ribd - 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).

- R
Published by magnusdv over 1 year ago

ribd - 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.

- R
Published by magnusdv over 2 years ago

ribd - 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).

- R
Published by magnusdv almost 3 years ago

ribd - ribd 1.5.0

Breaking changes

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

New features

• Several two-locus functions have been cleaned up, and many examples have been added.
• 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).

- R
Published by magnusdv over 3 years ago

ribd - 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, being replaced with an argument Xchrom in kinship(), inbreeding() and kappaIBD() respectively. This is also consistent with the new identityCoefs() (see below).

• 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 decimal places, 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() affecting pedigrees in nonstandard order.

- R
Published by magnusdv about 4 years ago

ribd - ribd 1.3.1

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

- R
Published by magnusdv over 4 years ago

ribd - 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.

- R
Published by magnusdv about 5 years ago

ribd - ribd 1.2.0

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

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

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

- R
Published by magnusdv almost 6 years ago

ribd - ribd 1.1.0

New features

• 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.

- R
Published by magnusdv almost 6 years ago