Showing papers by "Benjamin M. Bolker published in 2023"

The role of fire in terrestrial vertebrate richness patterns.

Abstract: Productivity is strongly associated with terrestrial species richness patterns, although the mechanisms underpinning such patterns have long been debated. Despite considerable consumption of primary productivity by fire, its influence on global diversity has received relatively little study. Here we examine the sensitivity of terrestrial vertebrate biodiversity (amphibians, birds and mammals) to fire, while accounting for other drivers. We analyse global data on terrestrial vertebrate richness, net primary productivity, fire occurrence (fraction of productivity consumed) and additional influences unrelated to productivity (i.e., historical phylogenetic and area effects) on species richness. For birds, fire is associated with higher diversity, rivalling the effects of productivity on richness, and for mammals, fire's positive association with diversity is even stronger than productivity; for amphibians, in contrast, there are few clear associations. Our findings suggest an underappreciated role for fire in the generation of animal species richness and the conservation of global biodiversity.

Comparing machine learning approaches to incorporate time-varying covariates in predicting cancer survival time

Abstract: The Cox proportional hazards 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 accuracy. In this retrospective, population-based, prognostic study of data from patients diagnosed with cancer from 2008 to 2015 in Ontario, Canada, we applied machine learning-based time-to-event prediction methods and compared their predictive performance in two sets of analyses: (1) yearly-cohort-based time-invariant and (2) fully time-varying covariates analysis. Machine learning-based methods-gradient boosting model (gbm), random survival forest (rsf), elastic net (enet), lasso and ridge-were compared to the traditional Cox proportional hazards (coxph) model and the prior study which used the yearly-cohort-based time-invariant analysis. Using Harrell's C index as our primary measure, we found that using both machine learning techniques and incorporating time-dependent covariates can improve predictive performance. Gradient boosting machine showed the best performance on test data in both time-invariant and time-varying covariates analysis.

Toward a comprehensive system for constructing compartmental epidemic models

Abstract: Compartmental models are valuable tools for investigating infectious diseases. Researchers building such models typically begin with a simple structure where compartments correspond to individuals with different epidemiological statuses, e.g., the classic SIR model which splits the population into susceptible, infected, and recovered compartments. However, as more information about a specific pathogen is discovered, or as a means to investigate the effects of heterogeneities, it becomes useful to stratify models further -- for example by age, geographic location, or pathogen strain. The operation of constructing stratified compartmental models from a pair of simpler models resembles the Cartesian product used in graph theory, but several key differences complicate matters. In this article we give explicit mathematical definitions for several so-called ``model products'' and provide examples where each is suitable. We also provide examples of model stratification where no existing model product will generate the desired result.