rollupTree
The recursive-computation engine under massProps grows the accessors its consumer needed
Comparison · Infra & APIs
PEIMAN2 vs tf
A side-by-side editorial comparison of PEIMAN2 and tf — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-packages
PEIMAN2 vs tf: 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 tf?
tf gave functional data a second dimension: curves whose values are vectors.
tf supplies the vector classes underneath the tidyfun stack — tfd for raw functional observations, tfb for basis-represented ones, both built on vctrs so curves sit in a data frame column and behave like any other vector. Until July that codomain was scalar. The 0.5.0 release adds tfd_mv and tfb_mv, classes for functions whose values are vectors in R^d, and rebuilds the analysis verbs to match.
PEIMAN2 vs tf: 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.
tf
0.0INFRA · APIS
tf gave functional data a second dimension: curves whose values are vectors.
◆ Current state
tf supplies the vector classes underneath the tidyfun stack — tfd for raw functional observations, tfb for basis-represented ones, both built on vctrs so curves sit in a data frame column and behave like any other vector. Until July that codomain was scalar. The 0.5.0 release adds tfd_mv and tfb_mv, classes for functions whose values are vectors in R^d, and rebuilds the analysis verbs to match.
◆ Where it's heading
The package is widening what a functional observation can be, then porting the toolkit onto it. Registration arrived first in 0.4.0 for univariate curves and immediately gained an srvf_mv method for aligning components jointly, and tfb_mfpc() ports principal component analysis to the multivariate case with a single set of scores shared across components. Alongside that runs steady dependency shedding — mvtnorm and pracma both replaced by inlined samplers that reproduce prior draws bit-for-bit, glue dropped for cli in the previous release — and an unusually long tail of NA-handling and edge-case fixes, several caught in pre-release review of the new classes.
◆ Prediction
The new classes ship with FPCA, registration and shape alignment but the release notes describe tidyfun::tf_unnest() as the consumer of one new export, so the visible next step is the rest of the tidyfun stack catching up to vector-valued columns. Expect follow-up patches on the vctrs casting paths, which is where most of this release's late fixes clustered.
Alternatives to PEIMAN2 and tf
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 tf.
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
Recent activity from PEIMAN2 and tf
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agotfVector-valued functional data becomes a first-class type ⚡
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 5mo agotfCurve registration, five depth measures and sub-domain splitting
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 2y agotfFix: tf_crosscov normalization
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
Frequently asked questions
What is the difference between PEIMAN2 and tf?
Both compete on the same themes — r-packages — within Infra & APIs. PEIMAN2 and tf 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 tf?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and tf 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 tf?
Top tf alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "tf alternatives" section above for the current picks, or visit /alternatives/tf for the full list with editorial commentary on each.