ELynx.Tree.Length

Creation date: Thu Jan 17 14:16:34 2019.

Non-negativity of lengths is not completely ensured. See the documentation of Length.

Non-negative length

data Length

Non-negative length.

However, non-negativity is only checked with toLength, and negative values can be obtained using the Num and related instances.

Safe conversion is roughly 50 percent slower.

benchmarking length/length sum foldl' with safe conversion
time                 110.4 ms   (109.8 ms .. 111.0 ms)
                     1.000 R²   (1.000 R² .. 1.000 R²)
mean                 110.2 ms   (110.0 ms .. 110.6 ms)
std dev              501.8 μs   (359.1 μs .. 730.0 μs)

benchmarking length/length sum foldl' num instance
time                 89.37 ms   (85.13 ms .. 94.27 ms)
                     0.996 R²   (0.992 R² .. 1.000 R²)
mean                 86.53 ms   (85.63 ms .. 88.52 ms)
std dev              2.239 ms   (1.069 ms .. 3.421 ms)

benchmarking length/double sum foldl'
time                 85.47 ms   (84.88 ms .. 86.42 ms)
                     1.000 R²   (0.999 R² .. 1.000 R²)
mean                 85.56 ms   (85.26 ms .. 86.02 ms)
std dev              611.9 μs   (101.5 μs .. 851.7 μs)

Instances

Enum Length

Defined in ELynx.Tree.Length

Methods

succ :: Length -> Length

pred :: Length -> Length

toEnum :: Int -> Length

fromEnum :: Length -> Int

enumFrom :: Length -> [Length]

enumFromThen :: Length -> Length -> [Length]

enumFromTo :: Length -> Length -> [Length]

enumFromThenTo :: Length -> Length -> Length -> [Length]

Eq Length

Defined in ELynx.Tree.Length

Methods

(==) :: Length -> Length -> Bool

(/=) :: Length -> Length -> Bool

Floating Length

Defined in ELynx.Tree.Length

Methods

pi :: Length

exp :: Length -> Length

log :: Length -> Length

sqrt :: Length -> Length

(**) :: Length -> Length -> Length

logBase :: Length -> Length -> Length

sin :: Length -> Length

cos :: Length -> Length

tan :: Length -> Length

asin :: Length -> Length

acos :: Length -> Length

atan :: Length -> Length

sinh :: Length -> Length

cosh :: Length -> Length

tanh :: Length -> Length

asinh :: Length -> Length

acosh :: Length -> Length

atanh :: Length -> Length

log1p :: Length -> Length

expm1 :: Length -> Length

log1pexp :: Length -> Length

log1mexp :: Length -> Length

Fractional Length

Defined in ELynx.Tree.Length

Methods

(/) :: Length -> Length -> Length

recip :: Length -> Length

fromRational :: Rational -> Length

Num Length

Defined in ELynx.Tree.Length

Methods

(+) :: Length -> Length -> Length

(-) :: Length -> Length -> Length

(*) :: Length -> Length -> Length

negate :: Length -> Length

abs :: Length -> Length

signum :: Length -> Length

fromInteger :: Integer -> Length

Ord Length

Defined in ELynx.Tree.Length

Methods

compare :: Length -> Length -> Ordering

(<) :: Length -> Length -> Bool

(<=) :: Length -> Length -> Bool

(>) :: Length -> Length -> Bool

(>=) :: Length -> Length -> Bool

max :: Length -> Length -> Length

min :: Length -> Length -> Length

Read Length

Defined in ELynx.Tree.Length

Methods

readsPrec :: Int -> ReadS Length

readList :: ReadS [Length]

readPrec :: ReadPrec Length

readListPrec :: ReadPrec [Length]

