make_relation_df: Simplify data frame to pedigree information
In samellisq/comparekin: Calculating relatedness in biological data

Description Usage Arguments Details Value Examples

Simple function to prepare a data frame of population.data data frame to be used in the make_kinship_network function.

1	make_relation_df(population.data, parents.to.use = "all.avaliable")

`population.data`	Data frame containing columns named id and one or both of 'mother' and 'father'.
`parents.to.use`	Either `"all.avaliable"`, `"mother.only"` or `father.only`. This defines the type of network that will be created and ultimately the type of relatedness calculated made either biparental, maternal only or paternal only. Option `"all.avaliable"` will use both mother and father if both columns are avalaible, otherwise will only use one or the other as are present in the population.data.

The function checks column names and trims a data frame to only include the necessary columns. If population.data already only has the necessary columns named correctly then this function is unnecessary, but will not do any harm.

Returns a dataframe with one column named id, and columns mother, father or both as appropriate.

#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

make_relation_df(test1, parents.to.use = "all.avaliable")
make_relation_df(test1, parents.to.use = "mother.only")
make_relation_df(test1, parents.to.use = "father.only")