Overview
1
Quick Start
1.1
Installing and Launching
PrioriTree
1.1.1
Installation
1.1.2
Launch the Shiny App (Browser Interface)
1.2
Interactively Specify
BEAST
Discrete-Geographic Phylodynamic Analyses Using Graphs of Priors
1.2.1
Step 1: Loading input files
1.2.2
Step 2: Specifying model and configuring basic analysis
1.2.3
Step 3: Specifying settings for basic analyses
1.2.4
Step 4: Saving Output
1.3
Assessing Prior Sensitivity
1.3.1
Estimating the induced prior
1.3.2
Robust Bayesian inference
1.3.3
Data cloning
1.4
Assessing Model Fit
1.4.1
Comparing the relative fit of competing models
1.4.2
Posterior-predictive checking
2
Detailed Guide
2.1
Model Specification and Related Theory
2.1.1
Discrete-geographic model
2.1.2
Inferring Biogeographic History
2.1.3
Accommodating Phylogenetic Uncertainty
2.2
Prior Specification and Related Theory
2.2.1
Inherent Prior Sensitivity of Biogeographic Inference
2.2.2
Prior on the Number of Dispersal Routes
2.2.3
Prior on the Average Dispersal Rate
2.3
MCMC Settings
2.3.1
The Metropolis–Hastings Algorithm
2.3.2
MCMC Sampling
2.3.3
Proposal Weights
2.4
Assessing Prior Sensitivity
2.4.1
Estimating the Prior
2.4.2
Robust Bayesian Inference
2.4.3
Data Cloning
2.5
Assessing Relative and Absolute Model Fit
2.5.1
Marginal-Likelihood Estimation
2.5.2
Posterior-Predictive Checking
2.6
Further UI features
References
PrioriTree: an Interactive Utility for Improving Geographic Phylodynamic Analyses in BEAST
1
Quick Start