Find unavailable subjects in a Pedigree

Find the identifiers of subjects in a Pedigree iteratively, as anyone who is not available and does not have an available descendant by successively removing unavailable terminal nodes.

Usage

# S4 method for class 'Ped'
find_unavailable(obj, avail = NULL)

# S4 method for class 'Pedigree'
find_unavailable(obj, avail = NULL)

Arguments

obj

A Ped or Pedigree object.

avail

A logical vector with the availability status of the individuals (i.e. FALSE = not available, TRUE = available, NA = unknown).

Value

Returns a vector of subject ids for who can be removed.

Details

If avail is null, then the function will use the corresponding Ped accessor.

Originally written as pedTrim by Steve Iturria, modified by Dan Schaid 2007, and now split into the two separate functions: find_unavailable(), and trim() to do the tasks separately. find_unavailable() calls exclude_stray_marryin() to find stray available marry-ins who are isolated after trimming their unavailable offspring, and exclude_unavail_founders(). If the subject ids are character, make sure none of the characters in the ids is a colon (":"), which is a special character used to concatenate and split subjects within the utility. The trim() functions is now replaced by the subset() function.

Side Effects

Relation matrix from subsetting is trimmed of any special relations that include the subjects to trim.

See also

shrink()

Examples

data(sampleped)
ped1 <- Pedigree(sampleped[sampleped$famid == "1",])
find_unavailable(ped1)
#>  [1] "1_101" "1_102" "1_107" "1_108" "1_111" "1_113" "1_121" "1_122" "1_123"
#> [10] "1_131" "1_132" "1_134" "1_139"