dumb error in fitness-function

app/Main.hs

@@ -38,7 +38,7 @@ exampleEnvironment addedC es pred tox =
     , maxCompound = maxCompoundWithoutGeneric + addedC
     , toxicCompounds = tox --[(Produced FPP,0.1)] ++ tox
     , possibleEnzymes = es -- [pps,fpps] ++ es
-    , settings = Settings { automimicry = False
+    , settings = Settings { automimicry = True
                           , predatorsRandom = False
                           , numPlants = 150
                           }
@@ -88,7 +88,6 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
     toxins = toxicCompounds env
     padded i str = take i $ str ++ repeat ' '
     printEvery = 10
-    addedConstFitness = 0.1
     loop' :: Int -> Int -> [Plant] -> Environment -> IO ()
     loop' loopAmount curLoop plants e = unless (loopAmount+1 == curLoop) $ do
       when (curLoop `mod` printEvery == 0) $ do
@@ -97,7 +96,7 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
         putStrLn ""
         putStrLn $ "Generation " ++ show curLoop ++ " of " ++ show loopAmount ++ ":"
       newPlants <- flip runReaderT e $ do
-          (!fs,cs) <- unzip . fmap (\(f,c) -> (f,c)) <$> fitness plants
+          (!fs,cs) <- unzip <$> fitness plants
           let fps = zip plants fs -- gives us plants & their fitness in a tuple
               sumFitness = sum fs
           when (curLoop `mod` printEvery == 0) $ liftIO $ do
@@ -126,16 +125,16 @@ main :: IO ()
 main = do
   hSetBuffering stdin NoBuffering
   --hSetBuffering stdout NoBuffering
-  randomCompounds <- makeHead (Substrate PPM) <$> generateTreeFromList 20 (toEnum <$> [(maxCompoundWithoutGeneric+1)..] :: [Compound]) -- generate roughly x compounds
+  randomCompounds <- makeHead (Substrate PPM) <$> generateTreeFromList 40 (toEnum <$> [(maxCompoundWithoutGeneric+1)..] :: [Compound]) -- generate roughly x compounds
   ds <- randoms <$> newStdGen
   probs <- randomRs (0.2,0.7) <$> newStdGen
   let poisonedTree     = poisonTree ds randomCompounds
-      poisonCompounds  = foldMap (\(a,b) -> [(b,a) | a > 0.2]) poisonedTree
+      poisonCompounds  = foldMap (\(a,b) -> [(b,a) | a > 0.5]) poisonedTree
   predators <- generatePredators 0.5 poisonedTree
   let env              = exampleEnvironment (getTreeSize randomCompounds) (generateEnzymeFromTree randomCompounds) (zip predators probs) poisonCompounds
       emptyPlants      = replicate (numPlants . settings $ env) emptyPlant
   enzs <- randomRs (0,length (possibleEnzymes env) - 1) <$> newStdGen
-  let startPlants      = randomGenome 10 enzs (possibleEnzymes env) emptyPlants
+  let startPlants      = randomGenome 1 enzs (possibleEnzymes env) emptyPlants
   printEnvironment env
   writeFile "poison.twopi" $ generateDotFromPoisonTree "poison" 0.5 poisonedTree
   putStr "\ESC[?1049h"
@@ -221,3 +220,6 @@ generateEnzymeFromTree t = (makeSimpleEnzyme c . getElement <$> sts)
   where
     c   = getElement t
     sts = getSubTrees t
+
+
+stepDebug a = liftIO $ print a >> void getChar

src/Environment.hs

@@ -175,14 +175,14 @@ fitness ps = do
                   return $ repeat 1
   dieRate <- mapM (dieToPredators (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
+      staticCostOfEnzymes = (\x -> 1 - 0.02*x) <$> sumEnzymes -- static cost of creating enzymes
   nutrientsAvailable <- fmap snd <$> asks soil
   let nutrientsLeft = (\p -> [p ! i | i <- [0..fromEnum (maxBound :: Nutrient)]]) <$> products
       nutrientRatio = minimum . zipWith (flip (/)) nutrientsAvailable <$> nutrientsLeft
-      costOfEnzymes = max 0 <$> zipWith (\s n -> s-n*0.01) staticCostOfEnzymes nutrientRatio -- cost to keep enzymes are static costs + amount of nutrient sucked out of the primary cycle
+      costOfEnzymes = max 0 <$> 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
       survivalRate = (1-) <$> dieRate
-  return $ (,) <$> zipWith (*) survivalRate costOfEnzymes
-               <*> products
+  return $ zip (zipWith (*) survivalRate costOfEnzymes)
+               (products)
 
 produceCompounds :: Plant -> [(Nutrient, Amount)] -> World (Vector Amount)
 produceCompounds (Plant genes _) substrate = do
@@ -210,9 +210,10 @@ dieToPredators :: [(Predator, Double)] -> Vector Amount -> World Probability
 dieToPredators [] _ = return 0 -- if no predator, no dying.
 dieToPredators appearingPredators compounds = do
   deters <- forM appearingPredators $ \(p,ahat) -> do
-    myDeter <- dieToPredator p compounds
-    return $ ahat * myDeter -- exp due to assumption that number of attacks are poisson-distributed.
-  return $ product deters
+    myDieRate <- dieToPredator p compounds
+    return $ exp $ -(ahat*numAttacks p) * myDieRate -- exp due to assumption that number of attacks are poisson-distributed.
+                                                    -- myDieRate = 1 - Survival = 1 - S(D) in the paper
+  return $ 1 - product deters
 
 
 dieToPredator :: Predator -> Vector Amount -> World Double