E. L. Ionides: Publications

Tan, K., Ionides, E. L. and Hooker, G. (2024). Accelerated inference for partially observed Markov processes using automatic differentiation. arxiv:2407.03085. Article source code on GitHub and Zenodo. Software on GitHub.

King A. A., Lin, Q. and Ionides, E. L. (2024). Exact phylodynamic likelihood via structured Markov genealogy processes. arxiv:2405.17032. Article source code on GitHub. Software on GitHub.

Hao, Y., Abkemeier, A. J. and Ionides, E. L. (2024). Poisson approximate likelihood compared to the particle filter. arxiv:2409.12173. Article source code on GitHub and Zenodo.

Tapia Granados, J. A. and Ionides, E. L. (2024). Income, health, and cointegration. arxiv:2407.15755.

Ning, N. and Ionides, E. L. (2024). Systemic infinitesimal over-dispersion on general stochastic graphical models. Statistics and Computing 34 147. doi. arxiv. Article source code on GitHub.

Breto, C., Wheeler, J., King, A. A., and Ionides, E. L. (2024). A tutorial on panel data analysis using partially observed Markov processes via the R package panelPomp. arxiv:2409.03876. Article source code included in the R package on GitHub and CRAN.

Asfaw, K., Park, J., King, A. A., and Ionides, E. L. (2024). spatPomp: An R package for spatiotemporal partially observed Markov process models. Journal of Open Source Software 9 7008. doi. R package on GitHub and CRAN. Website,

Asfaw, K., Park, J., King, A. A., and Ionides, E. L. (2024). A tutorial on spatiotemporal partially observed Markov process models via the R package spatPomp. arxiv:2101.01157v4. Article source code on GitHub.

Wheeler, J., Rosengart, A. L., Jiang, Z., Tan, K., Treutle, N. and Ionides, E. L. (2024). Informing policy via dynamic models: Cholera in Haiti. PLOS Computational Biology 20 e1012032. doi. arxiv. Article source code on GitHub and Zenodo. R package on GitHub and Zenodo.

Li, J., Ionides, E. L., King, A. A., Pascual, M. and Ning, N. (2024). Inference on spatiotemporal dynamics for coupled biological populations. Journal of the Royal Society Interface 21 20240217. doi. arxiv. Article source code on GitHub and Zenodo. R package on GitHub and Zenodo.

Wheeler, J. and Ionides, E. L. (2024). Likelihood Based Inference for ARMA Models. arxiv:2310.01198v5. R package arima2 on GitHub and CRAN.

Ionides, E. L., Ning, N. and Wheeler, J. (2024). An iterated block particle filter for inference on coupled dynamic systems with shared and unit-specific parameters. Statistica Sinica 34 1145-1166. doi. arxiv. Source code on GitHub.

Ionides, E. L., Asfaw, K., Park, J., and King, A. A. (2023). Bagged filters for partially observed interacting systems. Journal of the American Statistical Association 118 1078-1089. doi. arxiv. Source code on GitHub.

Ning, N. and Ionides, E. L. (2023). Iterated block particle filter for high-dimensional parameter learning: Beating the curse of dimensionality. Journal of Machine Learning Research 24(82) 1-76. pdf. arxiv. Tutorial with source code on GitHub.

Ionides, E. L. and Ritov, Y. (2022). The scientific method and p-values: Response to Mayo (2022). Conservation Biology, 36 e13984. doi.

King A. A., Lin, Q. and Ionides, E. L. (2022). Markov genealogy processes. Theoretical Population Biology, 143 77-91. doi. arxiv. Source code on Zenodo.

Ning, N., Ionides, E. L., and Ritov, Y. (2021). Scalable Monte Carlo inference and rescaled local asymptotic normality. Bernoulli, 27 2532-2555. doi. arxiv.

Kraay, A. N. M., Man, O., Levy, M. C., Levy, K., Ionides, E., Eisenberg, J. N. S. (2020). Understanding the Impact of Rainfall on Diarrhea: Testing the Concentration-Dilution Hypothesis Using a Systematic Review and Meta-Analysis. Environmental Health Perspectives, 128 126001. doi.

Subramanian, R., Romeo Aznar, V., Ionides, E., Codeco, C., and Pascual, M. (2020). Predicting re-emergence times of dengue epidemics at low reproductive numbers: DENV1 in Rio de Janeiro, 1986-1990. Journal of the Royal Society Interface, 17 20200273. doi. medRxiv

Kraay, A.N.M., Ionides, E.L., Lee, G.O., Trujillo, W.F.C. and Eisenberg, J.N.S. (2020). Effect of childhood rotavirus vaccinationon community rotavirus prevalence in rural Ecuador, 2008-13. International Journal of Epidemiology, 49 1691–1701. doi.

