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Comparison · Infra & APIs
ggdist vs phyloatlas
A side-by-side editorial comparison of ggdist and phyloatlas — release velocity, themes, recent moves, and the top alternatives to consider.
ggdist vs phyloatlas: at a glance
What is ggdist?
The grammar of uncertainty visualization, now drawing the uncertainty in its own estimates.
ggdist supplies ggplot2 with a compositional vocabulary for distributions — slabs, intervals, dotplots and the sub-geometries that combine them. The last three years moved it from a drawing library to an estimation library: bounded density estimation with Sheather-Jones bandwidth became the default, weights propagate through every density, interval and point summary, and blurred dotplots render Monte Carlo standard error as visual fuzz. The 2025 release rounds this out with per-geometry thickness subscales and settable global defaults.
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.
ggdist vs phyloatlas: editorial side-by-side
ggdist
0.0INFRA · APIS
The grammar of uncertainty visualization, now drawing the uncertainty in its own estimates.
◆ Current state
ggdist supplies ggplot2 with a compositional vocabulary for distributions — slabs, intervals, dotplots and the sub-geometries that combine them. The last three years moved it from a drawing library to an estimation library: bounded density estimation with Sheather-Jones bandwidth became the default, weights propagate through every density, interval and point summary, and blurred dotplots render Monte Carlo standard error as visual fuzz. The 2025 release rounds this out with per-geometry thickness subscales and settable global defaults.
◆ Where it's heading
Two threads run in parallel and keep converging. One is statistical: pluggable density estimators arrived first, then became the default, then gained weights and quantile histograms. The other is compositional: sub-geometries acquired their own guides, then their own scales, so a slab's thickness axis is now a first-class annotated dimension. Cadence has stretched from twice-yearly to roughly annual, with the recent work tightening existing surface rather than opening new.
◆ Prediction
Subguides gained subscales a release later, so the remaining asymmetry is in the sub-geometry system rather than the statistics; expect the next release to continue that fill-in work.
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 ggdist 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 ggdist 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 ggdist alternatives → · See all phyloatlas alternatives →
Recent activity from ggdist 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 ⚡
- 1y agoggdistPer-geometry thickness subscales and settable defaults
- 2y agoggdistBlurred dotplots draw Monte Carlo error; weights reach every estimator ⚡
- 2y agoggdistC++ dotplot binning and safer bandwidth fallbacks
- 3y agoggdistBounded density becomes the default; existing charts change ⚡
- 3y agoggdistCategorical distributions, hex layouts, pluggable density estimators
- 4y agoggdistComputed variables shared across sub-geometries
Frequently asked questions
What is the difference between ggdist and phyloatlas?
They serve adjacent needs but don't currently overlap on shipped themes. ggdist 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 ggdist better than phyloatlas?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. ggdist 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 ggdist?
Top ggdist alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "ggdist alternatives" section above for the current picks, or visit /alternatives/ggdist 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.