diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,13 @@
## Unreleased changes
+## Version 0.6.1.1
+
+- Remove plotting functionality (gnuplot incompatible with ghc921).
+- Read files strictly.
+- Refactor; flatten model hierarchy.
+
+
## Version 0.6.1.0
- Split `ELynx.Tools` into separate modules because the package will be reduced.
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.6.0.0.
+Version: 0.6.1.1.
Reproducible evolution made easy.
@@ -69,15 +69,16 @@
# Get help
- cabal exec slynx -- --help
+ cabal run slynx -- --help
# OR: stack exec slynx -- --help
# OR: slynx --help
- ELynx Suite version 0.6.0.0.
+ Up to date
+ ELynx Suite version 0.6.1.1.
Developed by Dominik Schrempf.
- Compiled on September 4, 2021, at 12:58 pm, UTC.
+ Compiled on February 22, 2022, at 15:10 pm, UTC.
- Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
+ Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
Analyze, and simulate multi sequence alignments.
@@ -138,18 +139,19 @@
The documentation of sub commands can be accessed separately:
- cabal exec slynx -- simulate --help
+ cabal run slynx -- simulate --help
# OR: stack exec slynx -- simulate --help
# OR: slynx simulate --help
- ELynx Suite version 0.6.0.0.
+ Up to date
+ ELynx Suite version 0.6.1.1.
Developed by Dominik Schrempf.
- Compiled on September 4, 2021, at 12:58 pm, UTC.
+ Compiled on February 22, 2022, at 15:10 pm, UTC.
- Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
- [-m|--mixture-model MODEL] [-e|--edm-file NAME]
- [-p|--siteprofile-files NAMES]
- [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
+ Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
+ [-m|--mixture-model MODEL] [-e|--edm-file NAME]
+ [-p|--siteprofile-files NAMES]
+ [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
[-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]
(-l|--length NUMBER) [-S|--seed [INT]]
Simulate multi sequence alignments.
diff --git a/elynx-markov.cabal b/elynx-markov.cabal
--- a/elynx-markov.cabal
+++ b/elynx-markov.cabal
@@ -1,6 +1,6 @@
-cabal-version: 2.2
+cabal-version: 3.0
name: elynx-markov
-version: 0.6.1.0
+version: 0.6.1.1
synopsis: Simulate molecular sequences along trees
description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at .
category: Bioinformatics
@@ -27,15 +27,15 @@
library
exposed-modules:
- ELynx.Data.MarkovProcess.AminoAcid
- ELynx.Data.MarkovProcess.CXXModels
- ELynx.Data.MarkovProcess.CXXModelsData
- ELynx.Data.MarkovProcess.GammaRateHeterogeneity
- ELynx.Data.MarkovProcess.MixtureModel
- ELynx.Data.MarkovProcess.Nucleotide
- ELynx.Data.MarkovProcess.PhyloModel
- ELynx.Data.MarkovProcess.RateMatrix
- ELynx.Data.MarkovProcess.SubstitutionModel
+ ELynx.MarkovProcess.AminoAcid
+ ELynx.MarkovProcess.CXXModels
+ ELynx.MarkovProcess.CXXModelsData
+ ELynx.MarkovProcess.GammaRateHeterogeneity
+ ELynx.MarkovProcess.MixtureModel
+ ELynx.MarkovProcess.Nucleotide
+ ELynx.MarkovProcess.PhyloModel
+ ELynx.MarkovProcess.RateMatrix
+ ELynx.MarkovProcess.SubstitutionModel
ELynx.Import.MarkovProcess.EDMModelPhylobayes
ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
ELynx.Simulate.MarkovProcess
@@ -66,9 +66,9 @@
type: exitcode-stdio-1.0
main-is: Spec.hs
other-modules:
- ELynx.Data.MarkovProcess.AminoAcidSpec
- ELynx.Data.MarkovProcess.NucleotideSpec
- ELynx.Data.MarkovProcess.RateMatrixSpec
+ ELynx.MarkovProcess.AminoAcidSpec
+ ELynx.MarkovProcess.NucleotideSpec
+ ELynx.MarkovProcess.RateMatrixSpec
ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
ELynx.Simulate.MarkovProcessAlongTreeSpec
diff --git a/src/ELynx/Data/MarkovProcess/AminoAcid.hs b/src/ELynx/Data/MarkovProcess/AminoAcid.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/AminoAcid.hs
+++ /dev/null
@@ -1,647 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.AminoAcid
--- Description : Amino acid rate matrices such as LG
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Jan 29 09:29:19 2019.
---
--- The order of amino acids is alphabetic.
-module ELynx.Data.MarkovProcess.AminoAcid
- ( -- * Amino acid substitution models
- lg,
- lgCustom,
- wag,
- wagCustom,
- poisson,
- poissonCustom,
- gtr20,
-
- -- * Convenience functions
- alphaToPamlVec,
- pamlToAlphaVec,
- )
-where
-
-import Data.ByteString.Internal (c2w)
-import Data.Maybe (fromMaybe)
-import qualified Data.Vector.Storable as V
-import Data.Word (Word8)
-import ELynx.Data.Alphabet.Alphabet
-import ELynx.Data.MarkovProcess.RateMatrix
-import ELynx.Data.MarkovProcess.SubstitutionModel
-import Numeric.LinearAlgebra
-
-n :: Int
-n = 20
-
--- Some matrices have to be converted from PAML order to alphabetical order. See
--- 'pamlToAlphaVec' and 'pamlToAlphaMat'.
-
--- Amno acids in alphabetical order.
-aaAlphaOrder :: V.Vector Word8
-aaAlphaOrder =
- V.map
- c2w
- $ V.fromList
- [ 'A',
- 'C',
- 'D',
- 'E',
- 'F',
- 'G',
- 'H',
- 'I',
- 'K',
- 'L',
- 'M',
- 'N',
- 'P',
- 'Q',
- 'R',
- 'S',
- 'T',
- 'V',
- 'W',
- 'Y'
- ]
-
--- Amino acids in PAML oder.
-aaPamlOrder :: V.Vector Word8
-aaPamlOrder =
- V.map
- c2w
- $ V.fromList
- [ 'A',
- 'R',
- 'N',
- 'D',
- 'C',
- 'Q',
- 'E',
- 'G',
- 'H',
- 'I',
- 'L',
- 'K',
- 'M',
- 'F',
- 'P',
- 'S',
- 'T',
- 'W',
- 'Y',
- 'V'
- ]
-
-alphaIndexToPamlIndex :: Int -> Int
-alphaIndexToPamlIndex i =
- fromMaybe
- (error $ "Could not convert index " ++ show i ++ ".")
- (V.elemIndex aa aaPamlOrder)
- where
- aa = aaAlphaOrder V.! i
-
-pamlIndexToAlphaIndex :: Int -> Int
-pamlIndexToAlphaIndex i =
- fromMaybe
- (error $ "Could not convert index " ++ show i ++ ".")
- (V.elemIndex aa aaAlphaOrder)
- where
- aa = aaPamlOrder V.! i
-
--- | Convert an amino acid vector in PAML order to a vector in alphabetical order.
-pamlToAlphaVec :: Vector R -> Vector R
-pamlToAlphaVec v = build n (\i -> v ! alphaIndexToPamlIndex (round i))
-
--- | Convert an amino acid vector in alphabetical order to a vector in PAML order.
-alphaToPamlVec :: Vector R -> Vector R
-alphaToPamlVec v = build n (\i -> v ! pamlIndexToAlphaIndex (round i))
-
--- Convert an amino acid matrix in PAML order to a matrix in alphabetical order.
-pamlToAlphaMat :: Matrix R -> Matrix R
-pamlToAlphaMat m =
- build
- (n, n)
- ( \i j -> m ! alphaIndexToPamlIndex (round i) ! alphaIndexToPamlIndex (round j)
- )
-
--- Lower triangular matrix of LG exchangeabilities in PAML order and in form of
--- a list.
-lgExchRawPaml :: [Double]
-lgExchRawPaml =
- [ 0.425093,
- 0.276818,
- 0.751878,
- 0.395144,
- 0.123954,
- 5.076149,
- 2.489084,
- 0.534551,
- 0.528768,
- 0.062556,
- 0.969894,
- 2.807908,
- 1.695752,
- 0.523386,
- 0.084808,
- 1.038545,
- 0.363970,
- 0.541712,
- 5.243870,
- 0.003499,
- 4.128591,
- 2.066040,
- 0.390192,
- 1.437645,
- 0.844926,
- 0.569265,
- 0.267959,
- 0.348847,
- 0.358858,
- 2.426601,
- 4.509238,
- 0.927114,
- 0.640543,
- 4.813505,
- 0.423881,
- 0.311484,
- 0.149830,
- 0.126991,
- 0.191503,
- 0.010690,
- 0.320627,
- 0.072854,
- 0.044265,
- 0.008705,
- 0.108882,
- 0.395337,
- 0.301848,
- 0.068427,
- 0.015076,
- 0.594007,
- 0.582457,
- 0.069673,
- 0.044261,
- 0.366317,
- 4.145067,
- 0.536518,
- 6.326067,
- 2.145078,
- 0.282959,
- 0.013266,
- 3.234294,
- 1.807177,
- 0.296636,
- 0.697264,
- 0.159069,
- 0.137500,
- 1.124035,
- 0.484133,
- 0.371004,
- 0.025548,
- 0.893680,
- 1.672569,
- 0.173735,
- 0.139538,
- 0.442472,
- 4.273607,
- 6.312358,
- 0.656604,
- 0.253701,
- 0.052722,
- 0.089525,
- 0.017416,
- 1.105251,
- 0.035855,
- 0.018811,
- 0.089586,
- 0.682139,
- 1.112727,
- 2.592692,
- 0.023918,
- 1.798853,
- 1.177651,
- 0.332533,
- 0.161787,
- 0.394456,
- 0.075382,
- 0.624294,
- 0.419409,
- 0.196961,
- 0.508851,
- 0.078281,
- 0.249060,
- 0.390322,
- 0.099849,
- 0.094464,
- 4.727182,
- 0.858151,
- 4.008358,
- 1.240275,
- 2.784478,
- 1.223828,
- 0.611973,
- 1.739990,
- 0.990012,
- 0.064105,
- 0.182287,
- 0.748683,
- 0.346960,
- 0.361819,
- 1.338132,
- 2.139501,
- 0.578987,
- 2.000679,
- 0.425860,
- 1.143480,
- 1.080136,
- 0.604545,
- 0.129836,
- 0.584262,
- 1.033739,
- 0.302936,
- 1.136863,
- 2.020366,
- 0.165001,
- 0.571468,
- 6.472279,
- 0.180717,
- 0.593607,
- 0.045376,
- 0.029890,
- 0.670128,
- 0.236199,
- 0.077852,
- 0.268491,
- 0.597054,
- 0.111660,
- 0.619632,
- 0.049906,
- 0.696175,
- 2.457121,
- 0.095131,
- 0.248862,
- 0.140825,
- 0.218959,
- 0.314440,
- 0.612025,
- 0.135107,
- 1.165532,
- 0.257336,
- 0.120037,
- 0.054679,
- 5.306834,
- 0.232523,
- 0.299648,
- 0.131932,
- 0.481306,
- 7.803902,
- 0.089613,
- 0.400547,
- 0.245841,
- 3.151815,
- 2.547870,
- 0.170887,
- 0.083688,
- 0.037967,
- 1.959291,
- 0.210332,
- 0.245034,
- 0.076701,
- 0.119013,
- 10.649107,
- 1.702745,
- 0.185202,
- 1.898718,
- 0.654683,
- 0.296501,
- 0.098369,
- 2.188158,
- 0.189510,
- 0.249313
- ]
-
--- Exchangeabilities of LG model in alphabetical order.
