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Comparison · Infra & APIs
phyloatlas vs sps
A side-by-side editorial comparison of phyloatlas and sps — release velocity, themes, recent moves, and the top alternatives to consider.
phyloatlas vs sps: 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 sps?
sps keeps sanding down sequential Poisson sampling rather than adding to it.
The package implements sequential Poisson sampling for survey design, covering inclusion probabilities, proportional allocation, replicate weights, and take-all strata. Recent releases are small and tightly scoped: a divisor method helper, an iterator that draws a sample one unit at a time, automatic selection of the replicate-weight parameter, and repeated performance work on inclusion probability calculation.
phyloatlas vs sps: 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.
sps
2.5INFRA · APIS
sps keeps sanding down sequential Poisson sampling rather than adding to it.
◆ Current state
The package implements sequential Poisson sampling for survey design, covering inclusion probabilities, proportional allocation, replicate weights, and take-all strata. Recent releases are small and tightly scoped: a divisor method helper, an iterator that draws a sample one unit at a time, automatic selection of the replicate-weight parameter, and repeated performance work on inclusion probability calculation.
◆ Where it's heading
Development is consolidation rather than expansion. Most releases either speed up an existing routine or remove a decision the user previously had to make by hand, such as picking the smallest parameter that keeps replicate weights non-negative. Documentation and tooling get comparable attention to the algorithms, with a dedicated vignette on inclusion probabilities and a recent switch of test and documentation infrastructure. The API surface has been essentially stable across the window.
◆ Prediction
Expect continued small ergonomic and performance releases against the existing function set rather than new sampling designs, which is the pattern every release in this window follows.
Alternatives to phyloatlas and sps
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 sps.
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 sps alternatives →
Recent activity from phyloatlas and sps
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agospsDocumentation polish; switches to tinytest and litedown
- 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 ⚡
- 9mo agospsFixes extra argument handling in sps_iterator()
- 0y agospsAdds divisor_method() and a one-unit-at-a-time sampling iterator
- 1y agospsAdds an inclusion-probability vignette and faster partial sorting
- 1y agospsAutomatic tau selection for replicate weights
- 2y agospsAdds becomes_ta() for take-all stratum sample sizes
Frequently asked questions
What is the difference between phyloatlas and sps?
They serve adjacent needs but don't currently overlap on shipped themes. sps 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 sps?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. sps 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 sps?
Top sps alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "sps alternatives" section above for the current picks, or visit /alternatives/sps for the full list with editorial commentary on each.