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Comparison · Infra & APIs
BayLum vs phyloatlas
A side-by-side editorial comparison of BayLum and phyloatlas — release velocity, themes, recent moves, and the top alternatives to consider.
BayLum vs phyloatlas: at a glance
What is BayLum?
Bayesian luminescence dating that finally replaced its folder-structure input format.
BayLum runs Bayesian age models for luminescence and combined OSL/C-14 dating on top of JAGS. The 2024 release rebuilt the front end: a single create_DataFile() replaces the separate single-grain and multi-grain generators, reads BIN/BINX and XSYG directly, and takes a YAML config in place of the old prescribed folder layout. Since then the work has been CRAN compliance and documentation.
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.
BayLum vs phyloatlas: editorial side-by-side
BayLum
0.0INFRA · APIS
Bayesian luminescence dating that finally replaced its folder-structure input format.
◆ Current state
BayLum runs Bayesian age models for luminescence and combined OSL/C-14 dating on top of JAGS. The 2024 release rebuilt the front end: a single create_DataFile() replaces the separate single-grain and multi-grain generators, reads BIN/BINX and XSYG directly, and takes a YAML config in place of the old prescribed folder layout. Since then the work has been CRAN compliance and documentation.
◆ Where it's heading
Two long-running threads have converged: making JAGS runs survivable (parallel methods, halved MCMC memory, injectable custom models) and making the inputs survivable (YAML config, consistency checks, auto-detected sample names). With the deprecated generators on their way out, the next phase is removal rather than addition. Release cadence is roughly annual and slowing.
◆ Prediction
The deprecated Generate_DataFile(), Generate_DataFile_MG() and LT_RegenDose() are the obvious next casualties; a release that drops them would be the first breaking change since the YAML rework.
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.
Alternatives to BayLum and phyloatlas
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 BayLum or phyloatlas.
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 BayLum alternatives → · See all phyloatlas alternatives →
Recent activity from BayLum and phyloatlas
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 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 ⚡
- 10mo agoBayLumCRAN anchor fixes and an R 4.4 floor
- 2y agoBayLumOne data-file function and a YAML config replace the folder layout ⚡
- 3y agoBayLumMCMC memory halved; density plots for age distributions
- 3y agoBayLumParallel JAGS runs and a file-scaffolding helper
- 4y agoBayLumCustom model injection and RNG control for parallel runs
- 5y agoBayLumParallel JAGS experiment plus IntCal20-era calibration data
Frequently asked questions
What is the difference between BayLum and phyloatlas?
They serve adjacent needs but don't currently overlap on shipped themes. BayLum and phyloatlas are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is BayLum better than phyloatlas?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. BayLum and phyloatlas are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Infra & APIs products to evaluate alongside.
What are the best alternatives to BayLum?
Top BayLum alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "BayLum alternatives" section above for the current picks, or visit /alternatives/baylum for the full list with editorial commentary on each.
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.