Benjamin M Bolker

Benjamin M Bolker
McMaster University | McMaster · Department of Mathematics and Statistics

About

126
Publications
42,773
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12,129
Citations
Citations since 2016
37 Research Items
6344 Citations
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Publications

Publications (126)
Preprint
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Maruotti et al. 2022 used a mark-recapture approach to estimate bounds on the true number of monkeypox infections in various countries. These approaches are fundamentally flawed; it is impossible to estimate undercounting based solely on a single stream of reported cases. Simulations based on a Richards curve for cumulative incidence show that, for...
Article
Full-text available
Predicting the combined effects of predators on shared prey has long been a focus of community ecology, yet quantitative predictions often fail. Failure to account for nonlinearity is one reason for this. Moreover, prey depletion in multiple predator effects (MPE) studies generates biased predictions in applications of common experimental and quant...
Preprint
The Cox proportional hazard model is commonly used in evaluating risk factors in cancer survival data. The model assumes an additive, linear relationship between the risk factors and the log hazard. However, this assumption may be too simplistic. Further, failure to take time-varying covariates into account, if present, may lower prediction accurac...
Article
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Testing individuals for pathogens can affect the spread of epidemics. Understanding how individual-level processes of sampling and reporting test results can affect community- or population-level spread is a dynamical modeling question. The effect of testing processes on epidemic dynamics depends on factors underlying implementation, particularly t...
Article
Inferring the relative strength (i.e. the ratio of reproduction numbers) and relative speed (i.e. the difference between growth rates) of new SARS-CoV-2 variants is critical to predicting and controlling the course of the current pandemic. Analyses of new variants have primarily focused on characterizing changes in the proportion of new variants, i...
Preprint
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A new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), has been identified based on genomic sequencing and epidemiological data in South Africa. Presumptive Omicron cases in South Africa have grown extremely rapidly, despite high prior exposure and moderate vaccination coverage. The available evidence suggests that Omicron spread is at least in...
Article
Popular songs are often said to be ‘contagious’, ‘infectious’ or ‘viral’. We find that download count time series for many popular songs resemble infectious disease epidemic curves. This paper suggests infectious disease transmission models could help clarify mechanisms that contribute to the ‘spread’ of song preferences and how these mechanisms un...
Preprint
Full-text available
1 Abstract Testing individuals for pathogens can affect the spread of epidemics. Understanding how individual-level processes of sampling and reporting test results can affect community-or population-level spread is a dynamical modeling question. The effect of testing processes on epidemic dynamics depends on factors underlying implementation, part...
Preprint
Full-text available
Inferring the relative strength (i.e., the ratio of reproduction numbers, ℛ var /ℛ wt ) and relative speed (i.e., the difference between growth rates, r var − r wt ) of new SARS-CoV-2 variants compared to their wild types is critical to predicting and controlling the course of the current pandemic. Multiple studies have estimated the relative stren...
Article
Full-text available
Background Patient age is one of the most salient clinical indicators of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reve...
Article
1. Parents providing care must sometimes choose between rearing locations that are most favourable for offspring versus those that are most favourable for them- selves. Here, we measured how both parental and offspring performance varied in nest sites distributed along an environmental gradient. 2. The plainfin midshipman fish Porichthys notatus n...
Article
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Significance The generation and serial interval distributions are key, but different, quantities in outbreak analyses. Recent studies suggest that the two distributions give different estimates of the reproduction number R as inferred from the observed growth rate r . Here, we show that estimating R based on r and the serial interval distribution,...
Preprint
Full-text available
Background: Patient age is the most salient clinical indicator of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reveal sour...
Article
Full-text available
Significance Epidemics of plague devastated Europe’s population throughout the Medieval and Renaissance periods. Genetic studies of modest numbers of skeletal remains indicate that the causative agent of all these epidemics was the bacterium Yersinia pestis , but such analyses cannot identify overall patterns of transmission dynamics. Analysis of t...
Preprint
Background Patient age is the most salient clinical indicator of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reveal sourc...
Article
Full-text available
A novel coronavirus (SARS-CoV-2) emerged as a global threat in December 2019. As the epidemic progresses, disease modellers continue to focus on estimating the basic reproductive number R 0 —the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of R 0...
Preprint
Full-text available
The reproduction number ℛ and the growth rate r are critical epidemiological quantities. They are linked by generation intervals, the time between infection and onward transmission. Because generation intervals are difficult to observe, epidemiologists often substitute serial intervals, the time between symptom onset in successive links in a transm...
Article
Many disease models focus on characterizing the underlying transmission mechanism but make simple, possibly naive assumptions about how infections are reported. In this note, we use a simple deterministic Susceptible-Infected-Removed (SIR) model to compare two common assumptions about disease incidence reports: Individuals can report their infectio...
Article
Full-text available
Context Animals' use of space and habitat selection emerges from their movement patterns, which are, in turn, determined by their behavioural or physiological states and extrinsic factors. Aim The aims of the present study were to investigate animal movement and incorporate the movement patterns into habitat selection analyses using Global Position...
