Laravel 5.5 Update a checkbox of many to many relationship model

I have a many to many relationship where I had a two models that belongsToMany to each other.

So I would like to update the pivot table but first I want to know if the two models are already existing on this pivot tables.

So here is the definition of my relationship in my two models below:

AnalysisRequest model

public function request_methods()
        {
            return $this->belongsToMany('App\Models\Methodologies')->withTimestamps();;
        }

and in my other model: Methodologies model

public function methods_requested()
    {
        return $this->belongsToMany('App\Models\AnalysisRequest')->withTimestamps();;
    }

So this two models has their own pivot table with all their ID attached. Now what I want to happen is when the two models has existing attached models to each other I want the checkbox to be checked on the view which I couldn't achieve.

Here is the pivot model

<?php

namespace App\Models;

use Eloquent as Model;
use Illuminate\Database\Eloquent\SoftDeletes;

class AnalysisRequestMethodologies extends Model
{

        public $table = 'analysis_request_methodologies';

        public $fillable = [
            'analysis_request_id',
            'methodologies_id',
        ];

        /**
         * The attributes that should be casted to native types.
         *
         * @var array
         */
        protected $casts = [
            'analysis_request_id' => 'integer',
            'methodologies_id' => 'integer',
        ];

        /**
         * Validation rules
         *
         * @var array
         */
        public static $rules = [
            'analysis_request_id' => 'required|unique_with:analysis_request_methodologies,methodologies_id',
            'methodologies_id' => 'required',
        ];
}

Here is my code controller below:

 public function edit($id)
{
    $analysis_request = $this->analysisrequestRepository->findWithoutFail($id);

    $checkeds = AnalysisRequest::find($id)->request_methods()->pluck('id');

    return view('encoder-dashboard.analysis-request-methods.create', compact('analysis_request', 'checkeds'));
}

And in my view

<div class="form-group col-sm-12">
    @forelse($analysis_request->category->methodology as $method)
    <label>
        <?php $checked = in_array($method->id, $checkeds) ? true : false; ?>
        {{ Form::checkbox('methodologies_id[]', $method->id) }}
        {{ $method->name }} with the lead time of {{ $method->lead_time }} and the DOH standard of {{ $method->doh_standard }}
    </label>
    @empty
        <h3>The category you selected has no method yet</h3>
    @endforelse
</div>

Anothere reference of question that can be related to my question.

I have an error in my view that sais:

Integrity constraint violation: 1052 Column 'id' in field list is ambiguous (SQL: select id from methodologies inner join analysis_request_methodologies on methodologies.id = analysis_request_methodologies.methodologies_id where analysis_request_methodologies.analysis_request_id = 10)

In the referenced question the solution said I need to use lists but it was depreciated in Laravel 5 I need to use pluck instead. But still can't solve the puzzle.

Appreciate if someone could help. Thanks in advance.