Your recipes should be clear and well illustrated. It helps to take the view of a line cook when crafting plate recipes. Batch recipes are a different breed. If you want to completely understand your operation, I recommend you spend most of your time on batch production recipes.
Basic prep activities should be carefully observed. Actual yields need to be compared to industry standards. Stocks are great for using the trim from your prep items. It's OK to assign the stock a zero cost for the usable trim. Some chefs like to give a credit for trim used in stocks when calculating the prep yields for the primary purpose. If you use this approach, you'll need to monitor the cost of the stock.
Secondary production activities include setups, mixes, sauces, stews, soups, portion cuts and other line items. If you build an explosive recipe model, you can save lots of time later if you need to make changes to your menu.
For example, a pizzeria could have a pizza sauce recipe, a pizza dough recipe, a standard weight for the shredded cheese and olive oil. A pizza setup would include 1 dough ball, 1 standard ladle of sauce, a standard portion of shredded cheese and the standard amount of oil. For a simple cheese pizza, the plate recipe could simply include 1 pizza setup. Pizzas with toppings could use 1 pizza setup and one or more topping portions.
Let's say you decide to change the shredded cheese mix and portion size. Instead of rebuilding every finished pizza recipe, you could simply change the one recipe for the shredded cheese portion. This change then explodes through the entire list of pizza recipes. Since the pizza setup is tied to each pizza and the setup includes the shredded cheese portion, you have updated the entire model with one change.
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