goat
A gene-set enrichment package that outgrew its human-only origins, then went quiet.
Comparison · Infra & APIs
rollupTree vs slendr
A side-by-side editorial comparison of rollupTree and slendr — release velocity, themes, recent moves, and the top alternatives to consider.
rollupTree vs slendr: at a glance
What is rollupTree?
The recursive-computation engine under massProps grows the accessors its consumer needed
rollupTree performs recursive computations over tree and DAG structures — the generic engine that its author's massProps package uses to roll mass properties up an assembly breakdown. It is small and moves slowly: five releases in a year, of which two are README and vignette work. The current surface added row-level get and set accessors by key and by id at 0.4.0.
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().
rollupTree vs slendr: editorial side-by-side
rollupTree
0.0INFRA · APIS
The recursive-computation engine under massProps grows the accessors its consumer needed
◆ Current state
rollupTree performs recursive computations over tree and DAG structures — the generic engine that its author's massProps package uses to roll mass properties up an assembly breakdown. It is small and moves slowly: five releases in a year, of which two are README and vignette work. The current surface added row-level get and set accessors by key and by id at 0.4.0.
◆ Where it's heading
The package develops in response to its one visible consumer. The 0.4.0 accessors appeared in January 2026 and massProps switched to them thirteen days later; 0.4.1 then fixed missing column names in the setters, which is the kind of defect only real use surfaces. Before that, 0.3.0's default_validate_dag() extended validation past strict trees to directed acyclic graphs, widening what structures the engine will accept.
◆ Prediction
On the established pattern the next release will be whatever massProps needs next, discovered by using it. A DAG validator suggests non-tree structures are in scope, but nothing in these notes says that path is being pushed further.
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 rollupTree 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 rollupTree or slendr.
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
See all rollupTree alternatives → · See all slendr alternatives →
Recent activity from rollupTree and slendr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoslendrEphemeral uv Python environments remove the setup step
- 6mo agorollupTreeMissing column names in the new row setters
- 6mo agorollupTreeRow-level get and set accessors by key and by id
- 7mo agoslendrgene_flow() separates migration rate from ancestry proportion
- 9mo agoslendrshiny made optional; SLiM 5.1 and Python 3.13 required
- 1y agoslendrconda activation reverted to a slower but reliable path
- 1y agorollupTreeMinor vignette improvements
- 1y agoslendrBackends raised to SLiM 5.0, tskit 0.6.4 and msprime 1.3.4
- 1y agorollupTreeBadges and GitHub Actions added to the README
- 1y agorollupTreedefault_validate_dag() extends validation past strict trees
- 1y agoslendrNon-neutral models arrive; slim() interface simplified ⚡
Frequently asked questions
What is the difference between rollupTree and slendr?
They serve adjacent needs but don't currently overlap on shipped themes. rollupTree 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 rollupTree better than slendr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. rollupTree 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 rollupTree?
Top rollupTree alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "rollupTree alternatives" section above for the current picks, or visit /alternatives/rolluptree 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.