Calculating Inbreeding on a 10 Generation Pedigree

Barand · December 11, 2015

In the code I posted, A - J would be in the sires array and O - U would be in the dams array, which would produce no common ancestors

Triple_Deuce · December 11, 2015

In the code I posted, A - J would be in the sires array and O - U would be in the dams array, which would produce no common ancestors

Yes, this is correct but I was talking about getting U's ICO...

Based on given info I get .5 (50%) as inbreeding on F_U (ID#: 59) instead of .375 (37.5%).

Edited December 11, 2015 by Triple_Deuce

Barand · December 11, 2015

I get these results, which look right to me

DOG: J
|     A |   0.0312 |   2 |   2 |
|     A |   0.0312 |   2 |   2 |
|     B |   0.0312 |   2 |   2 |
|     B |   0.0312 |   2 |   2 |
      COI : 0.1250


DOG: U
|     Q |   0.1250 |   1 |   1 |
|     O |   0.0312 |   2 |   2 |
|     O |   0.0312 |   2 |   2 |
|     P |   0.0312 |   2 |   2 |
|     P |   0.0312 |   2 |   2 |
|     R |   0.1250 |   1 |   1 |
      COI : 0.3750


DOG: Z
      COI : 0.0000

Triple_Deuce · December 11, 2015

Are you getting that on my thing?

http://play.ratsofnimh.com/pedigree/inbreeding2.php

or somewhere else?

Barand · December 11, 2015

Those results were from my own code.

Yours almost agrees with mine in that we both get

|  44 | A                  |   2,2|   2,2|

but I interpret that as

A | 0.03125 | 2 | 2 |

whereas you apparently have doubled it to

A | 0.03125 | 2 | 2 |

Triple_Deuce · December 11, 2015

Ok, as I was typing this, I think i see my error!

DogU is supposed to be .375 (37.5%)

DogO & DogP are only behind DogU TWICE.

I have my equation in a nested foreach() which is why I'm getting the 4 extra (2 of each) when I shouldnt.

 foreach($sires[$id] as $keyS => $valueS){
             	foreach($dams[$id] as $keyD => $valueD){
             		$ico = pow(.5,($valueS + $valueD + 1)) + $ico;
             	}
             }

What would be the best approach to break out of that and and potentially pair either $sires or $dams with empty $valueD/S?

Edited December 11, 2015 by Triple_Deuce

Triple_Deuce · December 11, 2015

Ok, I've put in the following:

 $c = array_map(function () {
		    return array_sum(func_get_args());
		}, $sires[$id], $dams[$id]);
		
		foreach($c AS $key =>$value){
			$ico = pow(.5,($value + 1)) + $ico;
		}
				
		print_r($c);

which calculates U correctly now... however J is now wrong, it's showing as 0.125 instead of .5 (full sibling x full sibling = .5 (50%)). What am I missing?

Barand · December 11, 2015

I'm struggling too. My method got U correct but not J. Using your nested foreach() method gets J correct but not U.

Time for a new algorithm?

Barand · December 13, 2015

This my best attempt yet. Instead of counting I store the traversed path then eliminate duplicates.

