Drezil/chemodiversity
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compiles, but metrics need to be checked.

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This commit is contained in:
Nicole Dresselhaus 2018-06-14 12:25:31 +02:00
parent 022b26e7a6
commit 62db90d3d9
Signed by: Drezil
GPG Key ID: 057D94F356F41E25
2 changed files with 19 additions and 18 deletions
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28
app/Main.hs
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@ -102,23 +102,23 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
putStrLn $ "Generation " ++ show curLoop ++ " of " ++ show loopAmount ++ ":" putStrLn $ "Generation " ++ show curLoop ++ " of " ++ show loopAmount ++ ":"
newPlants <- simulate s $ do newPlants <- simulate s $ do
(!fs,cs) <- unzip <$> fitness plants (!fs,cs) <- unzip <$> fitness 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 let fps = zip plants fs -- gives us plants & their fitness in a tuple
sumFitness = sum fs sumFitness = sum fs
-- $C_{\Sigma,mu}$: Durchschnittliche Menge an produzierten Stoffen -- $C_{\Sigma,mu}$: Durchschnittliche Menge an produzierten Stoffen
-- $C_{\Sigma,sigma}$: Durchschnittliche Varianz an produzierten Stoffen -- $C_{\Sigma,sigma}$: Durchschnittliche Varianz an produzierten Stoffen
(c_Sigma_mu, c_Sigma_sigma) = meanAndVar `from` sumProducedCompounds $ cs (c_sum_mu, c_sum_sigma) = meanAndVar `from` sumProducedCompounds $ cs
-- - $C_{i,\mu}$: Durchschnittliche Anzahl produzierter Komponenten -- - $C_{i,\mu}$: Durchschnittliche Anzahl produzierter Komponenten
-- - $C_{i,\sigma}$: Zusätzlich: Betrachtung der Varianz dieser Komponenten innerhalb der Population -- - $C_{i,\sigma}$: Zusätzlich: Betrachtung der Varianz dieser Komponenten innerhalb der Population
-- (Z.B. Stoff A wird immer mit $0.5$ produziert, hat also keine Varianz, -- (Z.B. Stoff A wird immer mit $0.5$ produziert, hat also keine Varianz,
-- wogegen Stoff B *im Schnitt* mit $0.5$ produziert wird, aber dies eine extreme -- wogegen Stoff B *im Schnitt* mit $0.5$ produziert wird, aber dies eine extreme
-- Varianz auslöst) -- Varianz auslöst)
-- c_mu_sigma :: [(Amount,Amount)]
(c_i_mu,c_i_sigma) = unzip $ meanAndVar `from` id <$> byProducts cs (c_i_mu,c_i_sigma) = unzip $ meanAndVar `from` id <$> byProducts cs
-- - $C_d$: Durchschnittliche Anzahl distinkter Produzierter Stoffe (sprich -- - $C_d$: Durchschnittliche Anzahl distinkter Produzierter Stoffe (sprich
-- nicht-endemisch, $#i | C_{i,\sigma} > \epsilon$ ) -- nicht-endemisch, $#i | C_{i,\sigma} > \epsilon$ )
isEndemic :: Vector Bool isEndemic :: Vector Bool
isEndemic = (> 0.01) <$> fromList c_i_sigma isEndemic = fromList $ (> 0.01) <$> c_i_sigma
(c_d_mu, c_d_sigma) = meanAndVar `from` (countWith isEndemic) $ cs (c_d_mu, c_d_sigma) = meanAndVar `from` countWith isEndemic $ cs
-- - $C_{\sigma,\{\mu/\sigma\}}$: Mittelwert/Varianz von $\C_{i,\sigma}$ -- - $C_{\sigma,\{\mu/\sigma\}}$: Mittelwert/Varianz von $\C_{i,\sigma}$
(c_sigma_mu, c_sigma_sigma) = meanAndVar `from` id $ c_i_sigma (c_sigma_mu, c_sigma_sigma) = meanAndVar `from` id $ c_i_sigma
-- - $\mathbf{E}[C_{\Sigma,plant} - C_{\Sigma,mu}]$: Durchschnittliche Abweichung der produzierten -- - $\mathbf{E}[C_{\Sigma,plant} - C_{\Sigma,mu}]$: Durchschnittliche Abweichung der produzierten
@ -127,21 +127,20 @@ loop loopAmount ps env = loop' loopAmount 0 ps env
-- mean and variance of fitness -- mean and variance of fitness
fns = meanAndVar `from` id $ fs fns = meanAndVar `from` id $ fs
-- - $P_\{\mu,\sigma\}$ Mittelwert/Varianz der Anteile der Stoffe in Pflanze i, die giftig sind -- - $P_\{\mu,\sigma\}$ Mittelwert/Varianz der Anteile der Stoffe in Pflanze i, die giftig sind
toxs = meanAndVar `from` percentagePoisonous $ cs toxs = meanAndVar `from` percentagePoisonous txns $ cs
when (curLoop `mod` printEvery == 0) $ liftIO $ do when (curLoop `mod` printEvery == 0) $ liftIO $ do
printPopulation stringe (zip3 plants fs cs) printPopulation (zip ((>0.01) <$> c_i_sigma) stringe) (zip3 plants fs cs)
putStrLn $ "Population statistics (mean,variance):" putStrLn $ "Population statistics (mean,variance):"
putStrLn $ "Amount of Components produced = " ++ (padded 50 . show $ spc) putStrLn $ "Amount of Components produced = " ++ (padded 50 . show $ (c_sum_mu,c_sum_sigma))
putStrLn $ "Number of distinct Components = " ++ (padded 50 . show $ ndc) putStrLn $ "Number of distinct Components = " ++ (padded 50 . show $ (c_d_mu, c_d_sigma))
putStrLn $ "Fitness = " ++ (padded 50 . show $ fns) putStrLn $ "Fitness = " ++ (padded 50 . show $ fns)
putStrLn $ show cstats
putStrLn $ show cstats'
hFlush stdout hFlush stdout
threadDelay $ 10*1000 -- sleep x*1000ns (=x ~ ms) threadDelay $ 10*1000 -- sleep x*1000ns (=x ~ ms)
tell $ show curLoop tell $ show curLoop
++ "," ++ show (fst spc) ++ "," ++ show (snd spc) ++ "," ++ show c_sum_mu ++ "," ++ show c_sum_sigma
++ "," ++ show (fst ndc) ++ "," ++ show (snd ndc) ++ "," ++ show c_d_mu ++ "," ++ show c_d_sigma
++ "," ++ show (fst fns) ++ "," ++ show (snd fns) ++ "," ++ show (fst fns) ++ "," ++ show (snd fns)
++ "," ++ show (fst toxs) ++ "," ++ show (snd toxs)
-- generate x new plants. -- generate x new plants.
