diversity 0.4.0.0 → 0.4.0.1

raw patch · 2 files changed

+15/−4 lines, 2 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• diversity.cabal +1/−1
• src/src-lib/Math/Diversity/Diversity.hs +14/−3

@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/  name:                diversity-version:             0.4.0.0+version:             0.4.0.1 synopsis:            Return the diversity at each position for all sequences in a fasta file description:         Find the diversity of a collection of entities, mainly for use with fasta sequences. Produces a binary which works on fasta files to find the diversity of any order and rarefaction curves for a sliding window across all positions in the sequences. To analyze just a collection of entities, just use the whole sequences and list flag. homepage:            https://github.com/GregorySchwartz/diversity

@@ -23,6 +23,16 @@ hamming :: String -> String -> Int hamming xs ys = length $ filter not $ zipWith (==) xs ys +-- | Fast product division+productDivision :: Double -> [Integer] -> [Integer] -> Double+productDivision acc [] []     = acc+productDivision acc [] (y:ys) = (acc / fromInteger y)+                              * productDivision acc [] ys+productDivision acc (x:xs) [] = acc * fromInteger x * productDivision acc xs []+productDivision acc (x:xs) (y:ys)+    | x == y    = productDivision acc xs ys+    | otherwise = (fromInteger x / fromInteger y) * productDivision acc xs ys+ -- | Returns the diversity of a list of things diversity :: (Ord b) => Double -> [b] -> Double diversity order sample@@ -39,9 +49,10 @@ -- | Binomial for small or large numbers (slow but works for big numbers, -- fast but works for small numbers) specialBinomial :: Bool -> Integer -> Integer -> Integer -> Double-specialBinomial False n_total g n = fromRational-    $ product [(n_total - g - n + 1)..(n_total - g)]-    % product [(n_total - n + 1)..n_total]+specialBinomial False n_total g n = productDivision 1 num den+  where+    num = [(n_total - g - n + 1)..(n_total - g)]+    den = [(n_total - n + 1)..n_total] specialBinomial True n_total g n = choose                                    (fromIntegral n_total - fromIntegral g)                                    (fromIntegral n)