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Comparison · Infra & APIs
lintr vs phyloatlas
A side-by-side editorial comparison of lintr and phyloatlas — release velocity, themes, recent moves, and the top alternatives to consider.
lintr vs phyloatlas: at a glance
What is lintr?
lintr makes the native pipe the default rule and clears out a decade of deprecations
lintr is the static analysis standard for R packages, and its 3.3.0 release does two things at once: it changes pipe_consistency_linter() to require the native pipe, following the Tidyverse Style Guide, and it completes a long deprecation program — six linters fully deprecated, several arguments defunct, and a batch of functions removed outright. The 3.1.x line before it was accuracy work and a maintainer handoff to Michael Chirico.
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.
lintr vs phyloatlas: editorial side-by-side
lintr
0.0INFRA · APIS
lintr makes the native pipe the default rule and clears out a decade of deprecations
◆ Current state
lintr is the static analysis standard for R packages, and its 3.3.0 release does two things at once: it changes pipe_consistency_linter() to require the native pipe, following the Tidyverse Style Guide, and it completes a long deprecation program — six linters fully deprecated, several arguments defunct, and a batch of functions removed outright. The 3.1.x line before it was accuracy work and a maintainer handoff to Michael Chirico.
◆ Where it's heading
The package has been consolidating: overlapping linters renamed and merged, configuration validated up front, and an experimental R-script config offered as a possible replacement for the DCF format. Alongside that, a sustained campaign against false positives and false negatives in individual linters, which is where most contributor effort goes.
◆ Prediction
Expect the six warning-deprecated linters to be removed in the next release as announced, and continued movement on the R-script configuration format if feedback supports it.
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 lintr 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 lintr 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 lintr alternatives → · See all phyloatlas alternatives →
Recent activity from lintr 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 ⚡
- 8mo agolintrNative pipe required by default; six linters deprecated ⚡
- 2y agolintrFalse positive and negative fixes; new CRAN maintainer
- 2y agolintrExperimental R-script configs; up-front config validation
- 3y agolintrLinter renames for consistency; Super-Linter config discovery
- 3y agolintrTest no longer leaves cache files behind
- 3y agolintrfunction_argument_linter() added; seq_linter() covers dplyr and data.table
Frequently asked questions
What is the difference between lintr and phyloatlas?
They serve adjacent needs but don't currently overlap on shipped themes. lintr 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 lintr better than phyloatlas?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. lintr 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 lintr?
Top lintr alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "lintr alternatives" section above for the current picks, or visit /alternatives/lintr 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.