Benjamin Bolker - McMaster Experts

Affiliations

Faculty of Science, McMaster University
Professor, Biology, Faculty of Science
Professor, Mathematics and Statistics, Faculty of Science
Associate Member, Psychology, Neuroscience & Behaviour, Faculty of Science

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selected scholarly activity

books
- Infectious Disease: A Very Short Introduction 2015
- Ecological models and data in R 2008
chapters
- Linear and generalized linear mixed models. 309-333. 2015
- Model-based, response-surface approaches to quantifying indirect interactions. 186-204. 2012
- 3 Continuous-Space Models for Population Dynamics. 45-69. 2004
- Continuous-Space Models for Population Dynamics. 45-69. 2004
- Moment Methods for Ecological Processes in Continuous Space. 388-411. 2000
- Microparasite Group Report. 123-143. 1995
- Spatial Dynamics Group Report. 399-420. 1995
conferences
- Predicting Predator Diversity Effects on Ecosystem Function. Integrative and Comparative Biology. E121-E121. 2015
- Are fluctuating asymmetry studies adequately sampled? Implications of a new model for size distribution. Integrative and Comparative Biology. 959-959. 2005
- Predator induced phenotypic plasticity: Influenced of prey size, density, and experience. Integrative and Comparative Biology. 1041-1041. 2005
- Management at a different scale: Marine ornamentals and local processes. Bulletin of Marine Science. 733-748. 2002
journal articles
- Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer. Bulletin of Mathematical Biology. 86:109. 2024
- Predicting the Temperature-Driven Development of Stage-Structured Insect Populations with a Bayesian Hierarchical Model. Journal of Agricultural, Biological, and Environmental Statistics. 29:536-552. 2024
- A simulation study of sampling in difficult settings: Statistical superiority of a little-used method. Statistical Journal of the IAOS. 40:375-385. 2024
- Multimodel Approaches Are Not the Best Way to Understand Multifactorial Systems. Entropy. 26:506-506. 2024
- The probability of epidemic burnout in the stochastic SIR model with vital dynamics. Proceedings of the National Academy of Sciences of the United States of America. 121:e2313708120-e2313708120. 2024
- The role of fire in terrestrial vertebrate richness patterns. Ecology Letters. 26:563-574. 2023
- Evaluating undercounts in epidemics: Response to Maruotti et al. (2022). Journal of Medical Virology. 95:e28474. 2023
- Comparing machine learning approaches to incorporate time-varying covariates in predicting cancer survival time. Scientific Reports. 13:1370. 2023
- A Simulation Study of Sampling in Difficult Settings: Statistical Superiority of Little-Used method 2022
- Testing and Isolation Efficacy: Insights from a Simple Epidemic Model. Bulletin of Mathematical Biology. 84:66. 2022
- The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants. Journal of the Royal Society Interface. 19:20220173. 2022
- Incorporating nonlinearity with generalized functional responses to simulate multiple predator effects. PeerJ. 10:e13920-e13920. 2022
- Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa 2021
- Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada. BMC International Health and Human Rights. 21:706. 2021
- Modelling song popularity as a contagious process. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 477:20210457-20210457. 2021
- Transmission dynamics are crucial to COVID-19 vaccination policy. Proceedings of the National Academy of Sciences of the United States of America. 118:e2105878118. 2021
- Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants 2021
- pcoxtime: Penalized Cox Proportional Hazard Model for Time-dependent Covariates 2021
- Consequences of nest site selection vary along a tidal gradient. Journal of Animal Ecology. 90:528-541. 2021
- Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. Proceedings of the National Academy of Sciences of the United States of America. 118:e2011548118. 2021
- Short Communication: Sensitivity Analysis of an Integrated Climate-Economic Model. SIAM Journal on Financial Mathematics. 12:SC44-SC57. 2021
- Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software. 67:28684-28691. 2020
- Acceleration of plague outbreaks in the second pandemic. Proceedings of the National Academy of Sciences of the United States of America. 117:27703-27711. 2020
- Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada 2020
- Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. Journal of the Royal Society Interface. 17:20200144-20200144. 2020
- Correction to ‘Interactive effects of tree size, crown exposure and logging on drought-induced mortality’. Philosophical Transactions of the Royal Society of London. Biological Sciences. 375:20200085-20200085. 2020
- A Curious Possible Prime Pattern. Mathematics Magazine. 93:132-135. 2020
- A Note on Observation Processes in Epidemic Models. Bulletin of Mathematical Biology. 82:37. 2020
- Corrigendum to: Incorporating movement patterns to discern habitat selection: black bears as a case study. Wildlife Research. 47:359-359. 2020
- Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada. BMC International Health and Human Rights. 19:1237. 2019
- Predicting West Nile virus transmission in North American bird communities using phylogenetic mixed effects models and eBird citizen science data. Parasites and Vectors. 12:395. 2019
- Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. Wildlife Monographs. 203:3-35. 2019
- Statistical modeling of patterns in annual reproductive rates. Ecology. 100:e02706. 2019
- I can see clearly now: Reinterpreting statistical significance. Methods in Ecology and Evolution. 10:756-759. 2019
- Bridging the gap between theory and data: the Red Queen Hypothesis for sex 2019
- Incorporating movement patterns to discern habitat selection: black bears as a case study. Wildlife Research. 46:76-76. 2019
- Interactive effects of tree size, crown exposure and logging on drought-induced mortality. Philosophical Transactions of the Royal Society of London. Biological Sciences. 373:20180189-20180189. 2018
- Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models. Proceedings of the National Academy of Sciences of the United States of America. 115:E7892-E7893. 2018
- Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches. Statistical Methods in Medical Research. 27:1956-1967. 2018
- The evolutionary response of virulence to host heterogeneity: a general model with application to myxomatosis in rabbits co-infected with intestinal helminths. Aegyptus. 19:257-278. 2018
- Phenotypic traits and resource quality as factors affecting male reproductive success in a toadfish. Behavioral Ecology. 29:496-507. 2018
- Two approaches to forecast Ebola synthetic epidemics. Epidemics. 22:36-42. 2018
- Reply. Psychotherapy and Psychosomatics. 87:180-180. 2018
- Incorporating periodic variability in hidden Markov models for animal movement. Movement Ecology. 5:1. 2017
- Penetrance of Polygenic Obesity Susceptibility Loci across the Body Mass Index Distribution. American Journal of Human Genetics. 101:925-938. 2017
- glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling. R Journal. 9:378-378. 2017
- Effects of environmental factors and landscape features on movement patterns of Florida black bears. Journal of Mammalogy. 98:1463-1478. 2017
- Modeling zero-inflated count data with glmmTMB 2017
- Can existing data on West Nile virus infection in birds and mosquitos explain strain replacement?. Ecosphere. 8. 2017
- Effects of contact structure on the transient evolution of HIV virulence. PLoS Computational Biology. 13:e1005453-e1005453. 2017
- Fitting mechanistic epidemic models to data: a comparison of simple Markov chain Monte Carlo approaches 2017
- The Mortality and Myocardial Effects of Antidepressants Are Moderated by Preexisting Cardiovascular Disease: A Meta-Analysis. Psychotherapy and Psychosomatics. 86:268-282. 2017
- Multicopy gene family evolution on primate Y chromosomes. BMC Genomics. 17:157. 2016
- Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity. Ecosphere. 7. 2016
- Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity. Ecosphere. 7. 2016
- The New Statistics with R: An Introduction for Biologists. By Andy Hector. Oxford and New York: Oxford University Press. $125.00 (hardcover); $49.95 (paper). xi + 199 p.; ill.; index. ISBN: 978-0-19-872905-1 (hc); 978-0-19-872906-8 (pb). 2015.. Quarterly Review of Biology. 91:204-205. 2016
- Inverse estimation of integral projection model parameters using time series of population‐level data. Methods in Ecology and Evolution. 7:147-156. 2016
- Fates of trees damaged by logging in Amazonian Bolivia. Forest Ecology and Management. 357:50-59. 2015
- Evolutionary Stability of Minimal Mutation Rates in an Evo-epidemiological Model. Bulletin of Mathematical Biology. 77:1985-2003. 2015
- Fitting Linear Mixed-Effects Models Using lme4 2015
