pedbuildr (version 0.3.0)

buildPeds: Build a list of pedigrees

Description

Build all pedigrees between a set of individuals, subject to given restrictions.

Usage

buildPeds(
  labs,
  sex = 1,
  extra = "parents",
  age = NULL,
  knownPO = NULL,
  knownSub = NULL,
  allKnown = FALSE,
  notPO = NULL,
  noChildren = NULL,
  connected = TRUE,
  maxInbreeding = 1/16,
  linearInb = FALSE,
  sexSymmetry = TRUE,
  verbose = TRUE
)

Value

A list of (possibly disconnected) pedigrees.

Arguments

labs

A character vector of ID labels.

sex

A vector of the same length as labs, with entries 1 (male) or 2 (female).

extra

Either the word "parents" (default), or a non-negative integer. See Details.

age

A numeric or character vector. If numeric, and age[i] < age[j], then individual i will not be an ancestor of individual j. The numbers themselves are irrelevant, only the partial ordering. (No inference is made about individuals of equal age.) Alternatively, for finer control, age may be a character vector of inequalities, e.g., age = c("1>2", "1>3").

knownPO

A list of vectors of length 2, containing the ID labels of pairs known to be parent-offspring. By default, both directions are considered; use age to force a specific direction.

knownSub

A ped object involving a subset of the labs individuals.

allKnown

A logical. If TRUE, no other pairs than knownPO will be assigned as parent-offspring. If FALSE (default), all pairs except those in notPO are treated as potential parent-offspring.

notPO

A list of vectors of length 2, containing the ID labels of pairs known not to be parent-offspring.

noChildren

A vector of ID labels, indicating individuals without children of their own.

connected

A logical. If TRUE (default), only connected pedigrees are returned.

maxInbreeding

A single numeric indicating the highest permitted inbreeding coefficient. Default: 1/16 (as with first-cousin parents.)

linearInb

A parameter controlling the maximum separation of linearly related spouses. Either TRUE (allow all linear inbreeding), FALSE (disallow all) or a non-negative integer. For example, linearInb = 1 allows parent/child mating, but not grandparent/grandchild or more distant linear relatives. Default: FALSE.

sexSymmetry

A logical. If TRUE (default), pedigrees which are equal except for the gender distribution of the added parents, are regarded as equivalent, and only one of each equivalence class is returned. Example: paternal vs. maternal half sibs.

verbose

A logical.

Details

The parameter extra controls which of two algorithms are used to create the pedigree list.

If extra is a nonnegative integer, it determines the number of extra individuals allowed in the iterative pedigree construction. These extras start off with undetermined sex, meaning that both males and females are used. It should be noted that the final pedigrees may contain additional extras, since missing parents are added at the end.

If extra is the word "parents", the algorithm is not iterative. It first generates all directed acyclic graphs between the original individuals. Then their parents are added and merged in all possible ways. This option has the advantage of not requiring an explicit/ad hoc number of "extras", but works best in smaller cases.

Examples

# Two individuals + 1 extra
plist = buildPeds(1:2, extra = 1, age = "1>2")
plot(plist)

# Allow disconnected
plist2 = buildPeds(1:2, extra = 1, age = "1>2", connected = FALSE)
plot(plist2, frames = TRUE)

# Note that full sibs require 2 extras
plist3 = buildPeds(1:2, extra = 2, age = "1>2")
plot(plist3)

# With 2 extras, allowing any inbreeding
plist4 = buildPeds(1:2, extra = 2, age = "1>2", maxInbreeding = 1)
plot(plist4)

# Full sibs are also included when `extra = "parents"`
plist5 = buildPeds(1:2, extra = "parents", age = "1>2")
plot(plist5)