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> 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> #
> # Test some twins data from Curtis Oswold
> #
> 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)
> 
> ## set up a fraternal twin set, and a set of triplets with kids from
> ## their marriages to test kinship coeff
> relate=data.frame(id1=c(101,102,104,203), id2=c(102,103,105,204), code=c(1,1,2,1))
> 
> tped <- with(twindat, pedigree(id, dadid, momid, sex,
+                                relation=relate))
> 
> 
> ## plot(tped)
> 
> ## should show kinship coeff of 0.5 for where MZ twins are
> ## ids: 102-103 and 203-204
> kinmat <- kinship(tped)
> 
> kinmat[c(10:16,19:23),c(10:16,19:23)]
      101   102   103   104   105   106  107    202    203    204    205    206
101 0.500 0.500 0.500 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.2500 0.2500
102 0.500 0.500 0.500 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.2500 0.2500
103 0.500 0.500 0.500 0.250 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.2500 0.2500
104 0.250 0.250 0.250 0.500 0.250 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
105 0.250 0.250 0.250 0.250 0.500 0.250 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
106 0.250 0.250 0.250 0.250 0.250 0.500 0.00 0.1250 0.1250 0.1250 0.1250 0.1250
107 0.000 0.000 0.000 0.000 0.000 0.000 0.50 0.0000 0.0000 0.0000 0.2500 0.0000
202 0.125 0.125 0.125 0.125 0.125 0.125 0.00 0.5000 0.2500 0.2500 0.0625 0.0625
203 0.125 0.125 0.125 0.125 0.125 0.125 0.00 0.2500 0.5000 0.5000 0.0625 0.0625
204 0.125 0.125 0.125 0.125 0.125 0.125 0.00 0.2500 0.5000 0.5000 0.0625 0.0625
205 0.250 0.250 0.250 0.125 0.125 0.125 0.25 0.0625 0.0625 0.0625 0.5000 0.1250
206 0.250 0.250 0.250 0.125 0.125 0.125 0.00 0.0625 0.0625 0.0625 0.1250 0.5000
>                                        
> 
> 
> 
> ## simple test case for kinship of MZ twins from Claus Ekstrom, 9/2012
> mydata <- data.frame(id=1:4, dadid=c(NA, NA, 1, 1),
+ momid=c(NA, NA, 2, 2), sex=c("male", "female", "male", "male"),
+ famid=c(1,1,1,1))
> relation <- data.frame(id1=c(3), id2=c(4), famid=c(1), code=c(1))
> 
> x <- pedigree(id=mydata$id, dadid=mydata$dadid, momid=mydata$momid, sex=mydata$sex, relation=relation)
> 
> #plot(x)
> 
> kinout <- kinship(x)
> kinship2:::kinship.pedigree(x)
     1    2    3    4
1 0.50 0.00 0.25 0.25
2 0.00 0.50 0.25 0.25
3 0.25 0.25 0.50 0.50
4 0.25 0.25 0.50 0.50
> 
> 
> proc.time()
   user  system elapsed 
   0.84    0.07    0.89