affinal_relatedness.R

## requires: kinship2 and igraph (because that's what I know)

## assumes inputs of :
## "parents" with columns Ego, Father, Mother, Sex (here, missing info coded as 0)
## "spouses" with columns Spouse1, Spouse2, and NotDivorced (yeah, stupidly reverse coded to make it easier to populate with 1s)
parents <- read.csv("parents.csv", header = TRUE, as.is = TRUE)
spouses <- read.csv("spouses.csv", header = TRUE, as.is = TRUE)

ped <- kinship2::pedigree(id = parents$Ego, dadid = parents$Father, momid = parents$Mother, sex = parents$Sex, missid = 0)

gen <- kinship2::kinship(ped)*2

## get immediate kin (parent/child and siblings)
imm <- (gen==0.5)*1

## if desired, exclude divorced people (that's how I've coded this). 
## NOTE: this effectively removes the *direct* connection between spouses, 
## but if they have had children, there will still be a value for affinal relatedness:  
## it will be half of what it otherwise would have been, as it will come through the longer path through the child
sp.mar <- subset(spouses, spouses$NotDivorced==1) 

sp.df <- as.data.frame(rbind(as.matrix(sp.mar[,c(1,2,3)]),as.matrix(sp.mar[,c(2,1,3)])))

## create matrix for spousal relationships, and populate with values from sp.df
sp.matrix <- matrix(data = 0, nrow = nrow(gen), ncol = nrow(gen))
rownames(sp.matrix) <- rownames(gen)
colnames(sp.matrix) <- rownames(gen)
  
for(i in 1:nrow(sp.df)){sp.matrix[rownames(sp.matrix)==sp.df[i,1],colnames(sp.matrix)==sp.df[i,2]] <- as.numeric(sp.df[i,3])}

## create matrix with immediate kin and spouses, and then create distance matrix from this
both <- imm + sp.matrix
net <- igraph::graph_from_adjacency_matrix(both, mode = "undirected", weighted = NULL)
aff_length <- igraph::distances(net, mode = "all")

## recode distance matrix to reflect affinal relatedness (so, spouses = 0.5, and all steps from there halve each time)
aff <- apply(aff_length, 1, function(x) 2^-x)
aff <- aff - gen

## Make sure that all relationships are accounted for in both the affinal and genetic relatedness inputs. 
## i.e., make sure all sets of parents appear in the partnerships file, unless you explicitly don't want them
## Not doing this (or purposefully censoring some, as for divorce) could potentially result in *negative* values, given the subtraction above
## Assuming that you may have only partial coverage of more distant relatedness, you may want to censor both matrices below some threshold (e.g., 0.125)