pr2database
The protist reference database keeps widening past the rRNA gene it was built on.
Comparison · Infra & APIs
jSDM vs slendr
A side-by-side editorial comparison of jSDM and slendr — release velocity, themes, recent moves, and the top alternatives to consider.
jSDM vs slendr: 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 slendr?
Population-genetic simulation in R, opened up to selection and finally easier to install.
slendr specifies spatial and non-spatial population-genetic models in R and simulates them through SLiM or msprime, returning tree sequences that tskit then analyses. Two threads dominate the current releases: keeping in step with fast-moving backends, with SLiM 5.1, pyslim 1.1.0 and Python 3.13 now required, and reducing the setup burden that its Python dependency imposes. Version 1.5.0 adds ephemeral uv-based virtual environments, so init_env(uv = TRUE) can stand in for creating a permanent environment with setup_env().
jSDM vs slendr: 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.
slendr
0.0INFRA · APIS
Population-genetic simulation in R, opened up to selection and finally easier to install.
◆ Current state
slendr specifies spatial and non-spatial population-genetic models in R and simulates them through SLiM or msprime, returning tree sequences that tskit then analyses. Two threads dominate the current releases: keeping in step with fast-moving backends, with SLiM 5.1, pyslim 1.1.0 and Python 3.13 now required, and reducing the setup burden that its Python dependency imposes. Version 1.5.0 adds ephemeral uv-based virtual environments, so init_env(uv = TRUE) can stand in for creating a permanent environment with setup_env().
◆ Where it's heading
Since the 1.0.0 release added non-neutral simulation, the work has shifted from capability to friction. A large share of recent notes concerns Python environment handling, conda activation races on Windows, dependency pruning that made shiny optional, and argument names that misled users, as when gene_flow()'s rate argument turned out to mean total ancestry proportion rather than a rate. That is the profile of a package whose scientific surface is settled and whose remaining problems are the ones users actually hit.
◆ Prediction
Expect the uv-based environment path to move from fallback to default once it has proven itself, given the notes already describe an environment variable for making it so. The deprecated rate argument in gene_flow() is explicitly slated for removal in a future major release, which is the clearest signal here of what a 2.0 would contain.
Alternatives to jSDM and slendr
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 slendr.
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 slendr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoslendrEphemeral uv Python environments remove the setup step
- 7mo agoslendrgene_flow() separates migration rate from ancestry proportion
- 9mo agoslendrshiny made optional; SLiM 5.1 and Python 3.13 required
- 9mo agojSDMjSDM CRAN release v0.2.7: Joint Species Distribution Models
- 1y agoslendrconda activation reverted to a slower but reliable path
- 1y agoslendrBackends raised to SLiM 5.0, tskit 0.6.4 and msprime 1.3.4
- 1y agoslendrNon-neutral models arrive; slim() interface simplified ⚡
- 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 slendr?
They serve adjacent needs but don't currently overlap on shipped themes. jSDM and slendr 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 slendr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. jSDM and slendr 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 slendr?
Top slendr alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "slendr alternatives" section above for the current picks, or visit /alternatives/slendr for the full list with editorial commentary on each.