# Comparing tree backends — when do they agree?

`prepR4pcm` can fetch a phylogenetic tree for your species from five different backends — external packages, each wrapped by `pr_get_tree()`, that supply a tree from a different reference source. The five backends draw on different reference trees, different taxonomies, and different calibration approaches, so the tree you get depends on which backend you pick. This vignette answers how much they disagree, and where.

This vignette walks through `pr_tree_compare()` and shows how to use it to make a defensible backend choice for your dataset — or to report which backend choice you made and what the alternatives would have given.

## Setup

Comparison requires multiple tree-retrieval backends installed. Each backend lives in a different package because each draws on a different reference tree or taxonomy:

- `rotl` (CRAN): client for the Open Tree of Life synthesis tree — the only backend with universal taxon coverage. Required for `source = "rotl"`.
- `fishtree` (CRAN): wraps the Fish Tree of Life (Rabosky et al. 2018), a time-calibrated ray-finned fish phylogeny. Required for `source = "fishtree"`.
- `rtrees` (github.com/daijiang/rtrees): grafts species onto taxon-specific mega-trees (mammals, birds, fish, amphibians, etc.). Required for `source = "rtrees"`.
- `clootl` (github.com/eliotmiller/clootl): supplies a phylogeny in the current Clements bird taxonomy. Required for `source = "clootl"`.
- `datelife`: synthesis chronograms assembled from many per-clade published trees. Required for `source = "datelife"`.

Install whichever you need. CRAN packages first, then GitHub-only backends via `pak`:

    library(prepR4pcm)
    # install.packages(c("rotl", "fishtree"))                 # CRAN
    # pak::pak("daijiang/rtrees")                             # GitHub
    # pak::pak("eliotmiller/clootl")                          # GitHub
    # pak::pak("phylotastic/datelife")                        # GitHub (heavy)

Check what’s installed and reachable in your session:

    pr_get_tree_status()
    #>     source installed version needs_network reachable
    #> 1     rotl      TRUE   3.1.1          TRUE        NA
    #> 2   rtrees      TRUE   1.0.4         FALSE        NA
    #> 3   clootl      TRUE   0.1.4         FALSE        NA
    #> 4 fishtree      TRUE   0.3.4          TRUE        NA
    #> 5 datelife     FALSE    <NA>         FALSE        NA
    #>                       install_hint                  source_repo
    #> 1         install.packages("rotl")                         CRAN
    #> 2      pak::pak("daijiang/rtrees")      github::daijiang/rtrees
    #> 3   pak::pak("eliotmiller/clootl")   github::eliotmiller/clootl
    #> 4     install.packages("fishtree")                         CRAN
    #> 5 pak::pak("phylotastic/datelife") github::phylotastic/datelife

## The recipe

Pick a small species list. Retrieve the same set from two or three backends. Compare.

    species <- c("Salmo salar", "Esox lucius", "Oncorhynchus mykiss",
                 "Gadus morhua", "Thunnus thynnus")

    # Three backends that all cover fish
    res_rotl     <- pr_get_tree(species, source = "rotl")
    res_fishtree <- pr_get_tree(species, source = "fishtree")
    res_rtrees   <- pr_get_tree(species, source = "rtrees", taxon = "fish")

About the `TNRS replaced ...` warning. `pr_get_tree()` runs the Open Tree of Life Taxonomic Name Resolution Service (TNRS) on the input names before passing them to the backend, so that minor spelling or capitalisation differences don’t cause a name to fall out of the tree silently. When TNRS finds a canonical form that differs from the input (e.g. an old binomial replaced by the current synonym), the wrapper substitutes the canonical form and emits a warning listing each replacement, so the substitution is visible in the run log. The retrieval still succeeds; the warning is informational.

The three results are independent. Now compare:

    cmp <- pr_tree_compare(
      rotl     = res_rotl,
      fishtree = res_fishtree,
      rtrees   = res_rtrees
    )
    cmp

The print method shows up to three pairwise matrices, depending on what is computable for your set of trees. Reading them:

