pr2database
The protist reference database keeps widening past the rRNA gene it was built on.
Comparison · Infra & APIs
jSDM vs valr
A side-by-side editorial comparison of jSDM and valr — release velocity, themes, recent moves, and the top alternatives to consider.
jSDM vs valr: at a glance
What is jSDM?
Joint species distribution models in Gibbs-sampled C++, quiet since 2023.
jSDM fits joint species distribution models by Gibbs sampling, with the sampler written in C++ against GSL and Armadillo and exposed through binomial probit, binomial logit, Poisson log and Gaussian entry points. The 0.2 line extended it with species traits, constrained factor loadings and residual-association plots. The one entry since 2023 carries only a compare link.
What is valr?
valr's interval verbs now read genomic files in place instead of demanding a loaded tibble.
valr reimplements bedtools-style genome interval arithmetic as tidyverse verbs backed by C++. Its long project has been closing the behavioural gap with bedtools — the book-ended interval semantics finally match in 0.10.0, three releases after the deprecation began. The July release also ends the assumption that intervals must be in memory: bed_map(), bed_intersect(), bed_subtract(), bed_coverage() and bed_window() accept a bigWig or bigBed path or URL where an interval table used to go.
jSDM vs valr: editorial side-by-side
jSDM
0.0INFRA · APIS
Joint species distribution models in Gibbs-sampled C++, quiet since 2023.
◆ Current state
jSDM fits joint species distribution models by Gibbs sampling, with the sampler written in C++ against GSL and Armadillo and exposed through binomial probit, binomial logit, Poisson log and Gaussian entry points. The 0.2 line extended it with species traits, constrained factor loadings and residual-association plots. The one entry since 2023 carries only a compare link.
◆ Where it's heading
The package built out its model family quickly and then stopped: five of the six visible entries are stamped the same day as a backfilled archive, and the only later release says nothing about its contents. The direction the 0.2 line was heading, toward trait-mediated species effects and better convergence on latent variable models, has no visible continuation.
◆ Prediction
The feed does not support a confident prediction; the latest entry publishes no notes, so whether the package is still developing or only being kept CRAN-clean cannot be read from it.
valr
0.0INFRA · APIS
valr's interval verbs now read genomic files in place instead of demanding a loaded tibble.
◆ Current state
valr reimplements bedtools-style genome interval arithmetic as tidyverse verbs backed by C++. Its long project has been closing the behavioural gap with bedtools — the book-ended interval semantics finally match in 0.10.0, three releases after the deprecation began. The July release also ends the assumption that intervals must be in memory: bed_map(), bed_intersect(), bed_subtract(), bed_coverage() and bed_window() accept a bigWig or bigBed path or URL where an interval table used to go.
◆ Where it's heading
Two arcs converge here. One is compatibility: min_overlap arrived with a deprecation warning in 0.9.0 and its default flipped from 0 to 1 in 0.10.0, so book-ended intervals are excluded by default as bedtools does, with the internal calculations in bed_closest() and friends deliberately left counting them. The other is the file-backed path, which grew out of the cpp11bigwig dependency adopted in 0.8.3 for read_bigwig() and re-exported in 0.9.0 — reading a file became querying one. Underneath, the C++ base keeps getting lighter: Rcpp swapped for cpp11, rlang cut to a single function, per-group memory copies removed from three verbs.
◆ Prediction
Only five verbs take a file argument today and bed_closest(), bed_glyph() and the statistical verbs do not, so extending the file-backed path across the rest of the API is the obvious follow-up. The deprecated tibble re-exports and the now-defunct n_fields argument suggest continued removal of the compatibility layer in the next minor release.
Alternatives to jSDM and valr
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 jSDM or valr.
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.
rsofun
An ecosystem model starts tracking carbon isotopes and land-use change.
usmap
Ten years in, US mapping splits its data out and finally adds Puerto Rico.
trackeR
Fitness-tracking analysis in slow maintenance, still absorbing upstream breakage.
Recent activity from jSDM and valr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agovalrInterval verbs read bigWig and bigBed files directly ⚡
- 7mo agovalrbed_slop() and bed_flank() preserve input row order
- 8mo agovalrmin_overlap introduced; C++ backend moves from Rcpp to cpp11
- 9mo agojSDMjSDM CRAN release v0.2.7: Joint Species Distribution Models
- 1y agovalrTest updated for ggplot2 3.6.0
- 1y agovalrread_bigwig() switches to cpp11bigwig; read_gtf() deprecated
- 1y agovalrCRAN Rd link NOTE and maintainer email change
- 3y agojSDMSpecies traits, constrained loadings and association plots
- 3y agojSDMFirst release: C++ Gibbs sampler for joint species models ⚡
- 3y agojSDMResidual correlation functions can filter to significant values
- 3y agojSDMjSDM_gaussian() fits continuous data with overdispersion
- 3y agojSDMFour versions of CRAN check corrections
Frequently asked questions
What is the difference between jSDM and valr?
They serve adjacent needs but don't currently overlap on shipped themes. jSDM and valr 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 jSDM better than valr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. jSDM and valr 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 jSDM?
Top jSDM alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "jSDM alternatives" section above for the current picks, or visit /alternatives/jsdm for the full list with editorial commentary on each.
What are the best alternatives to valr?
Top valr alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "valr alternatives" section above for the current picks, or visit /alternatives/valr for the full list with editorial commentary on each.