besthint {kinship} | R Documentation |
A pedigree structure can contain a hints
matrix
which helps to reorder the pedigree (e.g. left-to-right order of
children within family) so as to plot with minimal distortion.
This routine trys out a large number of configurations, finding the
best by brute force.
besthint(ped, wt=c(1000, 10, 1), tolerance=0)
ped |
a pedigree object |
wt |
relative weights for three types of "distortion" in a plotted pedigree. The final score for a pedigree is the weighted sum of these; the lowest score is considered the best. The three components are 1: the number of dotted lines, connecting two instances of the same person; 2: the lengths of those dotted lines; and 3: the horizontal offsets between parent/child pairs. |
tolerance |
the threshold for acceptance. If any of the orderings that are attempted have a score that is less than or equal to this value, the routine ceases searching for a better one. |
Assume that a pedigree has k founding couples, i.e., husband-wife pairs for
which neither has a parent in the pedigree.
The routine tries all k!/2 possible left to right orderings of the founders
(in random order), uses the autohint
function
to optimize the order of children within each family, and computes a
score.
The hints matrix for the first pedigree to match the tolerance
level is returned, or that for the best score found if none match the
tolerance.
a hints matrix
pedigree, plot.pedigree, autohint
## Not run: # Find a good plot, only trying to avoid dotted connectors myped$hints <- besthint(myped, wt=c(1000,100,0)) ## End(Not run)