Package index • prepR4pcm

Package overview

prepR4pcm prepR4pcm-package: prepR4pcm: Reconcile species names for phylogenetic comparative methods

Match species names

Build a reconciliation between your data and one or more reference sources (a tree, another dataset, or both). This is where most workflows begin.

reconcile_tree(): Reconcile species names between a dataset and a phylogenetic tree

reconcile_data(): Reconcile species names between two datasets

reconcile_to_trees(): Reconcile one dataset against multiple phylogenetic trees

reconcile_trees(): Reconcile tip labels between two phylogenetic trees

reconcile_multi(): Reconcile several datasets against one phylogenetic tree

Inspect and audit

Examine the results of a reconciliation: see what matched, what was flagged, and what is still unresolved. Produce reports for collaborators or supplementary materials.

reconcile_summary(): Print a reconciliation summary to the console

reconcile_mapping(): Extract the per-name mapping table from a reconciliation

reconcile_plot(): Plot the match composition of a reconciliation

reconcile_suggest(): Suggest near-miss matches for unresolved species

reconcile_diff(): Diff two reconciliations to see what changed

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

Corrections and crosswalks

Apply manual corrections by hand, in bulk, or from a published taxonomy crosswalk.

reconcile_override(): Manually override a single name in a reconciliation

reconcile_override_batch(): Apply many manual corrections to a reconciliation at once

reconcile_crosswalk(): Convert a published taxonomy crosswalk into an overrides table

Apply, merge, export

Turn a reconciliation into analysis-ready outputs — aligned data frames, pruned trees, merged datasets, or files on disk.

reconcile_apply(): Apply a reconciliation to produce an aligned data-tree pair

reconcile_merge(): Merge two reconciled datasets

reconcile_export(): Write an aligned dataset, tree, and mapping table to disk

Augment phylogenies (exploratory)

Graft unresolved species onto a tree using genus-level placement. For exploratory analyses only — always run sensitivity analyses with and without augmented tips.

reconcile_augment(): Graft missing species onto a phylogenetic tree (genus-level placement)

Name utilities

Low-level helpers for cleaning scientific names and pulling tip labels off trees. Useful outside a full reconciliation workflow.

pr_normalize_names(): Normalise scientific names to a canonical form

pr_extract_tips(): Extract tip labels from a phylogenetic tree

Tree retrieval, dating, and citation

Retrieve a candidate phylogeny for a reconciled species list, time-calibrate an existing topology, or format the citations for a tree result. Five pr_get_tree() backends ship: rotl (CRAN, Open Tree of Life synthesis), rtrees (GitHub, taxon-specific mega-trees), clootl (GitHub, bird Clements taxonomy), fishtree (CRAN, Rabosky et al. 2018 fish chronogram), and datelife (GitHub, Sanchez Reyes et al. 2024 chronogram database). Multi-tree support is backend-specific: fishtree and datelife honour n_tree, clootl requires an AvesData repo for n_tree > 1, rtrees returns whichever single tree or posterior its selected mega-tree provides, and rotl always returns the single Open Tree synthesis. Backends live in Suggests (or GitHub) and are installed on demand.

pr_get_tree(): Retrieve a candidate phylogeny for a species list

pr_date_tree(): Time-calibrate a topology using the DateLife chronogram database

pr_cite_tree(): Format the citations for a tree result

pr_tree_compare(): Compare two or more phylogenetic trees

pr_phylo_cor(): Phylogenetic correlation matrix from a tree

Tree-handling utilities

Helpers for the pr_get_tree() workflow: a backend health probe, an on-disk cache for repeat retrievals, and the source = "auto" / tnrs = "auto" controls (see ?pr_get_tree).

pr_get_tree_status(): Report the install status of every pr_get_tree() backend

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_cache_clear(): Clear the local tree-retrieval cache

Bundled bird data

Subsetted bird datasets and phylogenies used by the bird-workflow vignette. Full credit to the original data providers — each help page lists the citation, and the README has a consolidated list.

avonet_subset: AVONET morphological trait data (subset)

nesttrait_subset: Nest trait data (subset)

delhey_subset: Plumage lightness data (subset)

tree_jetz: Jetz (2012) phylogenetic tree (subset)

tree_clements25: Clements 2025 phylogenetic tree (subset)

crosswalk_birdlife_birdtree: BirdLife-BirdTree taxonomy crosswalk

Bundled mammal data

Subsetted mammal trait sources and an example phylogeny used by the db-assembly-workflow_mammals vignette. Each help page lists the citation; the mammal phylogeny has provenance pending confirmation (see the help page).

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)