NEWS.md

In pedprobr: Probability Computations on Pedigrees

pedprobr 0.8.0

New features

• Mutation models are now supported in likelihood2(), providing likelihood calculations for pairwise linked markers.

• New functions haldane() and kosambi().

Other

• Update README.

• Update package doc.

• Include license (GPL >= 2).

pedprobr 0.7.1

• reduceAlleles() is faster in some cases, due to the new pedmut::lumpedModel().

• A few minor speedups and code improvements.

pedprobr 0.7.0

New features

• merlin() gains argument checkpath. Set this to FALSE to avoid redundant checks of MERLIN availability.

• likelihoodMerlin() gains argument perChrom, used to parse the chromosome-wise likelihoods from the MERLIN output.

• lumpAlleles() gains argument always. By default lumping is skipped for markers where all individuals are genotyped, but this can cause problems e.g. with MERLIN which operates with an upper limit of allleles.

• Some efforts are done to check for (and warn about) underflow/overflow in MERLIN results.

pedprobr 0.6.1

Bug fixes

• Fixed a regression error involving the external program MINX (part of MERLIN). The new version of checkMerlin() by default checks that both merlin and minx are available on the system, and that they both come from the latest MERLIN version.

pedprobr 0.6.0

Breaking changes

• pedprobr now depends on R 4.1 and pedtools 1.1.0.

• The deprecated argument loop_breakers has been completely removed (renamed to loopBreakers)

New features

• likelihood.ped() gains a new argument lump, which activates allele lumping. This is TRUE by default, and should remain so in most cases.

• Using theta correction in pedigrees with inbred founders now gives an error.

• The internal peelingProcess() now checks for unbroken loops in the pedigree. (Of interest for developers mainly.)

Bug fixes

• Fixed bug affecting likelihood computations with theta correction.

Other changes

• When calling MERLIN, the window-centric and unnecessary .exe extensions has been removed.

• Many examples have been rewritten in simpler code, taking advantage of pedtools::addMarker and the pipe |>.

pedprobr 0.5.0

New features

• Removing/disabling mutation models is now easier, with setMutationModel(..., model = NULL).

Bug fixes

• Fixed bug in setMutationModel() affecting lists of multiple pedigrees.

pedprobr 0.4.0

Breaking changes

• likelihood() has been refactored, moving the treatment of (two) linked markers to a separate function, likelihood2().

New features

• Theta-correction is implemented in likelihood calculations, through the argument theta of likelihood().

• merlin() and likelihoodMerlin() have been overhauled.

• A new function checkMerlin() checks if MERLIN is installed and available.

• merlin() now has an argument linkageMap facilitating analysis of linked markers.

• likelihoodMerlin() gains arguments rho and logbase.

• New function lumpAlleles().

pedprobr 0.3.0

New features

• The likelihood() function now handles multiple marker inputs. For example, the call likelihood(x, 1:2) results in a vector of length 2 with the likelihoods of the first two markers attached to x.

• Recombination parameter theta is renamed to rho everywhere, to align with other ped suite packages. theta still works, though.

Other changes

• Many input checks have been added, giving more useful error messages.

• The data structure used in likelihood calculations is simplified and more efficient.

• Likelihood computation of two linked markers (and therefore also twoMarkerDistribution()) is much faster now.

pedprobr 0.2.0

New features

• New general MERLIN wrapper, merlin().

• Both likelihoodMerlin() and the new merlin() now accepts ped lists.

Bug fixes

• Fixed a bug affecting lumped mutation models.

pedprobr 0.1.0

• Initial CRAN release.

pedprobr documentation built on April 14, 2023, 12:31 a.m.