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Comparison · Analytics
ibdsim2 vs pedprobr
A side-by-side editorial comparison of ibdsim2 and pedprobr — release velocity, themes, recent moves, and the top alternatives to consider.
ibdsim2 vs pedprobr: at a glance
What is ibdsim2?
A pedigree IBD simulator that absorbed its own web app and now optimises for dense marker panels.
ibdsim2 simulates identity-by-descent sharing along chromosomes for arbitrary pedigrees, in both autosomal and X-chromosomal form, with downstream tools for segment statistics, pattern finding and distribution plots. Since 2.1.0 the Shiny front end lives inside the package and launches via launchApp() rather than sitting in a separate repository. The latest release is performance work, with profileSimIBD() substantially sped up for dense marker panels and ibdsim() skipping recombination in pedigree branches that cannot affect the result.
What is pedprobr?
pedprobr is the likelihood engine, and it keeps finding ways to compute what it previously could not.
pedprobr computes pedigree likelihoods for the ped suite. Version 1.1.0 updated its loop handling to match pedtools 2.11.0, including founder and repeated loop breakers, and improved the peeling algorithm with single-child shortcuts and lower memory use. Version 1.0.0 was the other expansion: special lumping lets markers with mutation models that are un-lumpable in the Kemeny-Snell sense be lumped anyway in certain cases, with alleleLimit as a fallback for the rest.
ibdsim2 vs pedprobr: editorial side-by-side
ibdsim2
2.5ANALYTICS
A pedigree IBD simulator that absorbed its own web app and now optimises for dense marker panels.
◆ Current state
ibdsim2 simulates identity-by-descent sharing along chromosomes for arbitrary pedigrees, in both autosomal and X-chromosomal form, with downstream tools for segment statistics, pattern finding and distribution plots. Since 2.1.0 the Shiny front end lives inside the package and launches via launchApp() rather than sitting in a separate repository. The latest release is performance work, with profileSimIBD() substantially sped up for dense marker panels and ibdsim() skipping recombination in pedigree branches that cannot affect the result.
◆ Where it's heading
Two long-running threads. One is the app as a first-class part of the package, which has been getting input validation, dependency checks and plotting fixes release after release, treating a research GUI as software to be maintained rather than a demo. The other is numerical care: the built-in recombination map was rebuilt in 2.3.0 with better chromosome endpoints and a thinning algorithm that cut it from about 38,000 points to 14,000 without losing accuracy, and IBD segment merging has been made consistent across the realised-coefficient functions. The maintainer flags repeatedly that seeded results may differ across versions, which is the right disclosure for a simulator used in published analyses.
◆ Prediction
The recent work points at further speed on dense panels and continued hardening of app input handling, both of which have appeared in each of the last several releases. Nothing here signals a new modelling capability on the way.
pedprobr
0.0ANALYTICS
pedprobr is the likelihood engine, and it keeps finding ways to compute what it previously could not.
◆ Current state
pedprobr computes pedigree likelihoods for the ped suite. Version 1.1.0 updated its loop handling to match pedtools 2.11.0, including founder and repeated loop breakers, and improved the peeling algorithm with single-child shortcuts and lower memory use. Version 1.0.0 was the other expansion: special lumping lets markers with mutation models that are un-lumpable in the Kemeny-Snell sense be lumped anyway in certain cases, with alleleLimit as a fallback for the rest.
◆ Where it's heading
Every significant release here removes a class of computation that used to be infeasible, either by making a marker lumpable or by making a loop breakable. The rest is steady peeling-algorithm optimization, which has been reducing memory footprint release after release since 0.9.2. The newly added .diagnostics option suggests the peeling internals are now complex enough that the maintainer needs to inspect them.
◆ Prediction
Since special lumping is documented as covering only some cases so far, expect further lumping situations to be implemented as pedmut adds them.
Alternatives to ibdsim2 and pedprobr
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 ibdsim2 or pedprobr.
spsurvey
spsurvey has spent four years consolidating after its 5.0.0 rewrite rather than adding to it
StreamCatTools
StreamCatTools is quietly moving off web services and onto cloud-native GeoParquet
reproducible
reproducible added a windowed read path so remote GeoTiffs never fully download
qcTAF
qcTAF is building an automated checklist for reproducible fisheries assessments, one criterion at a time
rpymat
After three dormant years, rpymat returned to fix the OpenMP crash that breaks R and conda together
See all ibdsim2 alternatives → · See all pedprobr alternatives →
Recent activity from ibdsim2 and pedprobr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11d agoibdsim2profileSimIBD() sped up for dense marker panels; segment merging fixed
- 1mo agopedprobrLoop handling updated for pedtools' new loop breakers
- 8mo agoibdsim2Segment-distribution merge argument, and function-valued parameters
- 1y agoibdsim2Built-in decode19 recombination map rebuilt, cutting 38k points to 14k
- 1y agopedprobrCRAN example rounding fix
- 1y agopedprobrSpecial lumping for previously un-lumpable mutation models
- 1y agopedprobrGenotype distributions gain sparse and table output
- 1y agoibdsim2Consistent IBD segment merging across the realised-coefficient functions
- 1y agoibdsim2Built-in pedigree labels revised; extra inbred examples added
- 1y agoibdsim2The Shiny front end moves into the package and gains X-chromosomal simulation ⚡
- 2y agopedprobrPeeling order bug fix
- 2y agopedprobrPartial genotype fix for singletons
Frequently asked questions
What is the difference between ibdsim2 and pedprobr?
They serve adjacent needs but don't currently overlap on shipped themes. ibdsim2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is ibdsim2 better than pedprobr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. ibdsim2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to ibdsim2?
Top ibdsim2 alternatives in Analytics are ranked by recent ship velocity. Browse the "ibdsim2 alternatives" section above for the current picks, or visit /alternatives/ibdsim2 for the full list with editorial commentary on each.
What are the best alternatives to pedprobr?
Top pedprobr alternatives in Analytics are ranked by recent ship velocity. Browse the "pedprobr alternatives" section above for the current picks, or visit /alternatives/pedprobr for the full list with editorial commentary on each.