# Prepare Data and Trees for Phylogenetic Comparative Methods

## Documentation for package ‘prepR4pcm’ version 1.0.0

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

## Help Pages

avonet_subset | AVONET morphological trait data (subset)
crosswalk_birdlife_birdtree | BirdLife-BirdTree taxonomy crosswalk
delhey_subset | Plumage lightness data (subset)
mammal_amniote_example | Amniote-style mammal life-history sample
mammal_pantheria_example | PanTHERIA-style mammal life-history sample
mammal_tetrapodtraits_example | TetrapodTraits-style mammal sample
mammal_tree_example | Mammal phylogenetic tree (example)
nesttrait_subset | Nest trait data (subset)
pr_cite_tree | Format the citations for a tree result
pr_date_tree | Time-calibrate a topology using the DateLife chronogram database
pr_extract_tips | Extract tip labels from a phylogenetic tree
pr_get_tree | Retrieve a candidate phylogeny for a species list
pr_get_tree_status | Report the install status of every 'pr_get_tree()' backend
pr_normalize_names | Normalise scientific names to a canonical form
pr_phylo_cor | Phylogenetic correlation matrix from a tree
pr_tree_cache_clear | Clear the local tree-retrieval cache
pr_tree_cache_dir | Get or set the local tree-retrieval cache directory
pr_tree_cache_status | Show the contents of the local tree-retrieval cache
pr_tree_compare | Compare two or more phylogenetic trees
reconcile_apply | Apply a reconciliation to produce an aligned data-tree pair
reconcile_augment | Graft missing species onto a phylogenetic tree (genus-level placement)
reconcile_crosswalk | Convert a published taxonomy crosswalk into an overrides table
reconcile_data | Reconcile species names between two datasets
reconcile_diff | Diff two reconciliations to see what changed
reconcile_export | Write an aligned dataset, tree, and mapping table to disk
reconcile_mapping | Extract the per-name mapping table from a reconciliation
reconcile_merge | Merge two reconciled datasets
reconcile_multi | Reconcile several datasets against one phylogenetic tree
reconcile_override | Manually override a single name in a reconciliation
reconcile_override_batch | Apply many manual corrections to a reconciliation at once
reconcile_plot | Plot the match composition of a reconciliation
reconcile_report | Write a self-contained HTML reconciliation report
reconcile_review | Interactively review reconciliation matches
reconcile_splits_lumps | Flag taxonomic splits and lumps in a reconciliation
reconcile_suggest | Suggest near-miss matches for unresolved species
reconcile_summary | Print a reconciliation summary to the console
reconcile_to_trees | Reconcile one dataset against multiple phylogenetic trees
reconcile_tree | Reconcile species names between a dataset and a phylogenetic tree
reconcile_trees | Reconcile tip labels between two phylogenetic trees
tree_clements25 | Clements 2025 phylogenetic tree (subset)
tree_jetz | Jetz (2012) phylogenetic tree (subset)