module Math.Diversity.Print ( printDiversity
, printRarefaction
, printRarefactionCurve ) where
import Data.List
import Data.Maybe
import qualified Data.Map.Strict as Map
import Math.Diversity.Types
import Math.Diversity.Diversity
printDiversity :: Label -> Order -> Window -> PositionMap -> String
printDiversity label order window positionMap = header ++ body
where
header = "label,order,window,position,weight,diversity\n"
body = unlines
. map mapLine
. Map.toAscList
$ positionMap
mapLine (p, xs) = intercalate "," . line p $ xs
line p xs = [ label
, show order
, show window
, show p
, show . Map.foldl' (+) 0 $ xs
, show . diversityOfMap order $ xs
]
printRarefaction :: Bool
-> Double
-> Label
-> Window
-> PositionMap
-> IO String
printRarefaction
bySample g label window positionMap = do
body <- fmap unlines . mapM mapLine . Map.toAscList $ positionMap
return (header ++ body)
where
header = "label,window,position,weight,\
\additional_sampling,g_proportion,richness,\
\S_est,S_est_var\n"
mapLine (p, xs) = fmap (intercalate ",") . line p $ xs
line p xs = do
return [ label
, show window
, show p
, show . Map.foldl' (+) 0 $ xs
, show . additionalSampling bySample $ xs
, show g
, show . sobs $ xs
, show . sest bySample $ xs
, show . var bySample $ xs
]
sest True xs = sobs xs + chao2 xs
sest False xs = sobs xs + chao1 xs
var True = chao2Var
var False = chao1Var
sobs = fromIntegral . richness
additionalSampling True = sampleG g
additionalSampling False = individualG g
printRarefactionCurve :: Bool
-> Bool
-> Bool
-> Int
-> Int
-> Int
-> Int
-> Label
-> Window
-> PositionMap
-> IO String
printRarefactionCurve
asDF bySample fastBin runs start interval end label window positionMap = do
body <- fmap unlines . mapM mapLine . Map.toAscList $ positionMap
return (header asDF ++ body)
where
header False = "label,window,position,weight,percent_above,\
\expected_richness,mad\n"
header True = "label,window,position,weight,percent_above,subsample,\
\expected_richness,mad\n"
mapLine (!p, !xs) = line asDF p xs
line False p xs = do
curve <- getRarefactionCurve bySample xs
return . intercalate "," $ [ label
, show window
, show p
, show . Map.foldl' (+) 0 $ xs
, show
. rarefactionViable
. map (maybe (1) snd . snd)
$ curve
, intercalate "/"
. map (maybe "NA" (show . fst) . snd)
$ curve
, intercalate "/"
. map (maybe "NA" (show . snd) . snd)
$ curve
]
line True p xs = do
curve <- getRarefactionCurve bySample xs
return . intercalate "\n"
. map ( \(!x, !y)
-> intercalate "," [ label
, show window
, show p
, show . Map.foldl' (+) 0 $ xs
, show
. rarefactionViable
. map (maybe (1) snd . snd)
$ curve
, show x
, maybe "NA" (show . fst) y
, maybe "NA" (show . snd) y
] )
$ curve
getRarefactionCurve True = rarefactionSampleCurve fastBin start interval end
getRarefactionCurve False = rarefactionCurve
fastBin
runs
(fromIntegral start)
(fromIntegral interval)
(fromIntegral end)