- Moving Beyond Too Little, Too Late: Managing Emerging Infectious Diseases in Wild Populations Requires International Policy and Partnerships. EcoHealth. 12:404-407. 2015
- Context‐dependent conservation responses to emerging wildlife diseases. Frontiers in Ecology and the Environment. 13:195-202. 2015
- Diet and cannibalism in plainfin midshipmanPorichthys notatus. Journal of Fish Biology. 86:1396-1415. 2015
- Hidden semi‐Markov models reveal multiphasic movement of the endangered Florida panther. Journal of Animal Ecology. 84:576-585. 2015
- A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects. PeerJ. 3:e1226-e1226. 2015
- Erratum to: Persistence of an invasive fish (Neogobius melanostomus) in a contaminated ecosystem. Biological Invasions. 16:2463-2463. 2014
- Persistence of an invasive fish (Neogobius melanostomus) in a contaminated ecosystem. Biological Invasions. 16:2449-2461. 2014
- Population-level effects of suppressing fever. Proceedings of the Royal Society of London. Biological Sciences. 281:20132570-20132570. 2014
- A general mathematical framework for the analysis of spatiotemporal point processes. Theoretical Ecology. 7:101-113. 2014
- Comparing population level sexual selection in a species with alternative reproductive tactics. Behavioral Ecology. 25:1524-1533. 2014
- Estimating Initial Epidemic Growth Rates. Bulletin of Mathematical Biology. 76:245-260. 2014
- Interspecific Dominance Via Vocal Interactions Mediates Altitudinal Zonation in Neotropical Singing Mice. The American Naturalist. 182:E161-E173. 2013
- Testing an autonomous acoustic telemetry positioning system for fine-scale space use in marine animals. Journal of Experimental Marine Biology and Ecology. 448:46-56. 2013
- Tundra ecosystems observed to be CO₂sources due to differential amplification of the carbon cycle. Ecology Letters. 16:1307-1315. 2013
- Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution. 4:501-512. 2013
- Translating Probability Density Functions: From R to BUGS and Back Again. R Journal. 5:207-207. 2013
- Gag (Mycteroperca microlepis) space-use correlations with landscape structure and environmental conditions. Journal of Experimental Marine Biology and Ecology. 443:1-11. 2013
- Predator density and timing of arrival affect reef fish community assembly. Ecology. 94:1057-1068. 2013
- Predator density and competition modify the benefits of group formation in a shoaling reef fish. Oikos. 122:171-178. 2013
- A Method for Detecting Positive Growth Autocorrelation without Marking Individuals. PLoS ONE. 8:e76389-e76389. 2013
- Virulence evolution in a host-parasite system in the absence of viral evolution.. Evolutionary Ecology Research. 15:883-901. 2013
- Multiple defender effects: synergistic coral defense by mutualist crustaceans. Oecologia. 169:1095-1103. 2012
- Experimental manipulation of seed shadows of an Afrotropical tree determines drivers of recruitment. Ecology. 93:500-510. 2012
- Incorporating spatial heterogeneity created by permafrost thaw into a landscape carbon estimate. Journal of Geophysical Research. 117. 2012
- Fire‐induced tree mortality in a neotropical forest: the roles of bark traits, tree size, wood density and fire behavior. Global Change Biology. 18:630-641. 2012
- Does genetic introgression improve female reproductive performance? A test on the endangered Florida panther. Oecologia. 168:289-300. 2012
- BISTABILITY AND LONG-TERM CURE IN A WITHIN-HOST MODEL OF HEPATITIS C. Journal of Biological Systems. 19:533-550. 2011
- Food Availability Alters the Effects of Larval Temperature on Aedes aegypti Growth. Journal of Medical Entomology. 48:974-984. 2011
- Decoupling the effects of logging and hunting on an Afrotropical animal community. Ecological Applications. 21:1819-1836. 2011
- Predicting Predation through Prey Ontogeny Using Size-Dependent Functional Response Models. The American Naturalist. 177:752-766. 2011
- Predicting local population distributions around a central shelter based on a predation risk-growth trade-off. Ecological Modelling. 222:1448-1455. 2011
- The prevalence and persistence of sigma virus, a biparentally transmitted parasite of Drosophila melanogaster.. Evolutionary Ecology Research. 13:323-345. 2011
- Benefits for Plants in Ant-Plant Protective Mutualisms: A Meta-Analysis. PLoS ONE. 5:e14308-e14308. 2010
- Effects of colonization asymmetries on metapopulation persistence. Theoretical Population Biology. 78:225-238. 2010
