Deardon, RobMahsin, MD2022-07-112022-07-112022-06Mahsin, MD (2022). Geographically dependent individual-level models for infectious disease transmission (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.http://hdl.handle.net/1880/114819Infectious disease models can be of great use for understanding the underlying mechanisms that influence the spread of diseases and predicting future disease progression. Modeling has been increasingly used to evaluate the potential impact of different control measures and to guide public health policy decisions. In recent years, there has been rapid progress in developing spatio-temporal modeling of infectious diseases and an example of such recent developments is the discrete time individual-level models (ILMs). These models are well developed and provide a common framework for modeling many disease systems, however, they assume the probability of disease transmission between two individuals depends only on their spatial separation and not on their spatial locations. In cases where spatial location itself is important for understanding the spread of emerging infectious diseases and identifying their causes, it would be beneficial to incorporate the effect of spatial location in the model. In this study, we thus generalize the ILMs to a new class of geographically-dependent ILMs (GD-ILMs), to allow for the evaluation of the effect of spatially varying risk factors (e.g., education, social deprivation, environmental), as well as unobserved spatial structure, upon the transmission of infectious disease. Specifically, we consider a conditional autoregressive (CAR) model to capture the effects of unobserved spatially structured latent covariates or measurement error. This results in flexible infectious disease models that can be used for formulating etiological hypotheses and identifying geographical regions of unusually high risk to formulate preventive action. The reliability of these models are investigated on a combination of simulated epidemic data and Alberta seasonal influenza outbreak data (2009). This new class of models is fitted to data within a Bayesian statistical framework using Markov chain Monte Carlo (MCMC) methods. We also developed the continuous-time GD-ILMs, allowing infection times and infectious periods to be treated as latent variables that are estimated using data-augmented Markov Chain Monte Carlo (MCMC) techniques within a Bayesian framework. This approach results in a flexible infectious disease modeling framework for formulating etiological hypotheses and identifying unusually high-risk geographical regions to develop preventive action. We evaluate the performance of these proposed models on a combination of simulated epidemic data and seasonal influenza data in Alberta in 2009. Finally, we proposed a special case of the GD-ILMs, termed as {\it small-area restricted} GD-ILMs for infectious disease modelling. The reliability of these models are investigated through simulation studies based on disease spread through the Canadian city of Calgary, Alberta.University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.Geographicallydependent individual-level models (GD-ILMs)Markov chain Monte Carlo (MCMC)Spatio-temporal infectious disease modelingData-augmented MCMCConditional autoregressive modelBiostatisticsEpidemiologyPublic HealthStatisticsdoctoral thesis10.11575/PRISM/39887