pedsize(x) returns the number of pedigree members in each component of
x.
generations(x) by default returns the number of generations in x,
defined as the number of individuals in the longest line of parent-child
links. (Note that this definition is valid also if x has loops.) If
maxOnly = FALSE, the output is a named integer vector, showing the
generation number of each pedigree member. If x has multiple components,
the output depends on the parameter maxComp. If this is FALSE, the output
is a vector containing the result for each component. If TRUE (default), only
the highest number is returned.
hasUnbrokenLoops(x) returns TRUE if x has loops, otherwise FALSE. (No
computation is done here; the function simply returns the value of
x$UNBROKEN_LOOPS).
hasInbredFounders(x) returns TRUE is founder inbreeding is specified for
x and at least one founder has positive inbreeding coefficient. See
founderInbreeding() for details.
hasSelfing(x) returns TRUE if the pedigree contains selfing events. This
is recognised by father and mother begin equal for some child. (Note that for
this to be allowed, the gender code of the parent must be 0.)
hasCommonAncestor(x) computes a logical matrix A whose entry A[i,j]
is TRUE if pedigree members i and j have a common ancestor in x, and FALSE
otherwise. By convention, A[i,i] is TRUE for all i.
subnucs(x) returns a list of all nuclear sub-pedigrees of x, wrapped as
nucleus objects. Each nucleus is a list with entries father, mother and
children.
peelingOrder(x) calls subnucs(x) and extends each entry with a link
individual, indicating a member linking the nucleus to the remaining
pedigree. One application of this function is the fact that if fails to
find a complete peeling order if and only if the pedigree has loops. (In fact
it is called each time a new ped object is created by ped() in order to
detect loops.) The main purpose of the function, however, is to prepare for
probability calculations in other packages, as e.g. in
pedprobr::likelihood.