tests/testthat/_snaps/align.md
In sinnweja/kinship2: Pedigree Functions
align.pedigree works
Code
align.pedigree(ped)
Output
$n
[1] 8 19 22 8
$nid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 5 6 7 8 35 36 42 43 0
[2,] 1 2 15 17 16 18 19 20 3
[3,] 9 10 29 30 31 32 33 34 10
[4,] 21 22 23 24 25 26 27 28 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 4 37 38 44 45 46 47
[3,] 11 12 18 14 15 39 40
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 48 50 49 0 0 0
[3,] 41 51 52 53 54 55
[4,] 0 0 0 0 0 0
$pos
[,1] [,2] [,3] [,4] [,5]
[1,] 3.750000e+00 4.75 6.50 7.50 11.75536
[2,] -4.541957e-13 1.00 2.00 3.00 4.00000
[3,] 1.000000e-02 1.01 2.01 3.01 4.01000
[4,] 1.939898e-16 1.00 2.00 3.00 10.01000
[,6] [,7] [,8] [,9] [,10] [,11]
[1,] 12.75536 17.71 18.71 0.00000 0.00000 0.00
[2,] 5.00000 6.00 7.00 10.50072 11.50072 13.01
[3,] 5.01000 6.01 7.01 8.01000 9.01000 10.01
[4,] 11.01000 12.01 13.01 0.00000 0.00000 0.00
[,12] [,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 14.01 15.01 16.01 17.01 18.01 19.01 20.01
[3,] 11.01 12.01 13.01 14.01 15.01 16.01 17.01
[4,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[,19] [,20] [,21] [,22]
[1,] 0.00 0.00 0.00 0.00
[2,] 21.01 0.00 0.00 0.00
[3,] 18.01 19.01 20.01 21.01
[4,] 0.00 0.00 0.00 0.00
$fam
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 0 0 0 0 0 0 0 0 0
[2,] 0 0 1 0 1 1 1 3 5
[3,] 1 0 4 7 7 7 7 7 9
[4,] 1 1 1 1 11 11 13 13 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 5 0 7 7 7
[3,] 9 9 0 9 0 11 11
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 7 0 7 0 0 0
[3,] 11 13 13 18 18 18
[4,] 0 0 0 0 0 0
$spouse
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 1 0 1 0 1 0 1 0 0
[2,] 1 0 0 1 0 0 1 0 1
[3,] 1 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 0 1 0 1 0 0 0
[3,] 0 1 0 1 0 0 0
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 0 1 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
test autohint works
Code
plist
Output
$n
[1] 8 19 22 8
$nid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 5 6 7 8 35 36 42 43 0 0 0 0 0 0
[2,] 1 2 15 17 16 18 19 20 3 4 37 38 44 45
[3,] 9 10 29 30 31 32 33 34 10 11 12 18 14 15
[4,] 21 22 23 24 25 26 27 28 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 46 47 48 50 49 0 0 0
[3,] 39 40 41 51 52 53 54 55
[4,] 0 0 0 0 0 0 0 0
$pos
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 3.750000e+00 4.75 6.50 7.50 11.75536 12.75536 17.71 18.71 0.00000
[2,] -4.541957e-13 1.00 2.00 3.00 4.00000 5.00000 6.00 7.00 10.50072
[3,] 1.000000e-02 1.01 2.01 3.01 4.01000 5.01000 6.01 7.01 8.01000
[4,] 1.939898e-16 1.00 2.00 3.00 10.01000 11.01000 12.01 13.01 0.00000
[,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 11.50072 13.01 14.01 15.01 16.01 17.01 18.01 19.01 20.01 21.01 0.00 0.00
[3,] 9.01000 10.01 11.01 12.01 13.01 14.01 15.01 16.01 17.01 18.01 19.01 20.01
[4,] 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[,22]
[1,] 0.00
[2,] 0.00
[3,] 21.01
[4,] 0.00
$fam
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 1 0 1 1 1 3 5 0 0 5 0 7
[3,] 1 0 4 7 7 7 7 7 9 9 9 0 9 0
[4,] 1 1 1 1 11 11 13 13 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 7 7 7 0 7 0 0 0
[3,] 11 11 11 13 13 18 18 18
[4,] 0 0 0 0 0 0 0 0
$spouse
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 0 1 0 1 0 1 0 0 0 0 0 0 0
[2,] 1 0 0 1 0 0 1 0 1 0 1 0 1 0
[3,] 1 0 0 0 0 0 0 0 0 0 1 0 1 0
[4,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 0 0 0 1 0 0 0 0
[3,] 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0
sinnweja/kinship2 documentation built on July 8, 2023, 11:26 p.m.
