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Comparison · Infra & APIs
PEIMAN2 vs surveytidy
A side-by-side editorial comparison of PEIMAN2 and surveytidy — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-packages
PEIMAN2 vs surveytidy: 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 surveytidy?
surveytidy taught every dplyr verb to operate on a whole collection of surveys at once.
surveytidy is the tidyverse-facing half of a two-package survey stack, wrapping survey design objects from surveycore so filter, mutate, select and the rest work on them while carrying variable labels, value labels and a transformation log alongside the data. The May release extended that verb surface to survey_collection, the abstraction surveycore uses to hold several surveys as one object, so a pipeline written once dispatches across every member.
PEIMAN2 vs surveytidy: 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.
surveytidy
0.0INFRA · APIS
surveytidy taught every dplyr verb to operate on a whole collection of surveys at once.
◆ Current state
surveytidy is the tidyverse-facing half of a two-package survey stack, wrapping survey design objects from surveycore so filter, mutate, select and the rest work on them while carrying variable labels, value labels and a transformation log alongside the data. The May release extended that verb surface to survey_collection, the abstraction surveycore uses to hold several surveys as one object, so a pipeline written once dispatches across every member.
◆ Where it's heading
The package is being built in two layers that arrive in order: vector-level transformations first, structural dispatch second. The make_* family in 0.4.0 handles the recoding that survey work actually consists of — labelled to factor, multi-level to dichotomous, scale reversal, valence flipping — with value labels propagating automatically. Collection support then applies data-masking, tidyselect, grouping, slicing and collapsing verbs per survey, with joins explicitly refused and a typed message reporting which surveys were skipped. Metadata fidelity is the recurring bug source: labels surviving across(), stale labels left behind by recoding, the transformation log keeping up with what the verbs did.
◆ Prediction
Joins are the one verb family that errors on collections, with users directed to join before constructing the collection, so that restriction is the clearest outstanding gap. The re-export of surveycore's collection constructors suggests the package is positioning itself as the single import users need, which points toward more re-exports as surveycore's stable API settles.
Alternatives to PEIMAN2 and surveytidy
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 surveytidy.
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 surveytidy alternatives →
Recent activity from PEIMAN2 and surveytidy
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 2mo agosurveytidymutate() syncs metadata for across() recodes
- 3mo agosurveytidydplyr and tidyr verbs dispatch across survey collections
- 5mo agosurveytidyFive label-aware recoding functions for use inside mutate()
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
Frequently asked questions
What is the difference between PEIMAN2 and surveytidy?
Both compete on the same themes — r-packages — within Infra & APIs. PEIMAN2 and surveytidy 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 surveytidy?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and surveytidy 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 surveytidy?
Top surveytidy alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "surveytidy alternatives" section above for the current picks, or visit /alternatives/surveytidy for the full list with editorial commentary on each.