-lgExch :: ExchangeabilityMatrix
-lgExch = pamlToAlphaMat $ exchFromListLower n lgExchRawPaml
-
-normalizeSumVec :: Vector Double -> Vector Double
-normalizeSumVec v = V.map (/ s) v
- where
- s = V.sum v
-{-# INLINE normalizeSumVec #-}
-
--- Stationary distribution in PAML order.
-lgStatDistPaml :: StationaryDistribution
-lgStatDistPaml =
- normalizeSumVec $
- fromList
- [ 0.079066,
- 0.055941,
- 0.041977,
- 0.053052,
- 0.012937,
- 0.040767,
- 0.071586,
- 0.057337,
- 0.022355,
- 0.062157,
- 0.099081,
- 0.064600,
- 0.022951,
- 0.042302,
- 0.044040,
- 0.061197,
- 0.053287,
- 0.012066,
- 0.034155,
- 0.069147
- ]
-
--- Stationary distribution of LG model in alphabetical order.
-lgStatDist :: StationaryDistribution
-lgStatDist = pamlToAlphaVec lgStatDistPaml
-
--- | LG substitution model.
-lg :: SubstitutionModel
-lg = substitutionModel Protein "LG" [] lgStatDist lgExch
-
--- | LG substitution model with maybe a name and a custom stationary distribution.
-lgCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
-lgCustom mnm d = substitutionModel Protein nm [] d lgExch
- where
- nm = fromMaybe "LG-Custom" mnm
-
--- WAG exchangeability list in PAML order.
-wagExchRawPaml :: [Double]
-wagExchRawPaml =
- [ 55.15710,
- 50.98480,
- 63.53460,
- 73.89980,
- 14.73040,
- 542.94200,
- 102.70400,
- 52.81910,
- 26.52560,
- 3.02949,
- 90.85980,
- 303.55000,
- 154.36400,
- 61.67830,
- 9.88179,
- 158.28500,
- 43.91570,
- 94.71980,
- 617.41600,
- 2.13520,
- 546.94700,
- 141.67200,
- 58.46650,
- 112.55600,
- 86.55840,
- 30.66740,
- 33.00520,
- 56.77170,
- 31.69540,
- 213.71500,
- 395.62900,
- 93.06760,
- 24.89720,
- 429.41100,
- 57.00250,
- 24.94100,
- 19.33350,
- 18.69790,
- 55.42360,
- 3.94370,
- 17.01350,
- 11.39170,
- 12.73950,
- 3.04501,
- 13.81900,
- 39.79150,
- 49.76710,
- 13.15280,
- 8.48047,
- 38.42870,
- 86.94890,
- 15.42630,
- 6.13037,
- 49.94620,
- 317.09700,
- 90.62650,
- 535.14200,
- 301.20100,
- 47.98550,
- 7.40339,
- 389.49000,
- 258.44300,
- 37.35580,
- 89.04320,
- 32.38320,
- 25.75550,
- 89.34960,
- 68.31620,
- 19.82210,
- 10.37540,
- 39.04820,
- 154.52600,
- 31.51240,
- 17.41000,
- 40.41410,
- 425.74600,
- 485.40200,
- 93.42760,
- 21.04940,
- 10.27110,
- 9.61621,
- 4.67304,
- 39.80200,
- 9.99208,
- 8.11339,
- 4.99310,
- 67.93710,
- 105.94700,
- 211.51700,
- 8.88360,
- 119.06300,
- 143.85500,
- 67.94890,
- 19.50810,
- 42.39840,
- 10.94040,
- 93.33720,
- 68.23550,
- 24.35700,
- 69.61980,
- 9.99288,
- 41.58440,
- 55.68960,
- 17.13290,
- 16.14440,
- 337.07900,
- 122.41900,
- 397.42300,
- 107.17600,
- 140.76600,
- 102.88700,
- 70.49390,
- 134.18200,
- 74.01690,
- 31.94400,
- 34.47390,
- 96.71300,
- 49.39050,
- 54.59310,
- 161.32800,
- 212.11100,
- 55.44130,
- 203.00600,
- 37.48660,
- 51.29840,
- 85.79280,
- 82.27650,
- 22.58330,
- 47.33070,
- 145.81600,
- 32.66220,
- 138.69800,
- 151.61200,
- 17.19030,
- 79.53840,
- 437.80200,
- 11.31330,
- 116.39200,
- 7.19167,
- 12.97670,
- 71.70700,
- 21.57370,
- 15.65570,
- 33.69830,
- 26.25690,
- 21.24830,
- 66.53090,
- 13.75050,
- 51.57060,
- 152.96400,
- 13.94050,
- 52.37420,
- 11.08640,
- 24.07350,
- 38.15330,
- 108.60000,
- 32.57110,
- 54.38330,
- 22.77100,
- 19.63030,
- 10.36040,
- 387.34400,
- 42.01700,
- 39.86180,
- 13.32640,
- 42.84370,
- 645.42800,
- 21.60460,
- 78.69930,
- 29.11480,
- 248.53900,
- 200.60100,
- 25.18490,
- 19.62460,
- 15.23350,
- 100.21400,
- 30.12810,
- 58.87310,
- 18.72470,
- 11.83580,
- 782.13000,
- 180.03400,
- 30.54340,
- 205.84500,
- 64.98920,
- 31.48870,
- 23.27390,
- 138.82300,
- 36.53690,
- 31.47300
- ]
-
--- WAG exchangeability matrix n alphabetical order.
-wagExch :: ExchangeabilityMatrix
-wagExch = pamlToAlphaMat $ exchFromListLower n wagExchRawPaml
-
--- WAG stationary distribution in PAML order.
-wagStatDistPaml :: StationaryDistribution
-wagStatDistPaml =
- normalizeSumVec $
- fromList
- [ 0.0866279,
- 0.043972,
- 0.0390894,
- 0.0570451,
- 0.0193078,
- 0.0367281,
- 0.0580589,
- 0.0832518,
- 0.0244313,
- 0.048466,
- 0.086209,
- 0.0620286,
- 0.0195027,
- 0.0384319,
- 0.0457631,
- 0.0695179,
- 0.0610127,
- 0.0143859,
- 0.0352742,
- 0.0708957
- ]
-
--- WAG stationary distribution in alphabetical order.
-wagStatDist :: StationaryDistribution
-wagStatDist = pamlToAlphaVec wagStatDistPaml
-
--- | LG substitution model.
-wag :: SubstitutionModel
-wag = substitutionModel Protein "WAG" [] wagStatDist wagExch
-
--- | LG substitution model with maybe a name and a custom stationary distribution.
-wagCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
-wagCustom mnm d = substitutionModel Protein nm [] d wagExch
- where
- nm = fromMaybe "WAG-Custom" mnm
-
-matrixSetDiagToZero :: Matrix R -> Matrix R
-matrixSetDiagToZero m = m - diag (takeDiag m)
-{-# INLINE matrixSetDiagToZero #-}
-
-uniformExch :: ExchangeabilityMatrix
-uniformExch = matrixSetDiagToZero $ matrix n $ replicate (n * n) 1.0
-
-poissonExch :: ExchangeabilityMatrix
-poissonExch = uniformExch
-
-uniformVec :: Vector Double
-uniformVec = V.replicate n (1 / fromIntegral n)
-
--- | Poisson substitution model.
-poisson :: SubstitutionModel
-poisson = substitutionModel Protein "Poisson" [] uniformVec poissonExch
-
--- | Poisson substitution model with maybe a name and a custom stationary distribution.
-poissonCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
-poissonCustom mnm d = substitutionModel Protein nm [] d poissonExch
- where
- nm = fromMaybe "Poisson-Custom" mnm
-
--- | General time reversible (GTR) substitution model for amino acids.
-gtr20 :: [Double] -> StationaryDistribution -> SubstitutionModel
-gtr20 es d = substitutionModel Protein "GTR" es d e
- where
- e = exchFromListUpper n es
diff --git a/src/ELynx/Data/MarkovProcess/CXXModels.hs b/src/ELynx/Data/MarkovProcess/CXXModels.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/CXXModels.hs
+++ /dev/null
@@ -1,146 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.CXXModels
--- Description : C10 to C60 models
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Feb 26 16:44:33 2019.
