PlanetsCentral

Mining: The maximum amount of minerals extracted from a planet's core depends on the mineral density.

Max_minerals_mined =
   Round(Mining_rate * Mine_count / 100)
   ...where Mining_rate = Round(RaceMiningRate * Mineral_density / 100) * RF
   ...with RF = 2 for Reptilian natives, 1 otherwise

Minerals_mined =
   Min(Max_minerals_mined, Minerals_in_core)

(4.1) PHost before version 4.1 used Trunc instead of Round here. The new formula always yields a little more minerals.

Supplies: Supplies are produced by factories, or by Bovinoid natives.

Supplies_made =
   Trunc((Factory_contribution + Bovinoid_contribution) * ProductionRate) / 100)
   ...where
      Factory_contribution =
         Factories
      Bovinoid_contribution =
         Min(Trunc(Native_clans / 100), Colonist_clans)
            ...if natives are Bovinoid
         0  ...otherwise

Trans-Uranium Decay: New minerals appear in the planet's core. Note that this happens after mining, so you cannot extract the new minerals the same turn. Trans-uranium decay happens separately for all four minerals.

New_minerals_in_core =
   Trunc((TransuraniumDecayRate * Mineral_density + 50) / 100)