np <- fromEnv (numPlants . settings) np <- fromEnv (numPlants . settings)
sequence . flip fmap [1..np] $ \_ -> do sequence . flip fmap [1..np] $ \_ -> do
@ -222,7 +221,7 @@ printEnvironment (Environment soil pred metaIter maxComp toxic possEnz settings)
putStrLn $ "Toxic: " ++ show toxic putStrLn $ "Toxic: " ++ show toxic
putStrLn $ "Settings: " ++ show settings putStrLn $ "Settings: " ++ show settings
printPopulation :: [(Enzyme,String)] -> [(Plant,Double,Vector Amount)] -> IO () printPopulation :: [(Bool,(Enzyme,String))] -> [(Plant,Double,Vector Amount)] -> IO ()
printPopulation es ps = do printPopulation es ps = do
let padded i str = take i $ str ++ repeat ' ' let padded i str = take i $ str ++ repeat ' '
n = length ps n = length ps
@ -232,7 +231,8 @@ printPopulation es ps = do
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) '█') forM_ ps $ \(_,f,_) -> putStr (printColor (f/maxFitness) '█')
putStrLn colorOff putStrLn colorOff
forM_ es $ \(e,s) -> do forM_ es $ \(b,(e,s)) -> do
if b then putStr ">" else putStr " "
putStr s putStr s
forM_ ps $ \(Plant g _,_,cs) -> do forM_ ps $ \(Plant g _,_,cs) -> do
let curE = sum $ map (\(_,q,a) -> fromIntegral q*a) let curE = sum $ map (\(_,q,a) -> fromIntegral q*a)

9
src/Evaluation.hs
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@ -38,13 +38,13 @@ numDistinctCompounds :: Functor f => f (LA.Vector Amount) -> f Amount
--numDistinctCompounds :: [LA.Vector Amount] -> [Amount] --numDistinctCompounds :: [LA.Vector Amount] -> [Amount]
numDistinctCompounds comps = sumElements . LA.cmap (\x -> if abs x < eps then 0 else 1) <$> comps numDistinctCompounds comps = sumElements . LA.cmap (\x -> if abs x < eps then 0 else 1) <$> comps
countWith :: Functor f => (LA.Vector Bool) -> f (LA.Vector Amount) -> f Amount countWith :: Functor f => LA.Vector Bool -> f (LA.Vector Amount) -> f Amount
countWith toSelect = fmap $ sumElements . LA.zipVectorWith (\selected _ -> if selected then 1 else 0) toSelect countWith toSelect = fmap $ sumElements . LA.zipVectorWith (\selected _ -> if selected then 1 else 0) toSelect
-- apply selection to set data to 1 or 0 -- apply selection to set data to 1 or 0
-- sum up 1 or 0s -- sum up 1 or 0s
-- for all data -- for all data
sumWith :: Functor f => (LA.Vector Bool) -> f (LA.Vector Amount) -> f Amount sumWith :: Functor f => LA.Vector Bool -> f (LA.Vector Amount) -> f Amount
sumWith toSelect = fmap $ sumElements . LA.zipVectorWith (\selected d -> if selected then d else 0) toSelect sumWith toSelect = fmap $ sumElements . LA.zipVectorWith (\selected d -> if selected then d else 0) toSelect
-- apply selection to set data to 1 or 0 -- apply selection to set data to 1 or 0
-- sum up data or 0s -- sum up data or 0s
@ -53,8 +53,9 @@ sumWith toSelect = fmap $ sumElements . LA.zipVectorWith (\selected d -> if sele
percentagePoisonous :: Functor f => [Int] -> f (LA.Vector Amount) -> f Amount percentagePoisonous :: Functor f => [Int] -> f (LA.Vector Amount) -> f Amount
percentagePoisonous poisons = fmap percentage percentagePoisonous poisons = fmap percentage
where where
percentage v = (\(tox,total) -> tox / total) $ foldl1' pfold [(if i `L.elem` poisons then v!i else 0, v!i) | i <- [1..LA.size v]] percentage v = uncurry (/) $ foldl1' pfold [(if i `L.elem` poisons then v!i else 0, v!i) | i <- [0..LA.size v-1]]
pfold (a,b) (a',b') = (a+a', b+b') -- uncurry (/) == (\(tox,total) -> tox / total), but exposes more laziness
pfold (a,b) (a',b') = (a+a', b+b')
-- | helper function for Foldl-Package. -- | helper function for Foldl-Package.
-- --