Copyright	2021 Dominik Schrempf
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

ELynx.Tree.Simulate.PointProcess

Description

Creation date: Tue Feb 13 13:16:18 2018.

See Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.

The point process can be used to simulate reconstructed trees under the birth and death process.

Synopsis

data PointProcess a b = PointProcess {
- points :: ![a]
- values :: ![b]
- origin :: !b
}
data TimeSpec
- = Random
- | Origin Time
- | Mrca Time
simulate :: StatefulGen g m => Int -> TimeSpec -> Rate -> Rate -> g -> m (PointProcess Int Double)
toReconstructedTree :: a -> PointProcess a Length -> Tree Length a
simulateReconstructedTree :: StatefulGen g m => Int -> TimeSpec -> Rate -> Rate -> g -> m (Tree Length Int)
simulateNReconstructedTrees :: StatefulGen g m => Int -> Int -> TimeSpec -> Rate -> Rate -> g -> m (Forest Length Int)

Documentation

data PointProcess a b Source #

A point process for $n$ points and of age $t_{or}$ is defined as follows. Draw $n$ points on the horizontal axis at $1,2,\ldots,n$. Pick $n-1$ points at locations $(i+1/2, s_i)$, $i=1,2,\ldots,n-1$; $0 < s_i < t_{or}$. There is a bijection between (ranked) oriented trees and the point process. Usually, a will be String (or Int) and b will be Double.

Constructors

PointProcess
Fields points :: ![a] values :: ![b] origin :: !b

Instances

Instances details

(Read a, Read b) => Read (PointProcess a b) Source #
Instance details Defined in ELynx.Tree.Simulate.PointProcess Methods readsPrec :: Int -> ReadS (PointProcess a b) # readList :: ReadS [PointProcess a b] # readPrec :: ReadPrec (PointProcess a b) # readListPrec :: ReadPrec [PointProcess a b] #
(Show a, Show b) => Show (PointProcess a b) Source #
Instance details Defined in ELynx.Tree.Simulate.PointProcess Methods showsPrec :: Int -> PointProcess a b -> ShowS # show :: PointProcess a b -> String # showList :: [PointProcess a b] -> ShowS #
(Eq a, Eq b) => Eq (PointProcess a b) Source #
Instance details Defined in ELynx.Tree.Simulate.PointProcess Methods (==) :: PointProcess a b -> PointProcess a b -> Bool # (/=) :: PointProcess a b -> PointProcess a b -> Bool #

data TimeSpec Source #

Tree height specification.

Constructors

Random	Sample time of origin from respective distribution.
Origin Time	Condition on time of origin.
Mrca Time	Condition on time of most recent common ancestor (MRCA).

simulate Source #

Arguments

:: StatefulGen g m
=> Int	Number of points (samples).
-> TimeSpec	Time of origin or MRCA.
-> Rate	Birth rate.
-> Rate	Death rate.
-> g
-> m (PointProcess Int Double)

Sample a point process using the BirthDeathDistribution. The names of the points will be integers.

toReconstructedTree :: a -> PointProcess a Length -> Tree Length a Source #

Convert a point process to a reconstructed tree. See Lemma 2.2.

simulateReconstructedTree Source #

Arguments

:: StatefulGen g m
=> Int	Number of points (samples)
-> TimeSpec	Time of origin or MRCA
-> Rate	Birth rate
-> Rate	Death rate
-> g
-> m (Tree Length Int)

Use the point process to simulate a reconstructed tree (see toReconstructedTree) possibly with specific height and a fixed number of leaves according to the birth and death process.

simulateNReconstructedTrees Source #

Arguments

:: StatefulGen g m
=> Int	Number of trees
-> Int	Number of points (samples)
-> TimeSpec	Time of origin or MRCA
-> Rate	Birth rate
-> Rate	Death rate
-> g
-> m (Forest Length Int)

See simulateReconstructedTree, but n times.