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


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Documentation for package ‘EvoPhylo’ version 0.3

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 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
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_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
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
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)