minor things before tests can start.

app/Main.hs

@@ -51,6 +51,12 @@ exampleEnvironment addedC es pred tox =
                           , predatorBehaviour = AttackInterval 10
                           , numPlants = 50
                           , logEveryNIterations = 10
+                          , mutationRate = 0.01
+                          , deletionDuplicationRate = 0.05
+                          , geneAddRate = 0.005
+                          , activationNoiseIntensity = 0.01
+                          , staticEnzymeCost = 0.01
+                          , nutrientImpact = 0.01
                           }
     }
 
@@ -252,7 +258,7 @@ main = do
   let emptyPlants      = replicate (numPlants . settings $ env) emptyPlant
       printEverything  = verbose opts
   enzs <- randomRs (0,length (possibleEnzymes env) - 1) <$> newStdGen
-  let startPlants      = randomGenome 1 enzs (possibleEnzymes env) emptyPlants
+  let startPlants      = randomGenome 2 enzs (possibleEnzymes env) emptyPlants
   --writeFile "poison.twopi" $ generateDotFromPoisonTree "poison" 0.5 poisonedTree
   LBS.writeFile "environment.json" . encode $ env
   when printEverything $ putStr "\ESC[?1049h"
@@ -272,7 +278,7 @@ randomGenome num inds enzs (p:ps) = p { genome = genes} : randomGenome num r enz
     i' = take num inds
     r  = drop num inds
     enzymes = (enzs!!) <$> i'
-    genes = (\e -> (e,1,1)) <$> enzymes
+    genes = (\e -> (e,1,0.5)) <$> enzymes
 
 
 generatePredators :: Double -> EnzymeTree s (Double,Compound) -> IO [Predator]
@@ -308,7 +314,7 @@ printPopulation endemic es ps = do
       fitnesses = (\(_,f,_) -> f) <$> ps
       meanFitness = sum fitnesses / fromIntegral n
       maxFitness = maximum fitnesses
-  putStr $ padded 50 ("Population: (fitness: mean " ++ padded 5 (show meanFitness) ++ ", max: " ++ padded 5 (show maxFitness) ++ ")")
+  putStr $ padded 50 (" Population: (fitness: mean " ++ padded 5 (show meanFitness) ++ ", max: " ++ padded 5 (show maxFitness) ++ ")")
   forM_ ps $ \(_,f,_) -> putStr (printColor (f/maxFitness) '█')
   putStrLn colorOff
   forM_ es $ \(e,s) -> do

environment2.json

@@ -495,8 +495,14 @@
         "numPlants": 100,
         "predatorBehaviour": {
             "contents": 10,
-            "tag": "AttackInterval"
+            "tag": "AlwaysAttack"
         }
+        , "mutationRate": 0.01
+        , "deletionDuplicationRate": 0.05
+        , "geneAddRate": 0.005
+        , "activationNoiseIntensity": 0.01
+        , "staticEnzymeCost": 0.01
+        , "nutrientImpact": 0.01
     },
     "soil": [
         [

src/Environment.hs

@@ -119,11 +119,20 @@ data PredatorBehaviour = AlwaysAttack
 instance FromJSON PredatorBehaviour
 instance ToJSON PredatorBehaviour
 
--- | Settings to enable/disable parts of the simulation
+--  | Settings to enable/disable parts of the simulation
-data Settings = Settings { automimicry :: Bool        -- ^ do we have automimicry-protection?
+--
-                         , predatorBehaviour :: PredatorBehaviour    -- ^ do predators always appear or according to their random distribution?
+--  Fitness is usually seen as relative Fitness (probability of survival), thus [0..1].
-                         , numPlants :: Int           -- ^ number of plants in starting population
+data Settings = Settings { automimicry              :: Bool              -- ^ do we have automimicry-protection?
-                         , logEveryNIterations :: Int -- ^ log status every @loopNumber `mod` logEveryNIterations == 0@
+                         , predatorBehaviour        :: PredatorBehaviour -- ^ do predators always appear or according to their random distribution?
+                         , numPlants                :: Int               -- ^ number of plants in starting population
+                         , logEveryNIterations      :: Int               -- ^ log status every @loopNumber `mod` logEveryNIterations == 0@
+                         , deletionDuplicationRate  :: Double            -- ^ Rate at wich genes get deleted or duplicated (e.g. 0.05 = 5% chance a gene gets deleted/duplicated. Independent per gene)
+                         , mutationRate             :: Double            -- ^ Rate at wich genes mutate to produce other enzymes. Independent per gene
+                         , geneAddRate              :: Double            -- ^ Rate at wich genes from the primary metabolims mutate to produce enzymes of the secondary metabolims
+                         , activationNoiseIntensity :: Double            -- ^ Intensity of activation mutatation. Enzymes produced are @#Genes * Activation@. Activation is clipped between @0@ and @1@.
+                                                                         --   New activation is @activation +- activationNoiseIntensity*[0..1)@ (random)
+                         , staticEnzymeCost         :: Double            -- ^ Penalty in Fitness per Enzyme created
+                         , nutrientImpact           :: Double            -- ^ Penalty in Fitness for using nutrients (@nutrientImpact * Ratio(nutrientsUsed : nutrientsAvailable)@)
                          }
                          deriving (Show, Eq, Generic)
 
