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Attackers in intervals now also work.

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This commit is contained in:
Nicole Dresselhaus 2018-06-21 16:15:43 +02:00
parent 6dfc7e1ae0
commit f478f0ecb6
Signed by: Drezil
GPG Key ID: AC88BB432537313A
4 changed files with 57 additions and 33 deletions
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4
TODO.md
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@ -20,13 +20,13 @@
- $\mathbf{E}[C_{plant} - C_#]$: Durchschnittliche Abweichung der produzierten
Stoffe gegenüber dem Schnitt der Gesamtpopulation
- Anteile der Stoffe, die giftig sind
- $#Plants$ die Angreifer X abwehren könnten
## Messung
- Ermitteln der Metriken für alle $x$ Generationen
- Stabilisieren sich die Metriken bei identischem Aufbau konsistent?
- $#Plants$ die Angreifer X abwehren könnten
- Ja, $\pm$ Random-Effekt
## Zu untersuchende Parameter

48
app/Main.hs
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@ -16,6 +16,7 @@ import System.IO
import System.Environment
import Data.Aeson
import qualified Data.ByteString as BS
import qualified Data.ByteString.Lazy as LBS
import Options.Applicative
import Data.Semigroup ((<>))
@ -47,10 +48,9 @@ exampleEnvironment addedC es pred tox =
, toxicCompounds = tox --[(Produced FPP,0.1)] ++ tox
, possibleEnzymes = es -- [pps,fpps] ++ es
, settings = Settings { automimicry = False
, predatorsRandom = False
, predatorBehaviour = AttackInterval 10
, numPlants = 50
, logEveryNIterations = 10
, verbose = True
}
}
@ -83,8 +83,8 @@ exampleEnvironment addedC es pred tox =
-- Running the simulation
-- ----------------------
loop :: Int -> [Plant] -> Simulation -> IO ()
loop loopAmount ps env = loop' loopAmount 0 ps env
loop :: Int -> [Plant] -> Simulation -> CLIOptions -> IO ()
loop loopAmount ps env opts = loop' loopAmount 0 ps env
where
-- cache enzyme colorful-strings
@ -96,7 +96,7 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
) <$> possibleEnzymes (snd env)
toxins :: [(Compound, Amount)]
toxins = toxicCompounds (snd env)
printEverything = verbose.settings.snd $ env
printEverything = verbose opts
padded i str = take i $ str ++ repeat ' '
printEvery = 10
loop' :: Int -> Int -> [Plant] -> Simulation -> IO ()
@ -107,15 +107,19 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
putStrLn ""
putStrLn $ "Generation " ++ show curLoop ++ " of " ++ show loopAmount ++ ":"
newPlants <- simulate s $ do
when (curLoop == 0) $
tell $ "num_iter"
++ ",c_sum_mu,c_sum_sigma"
++ ",c_d_mu,c_d_sigma"
++ ",e_d_mu,e_d_sigma"
++ ",fitness_mean,fitness_sigma"
++ ",percent_toxic_mean,percent_toxic_sigma"
when (curLoop == 0) $ do
preds <- length <$> fromEnv predators
--- generates "pred1,pred2,pred3,.....predN"
let additionalHeader = intercalate "," $ ("pred"++).show <$> [1..preds]
tell $ "num_iter"
++ ",c_sum_mu,c_sum_sigma"
++ ",c_d_mu,c_d_sigma"
++ ",e_d_mu,e_d_sigma"
++ ",fitness_mean,fitness_sigma"
++ ",percent_toxic_mean,percent_toxic_sigma"
++ "," ++ additionalHeader
logIter <- fromEnv $ logEveryNIterations . settings
(!fs,cs) <- unzip <$> fitness plants
(!fs,cs) <- unzip <$> fitness curLoop plants
txns <- fmap (fromEnum . fst) <$> fromEnv toxicCompounds -- [Int] of id's of toxic compounds
let fps = zip plants fs -- gives us plants & their fitness in a tuple
sumFitness = sum fs
@ -164,13 +168,17 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
putStrLn $ "Percentage of toxins in Cmpnds= " ++ show toxs
hFlush stdout
threadDelay $ 10*1000 -- sleep x*1000ns (=x ~ ms)
when (curLoop `mod` logIter == 0) $
when (curLoop `mod` logIter == 0) $ do
preds <- fmap fst <$> fromEnv predators
let numPlantsCanRepel = (\ir -> sum $ (\p -> if sum ((p LA.!) <$> ir) > 0 then 1 else 0) <$> cs) . fmap fromEnum . irresistance <$> preds
addedData = intercalate "," $ show <$> numPlantsCanRepel
tell $ show curLoop
++ "," ++ show c_sum_mu ++ "," ++ show c_sum_sigma
++ "," ++ show c_d_mu ++ "," ++ show c_d_sigma
++ "," ++ show e_d_mu ++ "," ++ show e_d_sigma
++ "," ++ show (fst fns) ++ "," ++ show (snd fns)
++ "," ++ show (fst toxs) ++ "," ++ show (snd toxs)
++ "," ++ addedData
-- generate x new plants.
np <- fromEnv (numPlants . settings)
sequence . flip fmap [1..np] $ \_ -> do
@ -190,6 +198,7 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
data CLIOptions = CLIOptions
{ environment :: Maybe FilePath
, logfile :: FilePath
, verbose :: Bool
}
cliOptParser :: Parser CLIOptions
@ -208,6 +217,11 @@ cliOptParser = CLIOptions
<> value "simulation.log"
<> help "Name for the logfile"
)
<*> switch
(long "verbose"
<> short 'v'
<> help "show 'gui' during process"
)
cliopts = info (cliOptParser <**> helper)
(fullDesc
@ -236,15 +250,15 @@ main = do
putStrLn $ "reading environment: " ++ file
decodeStrict' <$> BS.readFile file
let emptyPlants = replicate (numPlants . settings $ env) emptyPlant
printEverything = verbose.settings $ env
printEverything = verbose opts
enzs <- randomRs (0,length (possibleEnzymes env) - 1) <$> newStdGen
let startPlants = randomGenome 1 enzs (possibleEnzymes env) emptyPlants
--writeFile "poison.twopi" $ generateDotFromPoisonTree "poison" 0.5 poisonedTree
--writeFile "environment.json" . encode $ env
LBS.writeFile "environment.json" . encode $ env
when printEverything $ putStr "\ESC[?1049h"
loghandle <- openFile (logfile opts) WriteMode
putStrLn $ "logging to: " ++ logfile opts
loop 2000 startPlants (loghandle,env)
loop 2000 startPlants (loghandle,env) opts
hClose loghandle
when printEverything $ do
putStrLn "Simulation ended. Press key to exit."