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align.pedigree works
Code
align.pedigree(ped)
Output
$n
[1] 8 19 22 8
$nid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 5 6 7 8 35 36 42 43 0
[2,] 1 2 15 17 16 18 19 20 3
[3,] 9 10 29 30 31 32 33 34 10
[4,] 21 22 23 24 25 26 27 28 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 4 37 38 44 45 46 47
[3,] 11 12 18 14 15 39 40
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 48 50 49 0 0 0
[3,] 41 51 52 53 54 55
[4,] 0 0 0 0 0 0
$pos
[,1] [,2] [,3] [,4] [,5]
[1,] 3.750000e+00 4.75 6.50 7.50 11.75536
[2,] -4.541957e-13 1.00 2.00 3.00 4.00000
[3,] 1.000000e-02 1.01 2.01 3.01 4.01000
[4,] 1.939898e-16 1.00 2.00 3.00 10.01000
[,6] [,7] [,8] [,9] [,10] [,11]
[1,] 12.75536 17.71 18.71 0.00000 0.00000 0.00
[2,] 5.00000 6.00 7.00 10.50072 11.50072 13.01
[3,] 5.01000 6.01 7.01 8.01000 9.01000 10.01
[4,] 11.01000 12.01 13.01 0.00000 0.00000 0.00
[,12] [,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 14.01 15.01 16.01 17.01 18.01 19.01 20.01
[3,] 11.01 12.01 13.01 14.01 15.01 16.01 17.01
[4,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[,19] [,20] [,21] [,22]
[1,] 0.00 0.00 0.00 0.00
[2,] 21.01 0.00 0.00 0.00
[3,] 18.01 19.01 20.01 21.01
[4,] 0.00 0.00 0.00 0.00
$fam
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 0 0 0 0 0 0 0 0 0
[2,] 0 0 1 0 1 1 1 3 5
[3,] 1 0 4 7 7 7 7 7 9
[4,] 1 1 1 1 11 11 13 13 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 5 0 7 7 7
[3,] 9 9 0 9 0 11 11
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 7 0 7 0 0 0
[3,] 11 13 13 18 18 18
[4,] 0 0 0 0 0 0
$spouse
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 1 0 1 0 1 0 1 0 0
[2,] 1 0 0 1 0 0 1 0 1
[3,] 1 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0
[,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 0 0 0 0 0 0 0
[2,] 0 1 0 1 0 0 0
[3,] 0 1 0 1 0 0 0
[4,] 0 0 0 0 0 0 0
[,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0
[2,] 0 1 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
test autohint works
Code
plist
Output
$n
[1] 8 19 22 8
$nid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 5 6 7 8 35 36 42 43 0 0 0 0 0 0
[2,] 1 2 15 17 16 18 19 20 3 4 37 38 44 45
[3,] 9 10 29 30 31 32 33 34 10 11 12 18 14 15
[4,] 21 22 23 24 25 26 27 28 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 46 47 48 50 49 0 0 0
[3,] 39 40 41 51 52 53 54 55
[4,] 0 0 0 0 0 0 0 0
$pos
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,] 3.750000e+00 4.75 6.50 7.50 11.75536 12.75536 17.71 18.71 0.00000
[2,] -4.541957e-13 1.00 2.00 3.00 4.00000 5.00000 6.00 7.00 10.50072
[3,] 1.000000e-02 1.01 2.01 3.01 4.01000 5.01000 6.01 7.01 8.01000
[4,] 1.939898e-16 1.00 2.00 3.00 10.01000 11.01000 12.01 13.01 0.00000
[,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 11.50072 13.01 14.01 15.01 16.01 17.01 18.01 19.01 20.01 21.01 0.00 0.00
[3,] 9.01000 10.01 11.01 12.01 13.01 14.01 15.01 16.01 17.01 18.01 19.01 20.01
[4,] 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[,22]
[1,] 0.00
[2,] 0.00
[3,] 21.01
[4,] 0.00
$fam
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 1 0 1 1 1 3 5 0 0 5 0 7
[3,] 1 0 4 7 7 7 7 7 9 9 9 0 9 0
[4,] 1 1 1 1 11 11 13 13 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 7 7 7 0 7 0 0 0
[3,] 11 11 11 13 13 18 18 18
[4,] 0 0 0 0 0 0 0 0
$spouse
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 0 1 0 1 0 1 0 0 0 0 0 0 0
[2,] 1 0 0 1 0 0 1 0 1 0 1 0 1 0
[3,] 1 0 0 0 0 0 0 0 0 0 1 0 1 0
[4,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 0 0 0 0 0 0 0 0
[2,] 0 0 0 1 0 0 0 0
[3,] 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0
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Browse R Packages
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