Real Length

Defined in ELynx.Tree.Length

Methods

toRational :: Length -> Rational

RealFloat Length

Defined in ELynx.Tree.Length

Methods

floatRadix :: Length -> Integer

floatDigits :: Length -> Int

floatRange :: Length -> (Int, Int)

decodeFloat :: Length -> (Integer, Int)

encodeFloat :: Integer -> Int -> Length

exponent :: Length -> Int

significand :: Length -> Length

scaleFloat :: Int -> Length -> Length

isNaN :: Length -> Bool

isInfinite :: Length -> Bool

isDenormalized :: Length -> Bool

isNegativeZero :: Length -> Bool

isIEEE :: Length -> Bool

atan2 :: Length -> Length -> Length

RealFrac Length

Defined in ELynx.Tree.Length

Methods

properFraction :: Integral b => Length -> (b, Length)

truncate :: Integral b => Length -> b

round :: Integral b => Length -> b

ceiling :: Integral b => Length -> b

floor :: Integral b => Length -> b

Show Length

Defined in ELynx.Tree.Length

Methods

showsPrec :: Int -> Length -> ShowS

show :: Length -> String

showList :: [Length] -> ShowS

Generic Length

Defined in ELynx.Tree.Length

Associated Types

type Rep Length :: Type -> Type

Methods

from :: Length -> Rep Length x

to :: Rep Length x -> Length

Semigroup Length

Defined in ELynx.Tree.Length

Methods

(<>) :: Length -> Length -> Length

sconcat :: NonEmpty Length -> Length

stimes :: Integral b => b -> Length -> Length

Monoid Length

Defined in ELynx.Tree.Length

Methods

mempty :: Length

mappend :: Length -> Length -> Length

mconcat :: [Length] -> Length

NFData Length

Defined in ELynx.Tree.Length

Methods

rnf :: Length -> ()

ToJSON Length

Defined in ELynx.Tree.Length

Methods

toJSON :: Length -> Value

toEncoding :: Length -> Encoding

toJSONList :: [Length] -> Value

toEncodingList :: [Length] -> Encoding

FromJSON Length

Defined in ELynx.Tree.Length

Methods

parseJSON :: Value -> Parser Length

parseJSONList :: Value -> Parser [Length]

Splittable Length

Defined in ELynx.Tree.Length

Methods

split :: Length -> Length

HasLength Length

Defined in ELynx.Tree.Length

Methods

getLen :: Length -> Length

setLen :: Length -> Length -> Length

modLen :: (Length -> Length) -> Length -> Length

type Rep Length

Defined in ELynx.Tree.Length

type Rep Length = D1 ('MetaData "Length" "ELynx.Tree.Length" "elynx-tree-0.5.1.0-OnSTDMW2L1Ll7WyAwiVjK" 'True) (C1 ('MetaCons "Length" 'PrefixI 'True) (S1 ('MetaSel ('Just "fromLength") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

toLength :: Double -> Either String Length

Return Left if negative.

toLengthUnsafe :: Double -> Length

Do not check if value is negative.

class HasLength e where

A data type with measurable and modifiable values.

Methods

getLen :: e -> Length

Get length.

setLen :: Length -> e -> e

Set length.

modLen :: (Length -> Length) -> e -> e

Modify length.

Instances

HasLength Length

Defined in ELynx.Tree.Length

Methods

getLen :: Length -> Length

setLen :: Length -> Length -> Length

modLen :: (Length -> Length) -> Length -> Length

HasLength PhyloExplicit

Defined in ELynx.Tree.Phylogeny

Methods

getLen :: PhyloExplicit -> Length

setLen :: Length -> PhyloExplicit -> PhyloExplicit

modLen :: (Length -> Length) -> PhyloExplicit -> PhyloExplicit

height :: HasLength e => Tree e a -> Length

The maximum distance between origin and leaves.

The height includes the branch length of the stem.

rootHeight :: HasLength e => Tree e a -> Length

The maximum distance between root node and leaves.

Functions on trees

distancesOriginLeaves :: HasLength e => Tree e a -> [Length]

Distances from the origin of a tree to the leaves.

The distances include the branch length of the stem.

totalBranchLength :: HasLength e => Tree e a -> Length

Total branch length of a tree.

normalizeBranchLengths :: HasLength e => Tree e a -> Tree e a

Normalize branch lengths so that the sum is 1.0.

normalizeHeight :: HasLength e => Tree e a -> Tree e a

Normalize height of tree to 1.0.

ultrametric :: HasLength e => Tree e a -> Bool

Check if a tree is ultrametric.

makeUltrametric :: HasLength e => Tree e a -> Tree e a

Elongate terminal branches such that the tree becomes ultrametric.