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There are however many open regression problems, such as for instance re-testing of positive cases, a routine procedure nowadays.
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The student will be expected to implement and extend the models in Section 7.3 of [Bastos, Carvalho & Gomes (2021)](https://github.com/maxbiostat/papers/blob/master/PAPERS/2021_Bastos_Carvalho_Gomes.pdf) using both simulated and real-world data.
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Skills to be developed: Stan/NIMBLE, Multilevel modelling.
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References:
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- In addition to the references already given, Lucas Moschen's [honours thesis](https://github.com/lucasmoschen/rds-bayesian-analysis-tcc) is great resource.
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- [This](https://github.com/epiforecasts/inc2prev) repository might come in handy.
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Another aspect of epidemic surveillance is tracking the effective reproductive number (Rt) of the disease through time, as measure of risk of (exponential) disease spread.
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In this project, the student will couple the delay-correction nowcasting model of [Bastos et al. (2019)](https://onlinelibrary.wiley.com/doi/full/10.1002/sim.8303) and the Rt estimation methods in the R package [EpiEstim](https://github.com/mrc-ide/EpiEstim) to create a unified framework for accurate Rt calculation by explicitly modelling data misreporting.
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Skills to be developed: [INLA](https://www.r-inla.org/), R, Applied Bayesian Statistics.
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This is joint work with Drs [Leo Bastos](https://lsbastos.github.io/) and [Marcelo Gomes](https://scholar.google.com/citations?user=b018FBIAAAAJ&hl=en&authuser=1&oi=ao).
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The project will work along two axes: (i) realistically simulating sparse-but-correlated design matrices and (ii) developing memory-efficient implementations that scale with dimension.
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Skills to be developed: Stan and C++ programming, Bayesian statistics, Variable selection.
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This is joint work with [Aki Vehtari](https://users.aalto.fi/~ave/).
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References:
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A5) **General inference selection with multilevel models**
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A5) **General inference of natural selection with multilevel models**
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The question of identifying genes under natural selection is a central one in Evolutionary Biology.
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[Eilertson, Booth & Bustamante, (2012)](https://doi.org/10.1371/journal.pcbi.1002806) propose a method to use genome-wide polymorphism data to infer selection using a multilevel logistic model fitted to tens of thousands of (2x2) Mk matrices.

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