kinship2_alignped4

This is an internal helper function for pedigree alignment. It uses quadratic
programming to find optimal horizontal positions for subjects that minimize
the distance between parents and children while keeping spouses together and
respecting spacing constraints. Requires the quadprog package.

internal

Provides plotting functions for visualizing pedigrees and family trees. The package complements a behavior genetics package 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization. Due to the impending deprecation of kinship2, version 1.0 incorporates the layout helper functions from kinship2. The pedigree alignment algorithms are adapted from 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. We gratefully acknowledge the original authors: Jason Sinnwell, Terry Therneau, Daniel Schaid, and Elizabeth Atkinson for their foundational work.

S. Mason Garrison

ggpedigree

Visualizing Pedigrees with 'ggplot2' and 'plotly'

kinship2_alignped4 function

<dl><dt>rval</dt>
<dd>Aligned pedigree structure from previous alignment steps</dd>
<dt>spouse</dt>
<dd>Logical matrix indicating spouse connections</dd>
<dt>level</dt>
<dd>Integer vector of generation levels</dd>
<dt>width</dt>
<dd>Numeric, maximum width of the pedigree plot</dd>
<dt>align</dt>
<dd>Logical or numeric vector. If logical, uses default alignment parameters.
If numeric, should be a vector c(a1, a2) where a1 controls parent-child penalties
and a2 controls spouse penalties</dd></dl>

Arguments

Compute optimal horizontal spacing for pedigree alignment — kinship2_alignped4

<dl>

<dt>rval</dt>
<dd>Aligned pedigree structure from previous alignment steps</dd>


<dt>spouse</dt>
<dd>Logical matrix indicating spouse connections</dd>


<dt>level</dt>
<dd>Integer vector of generation levels</dd>


<dt>width</dt>
<dd>Numeric, maximum width of the pedigree plot</dd>


<dt>align</dt>
<dd>Logical or numeric vector. If logical, uses default alignment parameters.
If numeric, should be a vector c(a1, a2) where a1 controls parent-child penalties
and a2 controls spouse penalties</dd>

</dl>

kinship2_alignped4: Compute optimal horizontal spacing for pedigree alignment

Description

Usage

Value

Arguments