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

## Documentation for package ‘EvoPhylo’ version 0.3.5

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

## Help Pages

characters | A morphological phylogenetic data matrix
clade_membership | Designate clade membership for each tip for downstream analyses summarizing rates for each clade
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, 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
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)
write_partitioned_alignments2 | Write alignment partitions as separate alignment files for various data types