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Comparison · Infra & APIs
phyloatlas vs projoint
A side-by-side editorial comparison of phyloatlas and projoint — release velocity, themes, recent moves, and the top alternatives to consider.
phyloatlas vs projoint: at a glance
What is phyloatlas?
An atlas of the tree of life that keeps publishing what it got wrong, and stopped shipping the trees it does not own.
This is a curated deposit of species-level phylogenies — 264 trees across 62 partitions, 247 of them time-calibrated — paired with a species-name dictionary of roughly 638,000 standardized labels and per-tree provenance. It is moving through peer review at Methods in Ecology and Evolution, and the release stream is essentially a public erratum log: eight releases in five weeks, each reconciling the deposit against source papers, the manuscript, and its own metadata. The most recent replaced the turtle canonical with a 274-tip ultrametric chronogram after the previous tree failed time-calibration integrity checks.
What is projoint?
projoint spent a year on CRAN paperwork, then shipped a correctness fix it flagged itself.
projoint is an R package for analysing conjoint survey experiments, covering Qualtrics import, reshaping, and quantity-of-interest estimation with inter-rater reliability correction. Most of its release history is CRAN admission work — citation formats, DESCRIPTION fields, \value{} tags, vignette cleanups — with four tags backfilled within ninety seconds of each other on 15 July in non-monotonic version order, so neither tag order nor timestamps in this feed track the real sequence. The substantive releases are the ones fixing data-preparation bugs that silently corrupt estimates.
phyloatlas vs projoint: editorial side-by-side
phyloatlas
0.0INFRA · APIS
An atlas of the tree of life that keeps publishing what it got wrong, and stopped shipping the trees it does not own.
◆ Current state
This is a curated deposit of species-level phylogenies — 264 trees across 62 partitions, 247 of them time-calibrated — paired with a species-name dictionary of roughly 638,000 standardized labels and per-tree provenance. It is moving through peer review at Methods in Ecology and Evolution, and the release stream is essentially a public erratum log: eight releases in five weeks, each reconciling the deposit against source papers, the manuscript, and its own metadata. The most recent replaced the turtle canonical with a 274-tip ultrametric chronogram after the previous tree failed time-calibration integrity checks.
◆ Where it's heading
The project's defining decision is that it archives the recipe rather than the corpus. Since 1.0.3 the Zenodo deposit holds metadata, provenance, and standardization code while the tree files live at their original sources, and the same principle was applied again when the TimeTree-of-Life was removed at the TimeTree project's request and reduced to a citation. What makes the correction log unusual is its direction: partitions keep getting reclassified from dated to undated as verification confirms the source papers described chronograms they never deposited. The atlas is being built to be honest about archival uncertainty rather than to maximize coverage.
◆ Prediction
The release cadence is driven by the manuscript review cycle, so expect corrections to continue until MEE acceptance and then slow sharply; the open thread most likely to produce the next one is the remaining recoverable archival uncertainty flagged across non-Condamine dated source trees.
projoint
2.5INFRA · APIS
projoint spent a year on CRAN paperwork, then shipped a correctness fix it flagged itself.
◆ Current state
projoint is an R package for analysing conjoint survey experiments, covering Qualtrics import, reshaping, and quantity-of-interest estimation with inter-rater reliability correction. Most of its release history is CRAN admission work — citation formats, DESCRIPTION fields, \value{} tags, vignette cleanups — with four tags backfilled within ninety seconds of each other on 15 July in non-monotonic version order, so neither tag order nor timestamps in this feed track the real sequence. The substantive releases are the ones fixing data-preparation bugs that silently corrupt estimates.
◆ Where it's heading
The maintainer is hardening the path from raw Qualtrics export to estimate, which is where conjoint analysis quietly goes wrong. Three separate releases fix that path: dropped respondent-level weights in organize_data(), repeated-task reshaping in reshape_projoint(), and choice-to-profile mapping in 1.1.3. Each fix now arrives with regression tests and stricter validation rather than just a patch, and 1.1.3 adds an explicit .choice_map so the mapping is auditable instead of inferred.
◆ Prediction
Expect the validation-and-regression-test pattern to keep extending across the import path, with releases continuing to arrive in bursts around CRAN submission rather than on a cadence.
Alternatives to phyloatlas and projoint
Other Infra & APIs products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either phyloatlas or projoint.
forestploter
A forest plot package that keeps handing users control of one more graphical detail.
ggInterval
Interval-valued data plotting, spending 2026 making its function names and examples survive CRAN.
rgm
A microbiome network model that got itself un-archived by deleting the dependency that killed it.
contagionchannels
Three releases in ten days, every one of them a CRAN reviewer's correction rather than a code change.
tidyaudit
Pipeline provenance for tidyverse workflows, recording what changed at each step without keeping the data.
See all phyloatlas alternatives → · See all projoint alternatives →
Recent activity from phyloatlas and projoint
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 17d agoprojointExplicit .choice_map guards choice-to-profile mapping
- 1mo agoprojointCRAN submission housekeeping for DESCRIPTION and examples
- 1mo agoprojointCRAN formatting pass; minor make_projoint_data() fix
- 1mo agoprojointreshape_projoint() repeated-task bug fixed; validation tightened
- 1mo agoprojointCitation metadata updated with the CRAN DOI
- 1mo agophyloatlasv1.0.8 — turtle chronogram canonical; MEE integrity pass
- 1mo agophyloatlasv1.0.7 — restore species-name dictionary
- 1mo agophyloatlasv1.0.6 — data-integrity corrections + TimeTree de-redistribution
- 2mo agophyloatlasv1.0.5 — consistency corrections
- 2mo agophyloatlasv1.0.4 — data corrections + canonical succession (Supplementary Table S7)
- 2mo agophyloatlasv1.0.3 — title alignment, LICENSE, three-category framework, sensitivity bounds ⚡
- 5mo agoprojointorganize_data() no longer drops respondent-level weights
Frequently asked questions
What is the difference between phyloatlas and projoint?
They serve adjacent needs but don't currently overlap on shipped themes. projoint is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is phyloatlas better than projoint?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. projoint is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Infra & APIs products to evaluate alongside.
What are the best alternatives to phyloatlas?
Top phyloatlas alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "phyloatlas alternatives" section above for the current picks, or visit /alternatives/phylo-species-atlas for the full list with editorial commentary on each.
What are the best alternatives to projoint?
Top projoint alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "projoint alternatives" section above for the current picks, or visit /alternatives/projoint for the full list with editorial commentary on each.