alignped1: First routine alignement

In sinnweja/kinship2: Pedigree Functions

First routine alignement

Description

This is the first of the four co-routines.

Usage

alignped1(x, dad, mom, level, horder, packed, spouselist)

Arguments

spouselist

Details

It is called with a single subject, and returns the subtree founded on said subject, as though it were the only tree.

\item

Part 1In this routine the [[nid]] array consists of the final nid array + 1/2 of the final spouse array. Note that the [[spouselist]] matrix will only contain spouse pairs that are not yet processed. The logic for anchoring is slightly tricky. First, if row 4 of the spouselist matrix is 0, we anchor at the first opportunity. Also note that if spouselist[,3]==spouselist[,4] it is the husband who is the anchor (just write out the possibilities). \itemPart 2Create the set of 3 return structures, which will be matrices with (1+nspouse) columns. If there are children then other routines will widen the result. \itemPart 3Create the two complimentary lists lspouse and rspouse to denote those plotted on the left and on the right. For someone with lots of spouses we try to split them evenly. If the number of spouses is odd, then men should have more on the right than on the left, women more on the right. Any hints in the spouselist matrix override. We put the undecided marriages closest to [[x]], then add predetermined ones to the left and right. The majority of marriages will be undetermined singletons, for which nleft will be 1 for female (put my husband to the left) and 0 for male. In one bug found by plotting canine data, lspouse could initially be empty but length(rspouse)> 1. This caused nleft>length(indx). A fix was to not let indx to be indexed beyond its length, fix by JPS 5/2013. \itemPart 4For each spouse get the list of children. If there are any we call alignped2 to generate their tree and then mark the connection to their parent. If multiple marriages have children we need to join the trees. \itemPart 5 To finish up we need to splice together the tree made up from all the kids, which only has data from lev+1 down, with the data here. There are 3 cases: The first and easiest is when no children were found. The second is when the tree below is wider than the tree here, in which case we add the data from this level onto theirs. The third is when below is narrower, for instance an only child.

Value

A set of matrices along with the spouselist matrix. The latter has marriages removed as they are processed.

See Also

plot.pedigree, autohint

Examples

data(sample.ped)
ped <- with(sample.ped,pedigree(id, father, mother, sex, affected))
align.pedigree(ped)

sinnweja/kinship2 documentation built on July 8, 2023, 11:26 p.m.