Setup | Load the example sources | Step 1: Compare the source tables | Step 2: Standardise the sources | Step 3: Reconcile species names with the tree | Step 4: Add manual corrections | Step 5: Collapse to one row per species | Step 6: Align the database and the tree | Final database ready for model fitting | References
Package: prepR4pcm 1.0.0
Shinichi Nakagawa
prepR4pcm: Prepare Data and Trees for Phylogenetic Comparative Methods
Reconcile species names across datasets and phylogenetic trees for comparative biology workflows. Identifies mismatches due to formatting differences, taxonomic synonymy, and spelling errors. Produces detailed reports documenting how each name was resolved, which taxonomic authority was used, and what remains unresolved. Supports exact matching, name normalisation, synonym resolution via local taxonomic databases, and fuzzy matching for likely typos. Detects taxonomic splits and lumps. For methodological context, see Nakagawa et al. (2026) <doi:10.32942/X2468Z>.
Authors:
prepR4pcm_1.0.0.tar.gz
prepR4pcm_1.0.0.tar.gz(r-4.7-any)prepR4pcm_1.0.0.tar.gz(r-4.6-any)
prepR4pcm_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
prepR4pcm/json (API)
| # Install 'prepR4pcm' in R: |
| install.packages('prepR4pcm', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/itchyshin/prepr4pcm/issues
Pkgdown/docs site:https://itchyshin.github.io
Datasets:
- avonet_subset - AVONET morphological trait data
- crosswalk_birdlife_birdtree - BirdLife-BirdTree taxonomy crosswalk
- delhey_subset - Plumage lightness data
- 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
- nesttrait_subset - Nest trait data
- tree_clements25 - Clements 2025 phylogenetic tree
- tree_jetz - Jetz
Last updated from:b78fe29add. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 260 | ||
| source / vignettes | OK | 331 | ||
| linux-release-x86_64 | OK | 270 | ||
| wasm-release | OK | 187 |
Exports:pr_cite_treepr_date_treepr_extract_tipspr_get_treepr_get_tree_statuspr_normalize_namespr_phylo_corpr_tree_cache_clearpr_tree_cache_dirpr_tree_cache_statuspr_tree_comparereconcile_applyreconcile_augmentreconcile_crosswalkreconcile_datareconcile_diffreconcile_exportreconcile_mappingreconcile_mergereconcile_multireconcile_overridereconcile_override_batchreconcile_plotreconcile_reportreconcile_reviewreconcile_splits_lumpsreconcile_suggestreconcile_summaryreconcile_to_treesreconcile_treereconcile_trees
Dependencies:apeclidigestgluelatticelifecyclemagrittrnlmepillarpkgconfigRcpprlangtibbleutf8vctrs
Assembling mammal trait databases for phylogenetic comparative models
Last update: 2026-06-25
Started: 2026-06-25
Comparing tree backends — when do they agree?
Setup | The recipe | What actually works (status table) | Branch lengths and time-calibration | Where are the VertLife trees? | Note on tip labels before comparing | What to do with the result | When the backends return the same species set and similar topology (Jaccard ≈ 1, RF small) | When tip sets differ (Jaccard < 1) | When topologies disagree (RF large) | When branch-length correlation is low | Caching the comparisons | What pr_tree_compare() doesn't do (yet) | See also
Last update: 2026-06-25
Started: 2026-06-25
From Raw Data to PCM: A Complete Bird Trait Workflow
Setup | Part I: Core Workflow | Step 1: Load data and tree | Step 2: Reconcile data against the tree | Step 3: Produce aligned objects | Step 4: Run a comparative analysis | Phylogenetic generalised least squares (PGLS) | Phylogenetic generalised linear mixed model (PGLMM) | Part II: Advanced Topics | Reconciling two datasets | Multi-row species | Asymmetric datasets | Using a taxonomy crosswalk | Reconciling against multiple trees | Fuzzy matching for typos | Tree augmentation for missing species | Exporting to files | HTML reports | Key points | Data sources | References
Last update: 2026-06-25
Started: 2026-06-25
From species names to a phylogenetic posterior — prepR4pcm + pigauto
What we'll build | Step 1 — Retrieve a posterior of trees | Step 2 — Reconcile the data to the posterior | Step 3 — Format citations (do this before you submit) | Step 4 — Hand the posterior to pigauto | Choosing a backend | What's not in this pipeline | See also
Last update: 2026-06-25
Started: 2026-06-25
Getting Started with prepR4pcm
The problem | Installation | Example 1: Reconcile a dataset against a tree | Inspect the result | Apply manual overrides | Produce aligned objects | Example 2: Reconcile two datasets | Understanding match types | Example 3: Using a taxonomic authority | Example 4: Pre-built overrides | Example 5: Multiple datasets against one tree | Key design principles | Typical workflow | References
Last update: 2026-06-25
Started: 2026-06-25
Phylogenetic meta-analysis with rotl + prepR4pcm
A worked example: thermal-tolerance plasticity across animal classes | Setup | Step 1-3: topology -> bifurcating -> Grafen branches, in one call | The manual pipeline (without prepR4pcm) | The same in one call (with prepR4pcm) | Confirm the two pipelines produce the same tree | Step 4: phylogenetic correlation matrix | Step 5: fit the meta-analysis with metafor | Manual tree grafting when Open Tree of Life doesn't have a species | Why Grafen (and not DateLife / a time-calibrated tree)? | What this vignette deliberately doesn't cover | See also
Last update: 2026-06-25
Started: 2026-06-25