- Tip-set Jaccard — fraction of species both trees place. 1.0 = same species set. 0.0 = no overlap. If any pairwise value is < 1, the two trees do not cover the same species set, so the topological comparison below is restricted to the species both trees include.
- Robinson-Foulds distance — number of internal edges that differ between the two trees, restricted to their shared tip set. Lower = trees agree more. `NA` off-diagonal means the shared-tip subtree has fewer than four taxa (Robinson-Foulds is undefined below four shared tips), or one of the input trees could not be pruned to the shared subtree without becoming degenerate. Diagonal values are always 0 (a tree against itself).
- Branch-length correlation — Pearson correlation of sorted edge lengths after pruning to the shared subtree. Useful as a rough check on whether two chronograms use the same branch-length scale (e.g. millions of years vs unit-length placeholders). This matrix is only printed when at least one pair has computable branch lengths on both sides. If `rotl` trees (which carry unit-length placeholder branches) are part of the comparison, the matrix may collapse to NA and the print method drops it; that is why you sometimes see only two matrices rather than three.

## What actually works (status table)

Backends differ in coverage and in what `n_tree > 1` does. Verified on a clean macOS R 4.4 install on 2026-05-01. Column meanings:

- Backend — the value you pass as `source = "..."` to `pr_get_tree()`.
- Single tree — does `pr_get_tree(..., n_tree = 1)` (the default) return a single `ape::phylo` object cleanly?
- Multi-tree (`n_tree > 1`) — does the backend support returning a posterior or sample of trees? Some backends ship a single mega-tree and ignore `n_tree`; others support a true posterior sample.
- Notes — backend-specific gotchas worth knowing before you trust the result.

Backend | Single tree | Multi-tree (`n_tree > 1`) | Notes
--- | --- | --- | ---
`rotl` | ✅ | n/a — synthesis is a single tree | Returns lowercase tip labels (e.g. `salmo salar`) because Open Tree taxonomy names are case-folded; reconcile against the tree if your input mixes cases.
`rtrees` | ✅ | ✅ for taxa whose mega-tree is a posterior (e.g. `taxon = "bird"`, `"mammal"` → 100 trees); returns 1 tree for taxa with a single mega-tree (e.g. `taxon = "fish"`). | `n_tree` is informational only — `rtrees::get_tree()` has no `n_tree` argument, so the count is fixed by the chosen mega-tree.
`clootl` | ✅ | ❌ unless the AvesData repo is installed (run `clootl::get_avesdata_repo(".")` once). `n_tree = 1` calls `clootl::extractTree()` and works out of the box; `n_tree > 1` calls `clootl::sampleTrees(count = …)` and needs AvesData. | The single-tree path uses the v1.6 / 2025 taxonomy bundled with `clootl`. Posterior sampling caps at 100 upstream.
`fishtree` | ✅ | ✅ — `n_tree > 1` switches to `fishtree::fishtree_complete_phylogeny()` and returns the requested count. | Time-calibrated.
`datelife` | likely ✅ | likely ✅ | Untested in this run because `datelife` is in `Enhances` (heavy Bioconductor / BOLD deps). Install with `pak::pak("phylotastic/datelife")`.
`pr_date_tree()` | likely ✅ | likely ✅ | Same dependency story as `datelife`.

If you hit a broken row above on a fresh install, please open an issue at itchyshin/prepR4pcm with your `pr_get_tree_status()` output and the error.

## Branch lengths and time-calibration

Phylogenetic comparative methods (PGLS with Pagel’s λ, Brownian motion, OU, phylogenetic meta-analysis) need branch lengths that correspond to time — not just topology. Backends differ in what branch lengths they produce:

Backend | Branch lengths produced | Real time? | Taxonomic scope
--- | --- | --- | ---
`rotl` (default) | None — synthesis topology only | No | Universal
`rotl` + `resolve_polytomies = TRUE, branch_lengths = "grafen"` | Grafen ρ = 1 arbitrary depths | No (arbitrary) | Universal
`fishtree` | Yes — divergence times from Rabosky et al. 2018 | Yes | Ray-finned fish
`clootl` | Yes — Bird Tree consensus branches | Yes | Birds (current Clements)
`rtrees` (any `taxon`) | Yes — branches from `megatrees` posterior | Yes | Birds, mammals, fish, amphibians, reptiles, plants, sharks, bees, butterflies
`datelife` | Yes — SDM-summary chronograms or per-source candidates | Yes | Universal
`pr_date_tree(tree)` | Yes — calibrates your topology via DateLife | Yes | Universal
Manual `ape::chronos()` with user calibration points | Yes | Yes | Universal

The decision tree, in practice:

