Introduction to FnR
In FnR: Inbreeding and Numerator Relationship Coefficients

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(FnR)

Let's use the following example pedigree.

(ped <- data.frame(
  ID = 1:12,
  SIRE = c(0, 0, 0, 2, 2, 0, 4, 6, 0, 6, 10, 10),
  DAM = c(0, 0, 0, 1, 1, 0, 3, 5, 7, 8, 9, 0)
))

Let's assume that previously, 9 of 12 animals were in the pedigree, and inbreeding (f) and d coefficients (diagonal elements of the diagonal matrix D in $\mathbf A = \mathbf{TDT}'$) were calculated and saved.

oldped <- ped[1:9, ]
(oldrun <- resume_inbreed(oldped, export_d = TRUE))

Calculating inbreeding coefficients as if f and d coefficients from the previous analysis are not available:

resume_inbreed(ped)

Calculating inbreeding coefficients as if f coefficients from the previous analysis are available, but not d coefficients:

resume_inbreed(ped, f = oldrun$f)

Calculating inbreeding coefficients as if f and d coefficients from the previous analysis are available:

resume_inbreed(ped, f = oldrun$f, d = oldrun$d)

Let's calculate the numerator relationship coefficients between two groups of animals, one's members not among dams, and the members of the other not among sires.

calcR(ped, set1 = c(12, 6), set2 = c(11, 8), type = "notdam-notsire")

What is the inbreeding coefficient of a future progeny of 11 and 12? It is half of the relationship coefficient between the two individuals (0.320312/2).

Since "notdam-notsire" is the default type, type = "notdam-notsire" might be omitted. Where relationship coefficients between dams and between sires are needed, type = "dam-dam" and type = "sire-sire" are used, respectively.

Let's calculate the numerator relationship coefficients between dam 7 and dams 8 and 9.

calcR(ped, set1 = 7, set2 = 8:9, type = "dam-dam")

The relationship coefficients between sires 2 & 6 and sires 4 & 10 are calculated as:

calcR(ped, set1 = c(2, 6), set2 = c(4, 10), type = "sire-sire")

If inbreeding coefficients of the population or previous inbreeding estimates with a smaller pedigree are available, those can be used via the argument f to speed up the procedure. Similarly, if d coefficients are available, those can be used alongside the inbreeding coefficients via the argument d.

f <- rep(0, 12)
f[10] <- 0.25
f[11] <- 0.015625
d <- c(1, 1, 1, 0.5, 0.5, 1, 0.5, 0.5, 0.75, 0.5, 0.4375, 0.6875)
calcR(ped, set1 = c(2, 6), set2 = c(4, 10), type = "sire-sire", f = f, d = d)

For very large pedigree and small set1 and set2, one may consider extracting a sub-pedigree by tracing the pedigree upward from set1 and set2 (i.e., ggroups::pedup(ped, c(set1, set2))).