paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
ardlverse vs protr
A side-by-side editorial comparison of ardlverse and protr — release velocity, themes, recent moves, and the top alternatives to consider.
ardlverse vs protr: at a glance
What is ardlverse?
An outside audit against Stata found seven errors in ardlverse's panel estimator, including regressions with no intercept.
A small R package for autoregressive distributed lag models, with only three releases on record. The first two were administrative — a CRAN version note and a Zenodo metadata update. The third, 2.0.0, is a correction release built entirely from an external audit of panel_ardl() against Stata's xtpmg, and it is the only entry here with substantive content.
What is protr?
protr's feature set is finished; the work now is surviving Bioconductor's churn.
protr generates numerical descriptors from protein sequences for machine learning, plus alignment-based similarity between sequences. The descriptor functions have been stable for years. Recent releases divide cleanly into two kinds: extending the similarity computations to work under memory constraints, and absorbing the Bioconductor split that moved pairwise alignment out of Biostrings into pwalign.
ardlverse vs protr: editorial side-by-side
ardlverse
0.0ANALYTICS
An outside audit against Stata found seven errors in ardlverse's panel estimator, including regressions with no intercept.
◆ Current state
A small R package for autoregressive distributed lag models, with only three releases on record. The first two were administrative — a CRAN version note and a Zenodo metadata update. The third, 2.0.0, is a correction release built entirely from an external audit of panel_ardl() against Stata's xtpmg, and it is the only entry here with substantive content.
◆ Where it's heading
The package's direction is now set by verification against an established reference implementation rather than by feature work. The seven fixes bring panel_ardl() into strict alignment with the original Pesaran, Shin and Smith framework, and the most serious of them is structural: internal regressions used lm.fit(), which unlike lm() does not append an intercept, so every short-run regression across the PMG, MG and DFE estimators was forced through the origin. Design matrices now carry a column of ones and DFE reconstructs the grand-mean intercept to match standard fixed-effects output.
◆ Prediction
Expect the next releases to extend the same audit approach to the remaining estimators, since a package that has been validated against xtpmg on one function invites the same question about the rest.
protr
0.0ANALYTICS
protr's feature set is finished; the work now is surviving Bioconductor's churn.
◆ Current state
protr generates numerical descriptors from protein sequences for machine learning, plus alignment-based similarity between sequences. The descriptor functions have been stable for years. Recent releases divide cleanly into two kinds: extending the similarity computations to work under memory constraints, and absorbing the Bioconductor split that moved pairwise alignment out of Biostrings into pwalign.
◆ Where it's heading
The similarity side is where the remaining engineering goes, and it follows a consistent pattern — whatever parSeqSim() gained, crossSetSim() eventually gets. Batching, verbose progress and a disk-backed variant all arrived for the single-set case first and were mirrored for the cross-set case in 1.7-1. That is a maintainer closing feature-parity gaps rather than opening new directions, and the two most recent releases contain no user-facing change at all.
◆ Prediction
Expect the next release to react to another Bioconductor or R CMD check change, which accounts for three of the last four. The similarity functions now have parity, so there is no obvious internal backlog left.
Alternatives to ardlverse and protr
Other Analytics 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 ardlverse or protr.
geodist
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
errors
errors keeps making uncertainty print the way each scientific field expects.
CMAQ
CMAQ went global in v5.5, and has been patching that surface ever since.
enpls
enpls has not changed its statistics since 2016 — only its website, twice.
grex
grex is a lookup table with a version number — it ships when the annotation moves.
See all ardlverse alternatives → · See all protr alternatives →
Recent activity from ardlverse and protr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoardlverseSeven panel_ardl fixes after an audit against Stata's xtpmg
- 5mo agoardlverseZenodo metadata updated with ORCID
- 5mo agoardlverseardlverse v1.1.3
- 11mo agoprotrprotr 1.7-5 silences a Debian r-devel check note
- 1y agoprotrprotr 1.7-4 checks alignment dependencies upfront
- 1y agoprotrprotr 1.7-3 detects Biostrings version to find pwalign
- 2y agoprotrprotr 1.7-2 fixes citation key and vignette accessibility
- 2y agoprotrprotr 1.7-1 brings crossSetSim to parity with parSeqSim
- 2y agoprotrprotr 1.7-0 adds crossSetSim for two-set similarity
Frequently asked questions
What is the difference between ardlverse and protr?
They serve adjacent needs but don't currently overlap on shipped themes. ardlverse and protr 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 ardlverse better than protr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. ardlverse and protr 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 Analytics products to evaluate alongside.
What are the best alternatives to ardlverse?
Top ardlverse alternatives in Analytics are ranked by recent ship velocity. Browse the "ardlverse alternatives" section above for the current picks, or visit /alternatives/ardlverse-r for the full list with editorial commentary on each.
What are the best alternatives to protr?
Top protr alternatives in Analytics are ranked by recent ship velocity. Browse the "protr alternatives" section above for the current picks, or visit /alternatives/protr-r for the full list with editorial commentary on each.