minor things before tests can start.
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10
app/Main.hs
10
app/Main.hs
@ -51,6 +51,12 @@ exampleEnvironment addedC es pred tox =
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, predatorBehaviour = AttackInterval 10
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, numPlants = 50
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, logEveryNIterations = 10
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, mutationRate = 0.01
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, deletionDuplicationRate = 0.05
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, geneAddRate = 0.005
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, activationNoiseIntensity = 0.01
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, staticEnzymeCost = 0.01
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, nutrientImpact = 0.01
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}
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}
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@ -252,7 +258,7 @@ main = do
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let emptyPlants = replicate (numPlants . settings $ env) emptyPlant
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printEverything = verbose opts
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enzs <- randomRs (0,length (possibleEnzymes env) - 1) <$> newStdGen
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let startPlants = randomGenome 1 enzs (possibleEnzymes env) emptyPlants
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let startPlants = randomGenome 2 enzs (possibleEnzymes env) emptyPlants
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--writeFile "poison.twopi" $ generateDotFromPoisonTree "poison" 0.5 poisonedTree
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LBS.writeFile "environment.json" . encode $ env
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when printEverything $ putStr "\ESC[?1049h"
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@ -272,7 +278,7 @@ randomGenome num inds enzs (p:ps) = p { genome = genes} : randomGenome num r enz
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i' = take num inds
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r = drop num inds
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enzymes = (enzs!!) <$> i'
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genes = (\e -> (e,1,1)) <$> enzymes
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genes = (\e -> (e,1,0.5)) <$> enzymes
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generatePredators :: Double -> EnzymeTree s (Double,Compound) -> IO [Predator]
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@ -495,8 +495,14 @@
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"numPlants": 100,
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"predatorBehaviour": {
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"contents": 10,
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"tag": "AttackInterval"
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"tag": "AlwaysAttack"
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}
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, "mutationRate": 0.01
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, "deletionDuplicationRate": 0.05
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, "geneAddRate": 0.005
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, "activationNoiseIntensity": 0.01
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, "staticEnzymeCost": 0.01
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, "nutrientImpact": 0.01
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},
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"soil": [
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[
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@ -120,10 +120,19 @@ instance FromJSON PredatorBehaviour
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instance ToJSON PredatorBehaviour
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-- | Settings to enable/disable parts of the simulation
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--
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-- Fitness is usually seen as relative Fitness (probability of survival), thus [0..1].
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data Settings = Settings { automimicry :: Bool -- ^ do we have automimicry-protection?
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, predatorBehaviour :: PredatorBehaviour -- ^ do predators always appear or according to their random distribution?
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, numPlants :: Int -- ^ number of plants in starting population
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, logEveryNIterations :: Int -- ^ log status every @loopNumber `mod` logEveryNIterations == 0@
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, deletionDuplicationRate :: Double -- ^ Rate at wich genes get deleted or duplicated (e.g. 0.05 = 5% chance a gene gets deleted/duplicated. Independent per gene)
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, mutationRate :: Double -- ^ Rate at wich genes mutate to produce other enzymes. Independent per gene
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, geneAddRate :: Double -- ^ Rate at wich genes from the primary metabolims mutate to produce enzymes of the secondary metabolims
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, activationNoiseIntensity :: Double -- ^ Intensity of activation mutatation. Enzymes produced are @#Genes * Activation@. Activation is clipped between @0@ and @1@.
