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Abstract Reliable predictions of ectotherm responses to climatic warming are important because many of these organisms perform important roles that can directly impact human society.Thermal performance curves (TPCs) provide useful information on the physiological constraints that limit the capacity of these temperature‐sensitive organisms to exist and grow.NLS pipelines for fitting TPCs are widely available, but these approaches rely on assumptions that can yield unreliable parameter estimates.We presentbayesTPC, anRpackage for fitting TPCs to trait responses using thenimblelanguage and machinery as the underlying engine for Markov Chain Monte Carlo.bayesTPCaims to support the adoption of Bayesian approaches in thermal physiology, and promote TPC fitting that adequately quantifies uncertainty. 

Abstract The interactions of environmental, geographic, socio-demographic, and epidemiological factors in shaping mosquito-borne disease transmission dynamics are complex and changeable, influencing the abundance and distribution of vectors and the pathogens they transmit. In this study, 27 years of cross-sectional malaria survey data (1990–2017) were used to examine the effects of these factors onPlasmodium falciparumandPlasmodium vivaxmalaria presence at the community level in Africa and Asia. Monthly long-term, open-source data for each factor were compiled and analyzed using generalized linear models and classification and regression trees. Both temperature and precipitation exhibited unimodal relationships with malaria, with a positive effect up to a point after which a negative effect was observed as temperature and precipitation increased. Overall decline in malaria from 2000 to 2012 was well captured by the models, as was the resurgence after that. The models also indicated higher malaria in regions with lower economic and development indicators. Malaria is driven by a combination of environmental, geographic, socioeconomic, and epidemiological factors, and in this study, we demonstrated two approaches to capturing this complexity of drivers within models. Identifying these key drivers, and describing their associations with malaria, provides key information to inform planning and prevention strategies and interventions to reduce malaria burden. 

Abstract BackgroundAnopheles stephensiis a malaria-transmitting mosquito that has recently expanded from its primary range in Asia and the Middle East, to locations in Africa. This species is a competent vector of bothPlasmodium falciparumandPlasmodium vivaxmalaria. Perhaps most alarming, the characteristics ofAn.stephensi, such as container breeding and anthropophily, make it particularly adept at exploiting built environments in areas with no prior history of malaria risk. MethodsIn this paper, global maps of thermal transmission suitability and people at risk (PAR) for malaria transmission byAn.stephensiwere created, under current and future climate. Temperature-dependent transmission suitability thresholds derived from recently published species-specific thermal curves were used to threshold gridded, monthly mean temperatures under current and future climatic conditions. These temperature driven transmission models were coupled with gridded population data for 2020 and 2050, under climate-matched scenarios for future outcomes, to compare with baseline predictions for 2020 populations. ResultsUsing the Global Burden of Disease regions approach revealed that heterogenous regional increases and decreases in risk did not mask the overall pattern of massive increases of PAR for malaria transmission suitability withAn.stephensipresence. General patterns of poleward expansion for thermal suitability were seen for bothP.falciparumandP.vivaxtransmission potential. ConclusionsUnderstanding the potential suitability forAn.stephensitransmission in a changing climate provides a key tool for planning, given an ongoing invasion and expansion of the vector. Anticipating the potential impact of onward expansion to transmission suitable areas, and the size of population at risk under future climate scenarios, and where they occur, can serve as a large-scale call for attention, planning, and monitoring. 

Abstract In ecology, it is common for processes to be bounded based on physical constraints of the system. One common example is the positivity constraint, which applies to phenomena such as duration times, population sizes, and total stock of a system’s commodity. In this paper, we propose a novel method for parameterizing Lognormal state space models using an approach based on moment matching. Our method enforces the positivity constraint, allows for arbitrary mean evolution and variance structure, and has a closed-form Markov transition density which allows for more flexibility in fitting techniques. We discuss two existing Lognormal state space models and examine how they differ from the method presented here. We use 180 synthetic datasets to compare the forecasting performance under model misspecification and assess the estimation of precision parameters between our method and existing methods. We find that our models perform well under misspecification, and that fixing the observation variance both helps to improve estimation of the process variance and improves forecast performance. To test our method on a difficult problem, we compare the predictive performance of two Lognormal state space models in predicting the Leaf Area Index over a 151 day horizon by using a process-based ecosystem model to describe the temporal dynamics. We find that our moment matching model performs better than its competitor, and is better suited for intermediate predictive horizons. Overall, our study helps to inform practitioners about the importance of incorporating sensible dynamics when using models of complex systems to predict out-of-sample. 

Abstract Hierarchical probability models are being used more often than non-hierarchical deterministic process models in environmental prediction and forecasting, and Bayesian approaches to fitting such models are becoming increasingly popular. In particular, models describing ecosystem dynamics with multiple states that are autoregressive at each step in time can be treated as statistical state space models (SSMs). In this paper, we examine this subset of ecosystem models, embed a process-based ecosystem model into an SSM, and give closed form Gibbs sampling updates for latent states and process precision parameters when process and observation errors are normally distributed. Here, we use simulated data from an example model (DALECev) and study the effects changing the temporal resolution of observations on the states (observation data gaps), the temporal resolution of the state process (model time step), and the level of aggregation of observations on fluxes (measurements of transfer rates on the state process). We show that parameter estimates become unreliable as temporal gaps between observed state data increase. To improve parameter estimates, we introduce a method of tuning the time resolution of the latent states while still using higher-frequency driver information and show that this helps to improve estimates. Further, we show that data cloning is a suitable method for assessing parameter identifiability in this class of models. Overall, our study helps inform the application of state space models to ecological forecasting applications where (1) data are not available for all states and transfers at the operational time step for the ecosystem model and (2) process uncertainty estimation is desired.