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Comparison · Infra & APIs
cvms vs phyloatlas
A side-by-side editorial comparison of cvms and phyloatlas — release velocity, themes, recent moves, and the top alternatives to consider.
cvms vs phyloatlas: at a glance
What is cvms?
A cross-validation package whose real development has moved to its plotting function
cvms runs repeated cross-validation over model formulas and reports comparable metrics. The 2.0.0 release was a breaking correctness fix: every function accepting fold_cols mismatched training and testing data when fold indices were non-sequential, did not start at 1, or were strings, because the iteration index was compared against the raw fold value rather than its factor level index. 2.0.1 restored coefficient extraction for nnet::multinom and mixed models by supplying an environment containing the training data, and followed lme4's move of findbars() into the reformulas package.
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.
cvms vs phyloatlas: editorial side-by-side
cvms
0.0INFRA · APIS
A cross-validation package whose real development has moved to its plotting function
◆ Current state
cvms runs repeated cross-validation over model formulas and reports comparable metrics. The 2.0.0 release was a breaking correctness fix: every function accepting fold_cols mismatched training and testing data when fold indices were non-sequential, did not start at 1, or were strings, because the iteration index was compared against the raw fold value rather than its factor level index. 2.0.1 restored coefficient extraction for nnet::multinom and mixed models by supplying an environment containing the training data, and followed lme4's move of findbars() into the reformulas package.
◆ Where it's heading
Two threads run in parallel and only one is about cross-validation. The plotting function plot_confusion_matrix() has absorbed most feature work since 1.5.0 - custom gradient palettes, intensity limits, per-tile settings, dynamic font colors keyed to value thresholds, and arguments that accept functions rather than constants - to the point where a companion web application exists for using it without code. The cross-validation core, by contrast, sees maintenance: upstream compatibility fixes for pROC, ggnewscale and ggplot2, and the fold-matching correction that finally forced a major version.
◆ Prediction
Expect continued option growth in the confusion matrix plotting surface, since that is where nearly every release since 1.5.0 has spent its changes, with core cross-validation changes arriving only as upstream packages force them.
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 cvms 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 cvms 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 cvms alternatives → · See all phyloatlas alternatives →
Recent activity from cvms 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 agocvmsCoefficient extraction restored for multinom and mixed models
- 2mo agophyloatlasv1.0.4 — data corrections + canonical succession (Supplementary Table S7)
- 2mo agophyloatlasv1.0.3 — title alignment, LICENSE, three-category framework, sensitivity bounds ⚡
- 9mo agocvmsBreaking fix for mismatched folds with non-sequential fold IDs
- 11mo agocvmsTest compatibility with pROC 1.19 and a deprecation warning fix
- 1y agocvmsConfusion matrix fonts and colors can now be computed from the values
- 1y agocvmsTile intensity by row or column percentages
- 1y agocvmsMultinom coefficient extraction fix after a parameters update
Frequently asked questions
What is the difference between cvms and phyloatlas?
They serve adjacent needs but don't currently overlap on shipped themes. cvms 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 cvms better than phyloatlas?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. cvms 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 cvms?
Top cvms alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "cvms alternatives" section above for the current picks, or visit /alternatives/cvms 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.