paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
citeme vs protr
A side-by-side editorial comparison of citeme and protr — release velocity, themes, recent moves, and the top alternatives to consider.
citeme vs protr: at a glance
What is citeme?
Citation metadata machinery breaks out of INBO's checklist package to stand on its own.
citeme handles citation metadata for research software and organisations — building citation files, validating ORCIDs, RORs, licenses and URLs, and prompting for the pieces interactively. It was extracted from the checklist package in 0.1.0 and has spent the four releases since fleshing out organisational roles, most visibly publishers.
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.
citeme vs protr: editorial side-by-side
citeme
0.0ANALYTICS
Citation metadata machinery breaks out of INBO's checklist package to stand on its own.
◆ Current state
citeme handles citation metadata for research software and organisations — building citation files, validating ORCIDs, RORs, licenses and URLs, and prompting for the pieces interactively. It was extracted from the checklist package in 0.1.0 and has spent the four releases since fleshing out organisational roles, most visibly publishers.
◆ Where it's heading
Development is running in tight monthly increments along two tracks: modelling who is attached to a piece of research software, and smoothing the interactive prompts that collect it. The publisher role added in 0.1.1 propagated through validation, community detection and YAML handling over the next two releases, which is how this package tends to land a concept — introduce the class field, then follow it everywhere it needs to reach.
◆ Prediction
Expect the interactive ask_* family to keep growing alongside whatever metadata field is being modelled next, and further alignment with the checklist package it was carved out of.
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 citeme 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 citeme 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 citeme alternatives → · See all protr alternatives →
Recent activity from citeme and protr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agocitemeInteractive keyword prompts and YAML logical fixes
- 1mo agocitemeREADME parsing handles a missing language badge
- 2mo agocitemePublisher role reaches badges and README metadata
- 3mo agocitemeOrganisations can declare publisher requirements
- 4mo agocitemeciteme splits out of checklist as its own package ⚡
- 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 citeme and protr?
They serve adjacent needs but don't currently overlap on shipped themes. citeme 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 citeme better than protr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. citeme 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 citeme?
Top citeme alternatives in Analytics are ranked by recent ship velocity. Browse the "citeme alternatives" section above for the current picks, or visit /alternatives/citeme-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.