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) |