constants
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Comparison · Analytics
qqman vs ss3diags
A side-by-side editorial comparison of qqman and ss3diags — release velocity, themes, recent moves, and the top alternatives to consider.
qqman vs ss3diags: at a glance
What is qqman?
The Manhattan-plot package for GWAS results, finished and dormant since 2017.
qqman does two things: manhattan() and qq() plots for genome-wide association study results. Its six visible releases run from 2014 to a single 2017 packaging fix, and the last release with any user-facing change shipped in 2015. The archive is non-monotonic — a 0.0.0 tag published after 0.1.1 archives the pre-package standalone script — so version order and publication order disagree.
What is ss3diags?
A fisheries diagnostics package that lives and dies by one upstream dependency.
ss3diags provides residual, retrospective and hindcast cross-validation diagnostics for Stock Synthesis models, sitting directly on top of r4ss. Its recent history is dominated by that dependency: when r4ss 1.50.0 renamed columns across its read and write functions, ss3diags pinned itself to 1.49.3 only, then spent the following release adapting. It now requires r4ss 1.50.0 and above and has moved to native R pipes.
qqman vs ss3diags: editorial side-by-side
qqman
0.0ANALYTICS
The Manhattan-plot package for GWAS results, finished and dormant since 2017.
◆ Current state
qqman does two things: manhattan() and qq() plots for genome-wide association study results. Its six visible releases run from 2014 to a single 2017 packaging fix, and the last release with any user-facing change shipped in 2015. The archive is non-monotonic — a 0.0.0 tag published after 0.1.1 archives the pre-package standalone script — so version order and publication order disagree.
◆ Where it's heading
The real development window was 2014 to 2015. The 0.1.2 release did the substantive work, replacing the assumption that SNPs are evenly distributed across chromosomes and handing users control of axis limits, labels and log transformation; 0.1.3 then added annotation by p-value threshold and top-SNP-per-chromosome. After that the package stops. Notably, the archival 0.0.0 entry records that the original script had confidence intervals on QQ plots and richer highlighting than the released package ever regained.
◆ Prediction
With one packaging fix in the last decade, these entries support no prediction of further releases. The package reads as complete for its narrow purpose rather than abandoned mid-arc.
ss3diags
0.0ANALYTICS
A fisheries diagnostics package that lives and dies by one upstream dependency.
◆ Current state
ss3diags provides residual, retrospective and hindcast cross-validation diagnostics for Stock Synthesis models, sitting directly on top of r4ss. Its recent history is dominated by that dependency: when r4ss 1.50.0 renamed columns across its read and write functions, ss3diags pinned itself to 1.49.3 only, then spent the following release adapting. It now requires r4ss 1.50.0 and above and has moved to native R pipes.
◆ Where it's heading
The package is a downstream consumer whose release schedule is largely dictated by NOAA's r4ss. Between compatibility passes it has been shifting documentation from loose cookbook scripts into proper vignettes and shedding bundled Rdata in favour of objects generated at build time. Note that 2.0.3 and 2.1.0 were published the same day, so version order in this feed does not track chronology.
◆ Prediction
The next release most likely follows the next breaking r4ss change; between those, expect continued vignette and parameter-validation work.
Alternatives to qqman and ss3diags
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 qqman or ss3diags.
austraits
The R client for AusTraits spends its releases chasing the dataset it reads.
ggdemetra
A ggplot2 layer for seasonal adjustment output, filling in one plot type at a time.
fossilsim
A fossil-record simulator that quietly grew a trait-evolution engine.
tern.rbmi
Reference-based multiple imputation tables, shipping only what CRAN checks demand.
tern.mmrm
An MMRM tabulation package that has published nothing since its 2024 CRAN releases.
See all qqman alternatives → · See all ss3diags alternatives →
Recent activity from qqman and ss3diags
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1y agoss3diagsAdapts to r4ss 1.50.0 and drops the local binary fetcher
- 1y agoss3diagsPins r4ss to 1.49.3 after upstream breaking changes
- 2y agoss3diagsVignette tutorials replace cookbook scripts
- 3y agoss3diagsSSdeltaMVLN gains variance-covariance and bias options
- 3y agoss3diagsAligns with CRAN r4ss 1.44.0 and shared CI workflows
- 3y agoss3diagsSSrmse() split out as a standalone calculation
- 9y agoqqmanREADME image path fix for pandoc
- 11y agoqqmanAnnotate SNPs by p-value threshold or per-chromosome top hit
- 11y agoqqmanChromosome ticks stop assuming even SNP spacing; axis control opens up
- 12y agoqqmanArchival tag for the pre-package standalone script
- 12y agoqqmanVignette touch-up
- 12y agoqqmanZenodo archival tag, no code change
Frequently asked questions
What is the difference between qqman and ss3diags?
They serve adjacent needs but don't currently overlap on shipped themes. qqman and ss3diags 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 qqman better than ss3diags?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. qqman and ss3diags 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 qqman?
Top qqman alternatives in Analytics are ranked by recent ship velocity. Browse the "qqman alternatives" section above for the current picks, or visit /alternatives/qqman-r for the full list with editorial commentary on each.
What are the best alternatives to ss3diags?
Top ss3diags alternatives in Analytics are ranked by recent ship velocity. Browse the "ss3diags alternatives" section above for the current picks, or visit /alternatives/ss3diags for the full list with editorial commentary on each.