Prepare Data and Trees for Phylogenetic Comparative Methods

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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)