1. Is your taxon covered by a dedicated time-calibrated backend? For fish use `fishtree`; for birds, mammals, amphibians, squamates, sharks, or plants use `rtrees` with the matching `taxon`. These are pre-computed, pre-dated, and need no extra dependencies.
2. Is your taxon set cross-clade (e.g. a thermal-tolerance dataset spanning lampreys, bivalves, insects, fish, amphibians, reptiles)? Then your options are:
   1. `datelife` for a real time-calibrated solution. Install via `pak::pak("phylotastic/datelife")`. Heavy dependency tree (Bioconductor, BOLD); usually works on macOS / Linux with system libs, sometimes flaky on Windows.
   2. `rotl + resolve_polytomies = TRUE, branch_lengths = "grafen"` for Grafen pseudo-time. Defensible for phylogenetic meta- analysis where you mainly need a correlation structure, not real divergence times (this is the pattern Cinar et al. 2022 and Pottier et al. 2022 use). See the phylogenetic meta-analysis vignette for a worked example.
   3. Hand-curated calibration points + `ape::chronos()` if you have published divergence-time estimates for a small set of nodes.
3. Do you already have a topology you want time-calibrated? `pr_date_tree(your_tree)` wraps `datelife::datelife_use()` and has the same install requirement as the `datelife` backend.

If `datelife` is the option you want and it won’t install on your system, the practical fallbacks (in roughly preferred order) are: the dedicated taxon backend if one exists for your taxa; Grafen pseudo-time for meta-analysis-style use; or hand calibration for small, well-studied taxon sets.

## Where are the VertLife trees?

A common question: “I want the VertLife / Upham et al. 2019 mammal posterior — which backend has it?”

Short answer: `source = "rtrees"` has them. `rtrees` depends on the `megatrees` package, which ships 100 randomly-sampled posterior trees from each of the major VertLife datasets (mammals: Upham et al. 2019; amphibians: Jetz & Pyron 2018; squamates: Tonini et al. 2016; sharks: Stein et al. 2018; birds: Jetz et al. 2012). When you call `pr_get_tree(species, source = "rtrees", taxon = "mammal")`, the returned `multiPhylo` is exactly that 100-tree subset of the VertLife posterior, grafted to your species set.

If you need the full 10,000-tree posterior (rather than the 100-tree subset), you currently have to download the source archive manually from vertlife.org (each archive is 0.5–2 GB). A future round may add a `source = "vertlife"` backend that automates this caching step; for now, the 100-tree subset via `rtrees` is what you get out of the box, which is sufficient for the great majority of phylogenetic comparative analyses.

## Note on tip labels before comparing

The three backends use different conventions for tip labels:

- `rotl` appends an Open Tree OTT id to each tip (e.g. `Salmo_salar_ott854188`) and lower-cases the binomial.
- `fishtree` returns the canonical binomial with spaces (`Salmo salar`).
- `rtrees` returns the canonical binomial with underscores (`Salmo_salar`).

`pr_tree_compare()` matches tips by case- and separator-folded binomial (it strips `_ott<digits>`, converts underscores to spaces, and lower-cases) before computing Jaccard, so you do not need to clean the labels yourself for the comparison to work. The folded form is used only for matching; the original tip labels are preserved in each tree.

If you intend to use one of the returned trees downstream (e.g. feed it to `pr_phylo_cor()` and then to `metafor::rma.mv()`), you will usually want to strip those suffixes yourself with `gsub("_ott\\d+", "", tree$tip.label)` first. See the meta-analysis-with-rotl vignette for that workflow.

## What to do with the result

### When the backends return the same species set and similar topology (Jaccard ≈ 1, RF small)

The backends return the same species set (Jaccard ≈ 1) and broadly similar topologies (low Robinson-Foulds distance). Pick whichever backend best matches your taxonomic / temporal needs. Document the choice. Call `pr_cite_tree()` to capture the citation:

    pr_cite_tree(res_fishtree, format = "markdown")

### When tip sets differ (Jaccard < 1)

The backends disagree on which species are valid. Inspect the unique-to lists:

    cmp$unique_to$rotl     # species rotl placed but the others didn't
    cmp$unique_to$fishtree # species fishtree placed but the others didn't
    cmp$shared_tips        # species placed by all backends

Common causes:

- Taxonomy difference. rotl uses Open Tree taxonomy; fishtree uses its own; clootl uses Clements. The same species may have different canonical names.
- Coverage gap. A species is in one reference tree but not another (often a recently described species).
- Synonymy. One backend matches via synonymy, another doesn’t.

