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polyRAD

INFRA · APIS
Velocity0.0

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

github.com/lvclark/polyRAD ↗

Polyploid genotype calling went quiet for three years, then returned with a bug-fix tag.

polyploid-geneticsgenotype-callingbayesianbioinformaticscran
◆Current state
polyRAD calls genotypes from RAD sequencing data in polyploid and diploid populations using Bayesian estimation. Its capability surface has been settled since 2.0 in late 2022, which added support for ploidy that varies among individuals. The March 2026 release is a CRAN bug-fix sync after a three-and-a-half-year gap, with the substance deferred to NEWS.
◆Where it's heading
The releases between 1.0 and 2.0 followed a consistent pattern: add export paths to other tools in the polyploid genetics stack, add simulation controls, fix what CRAN checks caught. That expansion stopped at 2.0, and 2.0.1 does not resume it. The package reads as complete and maintained rather than under development.
◆Prediction
Continued low-frequency patch releases keeping the package on CRAN as R and its dependencies move. The release notes give no sign of a 2.1 feature line.

◆Recent moves

  1. 4mo ago

    Bug-fix sync with CRAN after a three-year gap

    A CRAN maintenance release described only as minor bug fixes, with the detail left in NEWS. Notable mostly for its timing: it ends a three-and-a-half-year silence without restarting the feature line that stopped at 2.0.

    View source ↗
  2. 3y ago

    Multiploidy support arrives and breaks saved RADdata objects

    ⚡ SPARK

    The release that set the package's current capability surface. Supporting ploidy that varies among individuals removes the assumption every prior version was built on, and it costs backward compatibility for serialised data.

    View source ↗
  3. 4y ago

    Contamination and error-rate simulation controls added

    The last release before the 2.0 line. Simulation functions gain contamRate and errorRate parameters so users can model cross contamination and sequencing error when generating read depths, and TestOverdispersion now returns the parameter it recommends instead of only printing advice.

    View source ↗
  4. 4y ago

    Mapping-population simulation and DArTag import added

    Five new functions broaden both ends of the pipeline: SimGenotypesMapping and ExpectedHindHeMapping extend the simulation and quality machinery to mapping populations, Export_polymapR_probs and readDArTag connect to neighbouring tools, and reverseComplement fills a utility gap.

    View source ↗
  5. 5y ago

    GWASpoly export gains continuous genotypes; adegenet export added

    Primarily a release to settle vignette dependency problems that were failing CRAN checks, but it also lets Export_GWASpoly emit continuous rather than discrete genotypes and adds an adegenet genind export. The export-path expansion is the through-line of this stretch of the package's history.

    View source ↗
  6. 5y ago

    polyRAD v1.3

    A CRAN sync whose body names no changes at all, deferring entirely to the NEWS page. It claims new features but identifies none, so nothing about the package's direction can be read from this entry.

    View source ↗