In ecological studies, the goal is often to describe and gain further insight into ecological processes underlying the data collected during observational studies. Because of the nature of observational data, it can often be difficult to separate the variation in the data from the underlying process or `state dynamics.' In order to better address this issue, it is becoming increasingly common for researchers to use hierarchical models. Hierarchical spatial, temporal, and spatio-temporal models allow for the simultaneous modeling of both first and second order processes, thus accounting for underlying autocorrelation in the system while still providing insight into overall spatial and temporal pattern. In this particular study, I use two species of interest, the lesser and greater scaup (Aythya affnis and Aythya marila), as an example of how hierarchical models can be utilized in wildlife management studies. Scaup are the most abundant and widespread diving duck in North America, and are important game species. Since 1978, the continental population of scaup has declined to levels that are 16% below the 1955-2010 average and 34% below the North American Waterfowl Management Plan goal. The greatest decline in abundance of scaup appears to be occurring in the western boreal forest, where populations may have depressed rates of reproductive success, survival, or both. In order to better understand the causes of the decline, and better understand the biology of scaup in general, a level of high importance has been placed on retrospective analyses that determine the spatial and temporal changes in population abundance. In order to implement Bayesian hierarchical models, I used a method called Integrated Nested Laplace Approximation (INLA) to approximate the posterior marginal distribution of the parameters of interest, rather than the more common Markov Chain Monte Carlo (MCMC) approach. Based on preliminary analysis, the data appeared to be overdispersed, containing a disproportionately high number of zeros along with a high variance relative to the mean. Thus, I considered two potential data models, the negative binomial and the zero-inflated negative binomial. Of these models, the zero-inflated negative binomial had the lowest DIC, thus inference was based on this model. Results from this model indicated that a large proportion of the strata were not decreasing (i.e., the estimated slope of the parameter was not significantly different from zero). However, there were important exceptions with strata in the northwest boreal forest and southern prairie parkland habitats. Several strata in the boreal forest habitat had negative slope estimates, indicating a decrease in breeding pairs, while some of the strata in the prairie parkland habitat had positive slope estimates, indicating an increase in this region. Additionally, from looking at plots of individual strata, it seems that the strata experiencing increases in breeding pairs are experiencing dramatic increases. Overall, my results support previous work indicating a decline in population abundance in the northern boreal forest of Canada, and additionally indicate that the population of scaup has increased rapidly in the prairie pothole region since 1957. Yet, by accounting for spatial and temporal autocorrelation in the data, it appears that declines in abundance are not as widespread as previously reported.

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This dissertation is concerned with effects dispersal and forest structure on forest insect population dynamics, and with identifying generating processes by comparing observed patterns to model predictions. In chapter 2, we investigated effects of changing forest landscape patterns on integro-difference models of host-parasitoid population dynamics. We demonstrated that removing habitat can increase herbivore density when herbivores don't disperse far, and parasitoids disperse further, due to differences in dispersal success between trophic levels. This is a novel potential explanation for why forest fragmentation increases the duration of forest tent caterpillar outbreaks. To better understand spatial model behaviour, we proposed a new local variation of the dispersal success approximation. The approximation successfully predicts effects of habitat loss and fragmentation on realistically complex landscapes, except when outbreak cycle amplitude is very large. Local dispersal success is useful in part because parameters can be estimated from widely available habitat data. In chapter 3, we investigated how well a discretized integro-difference model of mountain pine beetle population dynamics predicted the occurrence of new infestations in British Columbia. We found that a model with a large dispersal kernel, and high emigration from new, low severity infestations yielded the best predictions. However, we do not believe this to be convincing evidence that many beetles disperse from new, low severity infestations. Rather, we argued that differences in habitat quality, detection errors, and Moran effects can all confound dispersal patterns, making it difficult to infer dispersal parameters from observed infestation patterns. Nonetheless, predicting infestation risk is useful, and large kernels improve predictions. In chapter 4, we used generalized linear mixed models to characterize spatial and temporal variation in the propensity of jack pine trees to produce pollen cones, and account for confounding effects on the relationship between pollen cone production and previous defoliation by jack pine budworm. We found effects of stand age, and synchronous variation in pollen cone production among years. Accounting for background patterns in pollen cone production clarified that pollen cone production declines in with previous defoliation, as expected.