---
--- Quang, BL. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
--- phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
---
--- XXX: For now, I only provide Poisson exchangeabilities.
-module ELynx.Data.MarkovProcess.CXXModels
- ( cxx,
- )
-where
-
-import qualified Data.Vector as V
-import ELynx.Data.MarkovProcess.AminoAcid
-import ELynx.Data.MarkovProcess.CXXModelsData
-import qualified ELynx.Data.MarkovProcess.MixtureModel as M
-import ELynx.Data.MarkovProcess.RateMatrix
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-
--- | Create CXX model with given number of components and probably with custom
--- weights.
-cxx :: Int -> Maybe [M.Weight] -> M.MixtureModel
-cxx 10 (Just ws) = c10CustomWeights ws
-cxx 20 (Just ws) = c20CustomWeights ws
-cxx 30 (Just ws) = c30CustomWeights ws
-cxx 40 (Just ws) = c40CustomWeights ws
-cxx 50 (Just ws) = c50CustomWeights ws
-cxx 60 (Just ws) = c60CustomWeights ws
-cxx 10 Nothing = c10
-cxx 20 Nothing = c20
-cxx 30 Nothing = c30
-cxx 40 Nothing = c40
-cxx 50 Nothing = c50
-cxx 60 Nothing = c60
-cxx n _ =
- error $ "cxx: cannot create CXX model with " ++ show n ++ " components."
-
--- | C10 model.
-c10 :: M.MixtureModel
-c10 = cxxFromStatDistsAndWeights c10Weights c10StatDists
-
--- | C20 model.
-c20 :: M.MixtureModel
-c20 = cxxFromStatDistsAndWeights c20Weights c20StatDists
-
--- | C30 model.
-c30 :: M.MixtureModel
-c30 = cxxFromStatDistsAndWeights c30Weights c30StatDists
-
--- | C40 model.
-c40 :: M.MixtureModel
-c40 = cxxFromStatDistsAndWeights c40Weights c40StatDists
-
--- | C50 model.
-c50 :: M.MixtureModel
-c50 = cxxFromStatDistsAndWeights c50Weights c50StatDists
-
--- | C60 model.
-c60 :: M.MixtureModel
-c60 = cxxFromStatDistsAndWeights c60Weights c60StatDists
-
--- | C10 model with custom weights.
-c10CustomWeights :: [M.Weight] -> M.MixtureModel
-c10CustomWeights ws
- | length ws == 10 = cxxFromStatDistsAndWeights ws c10StatDists
- | otherwise = error "Number of weights does not match C10 model."
-
--- | C20 model with custom weights.
-c20CustomWeights :: [M.Weight] -> M.MixtureModel
-c20CustomWeights ws
- | length ws == 20 = cxxFromStatDistsAndWeights ws c20StatDists
- | otherwise = error "Number of weights does not match C20 model."
-
--- | C30 model with custom weights.
-c30CustomWeights :: [M.Weight] -> M.MixtureModel
-c30CustomWeights ws
- | length ws == 30 = cxxFromStatDistsAndWeights ws c30StatDists
- | otherwise = error "Number of weights does not match C30 model."
-
--- | C40 model with custom weights.
-c40CustomWeights :: [M.Weight] -> M.MixtureModel
-c40CustomWeights ws
- | length ws == 40 = cxxFromStatDistsAndWeights ws c40StatDists
- | otherwise = error "Number of weights does not match C40 model."
-
--- | C50 model with custom weights.
-c50CustomWeights :: [M.Weight] -> M.MixtureModel
-c50CustomWeights ws
- | length ws == 50 = cxxFromStatDistsAndWeights ws c50StatDists
- | otherwise = error "Number of weights does not match C50 model."
-
--- | C60 model with custom weights.
-c60CustomWeights :: [M.Weight] -> M.MixtureModel
-c60CustomWeights ws
- | length ws == 60 = cxxFromStatDistsAndWeights ws c60StatDists
- | otherwise = error "Number of weights does not match C60 model."
-
-cxxName :: Int -> String
-cxxName nComps = 'C' : show nComps
-
-componentName :: Int -> Int -> String
-componentName nComps comp = cxxName nComps ++ "; component " ++ show comp
-
--- Keep in mind, that when using different exchangeabilities, I have to decide
--- about global or local normalization.
-cxxSubstitutionModelFromStatDist ::
- Int -> Int -> StationaryDistribution -> S.SubstitutionModel
-cxxSubstitutionModelFromStatDist nComps comp d =
- poissonCustom
- (Just name)
- (normalizeSD d)
- where
- name = componentName nComps comp
-
-cxxSubstitutionModelsFromStatDists ::
- [StationaryDistribution] -> [S.SubstitutionModel]
-cxxSubstitutionModelsFromStatDists ds =
- zipWith
- (cxxSubstitutionModelFromStatDist nComp)
- [1 ..]
- ds
- where
- nComp = length ds
-
--- XXX: The use of `Data.List.NonEmpty.fromList` is daring, but since this
--- function is not exported and only applied to predefined non-empty lists, it
--- should be OK.
-cxxFromStatDistsAndWeights ::
- [M.Weight] -> [StationaryDistribution] -> M.MixtureModel
-cxxFromStatDistsAndWeights ws ds =
- M.fromSubstitutionModels
- (cxxName n)
- (V.fromList ws)
- sms
- where
- n = length ds
- sms = V.fromList $ cxxSubstitutionModelsFromStatDists ds
diff --git a/src/ELynx/Data/MarkovProcess/CXXModelsData.hs b/src/ELynx/Data/MarkovProcess/CXXModelsData.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/CXXModelsData.hs
+++ /dev/null
@@ -1,4724 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.CXXModelsData
--- Description : Stationary distributions and weights
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Feb 26 17:17:35 2019.
---
--- Quang, BL. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
--- phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
-module ELynx.Data.MarkovProcess.CXXModelsData
- ( c10StatDists,
- c10Weights,
- c20StatDists,
- c20Weights,
- c30StatDists,
- c30Weights,
- c40StatDists,
- c40Weights,
- c50StatDists,
- c50Weights,
- c60StatDists,
- c60Weights,
- )
-where
-
-import qualified Data.Vector.Storable as V
-import ELynx.Data.MarkovProcess.RateMatrix
-
--- | Stationary distribution of C10 model.
-c10StatDists :: [StationaryDistribution]
-c10StatDists =
- map
- V.fromList
- [ [ 0.408257,
- 0.0349388,
- 0.00698709,
- 0.00978467,
- 0.00616043,
- 0.122161,
- 0.00391518,
- 0.0125784,
- 0.00596702,
- 0.0158339,
- 0.00813132,
- 0.00962854,
- 0.0394156,
- 0.00752797,
- 0.0081783,
- 0.168245,
- 0.0658133,
- 0.0604427,
- 0.00187516,
- 0.00415797
- ],
- [ 0.102776,
- 0.0149663,
- 0.0155944,
- 0.0419667,
- 0.0180729,
- 0.0138806,
- 0.0158865,
- 0.106608,
- 0.0436344,
- 0.113194,
- 0.04378,
- 0.0213272,
- 0.0223251,
- 0.0440685,
- 0.0418664,
- 0.0529608,
- 0.108174,
- 0.160665,
- 0.00451472,
- 0.0137374
- ],
- [ 0.0351766,
- 0.00787065,
- 0.000676874,
- 0.00196868,
- 0.0126221,
- 0.00224206,
- 0.00128783,
- 0.351582,
- 0.00188565,
- 0.127818,
- 0.0242632,
- 0.00165915,
- 0.00297716,
- 0.00165596,
- 0.00196786,
- 0.00499981,
- 0.0255378,
- 0.388864,
- 0.00119078,
- 0.00375393
- ],
- [ 0.0408514,
- 0.00376029,
- 0.233381,
- 0.0901239,
- 0.00251082,
- 0.115833,
- 0.0373197,
- 0.00255236,
- 0.0485017,
- 0.00521646,
- 0.00225718,
- 0.218565,
- 0.0108334,
- 0.0380451,
- 0.0269887,
- 0.0804527,
- 0.030288,
- 0.00444811,
- 0.00108153,
- 0.00698909
- ],
- [ 0.0185493,
- 0.00704165,
- 0.000977506,
- 0.00248916,
- 0.073333,
- 0.00289529,
- 0.0040104,
- 0.163242,
- 0.00435709,
- 0.444308,
- 0.120282,
- 0.00248957,
- 0.00488276,
- 0.00835394,
- 0.00623624,
- 0.00516424,
- 0.0131807,
- 0.0968581,
- 0.00687598,
- 0.0144734
- ],
- [ 0.110675,
- 0.00148349,
- 0.163644,
- 0.263846,
- 0.00232568,
- 0.0325228,
- 0.0163804,
- 0.00683349,
- 0.0677158,
- 0.014068,
- 0.00489881,
- 0.0405186,
- 0.0298982,
- 0.0877962,
- 0.035219,
- 0.0562888,
- 0.0426922,
- 0.0181079,
- 0.0010339,
- 0.00405223
- ],
- [ 0.0522658,
- 0.0143325,
- 0.0297745,
- 0.0388387,
- 0.0624033,
- 0.0228101,
- 0.155164,
- 0.0187406,
- 0.0439469,
- 0.065378,
- 0.0207189,
- 0.0714837,
- 0.0145475,
- 0.073654,
- 0.0668295,
- 0.0549018,
- 0.037014,
- 0.0267512,
- 0.0193757,
- 0.111069
- ],
- [ 0.0116587,
- 0.0105341,
- 0.00217425,
- 0.00242511,
- 0.365099,
- 0.00347091,
- 0.0366787,
- 0.0187185,
- 0.00266947,
- 0.067649,
- 0.0143535,
- 0.00640111,
- 0.00311599,
- 0.00402037,
- 0.00509901,
- 0.00948485,
- 0.00737139,
- 0.0206341,
- 0.0509565,
- 0.357486
- ],
- [ 0.0627196,
- 0.00526629,
- 0.0236193,
- 0.0686285,
- 0.00391818,
- 0.0256175,
- 0.0332612,
- 0.0128968,
- 0.227084,
- 0.0305628,
- 0.0124037,
- 0.0428629,
- 0.0140441,
- 0.109811,
- 0.203878,
- 0.0483152,
- 0.0463378,
- 0.0197063,
- 0.00251435,
- 0.00655211
- ],
- [ 0.114552,
- 0.00985495,
- 0.0416192,
- 0.0364908,
- 0.0046606,
- 0.0503818,
- 0.0165233,
- 0.00929495,
- 0.0423027,
- 0.0139154,
- 0.00822408,
- 0.0750615,
- 0.0379222,
- 0.0339625,
- 0.0324009,
- 0.261065,
- 0.184583,
- 0.0195769,
- 0.0017549,
- 0.00585383
- ]
- ]
-
--- | Weights of C10 model.
