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Two ways to do it

Use of baker's percentage is fairly straightforward when there are no preferments involved. The weight of all the flour represents 100%, and the weight of each additional ingredient is expressed as a percentage by dividing its weight by the weight of the flour.

When a preferment is involved it is customary to treat the formula for making the preferment as if it were a complete formula. Thus, the flour in the preferment is 100%, etc.

Here are some links to additional explanations:

An alternative is to express all percentages, in final dough and preferments alike, as percentages of the dough in the overall formula. This is easier to do in a spreadsheet and that is what earlier versions of the Dough Calculator did. You may see examples of that in published PDF files from those earlier versions.

Dough Calculator's way

Dough Calculator treats each preferment and the final dough as standing on its own. In other words, the total flour in each is supposed to be 100%. It does mean, however, that Dough Calculator must be able to identify (in the Recipe worksheet) which ingredients belong to what preferment or final dough. This is the purpose of putting a value in the "Pre" column.

Dough Calculator will add up all percentages in a preferment or final dough to compute a total formula percentage. If the weight of a dough or preferment is known, the 100% flour weight is then computed by dividing by the total formula percentage. Once the weight for 100% is known, the weight for other ingredients follows a simple multiplication.

The weight for ingredients in the final dough is computed first. If an ingredient in the final dough refers to a listed preferment (names must be identical), the weight for the preferment is taken from the ingredient and is divided by the preferment's total percentage to arrive at its 100% weight.

Sometimes it is necessary, or useful, to look at the overall composition of a dough. In fact that is about the only way one can compare general characteristics of breads. If a formula uses preferments, the overall composition is not easily seen. Dough Calculator has a separate worksheet called "Analysis" that always contains an analysis of each preferment, as well as the overall dough. It also shows a cost and hydration analysis.