Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Convert clock rate tables from wide to long format
Plot clock rate distributions
Plot regression lines between sets of rates
Compute rate summary statistics across clades and clocks
Export character partitions to a Nexus file
Combine and filter (.p) log files from Mr.Bayes
Remove dummy tip from beast summary trees, accounting for metadata on ...
Remove dummy tip from Mr. Bayes summary trees, accounting for metadata...
Density plots for each FBD parameter
Inspect FBD parameter distributions visually
Convert an FBD posterior parameter table from wide to long format
Summarize FBD posterior parameter estimates
Test assumptions of normality and homoscedasticity for FBD posterior p...
Test for differences in FBD parameter values
Extract evolutionary rates from Bayesian clock trees produced by BEAST...
Extract evolutionary rates from a Bayesian clock tree produced by Mr. ...
Compute Gower distances between characters
Conduct pairwise t-tests between node rates and clock base rates from ...
Conduct pairwise t-tests between node rates and clock base rate from a...
Calculate silhouette widths index for various numbers of partitions
Estimate and plot character partitions
Convert trees produced by a BEAST2 FBD analysis with offset to trees w...
Convert trees produced by a BEAST2 FBD analysis with offset to trees w...
Plots distribution of background rates extracted from posterior log fi...
Plot Bayesian evolutionary tree with rate thresholds for selection mod...
Export multiple treedata objects (S4 class tree files) to BEAST NEXUS ...
Write character partitions as separate Nexus files (for use in BEAUti)
Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
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