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-- New activation is @activation +- activationNoiseIntensity*[0..1)@ (random)
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, staticEnzymeCost :: Double -- ^ Penalty in Fitness per Enzyme created
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, nutrientImpact :: Double -- ^ Penalty in Fitness for using nutrients (@nutrientImpact * Ratio(nutrientsUsed : nutrientsAvailable)@)
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}
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deriving (Show, Eq, Generic)
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@ -228,12 +237,14 @@ fitness iter ps = do
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else
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return $ repeat 1
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dieRate <- mapM (dieToPredators (zip appearingPredators popDefense)) products -- defeat predators with produced compounds
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sec <- fromEnv $ staticEnzymeCost . settings
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ni <- fromEnv $ nutrientImpact . settings
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let sumEnzymes = sum . fmap (\(_,q,a) -> fromIntegral q*a) . genome <$> ps -- amount of enzymes * activation = resources "wasted"
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staticCostOfEnzymes = (*0.01) <$> sumEnzymes -- static cost of creating enzymes
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staticCostOfEnzymes = (*sec) <$> sumEnzymes -- static cost of creating enzymes
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nutrientsAvailable <- fmap snd <$> fromEnv soil
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let nutrientsLeft = (\p -> [p ! i | i <- [0..fromEnum (maxBound :: Nutrient)]]) <$> products
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nutrientRatio = minimum . zipWith (flip (/)) nutrientsAvailable <$> nutrientsLeft
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costOfEnzymes = max 0 <$> zipWith (\s n -> 1-(s+n*0.1)) staticCostOfEnzymes nutrientRatio -- cost to keep enzymes are static costs + amount of nutrient sucked out of the primary cycle
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costOfEnzymes = max 0 <$> zipWith (\s n -> 1-(s+n*ni)) staticCostOfEnzymes nutrientRatio -- cost to keep enzymes are static costs + amount of nutrient sucked out of the primary cycle
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survivalRate = (1-) <$> dieRate
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return $ zip (zipWith (*) survivalRate costOfEnzymes) products
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@ -277,7 +288,6 @@ dieToPredator p comps = do
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-- Mating & Creation of diversity
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-- ------------------------------
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-- | mate haploid
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haploMate :: Plant -> World Plant
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haploMate (Plant genes abs) = do
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@ -293,6 +303,10 @@ haploMate (Plant genes abs) = do
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r4 <- liftIO digen
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r5 <- liftIO digen
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enzymes <- fromEnv possibleEnzymes
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ddr <- fromEnv $ deletionDuplicationRate.settings
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mr <- fromEnv $ mutationRate.settings
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ani <- fromEnv $ activationNoiseIntensity.settings
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gar <- fromEnv $ geneAddRate.settings
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re1 <- liftIO ((randomRs (0,length enzymes - 1) <$> newStdGen) :: IO [Int])
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re2 <- liftIO ((randomRs (0,length enzymes - 1) <$> newStdGen) :: IO [Int])
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let
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@ -304,7 +318,7 @@ haploMate (Plant genes abs) = do
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$ genes
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deleteGene :: [(Double,Int)] -> Genome -> Genome
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deleteGene _ [] = []
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deleteGene ((r,i):rs) g = if r < 0.05 then deleteGene rs (stay ++ go' ++ stay') else g
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deleteGene ((r,i):rs) g = if r < ddr then deleteGene rs (stay ++ go' ++ stay') else g
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where
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(stay, go:stay') = splitAt (i `mod` length g - 2) g
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go' = case go of
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@ -313,15 +327,15 @@ haploMate (Plant genes abs) = do
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duplicateGene :: [(Double,Int)] -> Genome -> Genome
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duplicateGene _ [] = []
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duplicateGene ((r,i):rs) g = if r < 0.05 then duplicateGene rs (stay ++ (e,q,a):(e,1,a):stay') else g
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duplicateGene ((r,i):rs) g = if r < ddr then duplicateGene rs (stay ++ (e,q,a):(e,1,a):stay') else g
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where
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(stay, (e,q,a):stay') = splitAt (i `mod` length g - 2) g
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addGene :: [Double] -> [Int] -> Genome -> Genome
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addGene (r:rs) (s:ss) g = if r < 0.005 then (enzymes !! s,1,0.5):g else g
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addGene (r:rs) (s:ss) g = if r < gar then (enzymes !! s,1,0.5):g else g
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noiseActivation :: [Double] -> Genome -> Genome
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noiseActivation (r:rs) ((e,q,a):gs) = (e,q,max 0 $ min 1 $ a-0.01+0.02*r):noiseActivation rs gs
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noiseActivation (r:rs) ((e,q,a):gs) = (e,q,max 0 $ min 1 $ a-ani+2*ani*r):noiseActivation rs gs
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noiseActivation _ [] = []
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mutateGene :: [Double] -> [Int] -> Genome -> Genome
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@ -331,9 +345,9 @@ haploMate (Plant genes abs) = do
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-- take q randoms from rs/ss, replace numMuts (<= q) with the enzymes in ss
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(rs',rs'') = splitAt q rs
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(ss',ss'') = splitAt q ss
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numMuts = length . filter (<0.01) $ rs'
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numMuts = length . filter (<mr) $ rs'
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newEnz = fmap ((\e' -> (e',1,a)).(enzymes!!).snd)
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. filter ((<0.01).fst)
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. filter ((<mr).fst)
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. zip rs' $ ss'
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g' = if q == numMuts then newEnz
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else (e,q-numMuts,a):newEnz
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