- Dispersers shape fruit diversity in Ficus (Moraceae). Proceedings of the National Academy of Sciences of the United States of America. 107:14668-14672. 2010
- Transient virulence of emerging pathogens. Journal of the Royal Society Interface. 7:811-822. 2010
- A Disease-Mediated Trophic Cascade in the Serengeti and its Implications for Ecosystem C. PLoS Biology. 7:e1000210-e1000210. 2009
- Learning hierarchical models: advice for the rest of us. Ecological Applications. 19:588-592. 2009
- Stem responses to damage: the evolutionary ecology of Quercus species in contrasting fire regimes. New Phytologist. 182:261-271. 2009
- Upper respiratory tract disease, force of infection, and effects on survival of gopher tortoises. Ecological Applications. 19:786-798. 2009
- Generalized linear mixed models: a practical guide for ecology and evolution. Trends in Ecology and Evolution. 24:127-135. 2009
- Effects of Sample Size on Estimates of Population Growth Rates Calculated with Matrix Models. PLoS ONE. 3:e3080-e3080. 2008
- A cross‐system synthesis of consumer and nutrient resource control on producer biomass. Ecology Letters. 11:740-755. 2008
- Modelling long‐distance seed dispersal in heterogeneous landscapes. Journal of Ecology. 96:599-608. 2008
- Trait‐mediated interactions: influence of prey size, density and experience. Journal of Animal Ecology. 77:478-486. 2008
- Effects of stem anatomical and structural traits on responses to stem damage: an experimental study in the Bolivian Amazon. Canadian Journal of Forest Research. 38:611-618. 2008
- Disease as a selective force precluding widespread cannibalism: A case study of an iridovirus of tiger salamanders, Ambystoma tigrinum (Evolutionary Ecology Research (2008) 10, 1, (105-128)). Evolutionary Ecology Research. 10:309. 2008
- Disease as a selective force precluding widespread cannibalism: a case study of an iridovirus of tiger salamanders, Ambystoma tigrinum (vol 10, pg 105, 2008). Evolutionary Ecology Research. 10:309-309. 2008
- Vaccine-induced pathogen strain replacement: what are the mechanisms?. Journal of the Royal Society Interface. 5:3-13. 2008
- Asymptotic profiles of the steady states for an SIS epidemic reaction-diffusion model. Discrete and Continuous Dynamical Systems. Series A. 21:1-20. 2008
- Disease as a selective force precluding widespread cannibalism:: a case study of an iridovirus of tiger salamanders, Ambystoma tigrinum. Evolutionary Ecology Research. 10:105-128. 2008
- Disturbance, invasion and re‐invasion: managing the weed‐shaped hole in disturbed ecosystems. Ecology Letters. 10:809-817. 2007
- Plants as Reef Fish: Fitting the Functional Form of Seedling Recruitment. The American Naturalist. 170:167-183. 2007
- On quantitative measures of indirect interactions. Ecology Letters. 10:264-271. 2007
- Incorporating multiple mixed stocks in mixed stock analysis: ‘many‐to‐many’ analyses. Molecular Ecology. 16:685-695. 2007
- Asymptotic Profiles of the Steady States for an SIS Epidemic Patch Model. SIAM Journal on Applied Mathematics. 67:1283-1309. 2007
- The Impact of the Allee Effect in Dispersal and Patch-Occupancy Age on the Dynamics of Metapopulations. Bulletin of Mathematical Biology. 69:135-156. 2007
- Evaluation of density-dependent processes and green turtle Chelonia mydas hatchling production at Tortuguero, Costa Rica. Marine Ecology Progress Series. 326:283-293. 2006
- Size correction: comparing morphological traits among populations and environments. Oecologia. 148:547-554. 2006
- Are Fluctuating Asymmetry Studies Adequately Sampled? Implications of a New Model for Size Distribution. The American Naturalist. 167:230-245. 2006
- Parasite establishment and host extinction in model communities. Oikos. 111:501-513. 2005
- Landscape Corridors: Possible Dangers?. Science. 310:779-783. 2005
- Landscape corridors: Possible dangers? Response. Science. 310:781-+. 2005
- COMPARATIVE SEED SHADOWS OF BIRD-, MONKEY-, AND WIND-DISPERSED TREES. Ecology. 86:2684-2694. 2005
- Intraspecific application of the mid‐domain effect model: spatial and temporal nest distributions of green turtles, Chelonia mydas, at Tortuguero, Costa Rica. Ecology Letters. 8:918-924. 2005
- Effects of Landscape Corridors on Seed Dispersal by Birds. Science. 309:146-148. 2005
- COMPENSATORY LARVAL RESPONSES SHIFT TRADE-OFFS ASSOCIATED WITH PREDATOR-INDUCED HATCHING PLASTICITY. Ecology. 86:1580-1591. 2005
- COMBINING GENETIC AND ECOLOGICAL DATA TO ESTIMATE SEA TURTLE ORIGINS. Ecological Applications. 15:315-325. 2005
