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PrioriTree: a utility for improving phylodynamic analyses in BEAST
- Gao, Jiansi;
- May, Michael R;
- Rannala, Bruce;
- Moore, Brian R
- Editor(s): Schwartz, Russell
Published Web Location
https://doi.org/10.1093/bioinformatics/btac849Abstract
Summary
Phylodynamic methods are central to studies of the geographic and demographic history of disease outbreaks. Inference under discrete-geographic phylodynamic models-which involve many parameters that must be inferred from minimal information-is inherently sensitive to our prior beliefs about the model parameters. We present an interactive utility, PrioriTree, to help researchers identify and accommodate prior sensitivity in discrete-geographic inferences. Specifically, PrioriTree provides a suite of functions to generate input files for-and summarize output from-BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets.Availability and implementation
PrioriTree is distributed as an R package available at https://github.com/jsigao/prioritree, with a comprehensive user manual provided at https://bookdown.org/jsigao/prioritree_manual/.Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.
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