-c10Weights :: [Double]
-c10Weights =
- [ 0.119134,
- 0.0874372,
- 0.103711,
- 0.0922585,
- 0.107049,
- 0.132995,
- 0.0538028,
- 0.0691986,
- 0.131994,
- 0.10242
- ]
-
--- | Stationary distribution of C20 model.
-c20StatDists :: [StationaryDistribution]
-c20StatDists =
- map
- V.fromList
- [ [ 0.0862413,
- 0.0130505,
- 0.0329909,
- 0.0184527,
- 0.00441553,
- 0.0366905,
- 0.0108013,
- 0.00979071,
- 0.0220195,
- 0.0112826,
- 0.00878215,
- 0.0791293,
- 0.0189273,
- 0.0169047,
- 0.0171944,
- 0.317815,
- 0.27117,
- 0.0179753,
- 0.00153173,
- 0.00483429
- ],
- [ 0.203558,
- 0.0348667,
- 0.00316561,
- 0.00708594,
- 0.0112429,
- 0.0195236,
- 0.0024392,
- 0.115257,
- 0.00423808,
- 0.0789777,
- 0.0309187,
- 0.00770524,
- 0.0164189,
- 0.00640441,
- 0.00509808,
- 0.0496777,
- 0.111895,
- 0.284906,
- 0.00177626,
- 0.00484482
- ],
- [ 0.0211547,
- 0.00481886,
- 0.000549287,
- 0.00145396,
- 0.0128252,
- 0.00114309,
- 0.00113464,
- 0.392846,
- 0.00135799,
- 0.125064,
- 0.0209789,
- 0.0012755,
- 0.00202472,
- 0.00123288,
- 0.00149462,
- 0.00262407,
- 0.0171914,
- 0.386068,
- 0.00115911,
- 0.0036028
- ],
- [ 0.0376904,
- 0.00640738,
- 0.0109469,
- 0.0358365,
- 0.00363498,
- 0.0191107,
- 0.0329514,
- 0.0101712,
- 0.289763,
- 0.0237496,
- 0.00965289,
- 0.0365411,
- 0.0105337,
- 0.0893564,
- 0.28852,
- 0.0356314,
- 0.0355927,
- 0.0144622,
- 0.00279252,
- 0.00665572
- ],
- [ 0.00845978,
- 0.0084909,
- 0.00244879,
- 0.00250555,
- 0.342046,
- 0.00242771,
- 0.0433214,
- 0.0097713,
- 0.0026741,
- 0.0380507,
- 0.00807248,
- 0.00725259,
- 0.00214187,
- 0.00427815,
- 0.00535899,
- 0.00804189,
- 0.00553221,
- 0.012141,
- 0.049484,
- 0.4375
- ],
- [ 0.17599,
- 0.00175587,
- 0.130126,
- 0.218217,
- 0.0025277,
- 0.0409535,
- 0.0130708,
- 0.00856221,
- 0.0542946,
- 0.0159531,
- 0.00540458,
- 0.0332846,
- 0.037102,
- 0.0707184,
- 0.0290429,
- 0.0793481,
- 0.0540083,
- 0.0249553,
- 0.00105921,
- 0.00362591
- ],
- [ 0.16344,
- 0.00886599,
- 0.0374273,
- 0.0220612,
- 0.00306413,
- 0.529672,
- 0.00900061,
- 0.00175694,
- 0.0167118,
- 0.00611563,
- 0.00293908,
- 0.0438702,
- 0.0126458,
- 0.0137555,
- 0.0195541,
- 0.0829343,
- 0.0142836,
- 0.00579857,
- 0.00286407,
- 0.00323983
- ],
- [ 0.0917469,
- 0.0284015,
- 0.0133819,
- 0.0196876,
- 0.0998479,
- 0.0249899,
- 0.0449766,
- 0.0583556,
- 0.0164916,
- 0.115501,
- 0.0395995,
- 0.0290699,
- 0.0209916,
- 0.0255085,
- 0.0265853,
- 0.0736483,
- 0.0661518,
- 0.0831856,
- 0.0246464,
- 0.0972327
- ],
- [ 0.0646701,
- 0.00771176,
- 0.0168734,
- 0.0544978,
- 0.0219148,
- 0.0148894,
- 0.0313852,
- 0.0505983,
- 0.0907931,
- 0.184428,
- 0.077484,
- 0.0228907,
- 0.0105004,
- 0.0996415,
- 0.0988016,
- 0.0321196,
- 0.0411766,
- 0.0505824,
- 0.0084303,
- 0.0206106
- ],
- [ 0.0135994,
- 0.010009,
- 0.00079517,
- 0.00180118,
- 0.264097,
- 0.00267946,
- 0.00724019,
- 0.0814027,
- 0.00251581,
- 0.366142,
- 0.0734965,
- 0.00184694,
- 0.00389941,
- 0.00464208,
- 0.00434084,
- 0.00436688,
- 0.00752485,
- 0.0573473,
- 0.0261565,
- 0.0660971
- ],
- [ 0.147804,
- 0.00488258,
- 0.0534743,
- 0.0727246,
- 0.00299039,
- 0.0907726,
- 0.0262289,
- 0.00357811,
- 0.105166,
- 0.0126777,
- 0.00596218,
- 0.072663,
- 0.0156558,
- 0.0757166,
- 0.0842845,
- 0.14599,
- 0.0634877,
- 0.00927198,
- 0.00159285,
- 0.00507607
- ],
- [ 0.0186377,
- 0.00549689,
- 0.00083297,
- 0.00202485,
- 0.0385383,
- 0.00217135,
- 0.0023666,
- 0.202081,
- 0.00291207,
- 0.437038,
- 0.124186,
- 0.00198652,
- 0.00406723,
- 0.00658901,
- 0.00420552,
- 0.00461774,
- 0.0149904,
- 0.118938,
- 0.00268717,
- 0.00563241
- ],
- [ 0.0477624,
- 0.00757917,
- 0.0141349,
- 0.0462688,
- 0.0130691,
- 0.00523279,
- 0.0165352,
- 0.17415,
- 0.0577575,
- 0.112125,
- 0.0330288,
- 0.0209574,
- 0.0124375,
- 0.0429297,
- 0.0505743,
- 0.0264989,
- 0.0951755,
- 0.20937,
- 0.00316605,
- 0.0112466
- ],
- [ 0.416419,
- 0.0406938,
- 0.00451317,
- 0.00632298,
- 0.00484384,
- 0.0946185,
- 0.00310574,
- 0.00764432,
- 0.00389418,
- 0.00998854,
- 0.00693232,
- 0.00917014,
- 0.0187841,
- 0.00613205,
- 0.00561008,
- 0.236077,
- 0.0746275,
- 0.0459225,
- 0.00121726,
- 0.00348258
- ],
- [ 0.0402296,
- 0.0124783,
- 0.0365524,
- 0.0372197,
- 0.0459095,
- 0.0233618,
- 0.210831,
- 0.00934787,
- 0.0482411,
- 0.0360561,
- 0.010029,
- 0.103665,
- 0.0098504,
- 0.0826558,
- 0.0735203,
- 0.0533383,
- 0.0310209,
- 0.015248,
- 0.0140077,
- 0.106438
- ],
- [ 0.0323453,
- 0.00359763,
- 0.24315,
- 0.0710274,
- 0.00244293,
- 0.101607,
- 0.0366225,
- 0.00314108,
- 0.0470129,
- 0.00519805,
- 0.00240287,
- 0.252045,
- 0.00948378,
- 0.0330831,
- 0.0236283,
- 0.0848355,
- 0.0359083,
- 0.00487046,
- 0.000873093,
- 0.00672477
- ],
- [ 0.147626,
- 0.00323272,
- 0.0403052,
- 0.0576893,
- 0.00471772,
- 0.0330851,
- 0.0146393,
- 0.0108267,
- 0.0451351,
- 0.0256201,
- 0.00586514,
- 0.0211973,
- 0.347371,
- 0.0371554,
- 0.0334507,
- 0.0892065,
- 0.0485899,
- 0.0282336,
- 0.00163587,
- 0.00441772
- ],
- [ 0.103145,
- 0.00617625,
- 0.0386402,
- 0.0923369,
- 0.00676664,
- 0.0202338,
- 0.0246762,
- 0.0376904,
- 0.0921699,
- 0.0376284,
- 0.0161883,
- 0.0435172,
- 0.0128302,
- 0.0786603,
- 0.0717748,
- 0.095145,
- 0.137857,
- 0.0740454,
- 0.00221447,
- 0.00830416
- ],
- [ 0.0837543,
- 0.00207351,
- 0.0804871,
- 0.194776,
- 0.00230634,
- 0.022903,
- 0.0268459,
- 0.00740798,
- 0.145929,
- 0.019025,
- 0.00673952,
- 0.0518811,
- 0.0085616,
- 0.14565,
- 0.0899383,
- 0.045574,
- 0.0451081,
- 0.0150303,
- 0.00107713,
- 0.00493253
- ],
- [ 0.0578736,
- 0.00111308,
- 0.294674,
- 0.34021,
- 0.00170349,
- 0.0293911,
- 0.0139817,
- 0.00305257,
- 0.0363365,
- 0.00626119,
- 0.0027296,
- 0.0491422,
- 0.0156106,
- 0.059825,
- 0.0138314,
- 0.0358045,
- 0.0249942,
- 0.00876742,
- 0.000866434,
- 0.0038313
- ]
- ]
-
--- | Weights of C20 model.
