Programming COI (Coefficient of Inbreeding)

D

deathmetal

New member
Hey all, I'm currently working on programming a game in PHP (in Laravel 9) that features an extensive and realistic breeding system. One of the most important aspects about such a system, in my eyes, is the implementation and handling of inbreeding in a manner that reflects reality.

I consider myself to be well versed in genetics, and I don't need help in terms of actually calculating the COI as I will probably implement a simpler but mostly identical system for the purpose of its existence in my game (AVK, Ancestor Loss Coefficient), however, I'm curious as to how others would tackle an issue I'm currently facing.

The calculation requires an array of all the ancestors of the animal, but I'm not sure what the best way to implement this would be. In my ideal scenario, the number would be calculated across an animal's entire pedigree, even if it's hundreds of generations long, but that doesn't sound like it'd be manageable, so I may have to settle on capping it for a specific number of generations to factor in for the calculation.

Assuming that the table contains 3 relevant fields, animal_id, sire_id, and dam_id, what is the best way to retrieve the entire list of ancestors for a particular animal in Laravel-y way? I can't come up with any solutions that wouldn't involve doing potentially hundreds of queries in rapid succession-would that be a performance killer? Maybe there's a way I can alter the animal table in a way where it includes more information on the ancestors so it doesn't need to be as many queries, but the thought of doing so many queries at once still sounds awful, and I'd like to keep the animals table as small as possible since it's already much larger with the genetic encoding system.

Any help or advice is appreciated, since my knowledge on designing such complicated tasks for scale is super limited.

 
@deathmetal You may want to make a table that has the most "ancient" ancestor mapped to a specific pet.  This would then allow you to see everyone who has at least one common ancestor.

Code: 
animal_ancestors
* animal_id (bigint)
* ancestor_animal_id (bigint)
* sire_or_dam (0/1)
* degrees_of_separation (bigint)
When inserting the animal in, you can then calculate the "degrees of separation" based on it's parents, which you would then use as a "marker" to figure out how many generations to go back.  Then when calculating breeding type things, you could say where "degrees of separation" is 10 less than my current or something for their "full" heritage.

This should also allow you to avoid the N+1 since you can eager load each of the animals with the first pass.

Personally I wouldn't put the genetics all on the animal table because I'm guessing it's pretty much "extra information" that isn't needed in 95% of the queries about the animal.  I don't know how you have it set up but I've seen an "animal" table with 400+ columns in it because of that and I cringed anytime I tried to do anything (phpmyadmin crawls).

 
Thank you @judda! That does seem like a good method, keeping track of which animals are related to which foundation animals to reference before going through an entire script.

Do you think it would get unruly after many generations of breeding? Such as if you had a generation 50 animal, would you keep track of every generation 1 ancestor in that entire lineage? I may have to end up capping it at something like 20 generations/degrees of separation to account for and keep track of, because it sounds like it would be really messy if every single animal had hundreds and hundreds of entries in a database just to keep track of all the foundation animals involved. Right now with the current plan of the game, anyone can create a foundation animal at any time, but it may be worth looking into ways to cap this globally so there aren't potentially hundreds of thousands of foundations that could be accounted for. (or would this be as much of an issue as I'm thinking it could be??)

And the genetics table is a good insight that I previously overlooked (I'm not as well versed in database design). The current way it's set up involves a large number of columns to determine things like the alleles and non-mendelian inheritable traits (stuff like specific shades or markings which don't take a lot of space to store), which I thought would be fine since this data is almost entirely tinyint, but it does make sense to separate it from the commonly accessed data, since the genetic information is most commonly referenced in generating images and breeding.

 
If they all stem from the same foundation animals or something (i.e. the foundation animals) then really the table shouldn't get unruly since you are only allowed to have 2 parents.  The only thing that I can see being a little bit of a pain is the initial seeding of it, but that would be a one time operation that takes probably a few minutes to run.  After that, you are able to use the "degree of separation" to calculate how far back.  Heck, I would even go fo far as to call the column "foundation_animal_id" instead of "ancestor_animal_id".

Please Note: The "ancestor_anmial_id" is the top-most (foundation), not each of an animal's ancestors duplicated.  If it was that then it would get bloated quickly with no real value.