Mitigation: re-run with `tnrs = "always"` to harmonise names via Open Tree’s TNRS first. See `?pr_get_tree`.

### When topologies disagree (RF large)

The trees agree on which species exist but disagree on how they’re related. This is the genuinely interesting case.

- For exploratory analyses, fit your model on each tree and report the range of estimates across them.
- For the analysis you intend to publish, pick the backend whose underlying phylogeny is the best-established for your taxon — the most recent, most densely sampled peer-reviewed tree for that group: `fishtree` for ray-finned fish, `clootl` for birds, and `datelife` for groups that need time-calibrated branch lengths and have no taxon-specific tree.

The companion package pigauto is built for this: hand it the multiPhylo of every backend’s tree, fit your model on each, and pool the results via Rubin’s rules. A single-tree analysis reports its confidence intervals as if the tree were known exactly — but it is not, and a different backend would have given a different tree. Pooling across the backends’ trees widens the intervals to absorb that tree-choice uncertainty, so the reported intervals are not falsely narrow.

    # Fitting across backends (not just within a backend's posterior)
    all_trees <- structure(list(res_rotl$tree, res_fishtree$tree,
                                res_rtrees$tree[[1]]),
                           class = "multiPhylo")
    # pigauto::multi_impute_trees(trait_data, all_trees, m_per_tree = 5)

### When branch-length correlation is low

The trees agree on topology but not on branch-length scale. Usually that is because one tree is time-calibrated (branch lengths in millions of years) and the other is not (branch lengths in unit-length placeholders, or in Grafen-units, or in some other non-time scale):

- `rotl` returns the synthesis tree with no calibration.
- `rtrees` grafts onto a reference tree; calibration is whatever the reference uses.
- `fishtree` and `clootl` and `datelife` all return time-calibrated trees.

If your downstream model expects calibrated branches (most BM / OU / lambda models do), use a calibrated backend. If the only calibrated option for your taxon is `datelife`, see `?pr_date_tree` for dating an existing topology.

## Caching the comparisons

Each retrieval is slow. If you’re going to compare backends, set `cache = TRUE` so re-running the vignette is instant:

    old_cache <- getOption("prepR4pcm.cache_dir", NULL)
    tmp_cache <- tempfile("prepR4pcm-cache-")
    pr_tree_cache_dir(tmp_cache)

    res_rotl     <- pr_get_tree(species, source = "rotl",
                                 cache = TRUE)
    res_fishtree <- pr_get_tree(species, source = "fishtree",
                                 cache = TRUE)
    res_rtrees   <- pr_get_tree(species, source = "rtrees",
                                 taxon  = "fish", cache = TRUE)

    # See what's cached
    pr_tree_cache_status()

    # Wipe just the rotl entries (e.g. after an OTT version refresh)
    pr_tree_cache_clear(source = "rotl", confirm = FALSE)

    options(prepR4pcm.cache_dir = old_cache)
    unlink(tmp_cache, recursive = TRUE)

By default the cache lives at `tools::R_user_dir()`. Pass an explicit temporary or project cache directory if you want a separate cache for a specific analysis:

    old_cache <- getOption("prepR4pcm.cache_dir", NULL)
    tmp_cache <- tempfile("prepR4pcm-cache-")
    pr_tree_cache_dir(tmp_cache)
    options(prepR4pcm.cache_dir = old_cache)
    unlink(tmp_cache, recursive = TRUE)

## What `pr_tree_compare()` doesn’t do (yet)

- Bipartition-matched branch-length correlation. The current implementation correlates sorted edge lengths, which is a coarse but defensible “do they agree on rate scale” check. A proper bipartition-matched correlation is a future-round refinement.
- Visualisation. Pair with `phytools::cophyloplot()` or `phangorn::densiTree()` for visual comparison of two or many trees.
- Three-or-more-tree consensus. For “what’s the median tree across these three backends?”, use `phangorn::consensus(c(res_rotl$tree, res_fishtree$tree, res_rtrees$tree[[1]]))`.

## See also

- `?pr_tree_compare` — full reference for the comparison function.
- `?pr_get_tree` — the main function for fetching a tree.
- `?pr_get_tree_status` — lists which backends are installed and reachable in your session.
- `?pr_tree_cache_dir` — manage the on-disk cache of retrieved trees.
- The posterior-tree pipeline vignette for the prepR4pcm → pigauto integration.