-c20Weights :: [Double]
-c20Weights =
- [ 0.0559911,
- 0.0514825,
- 0.0812922,
- 0.0721977,
- 0.0556719,
- 0.0331003,
- 0.0589502,
- 0.0263757,
- 0.0307584,
- 0.0376701,
- 0.0303058,
- 0.0808776,
- 0.0263349,
- 0.0579101,
- 0.0371248,
- 0.0586868,
- 0.0561479,
- 0.0349811,
- 0.0544937,
- 0.0596472
- ]
-
--- | Stationary distribution of C30 model.
-c30StatDists :: [StationaryDistribution]
-c30StatDists =
- map
- V.fromList
- [ [ 0.110045,
- 0.00190472,
- 0.159541,
- 0.109896,
- 0.00166295,
- 0.0684302,
- 0.0137951,
- 0.00262831,
- 0.0358554,
- 0.00733965,
- 0.00247064,
- 0.0640338,
- 0.166936,
- 0.0310187,
- 0.0171295,
- 0.138179,
- 0.0568343,
- 0.00823656,
- 0.000466112,
- 0.00359702
- ],
- [ 0.0874125,
- 0.00498264,
- 0.032612,
- 0.0951701,
- 0.00489966,
- 0.0144043,
- 0.0210627,
- 0.0399884,
- 0.11472,
- 0.0301585,
- 0.0126489,
- 0.0382152,
- 0.0137397,
- 0.0798169,
- 0.080632,
- 0.087377,
- 0.155862,
- 0.0793881,
- 0.00151228,
- 0.00539745
- ],
- [ 0.0225477,
- 0.00500182,
- 0.000595928,
- 0.00150305,
- 0.0089216,
- 0.0011571,
- 0.000937432,
- 0.394469,
- 0.00136009,
- 0.0889573,
- 0.0189103,
- 0.00130346,
- 0.0018312,
- 0.00114366,
- 0.00149005,
- 0.00283364,
- 0.0189813,
- 0.425056,
- 0.000669375,
- 0.00233037
- ],
- [ 0.0602158,
- 0.000952546,
- 0.290008,
- 0.361087,
- 0.00146256,
- 0.0281926,
- 0.0130501,
- 0.00305162,
- 0.0352705,
- 0.00604019,
- 0.00274606,
- 0.0414988,
- 0.0127175,
- 0.0621611,
- 0.0136833,
- 0.0318109,
- 0.022528,
- 0.00932584,
- 0.000794803,
- 0.00340246
- ],
- [ 0.0101224,
- 0.00859894,
- 0.000637919,
- 0.00112496,
- 0.278538,
- 0.00240852,
- 0.00477534,
- 0.0701153,
- 0.00167485,
- 0.413591,
- 0.0744863,
- 0.00129289,
- 0.00404666,
- 0.00350286,
- 0.00283449,
- 0.00370872,
- 0.00523793,
- 0.040886,
- 0.0200223,
- 0.0523939
- ],
- [ 0.133583,
- 0.00105145,
- 0.112578,
- 0.209957,
- 0.00167936,
- 0.0207552,
- 0.012133,
- 0.00735265,
- 0.0771772,
- 0.0133278,
- 0.00305717,
- 0.0213892,
- 0.18902,
- 0.0565844,
- 0.028479,
- 0.0484054,
- 0.0373318,
- 0.0225174,
- 0.000926699,
- 0.00269464
- ],
- [ 0.0408277,
- 0.0153918,
- 0.00306349,
- 0.00660109,
- 0.157505,
- 0.00581131,
- 0.0245212,
- 0.148751,
- 0.00759232,
- 0.16378,
- 0.0385527,
- 0.00804649,
- 0.00583522,
- 0.0102922,
- 0.0124492,
- 0.0151579,
- 0.033222,
- 0.154771,
- 0.0264937,
- 0.121334
- ],
- [ 0.246906,
- 0.103941,
- 0.00274183,
- 0.00549448,
- 0.0251776,
- 0.0373263,
- 0.00857523,
- 0.0292404,
- 0.00561231,
- 0.0535091,
- 0.0302246,
- 0.016893,
- 0.00780989,
- 0.0103988,
- 0.0106279,
- 0.164235,
- 0.123989,
- 0.0955868,
- 0.00531559,
- 0.0163954
- ],
- [ 0.0549429,
- 0.0099281,
- 0.00929153,
- 0.0417085,
- 0.024386,
- 0.0105564,
- 0.0363512,
- 0.0569585,
- 0.115252,
- 0.168183,
- 0.0592328,
- 0.0202958,
- 0.00830554,
- 0.0906036,
- 0.130543,
- 0.0283779,
- 0.0412594,
- 0.0592101,
- 0.00963554,
- 0.024978
- ],
- [ 0.0462773,
- 0.0172727,
- 0.0182504,
- 0.0224266,
- 0.133632,
- 0.0160971,
- 0.135785,
- 0.0164967,
- 0.0239396,
- 0.0598936,
- 0.0164507,
- 0.0412365,
- 0.0117413,
- 0.0348991,
- 0.0362984,
- 0.0454156,
- 0.0304388,
- 0.0253979,
- 0.0330338,
- 0.235016
- ],
- [ 0.047438,
- 0.00823324,
- 0.0112117,
- 0.0388101,
- 0.0116644,
- 0.00559986,
- 0.0149157,
- 0.183217,
- 0.0467851,
- 0.110069,
- 0.0356444,
- 0.0222454,
- 0.0100245,
- 0.0374051,
- 0.041018,
- 0.0317171,
- 0.111435,
- 0.219931,
- 0.00266856,
- 0.00996601
- ],
- [ 0.0213608,
- 0.00610249,
- 0.00129412,
- 0.00362973,
- 0.0371808,
- 0.0030017,
- 0.00384259,
- 0.130947,
- 0.00545678,
- 0.456699,
- 0.194784,
- 0.0039879,
- 0.00407473,
- 0.0139566,
- 0.00699762,
- 0.00769915,
- 0.0198019,
- 0.0693208,
- 0.00340864,
- 0.00645457
- ],
- [ 0.0919632,
- 0.0117031,
- 0.0306717,
- 0.0171908,
- 0.00415894,
- 0.0370685,
- 0.0100793,
- 0.00931237,
- 0.0205386,
- 0.0097241,
- 0.00757673,
- 0.0764682,
- 0.0179686,
- 0.016006,
- 0.0160005,
- 0.325447,
- 0.274438,
- 0.0178218,
- 0.00138874,
- 0.00447397
- ],
- [ 0.464925,
- 0.0233329,
- 0.00507317,
- 0.00579942,
- 0.00255882,
- 0.149524,
- 0.00232984,
- 0.00433612,
- 0.00285254,
- 0.00559955,
- 0.00393132,
- 0.00753048,
- 0.0186467,
- 0.00435713,
- 0.00430132,
- 0.215019,
- 0.047703,
- 0.0292668,
- 0.00090381,
- 0.00200872
- ],
- [ 0.205133,
- 0.00209159,
- 0.107098,
- 0.198973,
- 0.00182351,
- 0.0487574,
- 0.0127143,
- 0.00581247,
- 0.0667787,
- 0.0133472,
- 0.00437834,
- 0.0339418,
- 0.0110998,
- 0.0822742,
- 0.0439661,
- 0.0873962,
- 0.0519782,
- 0.0193174,
- 0.00073616,
- 0.00238214
- ],
- [ 0.026369,
- 0.00394624,
- 0.311772,
- 0.0694354,
- 0.00233519,
- 0.0799842,
- 0.0309615,
- 0.00275212,
- 0.0288631,
- 0.00385797,
- 0.00183637,
- 0.272716,
- 0.00624576,
- 0.0218979,
- 0.0133614,
- 0.0798729,
- 0.0324143,
- 0.00427053,
- 0.000722966,
- 0.00638577
- ],
- [ 0.15265,
- 0.00402153,
- 0.0237392,
- 0.0377949,
- 0.00585844,
- 0.0306214,
- 0.014193,
- 0.0123318,
- 0.0375543,
- 0.0290062,
- 0.00644732,
- 0.016823,
- 0.38645,
- 0.0341734,
- 0.0332784,
- 0.0880336,
- 0.0489543,
- 0.0313553,
- 0.00182526,
- 0.00488778
- ],
- [ 0.00802476,
- 0.00234121,
- 0.000338596,
- 0.000781895,
- 0.0311968,
- 0.000540383,
- 0.00100264,
- 0.317706,
- 0.00125983,
- 0.373789,
- 0.0488212,
- 0.00063274,
- 0.00206875,
- 0.00155079,
- 0.00174086,
- 0.00120951,
- 0.00656968,
- 0.19446,
- 0.00163092,
- 0.00433436
- ],
- [ 0.059995,
- 0.0016885,
- 0.0889731,
- 0.0962701,
- 0.00118007,
- 0.0588796,
- 0.0327277,
- 0.00214673,
- 0.182586,
- 0.00708764,
- 0.00339794,
- 0.133492,
- 0.0141408,
- 0.0864856,
- 0.100054,
- 0.0779002,
- 0.0448817,
- 0.00422414,
- 0.000624903,
- 0.00326411
- ],
- [ 0.0393521,
- 0.00990719,
- 0.0431198,
- 0.039464,
- 0.0188681,
- 0.0282866,
- 0.209572,
- 0.00761014,
- 0.0596434,
- 0.025834,
- 0.00845867,
- 0.142548,
- 0.00968405,
- 0.101979,
- 0.0838171,
- 0.0624999,
- 0.0347088,
- 0.0127686,
- 0.00546458,
- 0.0564145
- ],
- [ 0.00727155,
- 0.00678525,
- 0.00276038,