8
environment2.json
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@ -429,7 +429,7 @@
"fitnessImpact": 0.4901681711436634,
"irresistance": [
{
"contents": 27,
"contents": 26,
"tag": "GenericCompound"
}
],
@ -493,8 +493,10 @@
"automimicry": false,
"logEveryNIterations": 10,
"numPlants": 100,
"predatorsRandom": false,
"verbose": false
"predatorBehaviour": {
"contents": 10,
"tag": "AttackInterval"
}
},
"soil": [
[

30
src/Environment.hs
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@ -111,12 +111,19 @@ data Predator = Predator { irresistance :: [Compound]
instance FromJSON Predator
instance ToJSON Predator
data PredatorBehaviour = AlwaysAttack
| AttackRandom
| AttackInterval Int
deriving (Show, Eq, Generic)
instance FromJSON PredatorBehaviour
instance ToJSON PredatorBehaviour
-- | 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?
, 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@
, verbose :: Bool -- ^ print visual statistics instead of just logging
}
deriving (Show, Eq, Generic)
@ -199,19 +206,20 @@ instance Eq Plant where
type Fitness = Double
fitness :: [Plant] -> World [(Fitness, Vector Amount)]
fitness ps = do
fitness :: Int -> [Plant] -> World [(Fitness, Vector Amount)]
fitness iter ps = do
nutrients <- mapM absorbNutrients ps -- absorb soil
products <- sequenceA $ zipWith produceCompounds ps nutrients -- produce compounds
ds <- liftIO $ randoms <$> newStdGen
preds <- fromEnv predators
randPred <- fromEnv (predatorsRandom . settings)
predB <- fromEnv (predatorBehaviour . settings)
let
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
appearingPredators = case predB of
AttackRandom -> 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.
AttackInterval lngth -> fmap fst . filter (\(_,p) -> iter `mod` floor (fromIntegral lngth / p) < lngth) $ preds
-- attacker appears for length lngth iterations averaging out at p over longer timespans.
AlwaysAttack -> fst <$> preds -- else just forget about probabilities
automimicry <- fromEnv (automimicry . settings)
popDefense <- if automimicry then
forM appearingPredators $ \p -> do
@ -310,7 +318,7 @@ haploMate (Plant genes abs) = do
(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,1,1):g else g
addGene (r:rs) (s:ss) g = if r < 0.005 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