NeCamp, T., Sen, S., Frank, E., Walton, M. A., Ionides, E. L., Fang, Y., Tewari, A. and Wu, Z. (2020). Assessing real-time moderation for developing adaptive mobile health interventions for medical interns: Micro-randomized trial. Journal of Medical Internet Research 22 e15033. doi.

King A. A., Lin, Q. and Ionides, E. L. (2020). The sampled Moran genealogy process. arxiv:2002.11184v3.

Park, J., and Ionides, E. L. (2020). A guided intermediate resampling particle filter for inference on high dimensional systems. Statistics and Computing 30 1497-1522. doi. arxiv. Source code on GitHub.

Breto, C., Ionides, E. L., and King, A. A. (2019). Panel data analysis via mechanistic models. Journal of the American Statistical Association 115 1178-1188. doi. arxiv. R package on GitHub and CRAN. Source code as Supplemental material.

Marino, J.A. Jr., Peacor, S.D., Bunnell, D.B., Vanderploeg, H.A., Pothoven, S.A., Elgin, A.K., Bence, J.R., Jiao, J. and Ionides, E.L. (2019). Evaluating consumptive and nonconsumptive predator effects on prey density using field time series data. Ecology 100 e02583. doi. Source code.

Tapia Granados, J.A., Christine, P.J., Ionides, E.L., Carnethon, M.R., Diez Roux, A.V., Kiefe, C.I. and Schreiner, P.J., (2018). Cardiovascular risk factors, depression, and alcohol consumption during joblessness and during recessions in CARDIA young adults. American Journal of Epidemiology 187 2339-2345. doi.

Ionides, E. L., Breto, C., Park, J., Smith, R. A. and King, A. A. (2017). Monte Carlo profile confidence intervals for dynamic systems. Journal of the Royal Society Interface 14 1-10. doi. arxiv.

Smith, R. A., Ionides, E. L. and King, A. A. (2017). Infectious disease dynamics inferred from genetic data via sequential Monte Carlo. Molecular Biology and Evolution 34 2065-2084. doi. biorxiv. Source code.

Koopman, J. S., Henry, C. J., Park, J. H., Eisenberg, M. C., Ionides, E. L., and Eisenberg, J. N. (2017). Dynamics affecting the risk of silent circulation when oral polio vaccination is stopped. Epidemics 20 21-36. doi. bioarxiv.

Tapia Granados, J. A. and Ionides, E. L. (2017). Population health in expansion and recession: Mortality and the Great Recession in Europe. Health Economics 26 e219–e235. doi. Coverage in New York Times.

Ionides, E. L., Giessing, A., Ritov, Y., and Page, S. E. (2017). Response to the ASA's statement on p-values: context, process, and purpose. The American Statistician 71 88-89. doi. pdf.

Nguyen, D. and Ionides, E. L. (2017). A second-order iterated smoothing algorithm. Statistics and Computing 27 1677–1692. doi. pdf.

Tapia Granados, J. A. and Ionides, E. L. (2016). Statistical evidence shows that mortality tends to fall during recessions: A rebuttal to Catalano and Bruckner. International Journal of Epidemiology 45 1683-1686. doi. pdf.

King, A. A., Nguyen, D. and Ionides, E. L. (2016). Statistical inference for partially observed Markov processes via the R package pomp. Journal of Statistical Software 69. doi. pdf. Website. R package on GitHub and CRAN.

Ehsani, J.P., Ionides, E.L., Klauer, S.G., Perlus, J.G., and Gee, B. (2016). The Effectiveness of Cell Phone Restrictions for Young Drivers: A Review of the Evidence. Transportation Research Record: Journal of the Transportation Research Board 2602 35–42. doi.

Koopman, J.S., Singh, P. and Ionides, E. L. (2016). Transmission modeling to enhance surveillance system function. In Transforming Public Health Surveillance, edited by S. J. N. McNabb et al. Elsevier.

Bhadra, A. and Ionides, E. L. (2016). Adaptive particle allocation in iterated sequential Monte Carlo via approximating meta-models. Statistics and Computing. 26 393-407. doi.

Ionides, E. L., Nguyen, D., Atchade, Y., Stoev, S. and King, A. A. (2015). Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. Proceedings of the National Academy of Sciences of the USA 112 719-724. doi. pdf.

Romero-Severson, E. O., Petrie, C. L., Ionides, E. L., Albert, J. and Leitner, T. (2015). Trends of HIV-1 incidence with credible intervals in Sweden 2002-2009 reconstructed using a dynamic model of within-patient IgG growth. International Journal of Epidemiology 44 998-1006. doi. pdf.