- 0.00250694,
- 0.127148,
- 0.00808347,
- 0.0113218,
- 0.00566096,
- 0.00177351,
- 0.03942,
- 0.00798661,
- 0.00197568,
- 0.00410981,
- 0.00433393,
- 0.0140999,
- 0.00522444,
- 0.00430223,
- 0.00942264,
- 0.627357,
- 0.108456
- ],
- [ 0.090707,
- 0.00636999,
- 0.0745873,
- 0.0386802,
- 0.00288592,
- 0.475005,
- 0.016809,
- 0.00147211,
- 0.0343856,
- 0.00551498,
- 0.00246921,
- 0.0860678,
- 0.0112151,
- 0.0259377,
- 0.0290062,
- 0.073111,
- 0.0153706,
- 0.00392819,
- 0.00229148,
- 0.00418607
- ],
- [ 0.00552919,
- 0.00721059,
- 0.00114134,
- 0.000968304,
- 0.374409,
- 0.0016071,
- 0.0325831,
- 0.00829184,
- 0.00138494,
- 0.0353678,
- 0.00744868,
- 0.00460866,
- 0.00133746,
- 0.00226922,
- 0.00246263,
- 0.00574027,
- 0.00372796,
- 0.00988026,
- 0.0330334,
- 0.460998
- ],
- [ 0.244326,
- 0.027388,
- 0.00315909,
- 0.00767156,
- 0.00606194,
- 0.019609,
- 0.00201894,
- 0.101744,
- 0.00454923,
- 0.0468424,
- 0.0201286,
- 0.00624227,
- 0.0185219,
- 0.0053594,
- 0.00453866,
- 0.0497754,
- 0.11708,
- 0.310493,
- 0.000957725,
- 0.00353337
- ],
- [ 0.0863111,
- 0.00244198,
- 0.0600903,
- 0.20361,
- 0.00293931,
- 0.0175221,
- 0.0245245,
- 0.0105994,
- 0.148579,
- 0.027121,
- 0.00958244,
- 0.0313963,
- 0.00682768,
- 0.167235,
- 0.0984812,
- 0.03478,
- 0.0408211,
- 0.0202271,
- 0.00140013,
- 0.00551054
- ],
- [ 0.0643926,
- 0.00231659,
- 0.162821,
- 0.17627,
- 0.00430667,
- 0.0297139,
- 0.0303504,
- 0.0088163,
- 0.072714,
- 0.0148017,
- 0.00567484,
- 0.103121,
- 0.00992703,
- 0.0752535,
- 0.0369049,
- 0.0926434,
- 0.083313,
- 0.0161551,
- 0.00112371,
- 0.00938015
- ],
- [ 0.173668,
- 0.00835966,
- 0.0285985,
- 0.0483894,
- 0.0058274,
- 0.0781901,
- 0.0266135,
- 0.00686419,
- 0.0964012,
- 0.0219499,
- 0.0112303,
- 0.0520405,
- 0.0169661,
- 0.0722447,
- 0.0943629,
- 0.15478,
- 0.0751702,
- 0.0172524,
- 0.00287745,
- 0.00821304
- ],
- [ 0.0347857,
- 0.00627549,
- 0.00923552,
- 0.0323568,
- 0.00343035,
- 0.0170288,
- 0.0306439,
- 0.00919323,
- 0.302085,
- 0.0224429,
- 0.00937208,
- 0.0314157,
- 0.0104447,
- 0.0861073,
- 0.307598,
- 0.0326883,
- 0.0328713,
- 0.0130832,
- 0.00252449,
- 0.00641713
- ],
- [ 0.108774,
- 0.0247877,
- 0.00158232,
- 0.00417699,
- 0.0316523,
- 0.0134703,
- 0.00247658,
- 0.164346,
- 0.00270004,
- 0.233715,
- 0.0539213,
- 0.00326798,
- 0.0154887,
- 0.0057932,
- 0.0051781,
- 0.0188188,
- 0.0474912,
- 0.251283,
- 0.00376565,
- 0.00731064
- ],
- [ 0.110101,
- 0.00726998,
- 0.0579269,
- 0.0828181,
- 0.0269154,
- 0.0314463,
- 0.0308557,
- 0.0530866,
- 0.029386,
- 0.109679,
- 0.0458729,
- 0.0435099,
- 0.0296431,
- 0.0615197,
- 0.0324325,
- 0.0715888,
- 0.0685882,
- 0.0754042,
- 0.00623241,
- 0.0257238
- ]
- ]
-
--- | Weights of C30 model.
-c30Weights :: [Double]
-c30Weights =
- [ 0.00957833,
- 0.0248476,
- 0.0636309,
- 0.0537939,
- 0.0295886,
- 0.0117588,
- 0.0132013,
- 0.0236869,
- 0.0261688,
- 0.0239822,
- 0.0257101,
- 0.0465072,
- 0.0546795,
- 0.0536085,
- 0.0270623,
- 0.0403914,
- 0.0474213,
- 0.0458816,
- 0.0214037,
- 0.0290386,
- 0.0123392,
- 0.056935,
- 0.0419688,
- 0.0339027,
- 0.0388777,
- 0.0196344,
- 0.0233086,
- 0.0622723,
- 0.0184803,
- 0.0203395
- ]
-
--- | Stationary distribution of C40 model.
-c40StatDists :: [StationaryDistribution]
-c40StatDists =
- map
- V.fromList
- [ [ 0.066026,
- 0.00565867,
- 0.105447,
- 0.0440361,
- 0.00131048,
- 0.0711239,
- 0.0168195,
- 0.00390887,
- 0.036669,
- 0.0055316,
- 0.00374124,
- 0.159982,
- 0.0176359,
- 0.0273928,
- 0.0231862,
- 0.249769,
- 0.150708,
- 0.0065529,
- 0.000672321,
- 0.00382902
- ],
- [ 0.0232377,
- 0.00379875,
- 0.353209,
- 0.0739378,
- 0.00240321,
- 0.0576668,
- 0.0315867,
- 0.00310928,
- 0.0259363,
- 0.00387116,
- 0.00173556,
- 0.275965,
- 0.00631169,
- 0.0197339,
- 0.0122683,
- 0.0657068,
- 0.0270484,
- 0.00475317,
- 0.000760289,
- 0.00696025
- ],
- [ 0.0166487,
- 0.00366657,
- 0.000565145,
- 0.00133563,
- 0.00827757,
- 0.000889475,
- 0.000823185,
- 0.412937,
- 0.00119041,
- 0.0884689,
- 0.0186055,
- 0.00126222,
- 0.001403,
- 0.00106698,
- 0.00125948,
- 0.00213394,
- 0.0162167,
- 0.420686,
- 0.000608205,
- 0.00195532
- ],
- [ 0.239474,
- 0.0283812,
- 0.00447417,
- 0.010553,
- 0.00559911,
- 0.013511,
- 0.00389298,
- 0.0765957,
- 0.0071093,
- 0.0358495,
- 0.0199496,
- 0.0120537,
- 0.0114266,
- 0.00865589,
- 0.00729013,
- 0.0847799,
- 0.179728,
- 0.245468,
- 0.0009838,
- 0.00422407
- ],
- [ 0.119461,
- 0.0150527,
- 0.0134273,
- 0.0192173,
- 0.0550467,
- 0.0337676,
- 0.0214746,
- 0.0579002,
- 0.0147261,
- 0.144631,
- 0.0561243,
- 0.0294552,
- 0.0631355,
- 0.0301538,
- 0.0233256,
- 0.0925267,
- 0.083123,
- 0.0811758,
- 0.0131636,
- 0.0331118
- ],
- [ 0.0567044,
- 0.00089248,
- 0.29555,
- 0.379515,
- 0.00129723,
- 0.023047,
- 0.0118361,
- 0.0031182,
- 0.0314206,
- 0.00601375,
- 0.00285841,
- 0.0364734,
- 0.0124746,
- 0.0609517,
- 0.0117359,
- 0.0300335,
- 0.0227051,
- 0.00946396,
- 0.000773876,
- 0.00313438
- ],
- [ 0.0179027,
- 0.016076,
- 0.000887041,
- 0.00231821,
- 0.334486,
- 0.00398298,
- 0.0127293,
- 0.0404651,
- 0.00279947,
- 0.167614,
- 0.0424172,
- 0.00356977,
- 0.00201151,
- 0.00453955,
- 0.00409671,
- 0.00758416,
- 0.00682273,
- 0.0326045,
- 0.0518381,
- 0.245254
- ],
- [ 0.271217,
- 0.200383,
- 0.0021017,
- 0.002323,
- 0.020299,
- 0.0502501,
- 0.0053728,
- 0.0150685,
- 0.00206463,
- 0.0330003,
- 0.0154811,
- 0.0141045,
- 0.0045351,
- 0.00482641,
- 0.00564808,
- 0.17642,
- 0.0839578,
- 0.0741934,
- 0.00462652,
- 0.0141271
- ],
- [ 0.0894737,
- 0.00455383,
- 0.0272183,
- 0.127508,
- 0.00565902,
- 0.0115686,
- 0.0215746,
- 0.0469424,
- 0.138205,
- 0.0512035,
- 0.0147657,
- 0.0190192,
- 0.00955465,
- 0.116809,
- 0.104003,
- 0.0383954,
- 0.0836653,
- 0.0819556,
- 0.00170794,
- 0.00621813
- ],
- [ 0.0495441,
- 0.0182506,
- 0.0143641,
- 0.0215379,
- 0.141805,
- 0.01402,
- 0.110854,
- 0.0247066,
- 0.0258142,
- 0.0700288,
- 0.0188272,
- 0.0315864,
- 0.0112101,
- 0.0316504,
