inbreed function calculates the inbreeding coefficients for all individuals in a tidied pedigree.
Details
This function takes a pedigree tidied by the tidyped function and
calculates the inbreeding coefficients using an optimized C++ implementation of
the Sargolzaei & Iwaisaki (2005) LAP (Longest Ancestral Path) bucket algorithm.
This method is the fastest known direct algorithm for computing all inbreeding
coefficients: it replaces the O(\(N^2\)) linear scan of Meuwissen & Luo (1992)
with O(1) bucket pops and selective ancestor clearing, giving
\(O(\sum m_i)\) total work where \(m_i\) is the number of distinct
ancestors of individual \(i\). At \(N = 1{,}000{,}000\), the kernel
completes in approximately 0.12 s — over 10\(\times\) faster than the previous
Meuwissen & Luo (1992) implementation and on par with the pedigreemm
reference C implementation of the same algorithm.
It is the core engine used by both tidyped(..., inbreed = TRUE) and
pedmat(..., method = "f"), ensuring consistent results across the package.
Examples
library(visPedigree)
data(simple_ped)
ped <- tidyped(simple_ped)
ped_f <- inbreed(ped)
ped_f[f > 0, .(Ind, Sire, Dam, f)]
#> Warning: Subsetting removed parent records. Result is a plain data.table, not a tidyped.
#> Use tidyped(tp, cand = ids, trace = "up") to extract a valid sub-pedigree.
#> Ind Sire Dam f
#> <char> <char> <char> <num>
#> 1: J5X804 J4Y326 J4E185 0.00390625