EvoPhylo
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
Comparison · Analytics
qtl vs timeplyr
A side-by-side editorial comparison of qtl and timeplyr — release velocity, themes, recent moves, and the top alternatives to consider.
qtl vs timeplyr: at a glance
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.
What is timeplyr?
timeplyr cut everything that wasn't time, then rebuilt intervals as fixed-width vectors.
timeplyr is a time-aware companion to dplyr and data.table, built around a fixed-width time_interval vector class. The 1.0.0 rewrite removed most non-time functions and pushed the C++ layer out into the separate cheapr package, leaving a narrower surface than the 0.8.x line. Releases since have been small: one feature batch in 1.1.1 and a pair of bug fixes in 1.1.2.
qtl vs timeplyr: editorial side-by-side
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.
timeplyr
0.0ANALYTICS
timeplyr cut everything that wasn't time, then rebuilt intervals as fixed-width vectors.
◆ Current state
timeplyr is a time-aware companion to dplyr and data.table, built around a fixed-width time_interval vector class. The 1.0.0 rewrite removed most non-time functions and pushed the C++ layer out into the separate cheapr package, leaving a narrower surface than the 0.8.x line. Releases since have been small: one feature batch in 1.1.1 and a pair of bug fixes in 1.1.2.
◆ Where it's heading
The arc is consolidation, not expansion. Each release since 1.0.0 trims arguments, renames functions toward a single vocabulary (width, timespan, grid), or fixes an interaction with data.table's own rolling functions. The package increasingly acts as a thin time layer over cheapr and data.table rather than carrying its own implementation.
◆ Prediction
Expect continued small releases tracking cheapr and data.table changes rather than new function families; the entries show no in-progress feature work beyond the ggplot2-friendly breakpoint helpers introduced in 1.1.1.
Alternatives to qtl and timeplyr
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 qtl or timeplyr.
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 qtl alternatives → · See all timeplyr alternatives →
Recent activity from qtl and timeplyr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agotimeplyrLeap-day and time_complete(.by=) bug fixes
- 8mo agoqtlRemove R_ext/PrtUtil.h include flagged by CRAN
- 8mo agoqtlClearer cim() error when multiple phenotypes are passed
- 10mo agotimeplyrtime_breakpoints added; rolling calcs realigned to data.table
- 1y agotimeplyrFixed-width time intervals; non-time functions removed ⚡
- 1y agoqtlC memory calls migrated to R_Calloc/R_Realloc/R_Free
- 1y agotimeplyrtime_intervals on by default; year_month/year_quarter ggplot2 scales
- 2y agotimeplyrRegression fixes after the 0.8.0 refactor
- 2y agotimeplyrC++ layer moved to cheapr; time_interval class introduced
- 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 qtl and timeplyr?
They serve adjacent needs but don't currently overlap on shipped themes. qtl and timeplyr 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 qtl better than timeplyr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. qtl and timeplyr 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 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.
What are the best alternatives to timeplyr?
Top timeplyr alternatives in Analytics are ranked by recent ship velocity. Browse the "timeplyr alternatives" section above for the current picks, or visit /alternatives/timeplyr for the full list with editorial commentary on each.