note = {R~package, version~2.8},
url = {https://kingaa.github.io/pomp/},
}
@article{ga_2013,
author = {Luca Scrucca},
title = {{GA: A Package for Genetic Algorithms in R}},
journal = {Journal of Statistical Software, Articles},
volume = {53},
number = {4},
year = {2013},
keywords = {},
issn = {1548-7660},
pages = {1--37},
doi = {10.18637/jss.v053.i04},
url = {https://www.jstatsoft.org/v053/i04}
}
@article{ga_2017_hybridGA,
author = {Luca Scrucca},
title = {{On Some Extensions to GA Package: Hybrid Optimisation,
Parallelisation and Islands Evolution}},
year = {2017},
journal = {{The R Journal}},
doi = {10.32614/RJ-2017-008},
url = {https://doi.org/10.32614/RJ-2017-008},
pages = {187--206},
volume = {9},
number = {1}
}
@article{matthies1979solution,
title={The solution of nonlinear finite element equations},
author={Matthies, Hermann and Strang, Gilbert},
journal={International journal for numerical methods in engineering},
volume={14},
number={11},
pages={1613--1626},
year={1979},
publisher={Wiley Online Library}
}
@article{sobol1967distribution,
title={On the distribution of points in a cube and the approximate evaluation of integrals},
author={Sobol', Il'ya Meerovich},
journal={Zhurnal Vychislitel'noi Matematiki i Matematicheskoi Fiziki},
volume={7},
number={4},
pages={784--802},
year={1967},
publisher={Russian Academy of Sciences, Branch of Mathematical Sciences}
}
@article{sobol1976uniformly,
title={Uniformly distributed sequences with an additional uniform property},
author={Sobol, Ilya M},
journal={USSR Computational Mathematics and Mathematical Physics},
volume={16},
number={5},
pages={236--242},
year={1976},
publisher={Elsevier}
}
@article{suchard2018bayesian,
title={Bayesian phylogenetic and phylodynamic data integration using {BEAST} 1.10},
author={Suchard, Marc A and Lemey, Philippe and Baele, Guy and Ayres, Daniel L and Drummond, Alexei J and Rambaut, Andrew},
journal={Virus evolution},
volume={4},
number={1},
pages={vey016},
year={2018},
publisher={Oxford University Press}
}
@misc{CDC-influenza-overview,
title={{U.S.} Influenza Surveillance System: Purpose and Methods},
url={https://www.cdc.gov/flu/weekly/overview.htm},
note="\url{https://www.cdc.gov/flu/weekly/overview.htm}",
journal={Centers for Disease Control and Prevention}, publisher={Centers for Disease Control and Prevention}, year={2019},
month={October},
note = {Accessed: 2020-04-17}
}
@misc{CDC2020-web-week12,
title={Weekly {U.S.} Influenza Surveillance Report},
url={https://www.cdc.gov/flu/weekly/index.htm},
note="\url{https://www.cdc.gov/flu/weekly/index.htm}",
journal={Centers for Disease Control and Prevention}, publisher={Centers for Disease Control and Prevention}, year={2020},
month={March},
note = {Accessed: 2020-03-31}
}
@misc{CDC-Wonder-pop-proj,
title={Population Projections, {United States}, 2004 -- 2030, by state, age, and sex, on {CDC WONDER} Online Database},
url={http://wonder.cdc.gov/population-projections.html},
note= "\url{http://wonder.cdc.gov/population-projections.html}",
publisher={Centers for Disease Control and Prevention},
year={2005},
month={September},
note = {Accessed: 2019-08-16}
}
@misc{CDC-FluView-Feb28,
title={FluView Interactive},
url={https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html},
note="\url{https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html}",
publisher={Centers for Disease Control and Prevention},
year={2020},
month={February},
note = {Accessed: 2020-02-28}
}
@misc{CDC-FluView-age,
title={FluView Interactive},
url={https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html},
note="\url{https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html}",
publisher={Centers for Disease Control and Prevention},
year={2020},
month={June},
note = {Accessed: 2020-06-05}
}
@article{wood2015package,
title={Package 'mgcv'},
author={Wood, Simon and Wood, Maintainer Simon},
journal={R package version},
volume={1},
pages={29},
year={2015}
}
@article{yu2017ggtree,
title={ggtree: an {R} package for visualization and annotation of phylogenetic trees with their covariates and other associated data},
author={Yu, Guangchuang and Smith, David K and Zhu, Huachen and Guan, Yi and Lam, Tommy Tsan-Yuk},
journal={Methods in Ecology and Evolution},
volume={8},
number={1},
pages={28--36},
year={2017},
publisher={Wiley Online Library}
}
@article{an2015variational,
title={Variational autoencoder based anomaly detection using reconstruction probability},
author={An, Jinwon and Cho, Sungzoon},
journal={Special Lecture on IE},
volume={2},
number={1},
year={2015}
}
@inproceedings{sakurada2014anomaly,
title={Anomaly detection using autoencoders with nonlinear dimensionality reduction},
author={Sakurada, Mayu and Yairi, Takehisa},
booktitle={Proceedings of the MLSDA 2014 2nd Workshop on Machine Learning for Sensory Data Analysis},
pages={4--11},
year={2014}
}
@inproceedings{zhou2017anomaly,
title={Anomaly detection with robust deep autoencoders},
author={Zhou, Chong and Paffenroth, Randy C},
booktitle={Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
pages={665--674},
year={2017}
}