check_pedigree: Check the rules for a well-formed pedigree

In famuvie/breedR: Statistical Methods for Forest Genetic Resources Analysts

Check the rules for a well-formed pedigree

Description

This function performs sanity checks on a pedigree.

Usage

check_pedigree(ped)

Arguments

ped	a 'pedigree'-class object, a dataframe, a matrix, or anything that can be coerced into a 3-column, numeric dataframe.

Details

Rules are: the pedigree must be full (i.e. all the codes in the pedigree must appear once in the first column); the codes of the offspring must follow their parent's codes; the identity codes must be sorted in ascending order and this order must be consecutive beginning from 1.

If any check fails, the pedigree must be recoded/reordered to be used in analysis. build_pedigree(1:3, data = ped) should fix it.

Value

a named logical vector with the results of the checks

See Also

build_pedigree

Examples

# A well-formed pedigree
ped_ok <- data.frame(id   = 1:6,
                     dam  = c(NA,NA,1,1,4,4),
                     sire = c(NA,NA,2,2,3,5))
check_pedigree(ped_ok)  # passes all checks

# Sometimes founders are missing
(ped_notfull <- ped_ok[-c(1:2),])
check_pedigree(ped_notfull)  # fails full_ped

# Sometimes codes of parents are greater than their offspring
sw_23 <- c(1, 3, 2, 4:6)
(ped_messed <- as.data.frame(sapply(ped_ok, function(x) sw_23[x]))[sw_23,])
check_pedigree(ped_messed)        # fails offsp_follows

# Sometimes the pedigree is unordered
(ped_unordered <- ped_ok[sw_23, ])
check_pedigree(ped_unordered)   # fails codes_sorted

# Finally, sometimes codes are just not consecutive
(ped_notconsec <- transform(ped_ok, id = c(1:5, 10)))
check_pedigree(ped_notconsec)  # fails codes_consecutive

# Everything is fixed with build_pedigree()
check_pedigree(build_pedigree(1:3, data = ped_notfull))
check_pedigree(build_pedigree(1:3, data = ped_messed))
check_pedigree(build_pedigree(1:3, data = ped_unordered))
check_pedigree(build_pedigree(1:3, data = ped_notconsec))

famuvie/breedR documentation built on Aug. 6, 2024, 9:10 p.m.