- SPATIAL SIGNATURE OF ENVIRONMENTAL HETEROGENEITY, DISPERSAL, AND COMPETITION IN SUCCESSIONAL GRASSLANDS. Ecological Monographs. 75:199-214. 2005
- Mechanisms of disease‐induced extinction. Ecology Letters. 8:117-126. 2005
- Other People's Data. BioScience. 55:550-550. 2005
- Quantitative Bioscience for the 21st Century. BioScience. 55:511-511. 2005
- Natal homing in juvenile loggerhead turtles (Caretta caretta). Molecular Ecology. 13:3797-3808. 2004
- Uncertain climate thresholds and optimal economic growth. Journal of Environmental Economics and Management. 48:723-741. 2004
- The effects of disease dispersal and host clustering on the epidemic threshold in plants. Bulletin of Mathematical Biology. 66:341-371. 2004
- A smorgasbord of stochastic dynamics. Trends in Ecology and Evolution. 19:11-11. 2004
- Combining endogenous and exogenous spatial variability in analytical population models. Theoretical Population Biology. 64:255-270. 2003
- Spatial Dynamics in Model Plant Communities: What Do We Really Know?. The American Naturalist. 162:135-148. 2003
- SEA TURTLE STOCK ESTIMATION USING GENETIC MARKERS: ACCOUNTING FOR SAMPLING ERROR OF RARE GENOTYPES. Ecological Applications. 13:763-775. 2003
- CONNECTING THEORETICAL AND EMPIRICAL STUDIES OF TRAIT-MEDIATED INTERACTIONS. Ecology. 84:1101-1114. 2003
- Testing performance rank reversals among coexisting species: crossover point irradiance analysis. Functional Ecology. 17:276-281. 2003
- Canonical functions for dispersal-induced synchrony. Proceedings of the Royal Society of London. Biological Sciences. 267:1787-1794. 2000
- A Simple Model for Complex Dynamical Transitions in Epidemics. Science. 287:667-670. 2000
- Analytic Models for the Patchy Spread of Plant Disease. Bulletin of Mathematical Biology. 61:849-874. 1999
- Spatial Moment Equations for Plant Competition: Understanding Spatial Strategies and the Advantages of Short Dispersal. The American Naturalist. 153:575-602. 1999
- Book Reviews. Bulletin of Mathematical Biology. 61:597-600. 1999
- Cities and villages: infection hierarchies in a measles metapopulation. Ecology Letters. 1:63-70. 1998
- LINEAR ANALYSIS OF SOIL DECOMPOSITION: INSIGHTS FROM THE CENTURY MODEL. Ecological Applications. 8:425-439. 1998
- Linear Analysis of Soil Decomposition: Insights from the Century Model. Ecological Applications. 8:425-425. 1998
- Using Moment Equations to Understand Stochastically Driven Spatial Pattern Formation in Ecological Systems. Theoretical Population Biology. 52:179-197. 1997
- Modeling Juror Decay in a High Profile Criminal Trial. Math Horizons. 5:12-16. 1997
- Individual-based modelling: what is the difference?. Trends in Ecology and Evolution. 12:111-111. 1997
- Impact of vaccination on the spatial correlation and persistence of measles dynamics.. Proceedings of the National Academy of Sciences of the United States of America. 93:12648-12653. 1996
- Species diversity and ecosystem response to carbon dioxide fertilization: conclusions from a temperate forest model. Global Change Biology. 1:373-381. 1995
- Spatial heterogeneity, nonlinear dynamics and chaos in infectious diseases. Statistical Methods in Medical Research. 4:160-183. 1995
- Space, persistence and dynamics of measles epidemics. Philosophical Transactions of the Royal Society of London. Biological Sciences. 348:309-320. 1995
- Seasonality and extinction in chaotic metapopulations. Proceedings of the Royal Society of London. Biological Sciences. 259:97-103. 1995
- Measles as a case study in nonlinear forecasting and chaos. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 348:515-530. 1994
- Measles as a case study in nonlinear forecasting and chaos. Philosophical Transactions - Royal Society of London, A. 348:497-514. 1994
- Chaos and biological complexity in measles dynamics. Proceedings of the Royal Society of London. Biological Sciences. 251:75-81. 1993
- Chaos and complexity in measles models: A comparative numerical study. Mathematical Medicine and Biology. 10:83-95. 1993
- DETERMINATION OF THE SURFACE TO VOLUME RATIO IN HOMES FROM MEASUREMENTS OF RADON AND ITS PROGENY. Radiation Protection Dosimetry. 42:121-126. 1992
- ROYAL-STATISTICAL-SOCIETY MEETING ON CHAOS - DISCUSSION. Journal of The Royal Statistical Society Series B-statistical Methodology. 54:451-474. 1992
- Collective behavior of a coupled-map system with a conserved quantity. Physical Review A (PRA). 44:4923-4936. 1991
preprints