paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
geos vs protr
A side-by-side editorial comparison of geos and protr — release velocity, themes, recent moves, and the top alternatives to consider.
geos vs protr: at a glance
What is geos?
The thin GEOS binding for R adds terra interop after three years of compiler triage
geos is a low-overhead R binding to the GEOS geometry engine, exposing predicates, overlays and spatial indexes with minimal copying. Version 0.2.5 accepts terra SpatVector objects directly, alongside fixes for zero-length memcpy and plotting of invalid geometries. The releases between 0.2.0 and 0.2.5 contain almost no feature work — they are responses to compiler warnings, sanitiser findings and CRAN check failures.
What is protr?
protr's feature set is finished; the work now is surviving Bioconductor's churn.
protr generates numerical descriptors from protein sequences for machine learning, plus alignment-based similarity between sequences. The descriptor functions have been stable for years. Recent releases divide cleanly into two kinds: extending the similarity computations to work under memory constraints, and absorbing the Bioconductor split that moved pairwise alignment out of Biostrings into pwalign.
geos vs protr: editorial side-by-side
geos
0.0ANALYTICS
The thin GEOS binding for R adds terra interop after three years of compiler triage
◆ Current state
geos is a low-overhead R binding to the GEOS geometry engine, exposing predicates, overlays and spatial indexes with minimal copying. Version 0.2.5 accepts terra SpatVector objects directly, alongside fixes for zero-length memcpy and plotting of invalid geometries. The releases between 0.2.0 and 0.2.5 contain almost no feature work — they are responses to compiler warnings, sanitiser findings and CRAN check failures.
◆ Where it's heading
Feature development stopped after 0.2.0 and the package has since been kept alive against a moving toolchain: strict-prototypes warnings, a clang sanitiser error, format string checks, an M1 test failure. The 0.2.5 terra support breaks that pattern and came from an outside contributor, which suggests the package's direction is now set by what neighbouring spatial packages need from it rather than by GEOS feature coverage.
◆ Prediction
GEOS has released new capabilities since the 3.11 features wired up in 0.2.0, and none have been exposed since; whether the next release closes that gap or continues as interop-and-maintenance is the open question the history does not yet answer.
protr
0.0ANALYTICS
protr's feature set is finished; the work now is surviving Bioconductor's churn.
◆ Current state
protr generates numerical descriptors from protein sequences for machine learning, plus alignment-based similarity between sequences. The descriptor functions have been stable for years. Recent releases divide cleanly into two kinds: extending the similarity computations to work under memory constraints, and absorbing the Bioconductor split that moved pairwise alignment out of Biostrings into pwalign.
◆ Where it's heading
The similarity side is where the remaining engineering goes, and it follows a consistent pattern — whatever parSeqSim() gained, crossSetSim() eventually gets. Batching, verbose progress and a disk-backed variant all arrived for the single-set case first and were mirrored for the cross-set case in 1.7-1. That is a maintainer closing feature-parity gaps rather than opening new directions, and the two most recent releases contain no user-facing change at all.
◆ Prediction
Expect the next release to react to another Bioconductor or R CMD check change, which accounts for three of the last four. The similarity functions now have parity, so there is no obvious internal backlog left.
Alternatives to geos and protr
Other Analytics 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 geos or protr.
geodist
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
errors
errors keeps making uncertainty print the way each scientific field expects.
CMAQ
CMAQ went global in v5.5, and has been patching that surface ever since.
enpls
enpls has not changed its statistics since 2016 — only its website, twice.
grex
grex is a lookup table with a version number — it ships when the annotation moves.
Recent activity from geos and protr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 7mo agogeosAccepts terra SpatVector objects; invalid-geometry plotting fixed
- 11mo agoprotrprotr 1.7-5 silences a Debian r-devel check note
- 1y agoprotrprotr 1.7-4 checks alignment dependencies upfront
- 1y agoprotrprotr 1.7-3 detects Biostrings version to find pwalign
- 2y agoprotrprotr 1.7-2 fixes citation key and vignette accessibility
- 2y agoprotrprotr 1.7-1 brings crossSetSim to parity with parSeqSim
- 2y agogeosFix format string checks flagged by CRAN
- 2y agoprotrprotr 1.7-0 adds crossSetSim for two-set similarity
- 2y agogeosNA/NaN handling adjusted for waldo; M1 test fixed
- 3y agogeosSilence -Wstrict-prototypes warnings
- 3y agogeosFix clang address sanitizer error
- 3y agogeosGEOS 3.11 functions exposed; spatial tree and join helpers added
Frequently asked questions
What is the difference between geos and protr?
They serve adjacent needs but don't currently overlap on shipped themes. geos and protr 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 geos better than protr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. geos and protr 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 Analytics products to evaluate alongside.
What are the best alternatives to geos?
Top geos alternatives in Analytics are ranked by recent ship velocity. Browse the "geos alternatives" section above for the current picks, or visit /alternatives/geos-r for the full list with editorial commentary on each.
What are the best alternatives to protr?
Top protr alternatives in Analytics are ranked by recent ship velocity. Browse the "protr alternatives" section above for the current picks, or visit /alternatives/protr-r for the full list with editorial commentary on each.