simlandr
Potential landscape tooling settling onto standard R generics after two rounds of renaming.
Comparison · Analytics
gratia vs STACAS
A side-by-side editorial comparison of gratia and STACAS — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
gratia vs STACAS: at a glance
What is gratia?
The tidy front-end for GAMs, now stable enough that upstream ggplot2 sets its release calendar.
gratia wraps mgcv-fitted generalized additive models in tidy data frames and ggplot2 graphics — smooth_estimates(), fitted_values(), derivatives(), draw() and appraise() cover evaluation, prediction and diagnostics. The API reached its intended shape at 0.9.0, when every generated column was renamed to a dot-prefixed form, and 0.10.0 added conditional_values() for covariate-conditional prediction plots.
What is STACAS?
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
STACAS integrates single-cell RNA-seq datasets by finding and weighting anchors between them, with rPCA-distance-based downweighting and an optional semi-supervised mode that uses cell type labels to discard inconsistent anchors. IntegrateData.STACAS() performs the integration natively rather than handing off, and StandardizeGeneSymbols() normalises gene naming across datasets before anchors are computed.
gratia vs STACAS: editorial side-by-side
gratia
0.0ANALYTICS
The tidy front-end for GAMs, now stable enough that upstream ggplot2 sets its release calendar.
◆ Current state
gratia wraps mgcv-fitted generalized additive models in tidy data frames and ggplot2 graphics — smooth_estimates(), fitted_values(), derivatives(), draw() and appraise() cover evaluation, prediction and diagnostics. The API reached its intended shape at 0.9.0, when every generated column was renamed to a dot-prefixed form, and 0.10.0 added conditional_values() for covariate-conditional prediction plots.
◆ Where it's heading
The package has moved through a long rewrite cycle and out the other side. Successive releases replaced evaluate_smooth() with smooth_estimates(), rebuilt draw() on top of it, then renamed the entire output vocabulary to avoid colliding with user variables. That work is finished; 0.11.1 is driven almost entirely by ggplot2 4.0.0 compatibility, with new mgcv family support for quantile residuals riding along. Development now tracks upstream breakage rather than internal redesign.
◆ Prediction
Expect the next releases to continue absorbing ggplot2 4.x and mgcv changes, with incremental family coverage in quantile_residuals() as the visible new work. The entries give no signal on which mgcv families come next.
STACAS
0.0ANALYTICS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
◆ Current state
STACAS integrates single-cell RNA-seq datasets by finding and weighting anchors between them, with rPCA-distance-based downweighting and an optional semi-supervised mode that uses cell type labels to discard inconsistent anchors. IntegrateData.STACAS() performs the integration natively rather than handing off, and StandardizeGeneSymbols() normalises gene naming across datasets before anchors are computed.
◆ Where it's heading
The method work concentrated in version 2.0 and has been stable since; everything after is Seurat compatibility and operational robustness. Versions 2.1.1 through 2.3.0 track Seurat v5 assays, v3-to-v5 conversion, multi-layer objects and SCT normalisation, with the genuinely useful additions — a reference seed dataset, max.seed.datasets for large-scale integration, min.sample.size — arriving as side effects of that work. The package is from the same lab as GeneNMF, and its release rhythm follows the single-cell ecosystem's upstream churn rather than an internal roadmap.
◆ Prediction
Expect the next release to follow further Seurat object-model changes, which have driven the last three. Nothing in the entries indicates new anchor-scoring or correction methodology in progress.
Alternatives to gratia and STACAS
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 gratia or STACAS.
lavaanExtra
SEM reporting helpers converging on APA output, one CRAN resubmission at a time.
ibis.iSDM
A raster-to-terra migration is the only readable change in a feed of merge notes.
anyflights
A nycflights13 generator whose recent work is all about the data being right.
vinereg
Conditional density and log-likelihood fill out a vine copula regression package.
stringx
A drop-in string API for base R, kept alive by upstream check failures.
See all gratia alternatives → · See all STACAS alternatives →
Recent activity from gratia and STACAS
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agogratiaggplot2 4.0.0 compatibility, plus four more quantile-residual families
- 1y agoSTACASMulti-layer objects and Seurat v3-to-v5 conversion handled
- 1y agogratiaconditional_values() replaces vis.gam for conditional prediction plots
- 2y agogratiaparametric_effects() joins the dot-prefix rename; LSS families begin
- 2y agogratiaEvery generated column gains a dot prefix ⚡
- 2y agoSTACASscale.data option for extreme batch effects; gene name conversion table
- 3y agoSTACASReference seeding, gene symbol standardisation, large-scale integration path
- 3y agogratiaReal variable names in smooth_samples(), plus dplyr 1.1.0 fixes
- 4y agoSTACASSemi-supervised integration and rPCA anchor downweighting ⚡
- 4y agogratiaM1 example output fixes and confint tibble returns
- 5y agoSTACASSeurat 4.0.0 compatibility and SCTransform support
Frequently asked questions
What is the difference between gratia and STACAS?
Both compete on the same themes — r-package — within Analytics. gratia and STACAS 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 gratia better than STACAS?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. gratia and STACAS 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 gratia?
Top gratia alternatives in Analytics are ranked by recent ship velocity. Browse the "gratia alternatives" section above for the current picks, or visit /alternatives/gratia for the full list with editorial commentary on each.
What are the best alternatives to STACAS?
Top STACAS alternatives in Analytics are ranked by recent ship velocity. Browse the "STACAS alternatives" section above for the current picks, or visit /alternatives/stacas for the full list with editorial commentary on each.