R Under development (unstable) (2025-09-02 r88773 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require(kinship2)
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Warning: kinship2 package is deprecated for R <= 4.5; switch functionality to Pedixplorer from BioConductor> 
> twindat <- c(1,3,4,2,
+              2,0,0,1,
+              3,8,7,1,
+              4,6,5,2,
+              5,0,0,2,
+              6,0,0,1,
+              7,0,0,2,
+              8,0,0,1,
+              100,3,4,1,
+              101,3,4,2,
+              102,3,4,2,
+              103,3,4,2,
+              104,3,4,2,
+              105,3,4,2,
+              106,3,4,2,
+              107,0,0,1,
+              108,0,0,1,
+              201,2,1,1,
+              202,2,1,1,
+              203,2,1,1,
+              204,2,1,1,
+              205,107,102,1,
+              206,108,103,2)
> twindat <- matrix(twindat, ncol=4, byrow=T)
> dimnames(twindat) <- list(NULL, c('id', 'dadid', 'momid', 'sex'))
> twindat <- data.frame(twindat)
>  
> relate=data.frame(id1=c(101,102,101,104,203), id2=c(102,103,103,105,204), 
+                   code=c(1,1,1,2,1))
> #
> # Renumber everyone as 1,2,....; makes the all.equal checks easier
> indx <- sort(unique(unlist(twindat[,1:3])))
> twindat$id <- match(twindat$id, indx) -1
> twindat$dadid <- match(twindat$dadid, indx) -1
> twindat$momid <- match(twindat$momid, indx) -1
> relate$id1 <- match(relate$id1, indx) -1
> relate$id2 <- match(relate$id2, indx) -1
>  
> # Build the pedigree and kinship
> tped <- with(twindat, pedigree(id, dadid, momid, sex,
+                                relation=relate))
> kmat <- kinship(tped)
> 
> truth <- matrix(c(5,6, 0,
+                   5,4, .25,    #parent child
+                   10,11,.5,    # mz twins
+                   22,12, .25,  # aunt, mz with mother
+                   22, 13, .125, # aunt, dz
+                   13, 14, .25,  # dz twins
+                   20, 21, .5,   # mz twins
+                   19, 16, 0 ,   # marry in uncle
+                   19, 11, .125, # aunt who is a twin
+                   19, 3,  .125), #grandmother
+                 byrow=T, ncol=3)
> 
> all.equal(kmat[truth[,1:2]], truth[,3])
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.84    0.07    0.87