Preprint
Full-text available
Many disease models focus on characterizing the underlying transmission mechanism but make simple, possibly naive assumptions about how infections are reported. In this note, we use a simple deterministic Susceptible-Infected-Removed (SIR) model to compare two common assumptions about disease incidence reports: individuals can report their infectio...
Article
Full-text available
Background: Mathematical and statistical models are used to project the future time course of infectious disease epidemics and the expected future burden on health care systems and economies. Influenza is a particularly important disease in this context because it causes annual epidemics and occasional pandemics. In order to forecast health care u...
Article
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Background: West Nile virus (WNV) is a mosquito-transmitted disease of birds that has caused bird population declines and can spill over into human populations. Previous research has identified bird species that infect a large fraction of the total pool of infected mosquitoes and correlate with human infection risk; however, these analyses cover s...
Article
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Abundant evidence supports the benefits accrued to the Florida panther (Puma concolor coryi) population via the genetic introgression project implemented in South Florida, USA, in 1995. Since then, genetic diversity has improved, the frequency of morphological and biomedical correlates of inbreeding depression have declined, and the population size...
Preprint
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Sexual reproduction persists in nature despite its large cost. The Red Queen Hypothesis postulates that parasite pressure maintains sexual reproduction in the host population by selecting for the ability to produce rare genotypes that are resistant to infection. Mathematical models have been used to lay theoretical foundations for the hypothesis; e...
Article
Reproduction by individuals is typically recorded as count data (e.g. number of fledglings from a nest or inflorescences on a plant) and commonly modeled using Poisson or negative binomial distributions, which assume that variance is greater than or equal to the mean. However, distributions of reproductive effort are often underdispersed (i.e., var...
Article
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1.Null hypothesis significance testing (NHST) remains popular despite decades of concern about misuse and misinterpretation. There are many recent suggestions for mitigating problems arising from NHST, including calls for abandoning NHST in favor of Bayesian or information‐theoretic approaches. We believe that NHST will continue to be widely used,...
Article
Full-text available
Context Animals’ use of space and habitat selection emerges from their movement patterns, which are, in turn, determined by their behavioural or physiological states and extrinsic factors. Aim The aims of the present study were to investigate animal movement and incorporate the movement patterns into habitat selection analyses using Global Position...
Preprint
Full-text available
Null hypothesis significance testing remains popular despite decades of concern about misuse and misinterpretation. We believe that much of the problem is due to language: significance testing has little to do with other meanings of the word "significance". Despite the limitations of null-hypothesis tests, we argue here that they remain useful in m...
Article
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Simple mechanistic epidemic models are widely used for forecasting and parameter estimation of infectious diseases based on noisy case reporting data. Despite the widespread application of models to emerging infectious diseases, we know little about the comparative performance of standard computational-statistical frameworks in these contexts. Here...
Data
Supplemental material for Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches
Article
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We reply to Rosenblat, Smith & McIntyre, who critiqued our paper, "The mortality and myocardial effects of antidepressants are moderated by preexisting cardiovascular disease: a meta-analysis", published in Psychotherapy and Psychosomatics, 2017; 268-282.
Preprint
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Ecological phenomena are often measured in the form of count data. These data can be analyzed using generalized linear mixed models (GLMMs) when observations are correlated in ways that require random effects. However, count data are often zero-inflated , containing more zeros than would be expected from the standard error distributions used in GLM...
Article
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Background Clustering time-series data into discrete groups can improve prediction and provide insight into the nature of underlying, unobservable states of the system. However, temporal variation in probabilities of group occupancy, or the rates at which individuals move between groups, can obscure such signals. We use finite mixture and hidden Ma...
Conference Paper
Full-text available
Section 1: Background/Question/Methods Adaptive management requires for population viability analyses (PVAs) to be updated and reevaluated as conservation strategies are implemented, changes in the population or the environment occur, and new demographic data become available. The Florida panther (Puma concolor coryi) population has been monitored...
Article
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Emerging infectious diseases pose an important threat to wildlife. While established protocols exist for combating outbreaks of human and agricultural pathogens, appropriate management actions before, during, and after the invasion of wildlife pathogens have not been developed. We describe stage-specific goals and management actions that minimize d...
Article
The macroscopic and microscopic diversity of potential food items available in the nests of plainfin midshipman Porichthys notatus were quantified and compared with items that were found in the stomach and intestine (digestive tract) of the guarding males. In this species, males occur as one of two possible reproductive morphs: guarder males that c...
Article
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The description of a species’ mating patterns is often based on observations from a single exemplar population; however, environmental variation can lead to variation in mating patterns and to differences in the strength of sexual selection among populations. In this study, we explored how resource distribution across a species’ range affects compe...
Article
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Erratum to: Biol Invasions DOI 10.1007/s10530-014-0677-2Unfortunately, in the original publication one of the authors, Julie R. Marentette, has been misspelled as “Julie R. Marenette”. The correct version of the author name is provided in this erratum.