I don't beleive that having hundreds/thousands of foundation animals would pose a technical problem at all.  It could pose an issue with the "storyline" of the game but that's all I can see.

As for the genetics table, I would consider swapping it to, or something similar to this:

Code: 
animal_genetics
* animal_id
* trait_id
* trait_value
This could lead to code like:

<?php

class Animal extends Model
{
public function genetics(): HasMany {
return $this->hasMany(AnimalGenetics::class);
}
}

class GeneticTrait extends Model {

}

class AnimalGenetics extends Model
{
public function animal(): BelongsTo {
return $this->belongsTo(Animal::class);
}

public function geneticTrait(): BelongsTo {
return $this->belongsTo(GeneticTrait::class);
}
}

// If we have the "trait" column
$animalGenetics = $animal
->genetics
->with('geneticTrait')
->keyBy(
fn($g) => $g->geneticTrait->name
);


You could do:

Code: 
animal_genetics
* animal_id
* trait
* trait_value
Where "trait" is the column name you previously had.  It is true that this will make the table a fair bit bigger, but it could be a little easier to manage (though you could do that mapping with Laravel too).

<?php

class Animal extends Model
{
public function genetics(): HasMany {
return $this->hasMany(AnimalGenetics::class);
}
}

class AnimalGenetics extends Model
{
public function animal(): BelongsTo {
return $this->belongsTo(Animal::class);
}
}

// If we have the "trait" column
$animalGenetics = $animal->genetics->keyBy('trait');


This would get you the exact same view over the data (after retrieving every row) for a specific animal.

-=-=-=-=-=-=-=-

That being said, having them as columns all in 1 table does have it's potential advantage.  In both of the cases above, there is nothing in place guaranteeing that all genes are accounted for, so if you have a bug where you forget to insert a trait/gene then there is nothing to catch that other than other code since it as a mapping table.  Having it all as columns in the table buys you the benefit of having "NOT NULL" on the columns.  But that also gets gross because if you start moving into other species, for some animals they may not actually have it, which then means you need to make the columns NULLable and then the safety is gone.

-=-=-=-=-=-=-=-

Also note: Laravel by default does a "SELECT * FROM table", so if you have a dozen columns in your table just for genetics, whenever you pull the animal you will also pull all of those TINYINT columns which may not seem like much, but they do eat up memory and make the query take longer in order to retrieve all of the records (this is why most optimization guidelines say avoid "SELECT *" and grab only what you need).

My personal approach to this optimization is ignore it until it becomes an issue, because it's a microoptimization but it gets uber frustrating to develop with if you have to pick and choose what columns are actually needed.  At the very least, wait until the feature is done before even bothering to try this sort of optimization.

Hope this helps @deathmetal

Please Note: All code in this post is completely untested and just written to describe the point/approach I would take and should not be taken as "this will work out of the box".

 
Last edited by a moderator:
@juddaMy concern is more along the lines of how many entries would be required for a single animal, since the more generations there are, the number of unique foundation animals required grows exponentially - even a generation 4 animal would need 16 entries in a database to keep track of only related foundations (simplified answer assuming no inbreeding and you breed animals of the same generation together). Much of the game is also centered around bartering with other players and making it purposefully harder to accomplish your goals unless you outcross your lines, so it'd be common to have animals with a much higher generation than 4 as the generation number grows with more and more people breeding.

And yeah, the separate genetics table is a really good idea. It'd be really nice to be able to mass update genetics or be able to add new alleles/locii without having to mess with the table schema.

 
Totally never thought of that ... that's what I get for early morning thinking.  Honestly, with the right index it's probably fine because the COI will be dependent on a specific or two specific foundations so the heritage I wouldn't be too worried.  As long as the data types are all ints you will have fairly quick results, and we can always revise if it slows down :D

 
Haha, I totally understand. It's glad to know it wouldn't be that much of a problem! I imagine you could also organize the foundation list by 'litter' instead of by individual animal id, so full siblings would not need to duplicate on the data and hopefully minimize the size even more. Thanks for the input 😄

 
I do like that idea ... I was thinking of it less of litters and more of 1:1 births like a lot of different sites use. If you are able to have that abstraction then you are golden :D

 
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