Romero-Severson, E. O., Volz, E., Koopman, J. S., Leitner, T. and Ionides, E. L. (2015). Dynamic variation in sexual contact rates for a cohort of HIV-negative urban gay men. American Journal of Epidemiology 182 255-262. doi. Tutorial.

Katus, R. M., Liemohn, M. W., Ionides, E. L., Ilie, R., Welling, D. and Sarno-Smith, L. K. (2014). Statistical analysis of the geomagnetic response to different solar wind drivers and the dependence on storm intensity. Journal of Geophysical Research: Space Physics 120 310-327. doi.

Tapia Granados, J. A., House, J. S., Ionides, E. L., Burgard, S. and Schoeni, R. S. (2014). Individual Joblessness, Contextual Unemployment, and Mortality Risk. American Journal of Epidemiology 180 280-287. doi.

Ehsani, J. P, Bingham, C. R., Ionides, E. L. and Childers, D. (2014). The short-term impact of Michigan's text messaging restriction on motor vehicle crashes. Journal of Adolescent Health 54 S68-S74. doi.

Larson, P. S., Minakawa, N., Dida, G. O., Njenga, S. M., Ionides, E. L. and Wilson, M. L. (2014). Insecticide-treated net use before and after mass distribution in a fishing community along Lake Victoria, Kenya: successes and unavoidable pitfalls. Malaria Journal , 13 466. doi.

Volz, E. M., Ionides, E., Romero-Severson, E. O., Brandt, M.-G., Mokotoff, E. and Koopman, J. S. (2013). HIV-1 transmission during early infection in men who have sex with men: A phylodynamic analysis. PLoS Medicine 10 e1001568. doi. pdf.

Ionides, E. L., Wang, Z. and Tapia Granados, J. A. (2013). Macroeconomic effects on mortality revealed by panel analysis with nonlinear trends. Annals of Applied Statistics 7 1362-1385. doi. arxiv. pdf. supplement.

Roy, M., Bouma, M. J., Ionides, E. L., Dhiman, R. C., and Pascual, M. (2013). Relapse treatment and the transmission dynamics of Plasmodium vivax malaria in NW India. PLoS Neglected Tropical Diseases 7 e1979. doi.

Mayer, B. T., Eisenberg, J. N., Henry, C. J., Gomes, G. M., Ionides, E. L. and Koopman, J. S. (2012). Successes and shortcomings of polio eradication: A transmission modeling analysis. American Journal of Epidemiology 177 1236-1245. doi.

Chuang, T., Ionides, E. L., Knepper, R. G., Stanuszek, W. W., Walker, E. D. and Wilson, M. L. (2012). Cross-correlation map analyses show weather variation influences on mosquito abundance patterns in Saginaw county, Michigan, 1989-2005. Journal of Medical Entomology 49 851-858. doi.

Tapia Granados, J. A., Ionides, E. L. and Carpintero, O. (2012). Climate change and the world economy: Short-run determinants of atmospheric CO2. Environmental Science and Policy 21 50-62. doi. summary on simpleclimate. coverage by NBC News.

Lindstrom, E., Ionides, E. L., Frydendall, J., and Madsen, H. (2012). Efficient iterated filtering. 16th IFAC Symposium on System Identification (SYSID 2012). doi.

Breto, C., and Ionides, E. L. (2011). Compound Markov counting processes and their applications to modeling infinitesimally over-dispersed systems. Stochastic Processes and Their Applications 121 2571-2591. doi. arxiv.

Ionides, E. L, Bhadra, A., Atchade, Y. and King, A. A. (2011). Iterated filtering. Annals of Statistics 39 1776-1802. doi. pdf. arxiv.

Ionides, E. L. (2011). Discussion on "Feature Matching in Time Series Modeling" by Y. Xia and H. Tong. Statistical Science 26 49-52. doi. pdf.

Bhadra, A., Ionides, E. L., Laneri, K., Pascual, M., Bouma, M. and Dhiman, R. C. (2011). Malaria in Northwest India: Data analysis via partially observed stochastic differential equation models driven by Levy noise. Journal of the American Statistical Association 106 440-451. doi.

Mayer, B. T. Koopman, J. S., Ionides, E. L., Pujol, J. M. and Eisenberg, J. N. S. (2011). A dynamic dose–response model to account for exposure patterns in risk assessment: A case study in inhalation anthrax. Journal of the Royal Society Interface 8:506-517. doi.

