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Comparison · Infra & APIs
cofad vs polyRAD
A side-by-side editorial comparison of cofad and polyRAD — release velocity, themes, recent moves, and the top alternatives to consider.
cofad vs polyRAD: at a glance
What is cofad?
Contrast analysis with a Shiny front end, shipping about one release a year
cofad performs contrast analyses for factorial designs in both between- and within-subject forms, and ships a Shiny GUI alongside the R interface. The 0.3.0 release in 2024 was the substantial one: a helper for calculating differences between two sets of lambdas for competing contrast analysis, improved summary output, removal of the plyr dependency, a rebuilt Shiny interface using standard elements after the sortable drag-and-drop proved unstable, and a change of maintainer to Johannes Titz. The most recent release is a one-line patch fixing degrees of freedom in the t-test table.
What is polyRAD?
Polyploid genotype calling went quiet for three years, then returned with a bug-fix tag.
polyRAD calls genotypes from RAD sequencing data in polyploid and diploid populations using Bayesian estimation. Its capability surface has been settled since 2.0 in late 2022, which added support for ploidy that varies among individuals. The March 2026 release is a CRAN bug-fix sync after a three-and-a-half-year gap, with the substance deferred to NEWS.
cofad vs polyRAD: editorial side-by-side
cofad
0.0INFRA · APIS
Contrast analysis with a Shiny front end, shipping about one release a year
◆ Current state
cofad performs contrast analyses for factorial designs in both between- and within-subject forms, and ships a Shiny GUI alongside the R interface. The 0.3.0 release in 2024 was the substantial one: a helper for calculating differences between two sets of lambdas for competing contrast analysis, improved summary output, removal of the plyr dependency, a rebuilt Shiny interface using standard elements after the sortable drag-and-drop proved unstable, and a change of maintainer to Johannes Titz. The most recent release is a one-line patch fixing degrees of freedom in the t-test table.
◆ Where it's heading
Development is slow and correctness-led. The record runs from a JOSS publication in 2021 through a near three-year gap to a release that both extended the method and repaired the GUI, then a degrees-of-freedom fix. Maintainer and author order changed in 0.3.0, which typically marks a handover rather than a burst of new work, and the cadence since is consistent with that.
◆ Prediction
Expect low-frequency correctness releases; the competing contrast analysis helper added in 0.3.0 is the most likely thing to be extended if anything is.
polyRAD
0.0INFRA · APIS
Polyploid genotype calling went quiet for three years, then returned with a bug-fix tag.
◆ Current state
polyRAD calls genotypes from RAD sequencing data in polyploid and diploid populations using Bayesian estimation. Its capability surface has been settled since 2.0 in late 2022, which added support for ploidy that varies among individuals. The March 2026 release is a CRAN bug-fix sync after a three-and-a-half-year gap, with the substance deferred to NEWS.
◆ Where it's heading
The releases between 1.0 and 2.0 followed a consistent pattern: add export paths to other tools in the polyploid genetics stack, add simulation controls, fix what CRAN checks caught. That expansion stopped at 2.0, and 2.0.1 does not resume it. The package reads as complete and maintained rather than under development.
◆ Prediction
Continued low-frequency patch releases keeping the package on CRAN as R and its dependencies move. The release notes give no sign of a 2.1 feature line.
Alternatives to cofad and polyRAD
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 cofad or polyRAD.
Okta
Okta's developer blog is a Cross App Access campaign, now diluted by advocacy-team storytelling.
tealeaves
A leaf-temperature model that finished its job in 2020 and has stayed finished
Infisical
A credential platform assembled two or three pull requests at a time, never a headline
SigNoz
Search without knowing the field — SigNoz keeps lowering the cost of not knowing your schema
nmfspalette
A NOAA Fisheries colour palette that ships when the branding guide changes
See all cofad alternatives → · See all polyRAD alternatives →
Recent activity from cofad and polyRAD
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agopolyRADBug-fix sync with CRAN after a three-year gap
- 1y agocofadDegrees of freedom corrected in the t-test table
- 2y agocofadCompeting contrast helper, rebuilt Shiny GUI, maintainer change
- 3y agopolyRADMultiploidy support arrives and breaks saved RADdata objects ⚡
- 4y agopolyRADContamination and error-rate simulation controls added
- 4y agocofadDocumentation and references for JOSS publication
- 4y agocofadShiny GUI added; aggregated-data function and 0-variance fix
- 4y agopolyRADMapping-population simulation and DArTag import added
- 5y agopolyRADGWASpoly export gains continuous genotypes; adegenet export added
- 5y agopolyRADpolyRAD v1.3
Frequently asked questions
What is the difference between cofad and polyRAD?
They serve adjacent needs but don't currently overlap on shipped themes. cofad and polyRAD 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 cofad better than polyRAD?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. cofad and polyRAD 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 cofad?
Top cofad alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "cofad alternatives" section above for the current picks, or visit /alternatives/cofad for the full list with editorial commentary on each.
What are the best alternatives to polyRAD?
Top polyRAD alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "polyRAD alternatives" section above for the current picks, or visit /alternatives/polyrad for the full list with editorial commentary on each.