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) |