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
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
clade_membership        Designate clade membership for each tip for
                        downstream analyses summarizing rates for each
                        clade
clock_reshape           Convert clock rate tables from wide to long
                        format
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
cluster_to_nexus        Export character partitions to a Nexus file
combine_log             Combine and filter (.p) log files from
                        Mr.Bayes, BEAST2 and MCMCTREE
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
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_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
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
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)
write_partitioned_alignments2
                        Write alignment partitions as separate
                        alignment files for various data types
