Function reference • EvoPhylo

Functions

Character partitioning

See vignette("char-part") for a complete workflow that uses these functions to conduct automated morphological character partitioning as a pre-processing step for clock (time-calibrated) Bayesian phylogenetic analysis of morphological data using the programs Mr. Bayes or BEAST2.

get_gower_dist(): Compute Gower distances between characters

get_sil_widths() plot(<sil_width_df>): Calculate silhouette widths index for various numbers of partitions

make_clusters() plot(<cluster_df>): Estimate and plot character partitions

cluster_to_nexus(): Export character partitions to a Nexus file

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

Evolutionary rates & selection mode (MrBayes)

See vignette("rates-selection_MrBayes") for a complete workflow that uses these functions to extract evolutionary rate parameters estimated from relaxed clock Bayesian inference analyses produced by the program Mr. Bayes and use evolutionary rate based inference of selection mode (or strength) adapted to clock-based rates.

get_clockrate_table_MrBayes(): Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayes

clockrate_dens_plot(): Plot clock rate distributions

clockrate_reg_plot(): Plot regression lines between sets of rates

clockrate_summary(): Compute rate summary statistics across clades and clocks

combine_log(): Combine and filter (.p) log files from Mr.Bayes

clock_reshape(): Convert clock rate tables from wide to long format

plot_back_rates(): Plots distribution of background rates extracted from posterior log files.

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

Evolutionary rates & selection mode (BEAST2)

See vignette("rates-selection_BEAST2") for a complete workflow that uses these functions to extract evolutionary rate parameters estimated from relaxed clock Bayesian inference analyses produced by the program BEAST2 and use evolutionary rate based inference of selection mode (or strength) adapted to clock-based rates.

get_clockrate_table_BEAST2(): Extract evolutionary rates from Bayesian clock trees produced by BEAST2

clockrate_dens_plot(): Plot clock rate distributions

clockrate_reg_plot(): Plot regression lines between sets of rates

clockrate_summary(): Compute rate summary statistics across clades and clocks

clock_reshape(): Convert clock rate tables from wide to long format

plot_back_rates(): Plots distribution of background rates extracted from posterior log files.

get_pwt_rates_BEAST2(): Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.

plot_treerates_sgn(): Plot Bayesian evolutionary tree with rate thresholds for selection mode

Analyzing FBD parameters

See vignette("fbd-params") for a complete workflow that uses these functions to extract FBD parameters estimated from relaxed clock Bayesian inference analyses produced by Mr. Bayes and BEAST2.

combine_log(): Combine and filter (.p) log files from Mr.Bayes

FBD_dens_plot(): Density plots for each FBD parameter

FBD_normality_plot(): Inspect FBD parameter distributions visually

FBD_reshape(): Convert an FBD posterior parameter table from wide to long format

FBD_summary(): Summarize FBD posterior parameter estimates

FBD_tests1(): Test assumptions of normality and homoscedasticity for FBD posterior parameters

FBD_tests2(): Test for differences in FBD parameter values

Analyzing Trees With Offsets

See vignette("offset_handling") for a complete workflow that uses these functions to summarize trees with offsets (with fossil species only) as produced by the SA package in BEAST2.

drop.dummy.beast(): Remove dummy tip from beast summary trees, accounting for metadata on the tips

drop.dummy.mb(): Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tips

offset.to.dummy(): Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages.

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.

write.beast.treedata(): Export multiple treedata objects (S4 class tree files) to BEAST NEXUS file

Datasets

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)

characters: A morphological phylogenetic data matrix

post_trees: Multiple phylogenetic clock trees

posterior1p: Posterior parameter samples (single clock)

posterior3p: Posterior parameter samples (3 clock partions)

tree1p: Phylogenetic tree with a single clock partition

tree3p: Phylogenetic tree with 3 clock partitions

tree_clock1: BEAST2 phylogenetic tree with clock rates from partition 1

tree_clock2: BEAST2 phylogenetic tree with clock rates from partition 2