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Comparison · Infra & APIs
missSBM vs phyloatlas
A side-by-side editorial comparison of missSBM and phyloatlas — release velocity, themes, recent moves, and the top alternatives to consider.
missSBM vs phyloatlas: at a glance
What is missSBM?
missSBM returns after four dormant years with a stricter API and a new refinement step.
The package fits stochastic block models to networks with missing data, covering both missing-at-random and informative sampling designs. After a run of releases from 2019 to 2022, the feed goes quiet until this year's 1.1.0, which breaks the control interface, exposes the block split and merge operations as testable instance methods, and adds a node-swap refinement pass that runs after variational convergence.
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.
missSBM vs phyloatlas: editorial side-by-side
missSBM
2.5INFRA · APIS
missSBM returns after four dormant years with a stricter API and a new refinement step.
◆ Current state
The package fits stochastic block models to networks with missing data, covering both missing-at-random and informative sampling designs. After a run of releases from 2019 to 2022, the feed goes quiet until this year's 1.1.0, which breaks the control interface, exposes the block split and merge operations as testable instance methods, and adds a node-swap refinement pass that runs after variational convergence.
◆ Where it's heading
The new release is maintenance-driven in the best sense: it targets the parts of the codebase that were hard to test or easy to misuse. Replacing free-form control lists with a function of named, defaulted arguments turns silent typos into errors, and pulling the exploration logic out of the collection class makes the search algorithm independently testable without changing it. The polish step addresses a known weakness, reaching individually misclassified nodes that split and merge moves cannot fix.
◆ Prediction
Given the gap before this release, the near-term question is whether the cadence resumes at all; the refactoring it contains would support further algorithmic work if it does.
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 missSBM 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 missSBM 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 missSBM alternatives → · See all phyloatlas alternatives →
Recent activity from missSBM and phyloatlas
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 27d agomissSBMReplaces raw control lists with missSBM_param(), adds polish()
- 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 ⚡
- 3y agomissSBMAdapts to Matrix 1.4-2 and fixes HTML5 documentation
- 4y agomissSBMFixes linking against nloptR 2.0.0
- 5y agomissSBMRelaxes CRAN test tolerances to avoid random failures
- 5y agomissSBMRewrites optimisation in C++ armadillo with sparse matrices
- 5y agomissSBMRenames core functions and interfaces with the sbm package
Frequently asked questions
What is the difference between missSBM and phyloatlas?
They serve adjacent needs but don't currently overlap on shipped themes. missSBM 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 missSBM better than phyloatlas?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. missSBM 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 missSBM?
Top missSBM alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "missSBM alternatives" section above for the current picks, or visit /alternatives/misssbm 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.