Learn R Programming

EvoPhylo (version 0.3.5)

Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Description

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) .

Copy Link

Version

Install

install.packages('EvoPhylo')

Monthly Downloads

193

Version

0.3.5

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/tiago-simoes/EvoPhylo

Homepage

https://tiago-simoes.github.io/EvoPhylo/

Maintainer

Tiago Simoes

Last Published

August 27th, 2025

Functions in EvoPhylo (0.3.5)

Convert clock rate tables from wide to long format

clockrate_summary

Compute rate summary statistics across clades and clocks

Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tips

drop.dummy.beast

Remove dummy tip from beast summary trees, accounting for metadata on the tips

get_clockrate_table_MrBayes

Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayes

clockrate_dens_plot

Plot clock rate distributions

cluster_to_nexus

Export character partitions to a Nexus file

get_clockrate_table_BEAST2

Extract evolutionary rates from Bayesian clock trees produced by BEAST2

Combine and filter (.p) log files from Mr.Bayes, BEAST2 and MCMCTREE

clockrate_reg_plot

Plot regression lines between sets of rates

Multiple phylogenetic clock trees

Compute Gower distances between characters

get_pwt_rates_MrBayes

Conduct pairwise t-tests between node rates and clock base rate from a Mr.Bayes output.

plot_treerates_sgn

Plot Bayesian evolutionary tree with rate thresholds for selection mode

Calculate silhouette widths index for various numbers of partitions

plot_back_rates

Plots distribution of background rates extracted from posterior log files.

write_partitioned_alignments2

Write alignment partitions as separate alignment files for various data types

Estimate and plot character partitions

get_pwt_rates_BEAST2

Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.

offset.to.dummy.metadata

Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages, accounting for possible metadata on the tips.

offset.to.dummy

Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages.

BEAST2 phylogenetic tree with clock rates from partition 2

Posterior parameter samples (3 clock partions)

Phylogenetic tree with 3 clock partitions

Phylogenetic tree with a single clock partition

write_partitioned_alignments

Write character partitions as separate Nexus files (for use in BEAUti)

write.beast.treedata

Export multiple treedata objects (S4 class tree files) to BEAST NEXUS file

Posterior parameter samples (single clock)

BEAST2 phylogenetic tree with clock rates from partition 1

Test assumptions of normality and homoscedasticity for FBD posterior parameters

FBD_normality_plot

Inspect FBD parameter distributions visually

Test for differences in FBD parameter values

Density plots for each FBD parameter

clade_membership

Designate clade membership for each tip for downstream analyses summarizing rates for each clade

A morphological phylogenetic data matrix

Summarize FBD posterior parameter estimates

Convert an FBD posterior parameter table from wide to long format

RateTable_Means_1p_Clades

Mean clock rates by node and clade (single clock)

RateTable_Means_3p_Clades

Mean clock rates by node and clade (3 clock partitions)