gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
pedmut vs qqman
A side-by-side editorial comparison of pedmut and qqman — release velocity, themes, recent moves, and the top alternatives to consider.
pedmut vs qqman: at a glance
What is pedmut?
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
pedmut builds and transforms the mutation models used in pedigree likelihood calculations. Its recent arc is a toolkit of model transformations: makeReversible() with three methods, makeStationary() replacing the older stabilize(), adjustRate() for tuning overall mutation rate, and lumpMutSpecial() for lumping models that strong lumpability cannot handle. The most recent release is narrow, adding a programmatic output format to getParams().
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.
pedmut vs qqman: editorial side-by-side
pedmut
0.0ANALYTICS
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
◆ Current state
pedmut builds and transforms the mutation models used in pedigree likelihood calculations. Its recent arc is a toolkit of model transformations: makeReversible() with three methods, makeStationary() replacing the older stabilize(), adjustRate() for tuning overall mutation rate, and lumpMutSpecial() for lumping models that strong lumpability cannot handle. The most recent release is narrow, adding a programmatic output format to getParams().
◆ Where it's heading
The consistent goal is making models satisfy the mathematical properties downstream algorithms require. Reversibility, stationarity, and lumpability each unlock something in pedprobr, and the package keeps adding ways to coerce an arbitrary model into having them. lumpMutSpecial() is explicitly incomplete, described as covering only some cases with more possibly to follow, which sets up the main open thread.
◆ Prediction
Expect additional special lumping cases to be implemented, since the package documents the current coverage as partial and pedprobr's likelihood performance depends directly on it.
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.
Alternatives to pedmut and qqman
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 pedmut or qqman.
ducksemantics
ducksemantics puts an ontology graph and ColBERT retrieval inside DuckDB, callable from R.
dvir
dvir keeps making disaster victim identification a single call instead of a workflow.
pedbuildr
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
forrel
forrel is getting faster at the simulations forensic kinship work actually spends its time on.
pedFamilias
pedFamilias exists to read one legacy file format, and it has that job nearly finished.
See all pedmut alternatives → · See all qqman alternatives →
Recent activity from pedmut and qqman
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 2mo agopedmutgetParams() gains a programmatic output format
- 1y agopedmutSpecial lumping arrives for un-lumpable models
- 1y agopedmutReversibility transformations and rate adjustment
- 2y agopedmutMutation rate and boundedness diagnostics
- 3y agopedmutPM stabilisation and multi-lump strong lumpability
- 3y agopedmutlumpedModel() wrapper and lumping speedups
- 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 pedmut and qqman?
They serve adjacent needs but don't currently overlap on shipped themes. pedmut and qqman 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 pedmut better than qqman?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. pedmut and qqman 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 pedmut?
Top pedmut alternatives in Analytics are ranked by recent ship velocity. Browse the "pedmut alternatives" section above for the current picks, or visit /alternatives/pedmut for the full list with editorial commentary on each.
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.