STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
dubicube vs gratia
A side-by-side editorial comparison of dubicube and gratia — release velocity, themes, recent moves, and the top alternatives to consider.
dubicube vs gratia: at a glance
What is dubicube?
dubicube grew from a bootstrap helper into the uncertainty layer other B-Cubed packages call.
dubicube supplies bootstrapping and confidence-interval machinery for biodiversity data cubes in the B-Cubed project. The 0.10–0.12 series added the things a library needs to be depended on rather than copied: automatic detection of group-specific versus whole-cube bootstrapping, an optional boot backend, and then a second capability area in 0.12.0 with data quality diagnostics and cube filtering. The sibling indicator package b3gbi now delegates its confidence intervals here.
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.
dubicube vs gratia: editorial side-by-side
dubicube
0.0ANALYTICS
dubicube grew from a bootstrap helper into the uncertainty layer other B-Cubed packages call.
◆ Current state
dubicube supplies bootstrapping and confidence-interval machinery for biodiversity data cubes in the B-Cubed project. The 0.10–0.12 series added the things a library needs to be depended on rather than copied: automatic detection of group-specific versus whole-cube bootstrapping, an optional boot backend, and then a second capability area in 0.12.0 with data quality diagnostics and cube filtering. The sibling indicator package b3gbi now delegates its confidence intervals here.
◆ Where it's heading
Release notes are terse — usually one line and an issue number — but the direction is legible in what gets automated. Decisions the caller used to make explicitly are being inferred: resampling scope in 0.10.0, the no-bias option in 0.11.0, and process_cube_args threaded through filter_cube() so the filtering path matches cube processing. The diagnostics work in 0.12.x is the newer line, and 0.12.2's rename of the heatmap option to rule suggests that surface is still settling.
◆ Prediction
The diagnostics and filtering additions have needed a follow-up fix in each of the two releases since they landed, so the next release is most likely more consolidation there rather than a new capability area.
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.
Alternatives to dubicube and gratia
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 dubicube or gratia.
ggtrace
A debugger for ggplot2's internals, hardening its grip as the internals it traces keep moving.
kde1d
A univariate density estimator that added zero-inflated data and reopened its C++ API to do it.
svines
Stationary vine copulas for time series, released in lockstep with the rest of Nagler's vine stack.
gghighlight
A single-purpose ggplot2 extension that has spent six years tracking ggplot2 instead of growing.
rtrek
A Star Trek data package that became a Memory Alpha web client and has been patching scrapers ever since.
See all dubicube alternatives → · See all gratia alternatives →
Recent activity from dubicube and gratia
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agodubicubePackage build fixes
- 3mo agodubicubeFilter vignette documentation and rule-function fix
- 3mo agodubicubeprocess_cube_args in filter_cube(); heatmap option renamed to rule
- 4mo agodubicubeData quality diagnostics and cube filtering ⚡
- 5mo agodubicubeZenodo grant ID and metadata fixes
- 6mo agodubicubeNo-bias bootstrap option automated
- 11mo agogratiaggplot2 4.0.0 compatibility, plus four more quantile-residual families
- 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 ⚡
- 3y agogratiaReal variable names in smooth_samples(), plus dplyr 1.1.0 fixes
- 4y agogratiaM1 example output fixes and confint tibble returns
Frequently asked questions
What is the difference between dubicube and gratia?
They serve adjacent needs but don't currently overlap on shipped themes. dubicube and gratia 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 dubicube better than gratia?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. dubicube and gratia 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 dubicube?
Top dubicube alternatives in Analytics are ranked by recent ship velocity. Browse the "dubicube alternatives" section above for the current picks, or visit /alternatives/dubicube for the full list with editorial commentary on each.
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.