ArticleBioinformatics (Oxford, England)2023
PrioriTree: a utility for improving phylodynamic analyses in BEAST.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa.Nature communications · 2025Article
- Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal.PLoS computational biology · 2024Article
- A phylogenetic assessment of HIV-1 transmission trends among people who inject drugs from Coastal and Nairobi, Kenya.Virus evolution · 2024Article
- Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models.Molecular biology and evolution · 2023Article
- Model misspecification misleads inference of the spatial dynamics of disease outbreaks.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
summaryPhylodynamic 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/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.