example.php

<?php

require 'vendor/autoload.php';

use League\Fractal;
use League\Fractal\Manager;
use League\Fractal\Resource\Collection;
use League\Fractal\TransformerAbstract;
use League\Fractal\Serializer\JsonApiSerializer;

class ChildTransformer extends TransformerAbstract
{

    public function transform($item)
    {
        return ['id' => $item['id']];
    }
}

class ParentTransformer extends TransformerAbstract
{

    protected $defaultIncludes = [
        'childs',
    ];

    public function transform($item) {
        return ['id' => $item['id']];
    }

    public function includeChilds($item)
    {
        return $this->collection($item['data'], new ChildTransformer(), 'childs');
    }
}

$a = ['id' => 10];
$b = ['id' => 20];
$c = ['id' => 30];

$items = [
    ['id' => 1, 'data' => [$a, $b]],
    ['id' => 3, 'data' => [$c]],
    ['id' => 2, 'data' => []],
];

$manager = new Manager();
$manager->setSerializer(new JsonApiSerializer());

$resource = new Collection($items, new ParentTransformer(), 'parent');

$array = $manager->createData($resource)->toArray();

echo $manager->createData($resource)->toJson();

// output: {"parent":[{"id":1},{"id":3},{"id":2}],"linked":{"childs":[{"id":10},{"id":20},{"id":30},[]]}}
// expected: {"parent":[{"id":1},{"id":3},{"id":2}],"linked":{"childs":[{"id":10},{"id":20},{"id":30}]}}

// empty array on the end is not desired

Can you do this:

    public function includeChilds($item)
    {
        if (empty($item['data'])) return;
        return $this->collection($item['data'], new ChildTransformer(), 'childs');
    }