rollupTree
The recursive-computation engine under massProps grows the accessors its consumer needed
Comparison · Infra & APIs
PEIMAN2 vs stochvol
A side-by-side editorial comparison of PEIMAN2 and stochvol — release velocity, themes, recent moves, and the top alternatives to consider.
PEIMAN2 vs stochvol: 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 stochvol?
A Bayesian volatility sampler in its maintenance decade, paying for its own speed
stochvol runs MCMC for stochastic volatility models, with a C++ sampler underneath an R interface. Five years of releases in this window contain no new models: the work is compiler and dependency compatibility, CRAN check notes, and a steady trickle of corrections to the sampler itself. Its methodological milestone, the Journal of Statistical Software paper, is recorded in a 2021 tag.
PEIMAN2 vs stochvol: 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.
stochvol
0.0INFRA · APIS
A Bayesian volatility sampler in its maintenance decade, paying for its own speed
◆ Current state
stochvol runs MCMC for stochastic volatility models, with a C++ sampler underneath an R interface. Five years of releases in this window contain no new models: the work is compiler and dependency compatibility, CRAN check notes, and a steady trickle of corrections to the sampler itself. Its methodological milestone, the Journal of Statistical Software paper, is recorded in a 2021 tag.
◆ Where it's heading
This is what a finished computational package looks like. The formula interface arrived at 3.1.0 and nothing has been added since; what changes is the ground underneath — RcppArmadillo major versions, UBSan checks, error-handling conventions moving from Rf_error to Rcpp::stop for correct memory management. The recurring pattern worth watching is that several releases fix real errors in the sampler's proposal distributions, found by users and by CRAN's own instrumented checks rather than by the maintainer.
◆ Prediction
Nothing in these notes suggests new methodology. Expect the next release when RcppArmadillo or a CRAN check flavour forces one, and treat any bug report against the samplers as the more consequential event.
Alternatives to PEIMAN2 and stochvol
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 stochvol.
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
midr
A black-box interpreter reaches CRAN, then learns multi-class and survival responses
GeoThinneR
Spatial thinning grows a result object, and the API breaks to make room for it
See all PEIMAN2 alternatives → · See all stochvol alternatives →
Recent activity from PEIMAN2 and stochvol
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 5mo agostochvolSampler crash with constant parameters fixed, plus RcppArmadillo 15
- 1y agostochvolTwo CRAN check notes cleared
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 1y agostochvolProposal variance corrected in the centered parameterisation
- 2y agostochvolCRAN stochvol 3.2.4
- 2y agostochvolRolling-window indexing and inverse gamma prior validation fixed
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
- 3y agostochvolCore C++ sampler routines exported for reuse
Frequently asked questions
What is the difference between PEIMAN2 and stochvol?
They serve adjacent needs but don't currently overlap on shipped themes. PEIMAN2 and stochvol 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 stochvol?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and stochvol 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 stochvol?
Top stochvol alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "stochvol alternatives" section above for the current picks, or visit /alternatives/stochvol for the full list with editorial commentary on each.