get_nth_degree_ego_network: Create ego-pedigree

In samellisq/comparekin: Calculating relatedness in biological data

Description

get_nth_degree_ego_network trims the full population kinship-network down to only the ego network for a given id up to the nth relatedness degree.

Usage

get_nth_degree_ego_network(
  network,
  ego.id,
  r.degree = 2,
  seperate.lineages = FALSE
)

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.
ego.id	Character. id of the ego for whom the ego network will be drawn.
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).
seperate.lineages	If TRUE each node in the ego network is given a property lineage labeling each node as part of the lineage A, B or both. Where A and B are paternal and maternal lineages (order determined by the data).

Value

igraph network object showing showing all relatives to the r.degree of the ego.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

r.df = make_relation_df(test1)
net = make_kinship_network(r.df)

ego.network = get_nth_degree_ego_network(network = population.network,
ego.id = test1$id[5],
r.degree = 2,
seperate.lineages = TRUE)

plot_ego_network(ego.network, census.data = test1)

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