get_nth_degree_relatives: Find all nth degree relatives from a pedigree-network

In samellisq/comparekin: Calculating relatedness in biological data

Description

get_nth_degree_relatives derives the ids of all relatives within the nth degree for a given individual from a population kinship-network.

Usage

get_nth_degree_relatives(network, from.id, r.degree)

Arguments

network	A kinship-network derived from the make_kinship_network function. The type of network input - biparental, maternal only, paternal only - defines which side(s) of relatives are found.
from.id	Character. The id of the individual for whom nth degree relatives will be found
r.degree	degree of relationship to which to calculate relatedness ( https://en.wikipedia.org/wiki/Coefficient_of_relationship. Degree is calculated separately for each lineage i.e. half-sisters are considered equivalent to full-sisters in count (but not in relatedness calculation).

Value

Returns a character vector of the ids of all relatives up to the r.degree degree of the from.id. For example, where r.degree = 2 this will return a vector of all 1st and 2nd degree maternal and paternal relatives (if they are both present in the network). Vector also includes from.id.

Examples

#Example data taken from kinship2::kinship()
test1 <- data.frame(id  =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
                   mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6,  2,  0,  0, 12, 13),
                   dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3,  7,  0,  0, 11, 10),
                   sex =c(0, 1, 0, 1, 0, 1, 0, 1, 0,  0,  0,  1,  1,  1))
#some renaming
names(test1)[2] = "mother"
names(test1)[3] = "father"
test1$sex = ifelse(test1$sex ==1, "F", "M")
test1$id = as.character(test1$id)
test1$mother = ifelse(test1$mother!=0, as.character(test1$mother), "UNK")
test1$father = ifelse(test1$father!=0, as.character(test1$father), "UNK")
test1

population.network = make_kinship_network(make_relation_df(test1))
plot(population.network)
get_nth_degree_relatives(network = population.network, from.id = test1$id[5],
r.degree = 2)

samellisq/comparekin documentation built on Dec. 22, 2021, 10:11 p.m.