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added automimicry-effect

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Stefan Dresselhaus
2018-06-03 16:17:31 +02:00
parent 2b7d0e6682
commit 69895ffaab
2 changed files with 86 additions and 64 deletions
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64
src/Environment.hs
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@ -84,9 +84,19 @@ data Predator = Predator { irresistance :: [Compound]
, fitnessImpact :: Amount
-- ^ impact on the fitness of a plant
-- (~ agressiveness of the herbivore)
, numAttacks :: Amount
-- ^ Avarage number of attacks in a generation of appearance
-- (~ mean of poisson-distribution)
} deriving (Show, Eq)
-- The environment itself is just the soil and the predators. Extensions would be possible.
-- | Settings to enable/disable parts of the simulation
data Settings = Settings { automimicry :: Bool -- ^ do we have automimicry-protection?
, predatorsRandom :: Bool -- ^ do predators always appear or according to their random distribution?
, numPlants :: Int -- ^ number of plants in starting population
}
deriving (Show, Eq)
-- | The environment itself.
data Environment =
Environment
@ -108,6 +118,7 @@ data Environment =
-- Kills 100% of Predators above Amount.
, possibleEnzymes :: [Enzyme]
-- ^ All enzymes that can be created by genetic manipulation in this setting.
, settings :: Settings
} deriving (Show, Eq)
-- helper function. Allows for [0..maxCompoundWithoutGeneric] :: [Compound] with all non-generic Compounds
@ -151,23 +162,28 @@ fitness ps = do
products <- sequenceA $ zipWith produceCompounds ps nutrients -- produce compounds
ds <- liftIO $ randoms <$> newStdGen
preds <- asks predators
randPred <- asks (predatorsRandom . settings)
let
appearingPredators = fmap fst . filter (\((_,p),r) -> p > r) $ zip preds ds -- assign one probability to each predator, filter those who appear, throw random data away again.
-- appearingPredators is now a sublist of ps.
survivalRate <- mapM (deterPredators products preds) products -- defeat predators with produced compounds
appearingPredators = if randPred then
fmap (fst . fst) . filter (\((_,p),r) -> p > r) $ zip preds ds -- assign one probability to each predator, filter those who appear, throw random data away again.
-- appearingPredators is now a sublist of preds without the probability.
else
fst <$> preds -- else just forget about probabilities
automimicry <- asks (automimicry . settings)
popDefense <- if automimicry then
forM appearingPredators $ \p -> do
as <- mapM (deterPredator p) products -- how good can an individual deter p
return $ sum as / fromIntegral (length as) -- how good can the population deter p on average
else
return $ repeat 1
survivalRate <- mapM (deterPredators (zip appearingPredators popDefense)) products -- defeat predators with produced compounds
let sumEnzymes = sum . fmap (\(_,q,a) -> fromIntegral q*a) . genome <$> ps -- amount of enzymes * activation = resources "wasted"
staticCostOfEnzymes = (\x -> 1 - 0.01*x) <$> sumEnzymes -- static cost of creating enzymes
-- primaryEnzymes = filter (\(e,_,_) -> case (fst.fst.synthesis) e of -- select enzymes which use substrate
-- Substrate _ -> True
-- otherwise -> False)
-- (genome p)
nutrientsAvailable <- fmap snd <$> asks soil
let nutrientsLeft = (\p -> [p ! i | i <- [0..fromEnum (maxBound :: Nutrient)]]) <$> products
nutrientRatio = minimum . zipWith (flip (/)) nutrientsAvailable <$> nutrientsLeft
costOfEnzymes = max 0 <$> zipWith (\s n -> s-n*0.1) staticCostOfEnzymes nutrientRatio -- cost to keep enzymes are static costs + amount of nutrient sucked out of the primary cycle
return $ zipWith (*) survivalRate costOfEnzymes
-- can also be written as, but above is more clear.
-- fitness p = absorbNutrients p >>= produceCompounds p >>= deterPredators
produceCompounds :: Plant -> [(Nutrient, Amount)] -> World (Vector Amount)
produceCompounds (Plant genes _) substrate = do
@ -186,19 +202,23 @@ produceCompounds (Plant genes _) substrate = do
-- faster, because no inversions and optimized eig.
return final
-- Automimicry: see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275178/#__sec2title Formula 2.1
-- Note: F(D) is "costOfEnzymes", but in 'fitness' we multiply "costOfEnzymes" already,
-- so F(D) is omitted
-- A(d_hat) is ahat * numAttacks p, because ahat is only deterrence of the population
-- and does not incorporate the number of attacks, which A(d_hat) in the paper does.
deterPredators :: [(Predator, Double)] -> Vector Amount -> World Probability
deterPredators appearingPredators compounds = do
deters <- forM appearingPredators $ \(p,ahat) -> do
myDeter <- deterPredator p compounds
return $ exp $ negate $ numAttacks p * ahat * myDeter -- exp due to assumption that number of attacks are poisson-distributed.
return $ product deters
-- TODO:
-- - dampen full-force due to auto-mimicry-effect. => Fitness would not depend on single plant.
deterPredators :: [Vector Amount] -> [(Predator,Amount)] -> Vector Amount -> World Probability
deterPredators others appearingPredators cs = do
-- ps <- asks predators
ts <- asks toxicCompounds
let
deter :: Predator -> Double
-- multiply (toxicity of t with 100% effectiveness at l| for all toxins t; and t in p's irresistance-list)
deter p = product [1 - min 1 (cs ! fromEnum t / l) | (t,l) <- ts, t `elem` irresistance p]
-- multiply (probability of occurence * intensity of destruction / probability to deter predator | for all predators)
return $ product [min 1 ((1-prob) * fitnessImpact p / deter p) | (p,prob) <- appearingPredators]
deterPredator :: Predator -> Vector Amount -> World Double
deterPredator p comps = do
toxins <- asks toxicCompounds
return $ product [1 - min 1 (comps ! fromEnum t * l) | (t,l) <- toxins, t `elem` irresistance p]
-- Mating & Creation of diversity
-- ------------------------------