ELynx.Tree.Measurable

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 operations with conversion from and to length are 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.Measurable

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.Measurable

Methods

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

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

Floating Length

Defined in ELynx.Tree.Measurable

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.Measurable

Methods

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

recip :: Length -> Length

fromRational :: Rational -> Length

Num Length

Defined in ELynx.Tree.Measurable

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.Measurable

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.Measurable

Methods

readsPrec :: Int -> ReadS Length

readList :: ReadS [Length]

readPrec :: ReadPrec Length

readListPrec :: ReadPrec [Length]

Real Length

Defined in ELynx.Tree.Measurable

Methods

toRational :: Length -> Rational

RealFloat Length

Defined in ELynx.Tree.Measurable

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.Measurable

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.Measurable

Methods

showsPrec :: Int -> Length -> ShowS

show :: Length -> String

showList :: [Length] -> ShowS

Generic Length

Defined in ELynx.Tree.Measurable

Associated Types

type Rep Length :: Type -> Type

Methods

from :: Length -> Rep Length x

to :: Rep Length x -> Length

Semigroup Length

Defined in ELynx.Tree.Measurable

Methods

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

sconcat :: NonEmpty Length -> Length

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

Monoid Length

Defined in ELynx.Tree.Measurable

Methods

mempty :: Length

mappend :: Length -> Length -> Length

mconcat :: [Length] -> Length

NFData Length

Defined in ELynx.Tree.Measurable

Methods

rnf :: Length -> ()

ToJSON Length

Defined in ELynx.Tree.Measurable

Methods

toJSON :: Length -> Value

toEncoding :: Length -> Encoding

toJSONList :: [Length] -> Value

toEncodingList :: [Length] -> Encoding

FromJSON Length

Defined in ELynx.Tree.Measurable

Methods

parseJSON :: Value -> Parser Length

parseJSONList :: Value -> Parser [Length]

Splittable Length

Defined in ELynx.Tree.Measurable

Methods

split :: Length -> Length

Measurable Length

Defined in ELynx.Tree.Measurable

Methods

getLen :: Length -> Length

setLen :: Length -> Length -> Length

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

type Rep Length

Defined in ELynx.Tree.Measurable

type Rep Length = D1 ('MetaData "Length" "ELynx.Tree.Measurable" "elynx-tree-0.5.0-LNeltioHkaNAWvI1l3dP6J" 'True) (C1 ('MetaCons "Length" 'PrefixI 'True) (S1 ('MetaSel ('Just "fromLength") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Double)))

toLength :: Double -> Either String Length

Nothing if length is negative.

toLengthUnsafe :: Double -> Length

Do not check if support value is negative.

checkLength :: Length -> Either String Length

Nothing if length is negative.

class Measurable e where

A data type with measurable and modifiable length.

Methods

getLen :: e -> Length

Get length.

setLen :: Length -> e -> e

Set length.

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

Modify length.

Instances

Measurable Length

Defined in ELynx.Tree.Measurable

Methods

getLen :: Length -> Length

setLen :: Length -> Length -> Length

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

Measurable PhyloExplicit

Defined in ELynx.Tree.Phylogeny

Methods

getLen :: PhyloExplicit -> Length

setLen :: Length -> PhyloExplicit -> PhyloExplicit

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

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

The maximum distance between origin and leaves.

The height includes the branch length of the stem.

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

The maximum distance between root node and leaves.

Functions on trees

distancesOriginLeaves :: Measurable 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 :: Measurable e => Tree e a -> Length

Total branch length of a tree.

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

Normalize branch lengths so that the sum is 1.0.

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

Normalize height of tree to 1.0.

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

Check if a tree is ultrametric.

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

Elongate terminal branches such that the tree becomes ultrametric.