- 0.0375346,
- 0.0456094,
- 0.0361428,
- 0.0369178,
- 0.0371985,
- 0.222397
- ],
- [ 0.170431,
- 0.000974733,
- 0.109856,
- 0.253646,
- 0.00133213,
- 0.0249846,
- 0.010139,
- 0.00587494,
- 0.0903324,
- 0.0116526,
- 0.00365127,
- 0.0271109,
- 0.0293614,
- 0.09173,
- 0.0415784,
- 0.0561766,
- 0.0479046,
- 0.02033,
- 0.000669682,
- 0.00226373
- ],
- [ 0.0162725,
- 0.00506141,
- 0.00101821,
- 0.00251413,
- 0.0376246,
- 0.00219354,
- 0.00299143,
- 0.132817,
- 0.00401204,
- 0.490444,
- 0.192993,
- 0.00218762,
- 0.00343332,
- 0.0104414,
- 0.00548261,
- 0.00401221,
- 0.0127074,
- 0.064772,
- 0.00321076,
- 0.00581006
- ],
- [ 0.0823766,
- 0.00656943,
- 0.0311745,
- 0.0675531,
- 0.00647179,
- 0.0178962,
- 0.0251144,
- 0.0291162,
- 0.0982302,
- 0.0287904,
- 0.0168023,
- 0.059839,
- 0.0114045,
- 0.0686451,
- 0.0734226,
- 0.1303,
- 0.182037,
- 0.0540271,
- 0.00227246,
- 0.00795733
- ],
- [ 0.359497,
- 0.0251417,
- 0.00314844,
- 0.00649627,
- 0.00920205,
- 0.119468,
- 0.00229704,
- 0.0458767,
- 0.00501688,
- 0.0468054,
- 0.0215569,
- 0.00334215,
- 0.0443916,
- 0.00490143,
- 0.00724072,
- 0.0465271,
- 0.0477755,
- 0.194216,
- 0.00245402,
- 0.00464504
- ],
- [ 0.201558,
- 0.00323653,
- 0.095415,
- 0.153491,
- 0.00256433,
- 0.0667292,
- 0.0155219,
- 0.00677408,
- 0.0547323,
- 0.0165114,
- 0.0060163,
- 0.0425386,
- 0.00919706,
- 0.0772011,
- 0.0430162,
- 0.118598,
- 0.0625473,
- 0.0202798,
- 0.000956551,
- 0.003115
- ],
- [ 0.104273,
- 0.00224501,
- 0.242407,
- 0.177482,
- 0.00125703,
- 0.169782,
- 0.0132649,
- 0.00189295,
- 0.0220652,
- 0.00425426,
- 0.00164412,
- 0.0621646,
- 0.0317042,
- 0.0356499,
- 0.0147062,
- 0.0778636,
- 0.0288516,
- 0.00602502,
- 0.00069309,
- 0.00177419
- ],
- [ 0.0781183,
- 0.0194449,
- 0.00415417,
- 0.0116634,
- 0.0262794,
- 0.0111524,
- 0.00635894,
- 0.135453,
- 0.00937298,
- 0.245757,
- 0.108778,
- 0.015927,
- 0.0055294,
- 0.0240152,
- 0.0111498,
- 0.0408519,
- 0.0860514,
- 0.148276,
- 0.00315476,
- 0.00851085
- ],
- [ 0.0856592,
- 0.0136073,
- 0.0135062,
- 0.00786026,
- 0.0047153,
- 0.0245401,
- 0.00553791,
- 0.0100592,
- 0.0127319,
- 0.0103344,
- 0.00806758,
- 0.0441923,
- 0.0175274,
- 0.00925906,
- 0.0101233,
- 0.340648,
- 0.357329,
- 0.019367,
- 0.00142431,
- 0.00350998
- ],
- [ 0.0674595,
- 0.00216342,
- 0.0662588,
- 0.0865501,
- 0.00182127,
- 0.0368557,
- 0.0381149,
- 0.00332388,
- 0.189974,
- 0.009384,
- 0.00394874,
- 0.116311,
- 0.0151208,
- 0.093936,
- 0.116173,
- 0.0842204,
- 0.0565954,
- 0.00645142,
- 0.00071873,
- 0.00461894
- ],
- [ 0.0572262,
- 0.00153015,
- 0.179393,
- 0.199226,
- 0.00137018,
- 0.0316472,
- 0.0291392,
- 0.00458046,
- 0.101562,
- 0.010074,
- 0.00402046,
- 0.108388,
- 0.00636741,
- 0.0903669,
- 0.0494724,
- 0.0621143,
- 0.0496102,
- 0.00859413,
- 0.000666929,
- 0.00464976
- ],
- [ 0.00360202,
- 0.00454848,
- 0.00208716,
- 0.00178577,
- 0.0855715,
- 0.00563916,
- 0.00649688,
- 0.00292929,
- 0.00104198,
- 0.0232635,
- 0.00445923,
- 0.00134555,
- 0.0024992,
- 0.00327181,
- 0.0102713,
- 0.00306718,
- 0.00259003,
- 0.00586684,
- 0.761782,
- 0.067881
- ],
- [ 0.203202,
- 0.00981316,
- 0.0135012,
- 0.00838182,
- 0.00196196,
- 0.618489,
- 0.00277479,
- 0.00118285,
- 0.00445989,
- 0.00398268,
- 0.00206318,
- 0.0143744,
- 0.00858704,
- 0.00445146,
- 0.00838957,
- 0.073992,
- 0.0108922,
- 0.00607691,
- 0.00186061,
- 0.00156387
- ],
- [ 0.00508988,
- 0.00617765,
- 0.00161262,
- 0.00120404,
- 0.356313,
- 0.00163342,
- 0.0393461,
- 0.00590888,
- 0.00137137,
- 0.0249344,
- 0.00497952,
- 0.0057093,
- 0.00141364,
- 0.00246931,
- 0.00287408,
- 0.00595277,
- 0.00365368,
- 0.00819341,
- 0.0357987,
- 0.485365
- ],
- [ 0.0403336,
- 0.00815495,
- 0.00982186,
- 0.0375407,
- 0.0119141,
- 0.00479344,
- 0.0176736,
- 0.189342,
- 0.0607377,
- 0.105186,
- 0.03056,
- 0.0216052,
- 0.00775506,
- 0.0383639,
- 0.0540186,
- 0.025711,
- 0.100991,
- 0.221091,
- 0.002878,
- 0.0115277
- ],
- [ 0.0790086,
- 0.00249479,
- 0.0546012,
- 0.199788,
- 0.00237734,
- 0.0192656,
- 0.02707,
- 0.00756675,
- 0.155311,
- 0.0254542,
- 0.00980244,
- 0.0309384,
- 0.00566407,
- 0.184338,
- 0.106544,
- 0.0332371,
- 0.0359575,
- 0.0145306,
- 0.00116828,
- 0.00488208
- ],
- [ 0.0722241,
- 0.00647553,
- 0.119488,
- 0.134589,
- 0.0348233,
- 0.0287815,
- 0.0699011,
- 0.0173589,
- 0.0490342,
- 0.051987,
- 0.0154411,
- 0.067893,
- 0.0145597,
- 0.070897,
- 0.0489728,
- 0.058958,
- 0.0425973,
- 0.0317884,
- 0.00879138,
- 0.0554387
- ],
- [ 0.108584,
- 0.00125026,
- 0.152967,
- 0.166485,
- 0.00145535,
- 0.0336098,
- 0.0134902,
- 0.00388218,
- 0.0576227,
- 0.00898614,
- 0.0024339,
- 0.0441956,
- 0.19901,
- 0.0405398,
- 0.020645,
- 0.084675,
- 0.0454715,
- 0.0113416,
- 0.000590283,
- 0.00276502
- ],
- [ 0.0309526,
- 0.0065594,
- 0.00823521,
- 0.0291974,
- 0.00368916,
- 0.0154206,
- 0.0310385,
- 0.00982516,
- 0.306263,
- 0.02379,
- 0.00970717,
- 0.0301337,
- 0.00950291,
- 0.0832608,
- 0.319589,
- 0.0295285,
- 0.0303052,
- 0.0133037,
- 0.00281253,
- 0.00688506
- ],
- [ 0.00989537,
- 0.00282767,
- 0.000374823,
- 0.00091821,
- 0.0298607,
- 0.000699707,
- 0.00104195,
- 0.311504,
- 0.00139605,
- 0.375039,
- 0.0474451,
- 0.000730793,
- 0.00252963,
- 0.0017337,
- 0.00196045,
- 0.0014628,
- 0.0075739,
- 0.1973,
- 0.00167998,
- 0.00402599
- ],
- [ 0.116321,
- 0.00347923,
- 0.0731918,
- 0.138088,
- 0.00941177,
- 0.0193193,
- 0.0160241,
- 0.0712243,
- 0.035512,
- 0.0771474,
- 0.0242841,
- 0.0250164,
- 0.0508927,
- 0.0586677,
- 0.0273321,
- 0.047556,
- 0.0726552,
- 0.123571,
- 0.00268927,
- 0.0076166
- ],
- [ 0.128522,
- 0.0172929,
- 0.040275,
- 0.0250692,
- 0.0199118,
- 0.112703,
- 0.0606981,
- 0.010935,
- 0.028875,
- 0.0258416,
- 0.0167593,
- 0.117984,
- 0.0180675,
- 0.0439706,
- 0.0373073,
- 0.174149,
- 0.0648968,
- 0.0182067,
- 0.0063575,
- 0.0321772
- ],
- [ 0.0372287,
- 0.014494,
- 0.00237032,
- 0.00485851,
- 0.146377,
- 0.00464339,
- 0.0186795,
- 0.182046,
- 0.00581985,
- 0.17801,
