Does the Engineering Notebook have to be in chronological order or can it by organized by subsystem?

I was wondering because our robot is already built and we are going to start with the Engineering Notebook now.

A good Engineering Notebook should be a record of how you got your robot to where it is now. Generally it should be a chronological account of your design process from day one. A good Notebook will include all of your design ideas including those you didn’t use and document why you made the decisions you made and why you dumped other designs. It should also be a daily diary of what was accomplished each meeting and an idea of what to attempt to accomplish at your next meeting. Pictures, drawings and the mathematics that document your decisions are great to have along with samples of your code as your robot progresses. This is what MOST judges’ would want to see. Are there other possibilities? Yes, but they probably will not be looked upon in the same way as I have described above. There are some judges that prefer the notebook be handwritten (in ink is best), while others will accept printed versions.
I hope this helps. Good Luck

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@536Mentor is right on target.

That said, in order to follow his good advice you would need to go back in time. Creating a notebook after your bot is built is not the intent of the task. It should be a part of the process of design and team management, not a report after the fact of the things you remember about why your robot became what it is.

First, here is a thread that says the judges have to accept whatever you present as your notebook and evaluate it:

https://vexforum.com/t/handwritten-design-journal/39057/1

Although they must accept it and evaluate, they do not have to evaluate it highly. To that end, it would be best to familiarize yourself with the guidance documents judges are given for the evaluation. The REC Foundation makes available to everyone the materials the judges will be using to evaluate your notebook. You should get those documents and read them. They are here:

Judge Guide:
http://link.roboticseducation.org/vrceventdocuments_judgeresources_vrcjudgeguide

Design Award Rubric:

In the interests of providing some quick guidance, here is an excerpt from the VRC Judge Guide:

Also from the VRC Judge Guide:

And finally, one of the most informative parts of the VRC Judge Guide:

So, teams are allowed to do anything they like in their engineering notebooks. But the judges have some specific guidance about how to judge them.

You can’t turn back time. What you can do is this: Get the Design Award Rubric, and try to ensure you’ve done everything you can to score as high as you can in each of the eight listed criteria. Next year, start the notebook early, update it continuously, and use what you’ve learned this year to make it better.