This dissertation is concerned with effects dispersal and forest structure on forest insect population dynamics, and with identifying generating processes by comparing observed patterns to model predictions. In chapter 2, we investigated effects of changing forest landscape patterns on integro-difference models of host-parasitoid population dynamics. We demonstrated that removing habitat can increase herbivore density when herbivores don't disperse far, and parasitoids disperse further, due to differences in dispersal success between trophic levels. This is a novel potential explanation for why forest fragmentation increases the duration of forest tent caterpillar outbreaks. To better understand spatial model behaviour, we proposed a new local variation of the dispersal success approximation. The approximation successfully predicts effects of habitat loss and fragmentation on realistically complex landscapes, except when outbreak cycle amplitude is very large. Local dispersal success is useful in part because parameters can be estimated from widely available habitat data. In chapter 3, we investigated how well a discretized integro-difference model of mountain pine beetle population dynamics predicted the occurrence of new infestations in British Columbia. We found that a model with a large dispersal kernel, and high emigration from new, low severity infestations yielded the best predictions. However, we do not believe this to be convincing evidence that many beetles disperse from new, low severity infestations. Rather, we argued that differences in habitat quality, detection errors, and Moran effects can all confound dispersal patterns, making it difficult to infer dispersal parameters from observed infestation patterns. Nonetheless, predicting infestation risk is useful, and large kernels improve predictions. In chapter 4, we used generalized linear mixed models to characterize spatial and temporal variation in the propensity of jack pine trees to produce pollen cones, and account for confounding effects on the relationship between pollen cone production and previous defoliation by jack pine budworm. We found effects of stand age, and synchronous variation in pollen cone production among years. Accounting for background patterns in pollen cone production clarified that pollen cone production declines in with previous defoliation, as expected.

Cette thèse s’attache à développer des outils et modèles adaptés a l’étude de certains risques spatiaux et en réseaux. Elle est divisée en cinq chapitres. Le premier consiste en une introduction générale, contenant l’état de l’art au sein duquel s’inscrivent les différents travaux, ainsi que les principaux résultats obtenus. Le Chapitre 2 propose un nouveau générateur de précipitations multi-site. Il est important de disposer de modèles capables de produire des séries de précipitations statistiquement réalistes. Alors que les modèles précédemment introduits dans la littérature concernent essentiellement les précipitations journalières, nous développons un modèle horaire. Il n’implique qu’une seule équation et introduit ainsi une dépendance entre occurrence et intensité, processus souvent considérés comme indépendants dans la littérature. Il comporte un facteur commun prenant en compte les conditions atmosphériques grande échelle et un terme de contagion auto-regressif multivarié, représentant la propagation locale des pluies. Malgré sa relative simplicité, ce modèle reproduit très bien les intensités, les durées de sècheresse ainsi que la dépendance spatiale dans le cas de la Bretagne Nord. Dans le Chapitre 3, nous proposons une méthode d’estimation des processus maxstables, basée sur des techniques de vraisemblance simulée. Les processus max-stables sont très adaptés à la modélisation statistique des extrêmes spatiaux mais leur estimation s’avère délicate. En effet, la densité multivariée n’a pas de forme explicite et les méthodes d’estimation standards liées à la vraisemblance ne peuvent donc pas être appliquées. Sous des hypothèses adéquates, notre estimateur est efficace quand le nombre d’observations temporelles et le nombre de simulations tendent vers l’infini. Cette approche par simulation peut être utilisée pour de nombreuses classes de processus max-stables et peut fournir de meilleurs résultats que les méthodes actuelles utilisant la vraisemblance composite, notamment dans le cas où seules quelques observations temporelles sont disponibles et où la dépendance spatiale est importante / This thesis aims at developing tools and models that are relevant for the study of some spatial risks and risks in networks. The thesis is divided into five chapters. The first one is a general introduction containing the state of the art related to each study as well as the main results. Chapter 2 develops a new multi-site precipitation generator. It is crucial to dispose of models able to produce statistically realistic precipitation series. Whereas previously introduced models in the literature deal with daily precipitation, we develop a hourly model. The latter involves only one equation and thus introduces dependence between occurrence and intensity; the aforementioned literature assumes that these processes are independent. Our model contains a common factor taking large scale atmospheric conditions into account and a multivariate autoregressive contagion term accounting for local propagation of rainfall. Despite its relative simplicity, this model shows an impressive ability to reproduce real intensities, lengths of dry periods as well as the spatial dependence structure. In Chapter 3, we propose an estimation method for max-stable processes, based on simulated likelihood techniques. Max-stable processes are ideally suited for the statistical modeling of spatial extremes but their inference is difficult. Indeed the multivariate density function is not available and thus standard likelihood-based estimation methods cannot be applied. Under appropriate assumptions, our estimator is efficient as both the temporal dimension and the number of simulation draws tend towards infinity. This approach by simulation can be used for many classes of max-stable processes and can provide better results than composite-based methods, especially in the case where only a few temporal observations are available and the spatial dependence is high