forrel 1.9.0

New features

• Updated loop handling throughout the package, syncing with pedtools 2.11.0 and pedprobr 1.1.0. In particular, this enables analyses of certain complex pedigrees that were previously intractable.

• profileSim() now uses mirai for parallel computations. To activate parallelisation, users must start workers with mirai::daemons() before calling profileSim(). See ?profileSim for details and code examples.

• Simulations with profileSim() and markerSim() are significantly faster in many cases, due to better organisation of the internal likelihood calculations.

• profileSim() no longer preserves map attributes (chromosome and position) of the markers. This was an expensive operation that is rarely needed, and can be done afterwards with setMap() if required.

• New function fEstimate() for estimating the inbreeding coefficient of an individual from marker data.

• New function parentChildLikelihood() for fast likelihood calculations in simple parent-child cases.

• quickLR() now includes a first-cousin hypothesis by default.

• IBD contour plots gain support for additional graphical arguments.

Other

• Updated dependencies to pedtools 2.11.0 and pedprobr 1.1.0.
• Reduced risk of underflow in kinshipLR() by using log-likelihoods internally.
• Fixed an ordering bug in exclusionPower() affecting pedigrees with multiple components.
• Fixed handling of X-chromosomal maps.
• ibdEstimate() now preserves class "ibdEst" when adding maximum log-likelihood values.
• Removed the long-deprecated readFam() function.