ELynx.Data.Character.BoundaryMutation

The boundary mutation model is a discrete-state, continuous-time Markov process that allows mutations only when the population is monomorphic.

• Changelog

TODO: BM states can not be read and written with a single letter, like characters.

Types

data Nucleotide

Nucleotides.

Instances

Bounded Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

minBound :: Nucleotide

maxBound :: Nucleotide

Enum Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

succ :: Nucleotide -> Nucleotide

pred :: Nucleotide -> Nucleotide

toEnum :: Int -> Nucleotide

fromEnum :: Nucleotide -> Int

enumFrom :: Nucleotide -> [Nucleotide]

enumFromThen :: Nucleotide -> Nucleotide -> [Nucleotide]

enumFromTo :: Nucleotide -> Nucleotide -> [Nucleotide]

enumFromThenTo :: Nucleotide -> Nucleotide -> Nucleotide -> [Nucleotide]

Eq Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

(==) :: Nucleotide -> Nucleotide -> Bool

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

Ord Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

compare :: Nucleotide -> Nucleotide -> Ordering

(<) :: Nucleotide -> Nucleotide -> Bool

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

(>) :: Nucleotide -> Nucleotide -> Bool

(>=) :: Nucleotide -> Nucleotide -> Bool

max :: Nucleotide -> Nucleotide -> Nucleotide

min :: Nucleotide -> Nucleotide -> Nucleotide

Read Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

readsPrec :: Int -> ReadS Nucleotide

readList :: ReadS [Nucleotide]

readPrec :: ReadPrec Nucleotide

readListPrec :: ReadPrec [Nucleotide]

Show Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

showsPrec :: Int -> Nucleotide -> ShowS

show :: Nucleotide -> String

showList :: [Nucleotide] -> ShowS

Unbox Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Character Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

toWord :: Nucleotide -> Word8

fromWord :: Word8 -> Nucleotide

Vector Vector Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Nucleotide -> m (Vector Nucleotide)

basicUnsafeThaw :: PrimMonad m => Vector Nucleotide -> m (Mutable Vector (PrimState m) Nucleotide)

basicLength :: Vector Nucleotide -> Int

basicUnsafeSlice :: Int -> Int -> Vector Nucleotide -> Vector Nucleotide

basicUnsafeIndexM :: Monad m => Vector Nucleotide -> Int -> m Nucleotide

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Nucleotide -> Vector Nucleotide -> m ()

elemseq :: Vector Nucleotide -> Nucleotide -> b -> b

MVector MVector Nucleotide

Defined in ELynx.Data.Character.Nucleotide

Methods

basicLength :: MVector s Nucleotide -> Int

basicUnsafeSlice :: Int -> Int -> MVector s Nucleotide -> MVector s Nucleotide

basicOverlaps :: MVector s Nucleotide -> MVector s Nucleotide -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Nucleotide)

basicInitialize :: PrimMonad m => MVector (PrimState m) Nucleotide -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> Nucleotide -> m (MVector (PrimState m) Nucleotide)

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Nucleotide -> Int -> m Nucleotide

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Nucleotide -> Int -> Nucleotide -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) Nucleotide -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) Nucleotide -> Nucleotide -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Nucleotide -> MVector (PrimState m) Nucleotide -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Nucleotide -> MVector (PrimState m) Nucleotide -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Nucleotide -> Int -> m (MVector (PrimState m) Nucleotide)

newtype Vector Nucleotide

Defined in ELynx.Data.Character.Nucleotide

newtype Vector Nucleotide = V_Nucleotide (Vector Word8)

newtype MVector s Nucleotide

Defined in ELynx.Data.Character.Nucleotide

newtype MVector s Nucleotide = MV_Nucleotide (MVector s Word8)

type Allele = Nucleotide

Alleles are just nucleotides at the moment. However, I want to keep the code such that it can be extended easily to codons or amino acids.

type PopulationSize = Int

The population size has to be larger than one otherwise there be dragons.

type AlleleCount = Int

The absolute frequency of an allele.

data State

A boundary mutation model state is either a boundary state or a polymorphic state. The population size has to be larger than one; the allele count has to be larger than one and lower than the population size, otherwise there be dragons.

Another possibility would be: data State = Bnd Allele | Ply AlleleCount Allele Allele data StateComplete = StateComplete PopulationSize State But then, I think it is more important that the information is kept in one, at the cost of some overhead.

Constructors

Bnd

Fields

• bndN :: PopulationSize
• bndA :: Allele

  Population size.

Ply

Fields

• plyN :: PopulationSize
• plyI :: AlleleCount

  Population size.

• plyA :: Allele

  Allele count.

• plyB :: Allele

Instances

Bounded State

A fixed population size nFixed is assumed.

Defined in ELynx.Data.Character.BoundaryMutation

Methods

minBound :: State

maxBound :: State

Enum State

Enumeration only works when the population size is nFixed. Only then, toEnum . fromEnum == id can be guaranteed. This is because toEnum :: State is only defined if the population size is known. See also fromIndexWith, and toIndex, as well as, setPopulationSize.

Defined in ELynx.Data.Character.BoundaryMutation

Methods

succ :: State -> State

pred :: State -> State

toEnum :: Int -> State

fromEnum :: State -> Int

enumFrom :: State -> [State]

enumFromThen :: State -> State -> [State]

enumFromTo :: State -> State -> [State]

enumFromThenTo :: State -> State -> State -> [State]

Eq State

Defined in ELynx.Data.Character.BoundaryMutation

Methods

(==) :: State -> State -> Bool

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

Ord State

A total order on the boundary mutation model states. In general, Bnd < Ply. Then, sorting happens according to the order population size, first allele, second allele, allele count. It may be beneficial to reverse the allele count order (i.e., make a polymorphic state with higher allele count show up before a polymorphic state with lower allele count, this would move some polymorphic states closer to their respective boundaries),

Defined in ELynx.Data.Character.BoundaryMutation

Methods

compare :: State -> State -> Ordering

(<) :: State -> State -> Bool

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

(>) :: State -> State -> Bool

(>=) :: State -> State -> Bool

max :: State -> State -> State

min :: State -> State -> State

Read State

Defined in ELynx.Data.Character.BoundaryMutation

Methods

readsPrec :: Int -> ReadS State

readList :: ReadS [State]

readPrec :: ReadPrec State

readListPrec :: ReadPrec [State]

showCounts :: State -> ByteString

L.ByteString representation of State; without surrounding brackets.

nFixed :: Int

Fixed population size when converting a State to or from a number. In this case, a fixed population size is necessary so that toEnum . fromEnum == id. When converting from a number to State, the population size has to be given or assumed (see fromIndexWith) anyways. Especially when performing IO, the same number should always correspond to the same State (bijection). nFixed has been set such that the size of the state space is 256.

Functions

setPopulationSize :: PopulationSize -> State -> Maybe State

Set the population size of a State; validity of resulting State is checked.

fromIndexWith :: PopulationSize -> Int -> State

For a given population size PopulationSize, convert a number Int to State.

toIndex :: State -> Int

Convert State to a number Int for the given population size PopulationSize. Back conversion can be done with fromIndexWith, with the same population size.

stateSpace :: PopulationSize -> [State]

Sorted list of all possible PoMo states for a specific population size.

stateSpaceSize :: PopulationSize -> Int

The state space of the boundary mutation model for four alleles and a population size N is 4 + 6*(N-1).

neighbors :: State -> State -> Bool

Check if two states are connected. By definition, states are NOT connected with themselves.