Tapia Granados, J. A. and Ionides, E. L. (2011). Mortality and Macroeconomic Fluctuations in Contemporary Sweden. European Journal of Population 27 157-184. doi.

Laneri, K., Bhadra, A., Ionides, E. L., Bouma, M., Dhiman, R. C., Yadav, R. S. and Pascual, M. (2010). Forcing versus feedback: Epidemic malaria and monsoon rains in NW India. PLoS Computational Biology 6 e1000898. doi.

He, D., Ionides, E. L. and King, A. A. (2010). Plug-and-play inference for disease dynamics: Measles in large and small towns as a case study. Journal of the Royal Society Interface 7 271-283. doi.

Breto, C., He, D., Ionides, E. L. and King, A. A. (2009). Time series analysis via mechanistic models. Annals of Applied Statistics 3 319-348. doi. pdf. arxiv.

Schweigler, L. M., Desmond, J. S., McCarthy, M., Bukowski, K., Ionides, E. L., and Younger, J. G. (2009) Forecasting Models of Emergency Department Crowding. Academic Emergency Medicine 16 301-308. doi

King, A. A., Ionides, E. L., Pascual, M. and Bouma, M. J. (2008). Inapparent infections and cholera dynamics. Nature 454 877-880. doi.

Ionides, E. L. (2008). Truncated Importance Sampling. Journal of Computational and Graphical Statistics 17 295-311. doi.

Tapia Granados, J. A. and Ionides, E. L. (2008). The reversal of the relation between economic growth and health progress: Sweden in the 19th and 20th centuries. doi. Journal of Health Economics 27 544-563. Supplement and pdf.

Ionides, E. L., Breto, C. and King, A. A. (2007). Modeling Disease Dynamics: Cholera as a Case Study. Statistical Advances in the Biomedical Sciences, Chapter 8 (pp. 123-140). Edited by A. Biswas, S. Datta, J. Fine and M. Segal. Wiley, Hoboken NJ. pdf

Ionides, E. L., Breto, C. and King, A. A. (2006). Inference for nonlinear dynamical systems. Proceedings of the National Academy of Sciences 103 18438-18443. doi. Supporting online material. pdf and supporting text.

Greene, S. K., Ionides, E. L. and Wilson, M. L. (2006). Patterns of Influenza-Associated Mortality Among U.S. Elderly by Geographic Region and Virus Subtype, 1968-1998. American Journal of Epidemiology 163 316-326. pdf.

Ionides, E. L. (2005). Maximum Smoothed Likelihood Estimation. Statistica Sinica 15 1003-1014. pdf.

Gage, G. J., Ionides, E. L. and Kipke, D. (2005). Information Capacity of Brain Machine Interfaces. Proceedings of the 27th Conference of IEEE Engineering in Medicine and Biology Society 2110-2113. pdf.

Gage, G. J., Ludwig, K., Otto, K., Ionides, E. L. and Kipke, D. (2005). Naive coadaptive cortical control. Journal of Neural Engineering 2 52-63. doi. pdf.

Ionides, E. L., Fang, K.S., Isseroff, R.R. and Oster, G.F. (2004). Stochastic models for cell motion and taxis. Journal of Mathematical Biology 48, 23-37. doi. pdf.

Ionides, E. L. (2003). Inference and Filtering for Partially Observed Diffusion Processes via Sequential Monte Carlo. University of Michigan Statistics Department Technical Report #405. pdf. Updated version.

Ionides, E. L. (2001). Statistical Analysis of Cell Motion. University of California, Berkeley thesis. pdf.

Fang, K.S., Ionides, E., Oster, G., Nuccitelli, R. and Isseroff, R.R. (1999). Epidermal Growth Factor Relocalization and Kinase Activity Are Necessary for Directional Migration of Keratinocytes in DC Electric Fields. Journal of Cell Science 112, 1967-1978. doi.

Published commentaries

Frey, K., Ionides, E. L., and Wheeler, J. (2024). Reviews of "Efficacy, Public Health Impact and Optimal Use of the Takeda Dengue Vaccine." Rapid Reviews Infectious Diseases. doi.

Ionides, E.L. (2020). Peer review report for "Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate " [version 1; peer review]. Wellcome Open Reseach 5 288. doi.

Ionides, E. L. (2012). Comment: Cell motility models and inference for dynamic systems. Journal of the American Statistical Association 107 865-868. doi.

Ionides, E. L. (2007). Discussion of "Parameter Estimation for Differential Equations: A Generalized Smoothing Approach" (by J. O. Ramsay, G. Hooker, D. Campbell and J. Cao). Journal of the Royal Statistical Society, Series B (Statistical Methodology) 69 783-784. doi.