R Under development (unstable) (2025-09-02 r88773 ucrt) -- "Unsuffered Consequences"
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> 
> ## if all you have is maternal information, fill in for dads
> ## from user on 2/1/19
> 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> materdf <- data.frame(id=1:5, momid=c(0,1,1,2,2), sex=2)
> 
> materdf$dadid <- materdf$momid * 100
> materdf
  id momid sex dadid
1  1     0   2     0
2  2     1   2   100
3  3     1   2   100
4  4     2   2   200
5  5     2   2   200
> 
> peddf <- with(materdf, fixParents(id, dadid, momid, sex))
> peddf
   id momid dadid sex
1   1     0     0   2
2   2     1   100   2
3   3     1   100   2
4   4     2   200   2
5   5     2   200   2
6 100     0     0   1
7 200     0     0   1
> testped <- with(peddf, pedigree(id, dadid, momid, sex))
> as.data.frame(testped)
   id dadid momid    sex
1   1     0     0 female
2   2   100     1 female
3   3   100     1 female
4   4   200     2 female
5   5   200     2 female
6 100     0     0   male
7 200     0     0   male
> 
> 
> ## chars
> test1char <- data.frame(id=paste("fam", 101:111, sep=""),
+                 sex=c("male","female")[c(1,2,1,2,1, 1,2, 2,1,2, 1)],
+           father=c(0,0,"fam101","fam101","fam101", 0,0,"fam106","fam106","fam106", "fam109"),
+           mother=c(0,0,"fam102","fam102","fam102", 0,0,"fam107","fam107","fam107", "fam112"))
> test1newmom <- with(test1char, fixParents(id, father, mother, sex, missid="0"))
> newped <- with(test1newmom, pedigree(id, dadid, momid, sex, missid="0"))
> as.data.frame(newped)
       id  dadid  momid    sex
1  fam101      0      0   male
2  fam102      0      0 female
3  fam103 fam101 fam102   male
4  fam104 fam101 fam102 female
5  fam105 fam101 fam102   male
6  fam106      0      0   male
7  fam107      0      0 female
8  fam108 fam106 fam107 female
9  fam109 fam106 fam107   male
10 fam110 fam106 fam107 female
11 fam111 fam109 fam112   male
12 fam112      0      0 female
> 
> 
> data(sample.ped)
> datped2 <- sample.ped[sample.ped$ped %in% 2,]
> datped2[datped2$id %in% 203, "sex"] <- 2
> datped2 <- datped2[-which(datped2$id %in% 209),]
> ## this gets an error
> ##ped2 <- with(datped2, pedigree(id, father, mother, sex))
> fixped2 <- with(datped2, fixParents(id, father, mother, sex))
> fixped2
    id momid dadid sex
1  201     0     0   1
2  202     0     0   2
3  203     0     0   1
4  204   202   201   2
5  205   202   201   1
6  206   202   201   2
7  207   202   201   2
8  208   202   201   2
9  210   204   203   1
10 211   204   203   1
11 212   208   209   2
12 213   208   209   1
13 214   208   209   1
14 209     0     0   1
> ped2 <- with(fixped2, pedigree(id, dadid, momid, sex))
> 
> 
> proc.time()
   user  system elapsed 
   0.82    0.09    0.90