@@ -228,12 +237,14 @@ fitness iter ps = do
                 else
                   return $ repeat 1
   dieRate <- mapM (dieToPredators (zip appearingPredators popDefense)) products  -- defeat predators with produced compounds
+  sec <- fromEnv $ staticEnzymeCost . settings
+  ni  <- fromEnv $ nutrientImpact . settings
   let sumEnzymes = sum . fmap (\(_,q,a) -> fromIntegral q*a) . genome <$>  ps -- amount of enzymes * activation = resources "wasted"
-      staticCostOfEnzymes = (*0.01) <$> sumEnzymes -- static cost of creating enzymes
+      staticCostOfEnzymes = (*sec) <$> sumEnzymes -- static cost of creating enzymes
   nutrientsAvailable <- fmap snd <$> fromEnv soil
   let nutrientsLeft = (\p -> [p ! i | i <- [0..fromEnum (maxBound :: Nutrient)]]) <$> products
       nutrientRatio = minimum . zipWith (flip (/)) nutrientsAvailable <$> nutrientsLeft
-      costOfEnzymes = max 0 <$> zipWith (\s n -> 1-(s+n*0.1)) staticCostOfEnzymes nutrientRatio -- cost to keep enzymes are static costs + amount of nutrient sucked out of the primary cycle
+      costOfEnzymes = max 0 <$> 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
       survivalRate = (1-) <$> dieRate
   return $ zip (zipWith (*) survivalRate costOfEnzymes)  products
 
@@ -277,7 +288,6 @@ dieToPredator p comps = do
 -- Mating & Creation of diversity
 -- ------------------------------
 
-
 -- | mate haploid
 haploMate :: Plant -> World Plant
 haploMate (Plant genes abs) = do
@@ -293,6 +303,10 @@ haploMate (Plant genes abs) = do
   r4 <- liftIO digen
   r5 <- liftIO digen
   enzymes <- fromEnv possibleEnzymes
+  ddr <- fromEnv $ deletionDuplicationRate.settings
+  mr  <- fromEnv $ mutationRate.settings
+  ani <- fromEnv $ activationNoiseIntensity.settings
+  gar <- fromEnv $ geneAddRate.settings
   re1 <- liftIO ((randomRs (0,length enzymes - 1) <$> newStdGen) :: IO [Int])
   re2 <- liftIO ((randomRs (0,length enzymes - 1) <$> newStdGen) :: IO [Int])
   let
@@ -304,7 +318,7 @@ haploMate (Plant genes abs) = do
            $ genes
     deleteGene :: [(Double,Int)] -> Genome -> Genome
     deleteGene _ []                = []
-    deleteGene ((r,i):rs) g = if r < 0.05 then deleteGene rs (stay ++ go' ++ stay') else g
+    deleteGene ((r,i):rs) g = if r < ddr then deleteGene rs (stay ++ go' ++ stay') else g
                                           where
                                             (stay, go:stay') = splitAt (i `mod` length g - 2) g
                                             go' = case go of
@@ -313,15 +327,15 @@ haploMate (Plant genes abs) = do
 
     duplicateGene :: [(Double,Int)] -> Genome -> Genome
     duplicateGene _ []                = []
-    duplicateGene ((r,i):rs) g = if r < 0.05 then duplicateGene rs (stay ++ (e,q,a):(e,1,a):stay') else g
+    duplicateGene ((r,i):rs) g = if r < ddr then duplicateGene rs (stay ++ (e,q,a):(e,1,a):stay') else g
                                           where
                                             (stay, (e,q,a):stay') = splitAt (i `mod` length g - 2) g
 
     addGene :: [Double] -> [Int] -> Genome -> Genome
-    addGene (r:rs) (s:ss) g = if r < 0.005 then (enzymes !! s,1,0.5):g else g
+    addGene (r:rs) (s:ss) g = if r < gar then (enzymes !! s,1,0.5):g else g
 
     noiseActivation :: [Double] -> Genome -> Genome
-    noiseActivation (r:rs) ((e,q,a):gs) = (e,q,max 0 $ min 1 $ a-0.01+0.02*r):noiseActivation rs gs
+    noiseActivation (r:rs) ((e,q,a):gs) = (e,q,max 0 $ min 1 $ a-ani+2*ani*r):noiseActivation rs gs
     noiseActivation _ []                = []
 
     mutateGene :: [Double] -> [Int] -> Genome -> Genome
@@ -331,9 +345,9 @@ haploMate (Plant genes abs) = do
         -- take q randoms from rs/ss, replace numMuts (<= q) with the enzymes in ss
         (rs',rs'') = splitAt q rs
         (ss',ss'') = splitAt q ss
-        numMuts = length . filter (<0.01) $ rs'
+        numMuts = length . filter (<mr) $ rs'
         newEnz = fmap ((\e' -> (e',1,a)).(enzymes!!).snd) 
-               . filter ((<0.01).fst) 
+               . filter ((<mr).fst) 
                . zip rs' $ ss'
         g' = if q == numMuts then newEnz
                              else (e,q-numMuts,a):newEnz