diversity 0.6.2.1 → 0.6.3.0
raw patch · 2 files changed
+8/−4 lines, 2 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
diversity.cabal view
@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/ name: diversity-version: 0.6.2.1+version: 0.6.3.0 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
src/src-lib/Math/Diversity/Diversity.hs view
@@ -229,7 +229,9 @@ -- | Returns the number of individuals needed to get the proportion g of -- the estimated total richness of the assemblage. Sobs / Sest < g < 1 individualG :: Double -> Map.Map (Sample, Fragment) Int -> Double-individualG g sample = ((sobs * f1) / (2 * f2)) * log (f0 / ((1 - g) * sest))+individualG g sample+ | sobs / sest >= g = 0+ | otherwise = ((sobs * f1) / (2 * f2)) * log (f0 / ((1 - g) * sest)) where sest = sobs + f0 sobs = fromIntegral $ richness sample@@ -240,8 +242,10 @@ -- | Returns the number of samples needed to get the proportion g of -- the estimated total richness of the assemblage. Sobs / Sest < g < 1 sampleG :: Double -> Map.Map (Sample, Fragment) Int -> Double-sampleG g sample = log (1 - ((t / (t - 1)) * ((2 * q2) / (q1 ** 2)) * ((g * sest) - sobs)))- / log (1 - ((2 * q2) / (((t - 1) * q1) + (2 * q2))))+sampleG g sample+ | sobs / sest >= g = 0+ | otherwise = log (1 - ((t / (t - 1)) * ((2 * q2) / (q1 ** 2)) * ((g * sest) - sobs)))+ / log (1 - ((2 * q2) / (((t - 1) * q1) + (2 * q2)))) where t = fromIntegral . Map.size . Map.mapKeys fst $ sample sest = sobs + q0