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

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Documentation for package ‘EvoPhylo’ version 0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

characters	A morphological phylogenetic data matrix
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
cluster_to_nexus	Export character partitions to a Nexus file
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
get_clockrate_table	Extract evolutionary rates from a Bayesian clock tree
get_gower_dist	Compute Gower distances between characters
get_pwt_rates	Conduct pairwise t-tests between node rates and clock base rate
get_sil_widths	Calculate silhouette widths index for various numbers of partitions
make_clusters	Estimate and plot character partitions
plot.cluster_df	Estimate and plot character partitions
plot.sil_width_df	Calculate silhouette widths index for various numbers of partitions
plot_treerates_sgn	Plot Bayesian evolutionary tree with rate thresholds for selection mode
posterior1p	Posterior parameter samples (single clock)
posterior3p	Posterior parameter samples (3 clock partions)
rate_table_clades_means1	Mean clock rates by node and clade (single clock)
rate_table_clades_means3	Mean clock rates by node and clade (3 clock partitions)
tree1p	Phylogenetic tree with a single clock partition
tree3p	Phylogenetic tree with 3 clock partitions