Man pages for EvoPhylo
Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
| characters | A morphological phylogenetic data matrix |
| clade_membership | Designate clade membership for each tip for downstream... |
| 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... |
| drop.dummy.beast | Remove dummy tip from beast summary trees, accounting for... |
| drop.dummy.mb | Remove dummy tip from Mr. Bayes summary trees, accounting for... |
| 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... |
| FBD_summary | Summarize FBD posterior parameter estimates |
| FBD_tests1 | Test assumptions of normality and homoscedasticity for FBD... |
| FBD_tests2 | Test for differences in FBD parameter values |
| get_clockrate_table_BEAST2 | Extract evolutionary rates from Bayesian clock trees produced... |
| get_clockrate_table_MrBayes | Extract evolutionary rates from a Bayesian clock tree... |
| get_gower_dist | Compute Gower distances between characters |
| get_pwt_rates_BEAST2 | Conduct pairwise t-tests between node rates and clock base... |
| get_pwt_rates_MrBayes | Conduct pairwise t-tests between node rates and clock base... |
| get_sil_widths | Calculate silhouette widths index for various numbers of... |
| make_clusters | Estimate and plot character partitions |
| offset.to.dummy | Convert trees produced by a BEAST2 FBD analysis with offset... |
| offset.to.dummy.metadata | Convert trees produced by a BEAST2 FBD analysis with offset... |
| plot_back_rates | Plots distribution of background rates extracted from... |
| plot_treerates_sgn | Plot Bayesian evolutionary tree with rate thresholds for... |
| 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... |
| write_partitioned_alignments | Write character partitions as separate Nexus files (for use... |
| write_partitioned_alignments2 | Write alignment partitions as separate alignment files for... |
