gps2gtfs
gps2gtfs spent a release making its docs stop describing functions it does not have.
Comparison · Analytics
pedbuildr vs pedprobr
A side-by-side editorial comparison of pedbuildr and pedprobr — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:performance
pedbuildr vs pedprobr: at a glance
What is pedbuildr?
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
pedbuildr infers pedigree structure from marker data by scoring candidate pedigrees against likelihoods. Version 0.4.0 moved reconstruct() to mirai for parallel likelihood computation, deprecated the old numCores argument, and picked up the improved loop breaking from pedtools and pedprobr, which lets many complex looped pedigrees succeed where they previously failed. buildPeds() also got significantly faster in its default configuration where mating between lineally related individuals is disallowed.
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.
pedbuildr vs pedprobr: editorial side-by-side
pedbuildr
0.0ANALYTICS
pedbuildr reconstructs pedigrees from DNA, and it just got much faster at the search.
◆ Current state
pedbuildr infers pedigree structure from marker data by scoring candidate pedigrees against likelihoods. Version 0.4.0 moved reconstruct() to mirai for parallel likelihood computation, deprecated the old numCores argument, and picked up the improved loop breaking from pedtools and pedprobr, which lets many complex looped pedigrees succeed where they previously failed. buildPeds() also got significantly faster in its default configuration where mating between lineally related individuals is disallowed.
◆ Where it's heading
The package is bounded by two costs: how many candidate pedigrees it enumerates and how expensive each likelihood is. The recent release attacks both, parallelizing the likelihoods and speeding up enumeration in the common case. The earlier 0.3.0 release worked on the other end, adding inbreeding limits and a proper result class so the output of a large search is manageable. Releases are infrequent, roughly three years apart in this window.
◆ Prediction
Expect the candidate generation side to receive the same attention the likelihood side just did, since search space size is the remaining bound on what pedbuildr can reconstruct.
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 pedbuildr 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 pedbuildr or pedprobr.
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.
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.
pedmut
pedmut turns awkward mutation models into ones the likelihood engine can actually handle.
See all pedbuildr alternatives → · See all pedprobr alternatives →
Recent activity from pedbuildr and pedprobr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agopedbuildrmirai parallelism and faster pedigree enumeration
- 1mo agopedprobrLoop handling updated for pedtools' new loop breakers
- 1y agopedprobrCRAN example rounding fix
- 1y agopedprobrSpecial lumping for previously un-lumpable mutation models
- 1y agopedprobrGenotype distributions gain sparse and table output
- 2y agopedprobrPeeling order bug fix
- 2y agopedprobrPartial genotype fix for singletons
- 2y agopedbuildrpedCollection class and an inbreeding ceiling
Frequently asked questions
What is the difference between pedbuildr and pedprobr?
Both compete on the same themes — performance — within Analytics. pedbuildr and pedprobr 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 pedbuildr better than pedprobr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. pedbuildr and pedprobr 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 pedbuildr?
Top pedbuildr alternatives in Analytics are ranked by recent ship velocity. Browse the "pedbuildr alternatives" section above for the current picks, or visit /alternatives/pedbuildr 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.