EvoPhylo
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
Comparison · Analytics
deeptime vs qtl
A side-by-side editorial comparison of deeptime and qtl — release velocity, themes, recent moves, and the top alternatives to consider.
deeptime vs qtl: at a glance
What is deeptime?
A geologic-time plotting layer that outgrew time axes and became a geology rendering toolkit.
deeptime extends ggplot2 with geological time scales, radial deep-time coordinates and phylogeny-aware geoms, and since 2.0.0 it also renders standardized FGDC/USGS geologic patterns as ggplot2 fills. The current 2.4.0 release adds geom_text_clade() for labeling clades on radial phylogenies and repairs long-standing coord_trans_xy() and scale-placement edge cases.
What is qtl?
R/qtl is in pure custodial mode: every recent release answers a compiler, not a user
R/qtl is the long-established R package for QTL mapping in experimental crosses, covering interval mapping, composite interval mapping, multiple-QTL model fitting and the associated cross data formats. Nothing in the recent release history adds capability. Version 1.74 removes an include that started warning on CRAN, 1.72 improves an error message in cim(), and 1.70 migrates the C code from Calloc/Realloc/Free to their R_-prefixed equivalents for R-devel.
deeptime vs qtl: editorial side-by-side
deeptime
0.0ANALYTICS
A geologic-time plotting layer that outgrew time axes and became a geology rendering toolkit.
◆ Current state
deeptime extends ggplot2 with geological time scales, radial deep-time coordinates and phylogeny-aware geoms, and since 2.0.0 it also renders standardized FGDC/USGS geologic patterns as ggplot2 fills. The current 2.4.0 release adds geom_text_clade() for labeling clades on radial phylogenies and repairs long-standing coord_trans_xy() and scale-placement edge cases.
◆ Where it's heading
The package is converging on two jobs: being the canonical R renderer for stratigraphic drawing conventions, and keeping pace with ggplot2's own churn. A sustained deprecation program — gggeo_scale(), coord_geo_polar(), getScaleData(), now disparity_through_time() — is trimming the surface down to coord_geo(), coord_geo_radial() and the pattern functions. Roughly half of each recent release is ggplot2 4.0 compatibility work.
◆ Prediction
Expect disparity_through_time() and coord_geo_polar() to be removed outright in the next major version, and further geoms aimed at annotating radial phylogenies.
qtl
0.0ANALYTICS
R/qtl is in pure custodial mode: every recent release answers a compiler, not a user
◆ Current state
R/qtl is the long-established R package for QTL mapping in experimental crosses, covering interval mapping, composite interval mapping, multiple-QTL model fitting and the associated cross data formats. Nothing in the recent release history adds capability. Version 1.74 removes an include that started warning on CRAN, 1.72 improves an error message in cim(), and 1.70 migrates the C code from Calloc/Realloc/Free to their R_-prefixed equivalents for R-devel.
◆ Where it's heading
The package is being maintained, not developed. The work divides cleanly into keeping the compiled code building against successive R and toolchain versions, and fixing narrow bugs reported through the issue tracker. The C-level migrations in particular are compliance with R's tightening of its C interface rather than anything chosen. Users should read the stability as maturity: the analysis surface has been fixed for years and the maintainer is keeping it installable.
◆ Prediction
R has continued to restrict its non-API C entry points, and this package has already made two such migrations, so further compile-time compliance work is the most likely content of the next release.
Alternatives to deeptime and qtl
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 deeptime or qtl.
treespace
treespace ships once every year or two, and only when CRAN or a user forces it.
Rpath
Rpath 1.1.0 learns to read Ecopath's own files, easing migration off the desktop tool.
TAF
TAF keeps turning ICES stock assessments into reproducible, dependency-pinned projects.
parallelDist
parallelDist is in pure preservation mode — one build fix every few years.
cairo
Cairo finally catches R's graphics engine, all the way to GE API 16.
See all deeptime alternatives → · See all qtl alternatives →
Recent activity from deeptime and qtl
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agodeeptimegeom_text_clade() labels clades on radial phylogenies
- 8mo agoqtlRemove R_ext/PrtUtil.h include flagged by CRAN
- 8mo agodeeptimeArgument renames for ggplot2 4.0 parity
- 8mo agodeeptimePattern code dictionary and time-scale theming
- 8mo agoqtlClearer cim() error when multiple phenotypes are passed
- 1y agodeeptimegeom_text_phylo() arrives with ggplot2 4 compatibility
- 1y agodeeptimeContrast-aware label colors across the built-in scales
- 1y agoqtlC memory calls migrated to R_Calloc/R_Realloc/R_Free
- 1y agodeeptimeFGDC geologic patterns become ggplot2 fills ⚡
- 2y agoqtlFix Rprintf call and remaining compiler warnings
- 2y agoqtlFix summary.scanone() thresholds and csvs phenotype reading
- 3y agoqtlFix addint()/addcovarint() with X chromosome QTL and missing phenotypes
Frequently asked questions
What is the difference between deeptime and qtl?
They serve adjacent needs but don't currently overlap on shipped themes. deeptime and qtl 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 deeptime better than qtl?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. deeptime and qtl 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 deeptime?
Top deeptime alternatives in Analytics are ranked by recent ship velocity. Browse the "deeptime alternatives" section above for the current picks, or visit /alternatives/deeptime-r for the full list with editorial commentary on each.
What are the best alternatives to qtl?
Top qtl alternatives in Analytics are ranked by recent ship velocity. Browse the "qtl alternatives" section above for the current picks, or visit /alternatives/qtl-r for the full list with editorial commentary on each.