pr2database
The protist reference database keeps widening past the rRNA gene it was built on.
Comparison · Infra & APIs
PEIMAN2 vs usmap
A side-by-side editorial comparison of PEIMAN2 and usmap — release velocity, themes, recent moves, and the top alternatives to consider.
PEIMAN2 vs usmap: 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 usmap?
Ten years in, US mapping splits its data out and finally adds Puerto Rico.
usmap plots US state and county maps in an Alaska- and Hawaii-inset projection and joins user data to them by FIPS code. Over the last two years it has been rebuilt underneath: the map data moved out to a companion usmapdata package, the geometry became sf, and a data_year parameter lets a plot match the vintage of the data being plotted. Version 1.0.0 marks ten years of the project and adds Puerto Rico across every function.
PEIMAN2 vs usmap: 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.
usmap
0.0INFRA · APIS
Ten years in, US mapping splits its data out and finally adds Puerto Rico.
◆ Current state
usmap plots US state and county maps in an Alaska- and Hawaii-inset projection and joins user data to them by FIPS code. Over the last two years it has been rebuilt underneath: the map data moved out to a companion usmapdata package, the geometry became sf, and a data_year parameter lets a plot match the vintage of the data being plotted. Version 1.0.0 marks ten years of the project and adds Puerto Rico across every function.
◆ Where it's heading
The package has separated what it draws from how it draws, and that separation is what makes the recent releases possible: annual map vintages ship in usmapdata without touching usmap, and Puerto Rico could be backfilled into every existing year at once. The remaining work is coverage and defaults rather than architecture, and the Puerto Rico exclusion default is already governed by an environment variable rather than a code change.
◆ Prediction
Expect the annual map vintage to keep arriving through usmapdata, with usmap itself changing only where a new territory or a projection default needs handling.
Alternatives to PEIMAN2 and usmap
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 usmap.
ggalign
Composable aligned layouts, rebuilt on S7 while ggplot2 4.0 lands underneath.
prioritizr
Conservation planning absorbs the literature's target-setting rules as code.
jSDM
Joint species distribution models in Gibbs-sampled C++, quiet since 2023.
rsofun
An ecosystem model starts tracking carbon isotopes and land-use change.
trackeR
Fitness-tracking analysis in slow maintenance, still absorbing upstream breakage.
See all PEIMAN2 alternatives → · See all usmap alternatives →
Recent activity from PEIMAN2 and usmap
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 11mo agousmapPuerto Rico added across every usmap function and map year
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 1y agousmapdata_year parameter threaded through the plotting functions
- 2y agousmapPopulation and poverty data refreshed; ggplot2 3.5 legend fix
- 2y agousmapMap data becomes sf; usmap_transform() returns geometry ⚡
- 2y agousmapDocumentation links updated
- 2y agousmapMap data extracted to a companion usmapdata package ⚡
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
Frequently asked questions
What is the difference between PEIMAN2 and usmap?
They serve adjacent needs but don't currently overlap on shipped themes. PEIMAN2 and usmap 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 usmap?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. PEIMAN2 and usmap 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 usmap?
Top usmap alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "usmap alternatives" section above for the current picks, or visit /alternatives/usmap for the full list with editorial commentary on each.