<?php
//
// ARRAY OF DOGS
//   id => [sire, dam, name]
//
$dogs = array ( 
    1 => array ( 0 => '2', 1 => '3', 2 => 'Nimh\'s Delorean', ), 
    2 => array ( 0 => '4', 1 => '9', 2 => 'Dog B', ), 
    3 => array ( 0 => '7', 1 => '8', 2 => 'Dog C', ), 
    4 => array ( 0 => '7', 1 => '9', 2 => 'Dog E', ), 
    5 => array ( 0 => '10', 1 => '11', 2 => 'Dog F', ), 
    7 => array ( 0 => '14', 1 => '15', 2 => 'Dog H', ), 
    8 => array ( 0 => '16', 1 => '17', 2 => 'Dog I', ), 
    9 => array ( 0 => '16', 1 => '17', 2 => 'Dog J', ), 
    10 => array ( 0 => '18', 1 => '19', 2 => 'Dog K', ), 
    11 => array ( 0 => '20', 1 => '21', 2 => 'Dog L', ), 
    14 => array ( 0 => '20', 1 => '17', 2 => 'Dog O', ), 
    15 => array ( 0 => '0', 1 => '0', 2 => 'Dog P', ), 
    16 => array ( 0 => '14', 1 => '17', 2 => 'Dog Q', ), 
    17 => array ( 0 => '0', 1 => '0', 2 => 'Dog R', ), 
    18 => array ( 0 => '0', 1 => '0', 2 => 'Dog S', ), 
    19 => array ( 0 => '0', 1 => '0', 2 => 'Dog T', ), 
    20 => array ( 0 => '0', 1 => '0', 2 => 'Dog U', ), 
    21 => array ( 0 => '0', 1 => '0', 2 => 'Dog V', ), 
    22 => array ( 0 => '0', 1 => '0', 2 => 'Dog W', ), 
    23 => array ( 0 => '0', 1 => '0', 2 => 'Dog X', ), 
    24 => array ( 0 => '25', 1 => '26', 2 => 'Cedric', ), 
    25 => array ( 0 => '27', 1 => '0', 2 => 'Phantom', ), 
    26 => array ( 0 => '27', 1 => '0', 2 => 'Walton Mare', ), 
    27 => array ( 0 => '0', 1 => '0', 2 => 'Walton', ), 
    28 => array ( 0 => '0', 1 => '0', 2 => 'A', ), 
    29 => array ( 0 => '0', 1 => '0', 2 => 'B', ), 
    30 => array ( 0 => '29', 1 => '28', 2 => 'C', ), 
    31 => array ( 0 => '29', 1 => '28', 2 => 'D', ), 
    32 => array ( 0 => '0', 1 => '30', 2 => 'E', ), 
    33 => array ( 0 => '0', 1 => '31', 2 => 'F', ), 
    34 => array ( 0 => '33', 1 => '32', 2 => 'I', ), 
    35 => array ( 0 => '0', 1 => '0', 2 => 'J', ), 
    36 => array ( 0 => '0', 1 => '0', 2 => 'K', ), 
    37 => array ( 0 => '0', 1 => '0', 2 => 'L', ), 
    38 => array ( 0 => '0', 1 => '0', 2 => 'M', ), 
    39 => array ( 0 => '0', 1 => '0', 2 => 'N', ), 
    40 => array ( 0 => '0', 1 => '0', 2 => 'Dog1', ), 
    41 => array ( 0 => '0', 1 => '0', 2 => 'Dog2', ), 
    42 => array ( 0 => '40', 1 => '41', 2 => 'Dog3', ), 
    43 => array ( 0 => '42', 1 => '41', 2 => 'Dog4', ), 
    44 => array ( 0 => '0', 1 => '0', 2 => 'O', ), 
    45 => array ( 0 => '0', 1 => '0', 2 => 'P', ), 
    46 => array ( 0 => '44', 1 => '45', 2 => 'Q', ), 
    47 => array ( 0 => '44', 1 => '45', 2 => 'R', ), 
    48 => array ( 0 => '46', 1 => '47', 2 => 'S', ), 
    49 => array ( 0 => '46', 1 => '47', 2 => 'T', ), 
    50 => array ( 0 => '48', 1 => '49', 2 => 'U', ), 
    51 => array ( 0 => '0', 1 => '0', 2 => 'A', ), 
    52 => array ( 0 => '0', 1 => '0', 2 => 'B', ), 
    53 => array ( 0 => '51', 1 => '52', 2 => 'C', ), 
    54 => array ( 0 => '51', 1 => '52', 2 => 'D', ), 
    55 => array ( 0 => '51', 1 => '52', 2 => 'E', ), 
    56 => array ( 0 => '51', 1 => '52', 2 => 'G', ), 
    57 => array ( 0 => '53', 1 => '54', 2 => 'H', ), 
    58 => array ( 0 => '55', 1 => '56', 2 => 'I', ), 
    59 => array ( 0 => '57', 1 => '58', 2 => 'J', ), 
    60 => array ( 0 => '59', 1 => '50', 2 => 'Z', )
);

