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NEWS.md

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ribd 1.7.1

New features

  • kappaIBD() gains a logical argument acrossComps. Switching this off will compute the IBD coefficients only between individuals in the same connected component, which is often better for large pedigrees.

  • Update and improve documentation of multiPersonIBD().

  • Several tweaks of the plotly version of IBD triangles.

Other

  • Now using Rhub v2 for testing.
  • Increased pedtools dependency to 2.6.0, for labels(..., unlist = TRUE).

ribd 1.7.0

Th main focus of this version is an overhaul of the IBD triangle plots, and implementing such plots also in ggplot2 and plotly.

New features

  • ibdTriangle() and showInTriangle() gain an argument plotType, with permitted values "base" (default), "ggplot2" and "plotly".

  • ibdTriangle() now supports graphic parameters las, mar and title. (These work for base plots and also ggplot2.)

  • showInTriangle() has a new argument ped, for adding an inset pedigree in the top right corner.

  • Improved handling of labels in showInTriangle().

  • New dataset basicRelationships, which is called by ibdTriangle().

  • In kinship(x, ids), ids is no longer restricted to length 2.

  • Improve documentation of kappaIBD().

Bug fixes

  • kinship(x) now catches duplicated ID labels across components when x is a pedlist.

ribd 1.6.1

New features

  • ibdTriangle() gains argument shortLines, restricting kinship lines to the interior of the triangle.

  • ibdDraw() now automatically calculates sensible plot margins.

  • Add citation info.

Bug fixes

  • kappaIBD(x, ids, simplify = TRUE) now works as intended when x is a ped list and ids has length 2.

  • Fixed printing of two-locus kinship patterns in twoLocusIBD(..., verbose = TRUE).

ribd 1.5.0

Breaking changes

  • In the output of coeffTable() several columns have been renamed.

New features

  • New function twoLocusInbreeding().

  • New function: realisedIbdVariance().

  • New function ELR(), implementing method of Egeland & Slooten (2016).

  • All two-locus functions have been cleaned up and improved, and new examples have been added.

Bug fixes

  • Check that the input vector to detailed2condensed() has sum 1 (#14).

  • Fixed edge-case bug in twoLocusIdentity() (#9).

ribd 1.4.0

Breaking changes

  • The function idcoefs() was removed, since it relied on the no-longer-available package identity.

  • The deprecated kinshipX(), inbreedingX() and kappaIbdX() were removed, and replaced with an argument Xchrom in kinship(), inbreeding() and kappaIBD().

  • The function generalisedKinship() has been replaced with the much more versatile gKinship() (see below).

New features

  • New function identityCoefs() for computing condensed and detailed identity coefficients ("Jacquard coefficients"). Both autosomal and X-chromosomal versions are supported. This function supersedes condensedIdentity() and condensedIdentityX(), which will continue to exist, nonetheless.

  • condensedIdentity() gains arguments simplify and self, to match the new identityCoefs().

  • Computation of identity coefficients by MERLIN (via the "--extended" feature) is implemented in identityCoefs() with the option method = "merlin". Note that MERLIN rounds the output to 3 decimals, reducing its utility somewhat.

  • New function gKinship() for computing generalised kinship coefficients. Several algorithms are implemented, supporting various flavours (random vs. deterministic; distinct vs. non-distinct groups; autosomal vs. X).

  • New container class gip for generalised IBD patterns. Includes a print method.

  • New function coeffTable() collecting various pedigree coefficients in a single table.

  • New function kin2deg() computing the degree of relatedness, as used e.g. by the software KING.

Bug fixes

  • Fixed bug in kinship(x, ids) affecting pedigrees in nonstandard order.

ribd 1.3.1

  • kinship() now accepts a list of pedigrees as input.

ribd 1.3.0

  • The README has been rewritten and substantially expanded.

  • kappaIBD() now accepts ped lists as input.

  • In inbreeding() the argument id is renamed to ids and accepts vectors of length > 1.

ribd 1.2.0

  • New function ibdDraw() for illustrating IBD patterns in a pedigree. IBD alleles are represented as coloured dots or as letters.

  • New function ibdTriangle(), which replaces forrel::IBDtriangle().

  • constructPedigree() now gives a textual description of the (usually double-half-cousin-like) pedigree it produces.

ribd 1.1.0

  • New function constructPedigree(), which constructs a pedigree yielding a prescribed set of IBD coefficients. This implements the algorithm described in https://doi.org/10.1007/s00285-020-01505-x.

  • kinship() gains a new argument ids, which is handy when you only want the kinship coefficient between two individuals (and not the whole kinship matrix)

  • Similarly, inbreeding() gains the argument id for computing the inbreeding coefficient of a single individual.

ribd 1.0.1

  • This is a minor release, resolving a CRAN request to fix a documentation issue.

ribd 1.0.0

  • Initial CRAN release