Changes in version 1.7.1 (2025-02-08)                  

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).

                 Changes in version 1.7.0 (2024-03-26)                  

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.

                 Changes in version 1.6.1 (2023-08-10)                  

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).

                 Changes in version 1.5.0 (2022-09-14)                  

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).

                 Changes in version 1.4.0 (2022-04-16)                  

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.

                 Changes in version 1.3.1 (2021-11-26)                  

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

                 Changes in version 1.3.0 (2021-05-28)                  

  - 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.

                 Changes in version 1.2.0 (2020-08-02)                  

  - 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.

                 Changes in version 1.1.0 (2020-06-19)                  

  - 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.

                 Changes in version 1.0.1 (2020-02-03)                  

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

                 Changes in version 1.0.0 (2019-11-01)                  

  - Initial CRAN release