High-Performance Open-Source Archive
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.
labels(..., unlist = TRUE).Th main focus of this version is an overhaul of the IBD triangle
plots, and implementing such plots also in ggplot2 and
plotly.
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().
kinship(x) now catches duplicated ID labels across
components when x is a pedlist.ibdTriangle() gains argument
shortLines, restricting kinship lines to the interior of
the triangle.
ibdDraw() now automatically calculates sensible plot
margins.
Add citation info.
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).
coeffTable() several columns have been
renamed.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.
Check that the input vector to detailed2condensed()
has sum 1 (#14).
Fixed edge-case bug in twoLocusIdentity()
(#9).
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 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.
kinship(x, ids) affecting pedigrees in
nonstandard order.kinship() now accepts a list of pedigrees as
input.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.
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.
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.
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