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

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Documentation for package ‘EvoPhylo’ version 0.3.2

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

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
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
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_BEAST2	Extract evolutionary rates from Bayesian clock trees produced by BEAST2
get_clockrate_table_MrBayes	Extract evolutionary rates from a Bayesian clock tree produced by Mr. Bayes
get_gower_dist	Compute Gower distances between characters
get_pwt_rates_BEAST2	Conduct pairwise t-tests between node rates and clock base rates from a BEAST2 output.
get_pwt_rates_MrBayes	Conduct pairwise t-tests between node rates and clock base rate from a Mr.Bayes output.
get_sil_widths	Calculate silhouette widths index for various numbers of partitions
make_clusters	Estimate and plot character partitions
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.
plot.cluster_df	Estimate and plot character partitions
plot.sil_width_df	Calculate silhouette widths index for various numbers of partitions
plot_back_rates	Plots distribution of background rates extracted from posterior log files.
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)
post_trees	Multiple phylogenetic clock trees
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)
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
write.beast.treedata	Export multiple treedata objects (S4 class tree files) to BEAST NEXUS file
write_partitioned_alignments	Write character partitions as separate Nexus files (for use in BEAUti)