Article
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Post-establishment dynamics of invasive species have been under-studied. However, understanding these dynamics is particularly important for the management of invasive species known to impact native communities. Following the invasion of a highly invasive species, the round goby (Neogobius melanostomus), we document long-term population changes aft...
Article
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Emerging infectious diseases (EIDs) are on the rise due to multiple factors, including human facilitated movement of pathogens, broad-scale landscape changes, and perturbations to ecological systems (Jones et al. 2008; Fisher et al. 2012). Epidemics in wildlife are problematic because they can lead to pathogen spillover to new host organisms, erode...
Article
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Animals must move to find food and mates, and to avoid predators; movement thus influences survival and reproduction, and ultimately determines fitness. Precise description of movement and understanding of spatial and temporal patterns as well as relationships with intrinsic and extrinsic factors is important both for theoretical and applied reason...
Article
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Question: How does virulence evolve in the Drosophila melanogaster/sigma virus (DMelSV) system? Organisms: Drosophila melanogaster (host) and DMelSV (parasite). Empirical methods: Artificial selection on whole-carcass viral titre of infected flies, including two selection regimes (maternal and biparental transmission) and three treatments with...
Article
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Spatial and stochastic models are often straightforward to simulate but difficult to analyze mathematically. Most of the mathematical methods available for nonlinear stochastic and spatial models are based on heuristic rather than mathematically justified assumptions, so that, e.g., the choice of the moment closure can be considered more of an art...
Article
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Fever is commonly attenuated with antipyretic medication as a means to treat unpleasant symptoms of infectious diseases. We highlight a potentially important negative effect of fever suppression that becomes evident at the population level: reducing fever may increase transmission of associated infections. A higher transmission rate implies that a...
Code
https://cran.r-project.org/package=DescTools
Article
The initial exponential growth rate of an epidemic is an important measure of disease spread, and is commonly used to infer the basic reproduction number [Formula: see text]. While modern techniques (e.g., MCMC and particle filtering) for parameter estimation of mechanistic models have gained popularity, maximum likelihood fitting of phenomenologic...
Article
Abstract Interspecific aggression between ecologically similar species may influence geographic limits by mediating competitive exclusion at the range edge. Advertisement signals that mediate competitive interactions within species may also provide social information that contributes to behavioral dominance and spatial segregation among species. We...
Article
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In most ecological studies, within-group variation is a nuisance that obscures patterns of interest and reduces statistical power. However, patterns of within-group variability often contain information about ecological processes. In particular, such patterns can be used to detect positive growth autocorrelation (consistent variation in growth rate...
Article
We tested the capabilities and limitations of a novel autonomous acoustic positioning telemetry system with data from fifteen field deployments off the Florida coast. Telemetry array coverage areas ranged between 100 and 300 m across. For fixed transmitters within the array, the fraction of transmissions leading to high-quality calculated position...
Article
Are tundra ecosystems currently a carbon source or sink? What is the future trajectory of tundra carbon fluxes in response to climate change? These questions are of global importance because of the vast quantities of organic carbon stored in permafrost soils. In this meta-analysis, we compile 40 years of CO2 flux observations from 54 studies spanni...
Article
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1. Ecologists often use nonlinear fitting techniques to estimate the parameters of complex ecological models, with attendant frustration. This paper compares three open-source model fitting tools and discusses general strategies for defining and fitting models. 2. R is convenient and (relatively) easy to learn, AD Model Builder is fast and robust b...
Article
To explore variation in space use under different environmental conditions, we acoustically tagged gag (Mycteroperca microlepis) established on experimental artificial reefs in the Gulf of Mexico and used an acoustic positioning array to record animal positions during the winters of 2007 and 2008. From side-scan sonar imagery, we created a categori...
Article
Full-text available
Most empirical studies of predation use simple experimental approaches to quantify the effects of predators on prey (e.g., using constant densities of predators, such as ambient vs. zero). However, predator densities vary in time, and these effects may not be well represented by studies that use constant predator densities. Although studies have in...
Data
Synthesis Predation risk experienced by individuals living in groups depends on the balance between predator dilution, competition for refuges, and predator interference or synergy. These interactions operate between prey species as well: the benefits of group living decline in the presence of an alternative prey species. We apply a novel model-fit...
Article
The future carbon balance of high-latitude ecosystems is dependent on the sensitivity of biological processes (photosynthesis and respiration) to the physical changes occurring with permafrost thaw. Predicting C exchange in these ecosystems is difficult because the thawing of permafrost is a heterogeneous process that creates a complex landscape. W...
Article
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The majority of our understanding of mutualisms comes from studies of pairwise interactions. However, many hosts support mutualist guilds, and interactions among mutualists make the prediction of aggregate effects difficult. Here, we apply a factorial experiment to interactions of 'guard' crustaceans that defend their coral host from seastar predat...
Article
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Genetic introgression has been suggested as a management tool for mitigating detrimental effects of inbreeding depression, but the role of introgression in species conservation has been controversial, partly because population-level impacts of genetic introgressions are not well understood. Concerns about potential inbreeding depression in the enda...