//
// CALCULATE INBREEDING COEFFICIENTS
//
$doglist = [4,9,34,50,59,60];
echo "<pre>\n";
foreach ($doglist as $dogid) {
    printf("%-20s (#%03d)  COI : %0.4f<br>", $dogs[$dogid][2], $dogid, COI($dogid, $dogs));
    
}
echo "</pre>\n";


//
// FUNCTIONS
//

function getAncestors($id, &$dogs, &$ancests, $path)
{   
    if ($id==0) return;

    $ancests[$id][] = $path;
    if (isset($dogs[$id]) ) {
        
        getAncestors($dogs[$id][0], $dogs, $ancests, $path.$dogs[$id][0].',');
        getAncestors($dogs[$id][1], $dogs, $ancests, $path.$dogs[$id][1].',');
    }
}

function COI($id, &$dogs)
{
    if ($id==0) return 0;
    $sires = $dams = [];
    getAncestors($dogs[$id][0], $dogs, $sires, '');
    getAncestors($dogs[$id][1], $dogs, $dams, '');
    $result=0;
    
    foreach ($sires as $did=>$dists) {
        if (isset($dams[$did])) {
            $distd = $dams[$did];
            foreach ($dists as $paths) {
                foreach ($distd as $pathd) {
                    $ds = count(explode(',', $paths));
                    $dd = count(explode(',', $pathd));
                    if ($paths==$pathd && $ds>2) continue;
                    $sumd = $ds + $dd-1;
                    $intermed = pow(0.5, $sumd) * (1 + COI($did, $dogs));
                    $result += $intermed;
                 // printf("| %5s | %8.4f | %12s | %12s |\n", $dogs[$did][2], $intermed, $paths, $pathd);
                }
            }
        }
    }
    return $result;
}

Results

Dog E                (#004)  COI : 0.1875
Dog J                (#009)  COI : 0.3750
I                    (#034)  COI : 0.0625
U                    (#050)  COI : 0.3750
J                    (#059)  COI : 0.2500
Z                    (#060)  COI : 0.0000

Triple_Deuce · December 14, 2015

Is there anyway to get the $sires & $dams arrays to properly display like this when necessary? It looks like it's not tracking all occurrences.

DOG ID: 52

|  ID |      NAME          | SIRE | DAM  |
|     |                    | DIST | DIST |
|-----|--------------------|------|------|
|  44 | A                  |   2,2,2,2|   2,2,2,2|
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125

|  45 | B                  |   2,2,2,2|   2,2,2,2|
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125
.5^(4+1) = 0.03125

total ICO: 0.25

Yranac · November 9, 2016

why i get my post deleted?

Jacques1 · November 9, 2016

Because you're not supposed to hijack threads of other users or dig out discussions from 2015.

Create your own thread. It's not that hard. You can still link to this thread if you feel it's relevant.

Got it now?

Yranac · November 9, 2016

yes, much more easy when you explain it

Beluga · May 7, 2020

On 12/8/2015 at 8:24 PM, Barand said:

Hi
Anybody see this topic?
I need little help for my database.
I have a planner and i wouldlike showing the COI, if possible.
Thank you.

Barand · May 7, 2020

@Beluga

Don't attribute things to me that I didn't say.
Don't hijack other people's threads
Don't resurrect old topics.

Beluga · May 7, 2020

sorry, can you deleted

Edited May 7, 2020 by Beluga

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Calculating Inbreeding on a 10 Generation Pedigree

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