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For example, Exotic bee has a 30% chance in the database to produce a Silky Comb, but the Edenic bee (one evolution up) only has a 20% chance. I also notice that they have differing production speeds - does this have an effect on the so-called 'base' chance?

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The article on Bee Breeding in the FTB Wiki has a very good explanation on how comb production works.

Every bee tick (550 minecraft ticks, or 27.5 seconds), the bee has a chance to produce items. This is calculated separately for each item type the bee produces. The chance is given by the following formula:

P = (bee speed) * (production modifier) * (item probability)

P is the probability of the bee producing items during this tick. If P >= 1.0, then the bee will always produce items every bee tick. Bee speed is determined by the "Speed" trait of the queen, using the following table for the conversion:

Speed trait    Bee speed
Slowest        0.3
Slower         0.6
Slow           0.8
Normal         1.0
Fast           1.2
Faster         1.4
Fastest        1.7

The production modifier is determined by the following algorithm:

  1. Set the production modifier to 0.1 for an apiary, or 1.0 for an alveary
  2. For each default Forestry frame (Untreated Frame, Impregnated Frame or Proven Frame), multiply production chance by two

The last variable, item probability, is a constant value for each type of item produced for each bee. For example, for industrious bees, the item probability is 0.2 for honey combs, and 0.15 for pollen.

The total chance of producing an item with a given queen is acquired by multiplying the production modifier by the base chance of producing an item (e.g. 20% for honey combs, 15% for pollen) by the speed trait of the queen (e.g., multiply by 1.7 for a queen with Fastest Worker) and then doubling the resultant value once for every frame present in the Apiary/Alveary.

(Production Modifier * Base Item Production Chance * Speed Trait of Queen) * 2^Quantity of Default Forestry Frames = Chance of Producing Given Item per Cycle with Given Bee

Once every 27.5 seconds (the length of a cycle) this formula is checked and the bee has a chance of producing an item. Any frames in an Apiary/Alveary also take one point of damage, five if in an Alveary. If the resultant value of the above formula is greater than or equal to one, the bee will always produce one item every 27.5 seconds it is in an Apiary or Alveary.

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so what this is saying is that the species of bee is irrelevant to the production speed - it only determines the default productivity speed (which can be changed via extrabees). –  Phill.Zitt Jun 24 '13 at 6:16

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