Math.Diversity.Diversity

Collection of functions pertaining to finding the diversity of samples.

Documentation

hamming :: String -> String -> Int

Takes two strings, returns Hamming distance

richness :: (Ord a, Ord b) => Map (a, b) c -> Int

Returns the richness of the observed data

diversity :: Ord a => Double -> [a] -> Double

Returns the diversity of a list of things

diversityOfMap :: Ord a => Double -> Map a Int -> Double

Returns the diversity of a map of the species and how many times it appears

diversityOfMapWithContribution :: Ord a => Double -> Map a Int -> (Double, Map a Double)

Returns the diversity of a map of the species and how many times it appears, along with the contribution of each species.

chao1 :: Ord a => Map a Int -> Double

Returns the chao1 estimator of a map of the species and how many times it appears

chao2 :: (Ord a, Ord b) => Map (a, b) Int -> Double

Returns the chao2 estimator of a map of the sample labeled species (sample, species) and how many times it appears. This will calculate the overlap for you, so if you don't have the number of times it appears it does not matter, you can set it to 1 and get the same result as it's all about overlapping samples.

chao1Var :: Ord a => Map a Int -> Double

Returns the chao1 estimator variance of a map of the species and how many times each one appears.

chao2Var :: (Ord a, Ord b) => Map (a, b) Int -> Double

Returns the chao2 estimator variance of a map of the sample labeled species (sample, species) and how many times it appears.

rarefactionCurve :: Bool -> Int -> Integer -> Integer -> Integer -> Map (Sample, Fragment) Int -> IO [(Int, Maybe (Double, Double))]

Returns the rarefaction curve for each position in a list

rarefactionSampleCurve :: Bool -> Int -> Int -> Int -> Map (Sample, Fragment) Int -> IO [(Int, Maybe (Double, Double))]

Returns the rarefaction curve for each position in a list

rarefactionViable :: [Double] -> Double

Calculates the percent of the curve that is above 95% of height of the curve

individualG :: Double -> Map (Sample, Fragment) Int -> Double

Returns the number of individuals needed to get the proportion g of the estimated total richness of the assemblage. Sobs / Sest < g < 1

sampleG :: Double -> Map (Sample, Fragment) Int -> Double

Returns the number of samples needed to get the proportion g of the estimated total richness of the assemblage. Sobs / Sest < g < 1

minRarefaction :: Bool -> Bool -> Int -> Map (Sample, Fragment) Int -> Double -> Int -> IO Int

Returns the number of samples needed before a new sample returns less than x new species. Warning, goes forever until threshold is met!