paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
EpiNow2 vs qtl
A side-by-side editorial comparison of EpiNow2 and qtl — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
EpiNow2 vs qtl: at a glance
What is EpiNow2?
EpiNow2 unified its model interface, then went back to deepen the estimators behind it
EpiNow2 estimates reproduction numbers, infections and delay distributions from incomplete epidemiological reporting data. 1.8.0 was the structural turning point: every main modelling function now returns a consistent S3 object with `fit`, `args` and `observations`, reachable through shared accessors. The releases either side of it work on estimator quality — accumulation of irregularly reported data in 1.7.0, and a substantial expansion of `estimate_truncation()` in 1.9.0.
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.
EpiNow2 vs qtl: editorial side-by-side
EpiNow2
0.0ANALYTICS
EpiNow2 unified its model interface, then went back to deepen the estimators behind it
◆ Current state
EpiNow2 estimates reproduction numbers, infections and delay distributions from incomplete epidemiological reporting data. 1.8.0 was the structural turning point: every main modelling function now returns a consistent S3 object with `fit`, `args` and `observations`, reachable through shared accessors. The releases either side of it work on estimator quality — accumulation of irregularly reported data in 1.7.0, and a substantial expansion of `estimate_truncation()` in 1.9.0.
◆ Where it's heading
The package spent this window paying down interface debt and is now extending from the tidier base. Options that existed only for `estimate_infections()` have been propagated outward: `estimate_truncation()` gained the full `dist_spec` delay families, `obs_opts()` observation model selection between Poisson and negative binomial, and the `likelihood` and `return_likelihood` settings that make prior-only fits and loo-compatible output possible. Hardcoded assumptions are being replaced by specifiable ones in the same motion — the truncation model's additive noise term was a fixed `sigma ~ normal(0, 1)` prior and is now a `dist_spec` argument.
◆ Prediction
Expect the remaining modelling functions to keep converging on the shared options interface, since the last two releases have each moved another function onto it. A new `estimate_dist()` for interval-censored linelist data suggests delay estimation is the area still gaining surface.
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 EpiNow2 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 EpiNow2 or qtl.
geodist
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
errors
errors keeps making uncertainty print the way each scientific field expects.
CMAQ
CMAQ went global in v5.5, and has been patching that surface ever since.
enpls
enpls has not changed its statistics since 2016 — only its website, twice.
grex
grex is a lookup table with a version number — it ships when the annotation moves.
Recent activity from EpiNow2 and qtl
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agoEpiNow2estimate_truncation gains full delay and observation options
- 6mo agoEpiNow2Unified return objects and shared accessors across all models ⚡
- 8mo agoqtlRemove R_ext/PrtUtil.h include flagged by CRAN
- 8mo agoqtlClearer cim() error when multiple phenotypes are passed
- 1y agoEpiNow2Patch for an upstream rstan issue
- 1y agoEpiNow2Accumulation for irregularly reported data; unified priors
- 1y agoEpiNow2Matern kernel spectral density fix and GP prior revert
- 1y agoEpiNow2Gaussian Process model improvements and explicit defaults
- 1y agoqtlC memory calls migrated to R_Calloc/R_Realloc/R_Free
- 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 EpiNow2 and qtl?
Both compete on the same themes — r-package — within Analytics. EpiNow2 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 EpiNow2 better than qtl?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. EpiNow2 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 EpiNow2?
Top EpiNow2 alternatives in Analytics are ranked by recent ship velocity. Browse the "EpiNow2 alternatives" section above for the current picks, or visit /alternatives/epinow2 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.