rollupTree
The recursive-computation engine under massProps grows the accessors its consumer needed
Comparison · Infra & APIs
PEIMAN2 vs ShortForm
A side-by-side editorial comparison of PEIMAN2 and ShortForm — release velocity, themes, recent moves, and the top alternatives to consider.
PEIMAN2 vs ShortForm: at a glance
What is PEIMAN2?
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
What is ShortForm?
Automated scale shortening with lavaan, spending its releases repairing its own search algorithms.
ShortForm automates the creation of short-form psychometric scales by searching for well-fitting subsets of items, using ant colony optimization, simulated annealing and Tabu search over lavaan models. The recent releases are corrective: 0.5.7 fixed the ant colony algorithm failing to update its best model and the simulated annealing routine mis-specifying models containing factor relationships or outcome variables, and 0.5.8 fixed Tabu search under parallel workflows and with multidimensional models. Each release note carries an explicit roadmap listing refactoring for 0.6.0 and input standardisation for 0.7.0, neither of which has shipped.
PEIMAN2 vs ShortForm: editorial side-by-side
PEIMAN2
0.0INFRA · APIS
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
◆ Current state
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
◆ Where it's heading
The package has been moving from a fixed snapshot toward versioned, user-selectable data. Earlier releases updated the bundled database in place — 1.0.0 shipped the March 2025 version and said little else — which meant the annotation vintage was whatever the package version implied. Now update_peiman_database() downloads and caches external database files and UniProt PTM lists, enrichment workflows take a database_version argument, and the mass-spec translators take a ptmlist_version, so an analysis can pin a dated database rather than a package release. The CRAN-safe default is preserved deliberately: loading, examples and checks still use the bundled internal data and need no network.
◆ Prediction
Version pinning is now expressible but the release notes do not describe how a chosen version is recorded in output, so surfacing the active database version in results is the natural companion. The database and the UniProt PTM list are versioned separately, which leaves room for a combined manifest.
ShortForm
0.0INFRA · APIS
Automated scale shortening with lavaan, spending its releases repairing its own search algorithms.
◆ Current state
ShortForm automates the creation of short-form psychometric scales by searching for well-fitting subsets of items, using ant colony optimization, simulated annealing and Tabu search over lavaan models. The recent releases are corrective: 0.5.7 fixed the ant colony algorithm failing to update its best model and the simulated annealing routine mis-specifying models containing factor relationships or outcome variables, and 0.5.8 fixed Tabu search under parallel workflows and with multidimensional models. Each release note carries an explicit roadmap listing refactoring for 0.6.0 and input standardisation for 0.7.0, neither of which has shipped.
◆ Where it's heading
The defects being fixed are in the search itself rather than around it. An optimizer that does not correctly retain its best candidate, and a search that mis-specifies models after the first iteration, both produce plausible-looking short forms that are not the ones the method should have found, which is a harder class of problem to notice than a crash. Alongside that the package is shedding dependencies, with ggplot2, ggrepel and tidyr dropped from the plotting methods in 0.5.8. The stated intent to refactor the major functions and standardise their arguments suggests the maintainer regards the current interface as the obstacle to further work.
◆ Prediction
The roadmap repeated across these notes points to a 0.6.0 focused on refactoring the major functions, with argument and output standardisation deferred to 0.7.0. On the evidence of this window, more unit tests and further algorithm-level fixes are likelier to arrive first than either milestone.
Alternatives to PEIMAN2 and ShortForm
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 PEIMAN2 or ShortForm.
massProps
A mass-properties rollup spends a year on documentation and follows its sibling's API
writeAlizer
Six months of releases and not one of them touched the scoring models
samplr
A cognitive-science sampling package ships once, then goes quiet for eighteen months
stochvol
A Bayesian volatility sampler in its maintenance decade, paying for its own speed
midr
A black-box interpreter reaches CRAN, then learns multi-class and survival responses
See all PEIMAN2 alternatives → · See all ShortForm alternatives →
Recent activity from PEIMAN2 and ShortForm
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 3mo agoShortFormTabu search fixed for parallel and multidimensional models
- 3mo agoShortFormAnt colony search failed to retain its best model
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 1y agoShortFormlavaan model specification defaults made forgiving
- 2y agoShortFormCompatibility fixes for a new lavaan release
- 2y agoShortFormAdapted to changed lavaan error and warning messages
- 2y agoShortFormDefault specification tweaks and documentation fixes
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
Frequently asked questions
What is the difference between PEIMAN2 and ShortForm?
They serve adjacent needs but don't currently overlap on shipped themes. PEIMAN2 and ShortForm 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 PEIMAN2 better than ShortForm?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and ShortForm 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 PEIMAN2?
Top PEIMAN2 alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "PEIMAN2 alternatives" section above for the current picks, or visit /alternatives/peiman2 for the full list with editorial commentary on each.
What are the best alternatives to ShortForm?
Top ShortForm alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "ShortForm alternatives" section above for the current picks, or visit /alternatives/shortform for the full list with editorial commentary on each.