- 0.0371334,
- 0.00533773,
- 0.00485386,
- 0.00790971,
- 0.0094528,
- 0.0103571,
- 0.0284162,
- 0.184992,
- 0.0211294,
- 0.0958905
- ],
- [ 0.0535644,
- 0.00962562,
- 0.0113537,
- 0.0391699,
- 0.0264214,
- 0.0120279,
- 0.0384888,
- 0.0522748,
- 0.0996038,
- 0.189239,
- 0.0712219,
- 0.0239173,
- 0.00837206,
- 0.0928585,
- 0.11598,
- 0.0299114,
- 0.0389485,
- 0.0500948,
- 0.0104232,
- 0.026503
- ],
- [ 0.133242,
- 0.0246514,
- 0.00127392,
- 0.00404615,
- 0.0156995,
- 0.00891392,
- 0.00158647,
- 0.197128,
- 0.00237132,
- 0.125129,
- 0.0286947,
- 0.0022705,
- 0.0118846,
- 0.00308435,
- 0.00331477,
- 0.0171462,
- 0.0563298,
- 0.356621,
- 0.00173418,
- 0.00487784
- ],
- [ 0.149866,
- 0.00354374,
- 0.0280355,
- 0.0435381,
- 0.00475339,
- 0.0311113,
- 0.0140626,
- 0.0101953,
- 0.0393125,
- 0.0251434,
- 0.00515483,
- 0.0176453,
- 0.39238,
- 0.0348151,
- 0.0326607,
- 0.0874497,
- 0.0473307,
- 0.0271597,
- 0.00152152,
- 0.00432083
- ],
- [ 0.421437,
- 0.018761,
- 0.00733051,
- 0.00868378,
- 0.00271561,
- 0.0902333,
- 0.0030262,
- 0.00393628,
- 0.00515087,
- 0.00471933,
- 0.00383066,
- 0.012159,
- 0.020894,
- 0.00727486,
- 0.0061426,
- 0.290119,
- 0.0651922,
- 0.0252211,
- 0.000810824,
- 0.00236228
- ],
- [ 0.177071,
- 0.00783489,
- 0.02265,
- 0.0509767,
- 0.00405142,
- 0.089739,
- 0.0220667,
- 0.00595198,
- 0.125769,
- 0.020537,
- 0.00929825,
- 0.0311657,
- 0.0264088,
- 0.0752471,
- 0.133278,
- 0.116959,
- 0.0565567,
- 0.0165087,
- 0.00299471,
- 0.00493467
- ],
- [ 0.0293984,
- 0.00317291,
- 0.109971,
- 0.046427,
- 0.00150396,
- 0.422242,
- 0.0272495,
- 0.000799733,
- 0.0622314,
- 0.00376343,
- 0.00166571,
- 0.148362,
- 0.00564818,
- 0.0388688,
- 0.0370902,
- 0.0472252,
- 0.0086569,
- 0.00203639,
- 0.000917602,
- 0.00276931
- ],
- [ 0.0265779,
- 0.0101369,
- 0.0280314,
- 0.0269057,
- 0.0276961,
- 0.0173377,
- 0.281513,
- 0.0064647,
- 0.0474749,
- 0.026821,
- 0.00723753,
- 0.13186,
- 0.0083015,
- 0.0989711,
- 0.0791105,
- 0.0426277,
- 0.0259043,
- 0.0100147,
- 0.00785289,
- 0.0891598
- ],
- [ 0.00960965,
- 0.00773017,
- 0.000633186,
- 0.00104719,
- 0.263017,
- 0.00202274,
- 0.00390014,
- 0.0733098,
- 0.00149315,
- 0.445169,
- 0.0732575,
- 0.00131044,
- 0.00427681,
- 0.00338994,
- 0.00271362,
- 0.00361174,
- 0.00579284,
- 0.0425173,
- 0.0181276,
- 0.0370698
- ]
- ]
-
--- | Weights of C40 model.
-c40Weights :: [Double]
-c40Weights =
- [ 0.0223854,
- 0.0338892,
- 0.0577169,
- 0.0252416,
- 0.0108608,
- 0.0462374,
- 0.0102293,
- 0.0147524,
- 0.0143161,
- 0.0182303,
- 0.0204025,
- 0.0425505,
- 0.0248627,
- 0.0105893,
- 0.0188239,
- 0.00866634,
- 0.0148496,
- 0.0343037,
- 0.0225335,
- 0.0174069,
- 0.0112208,
- 0.0443532,
- 0.0392573,
- 0.0196757,
- 0.028769,
- 0.0114441,
- 0.0112339,
- 0.0582694,
- 0.0444272,
- 0.0112011,
- 0.0145176,
- 0.0114629,
- 0.0239628,
- 0.0266266,
- 0.0481201,
- 0.0371147,
- 0.0160477,
- 0.0237249,
- 0.0235226,
- 0.0261998
- ]
-
--- | Stationary distribution of C50 model.
-c50StatDists :: [StationaryDistribution]
-c50StatDists =
- map
- V.fromList
- [ [ 0.115682,
- 0.00212412,
- 0.125699,
- 0.0919063,
- 0.0016175,
- 0.0391977,
- 0.0108596,
- 0.00344834,
- 0.0344439,
- 0.0125587,
- 0.00467132,
- 0.0530851,
- 0.206661,
- 0.0264814,
- 0.0147638,
- 0.154493,
- 0.0841319,
- 0.0134754,
- 0.000392551,
- 0.00430762
- ],
- [ 0.0983768,
- 0.00160659,
- 0.0456633,
- 0.0935028,
- 0.00112009,
- 0.0251388,
- 0.0191777,
- 0.00367483,
- 0.151407,
- 0.0115555,
- 0.00258422,
- 0.0266318,
- 0.229718,
- 0.0694385,
- 0.0855866,
- 0.0696565,
- 0.0498854,
- 0.0123983,
- 0.00069296,
- 0.00218381
- ],
- [ 0.0214598,
- 0.00446298,
- 0.000555089,
- 0.00135258,
- 0.00855351,
- 0.00112246,
- 0.000813505,
- 0.399631,
- 0.00128242,
- 0.0868331,
- 0.0170323,
- 0.00117488,
- 0.00183519,
- 0.00101872,
- 0.00142423,
- 0.00233511,
- 0.0161891,
- 0.430205,
- 0.00061736,
- 0.00210206
- ],
- [ 0.117155,
- 0.032654,
- 0.00620066,
- 0.00998032,
- 0.0657132,
- 0.0333659,
- 0.0134621,
- 0.0557335,
- 0.00794829,
- 0.199356,
- 0.0938018,
- 0.0221831,
- 0.0115415,
- 0.0204903,
- 0.0146873,
- 0.0842555,
- 0.0920314,
- 0.0798031,
- 0.0127314,
- 0.0269048
- ],
- [ 0.0371284,
- 0.0131607,
- 0.00255462,
- 0.00465054,
- 0.156922,
- 0.00416133,
- 0.019977,
- 0.178808,
- 0.00498614,
- 0.165159,
- 0.0352649,
- 0.0057612,
- 0.00512406,
- 0.00679862,
- 0.00826841,
- 0.0102949,
- 0.0275498,
- 0.181807,
- 0.0221255,
- 0.109498
- ],
- [ 0.0540087,
- 0.000836323,
- 0.306245,
- 0.38187,
- 0.00111469,
- 0.0245756,
- 0.0116353,
- 0.00254509,
- 0.030937,
- 0.00536416,
- 0.00256903,
- 0.0359123,
- 0.0122515,
- 0.0586791,
- 0.0115134,
- 0.0277199,
- 0.020314,
- 0.00828799,
- 0.000720693,
- 0.00290032
- ],
- [ 0.0404572,
- 0.028652,
- 0.00495693,
- 0.0068813,
- 0.242849,
- 0.0103569,
- 0.0318377,
- 0.0329142,
- 0.0105561,
- 0.143431,
- 0.0485779,
- 0.0105988,
- 0.00489299,
- 0.0118557,
- 0.0126873,
- 0.0229136,
- 0.0212457,
- 0.0349069,
- 0.0593874,
- 0.220042
- ],
- [ 0.319667,
- 0.138968,
- 0.00144847,
- 0.00200138,
- 0.00997903,
- 0.0503464,
- 0.00296588,
- 0.0182219,
- 0.00202126,
- 0.0260477,
- 0.0136422,
- 0.00936868,
- 0.00591365,
- 0.00358722,
- 0.00435407,
- 0.1656,
- 0.118413,
- 0.0996664,
- 0.00164228,
- 0.00614589
- ],
- [ 0.0977328,
- 0.00251083,
- 0.0724816,
- 0.197027,
- 0.00556062,
- 0.0117997,
- 0.0154288,
- 0.0563751,
- 0.0613631,
- 0.047368,
- 0.0159721,
- 0.0241106,
- 0.0149,
- 0.0909736,
- 0.034432,
- 0.0408092,
- 0.0929289,
- 0.111482,
- 0.00122744,
- 0.00551621
- ],
- [ 0.0195453,
- 0.0107627,
- 0.0127492,
- 0.011794,
- 0.14032,
- 0.0061666,
- 0.215761,
- 0.00826718,
- 0.0118897,
- 0.0328258,
- 0.00664433,
- 0.0423533,
- 0.00528472,
- 0.0258824,
- 0.024497,
- 0.0203711,
- 0.0124449,
- 0.0133889,
- 0.0330587,
- 0.345993
- ],
- [ 0.185338,
- 0.00185224,
- 0.161345,
- 0.234878,
- 0.00192286,
- 0.054278,
- 0.0109591,
- 0.00550122,
- 0.0382027,
- 0.00925008,
- 0.00343293,
- 0.033406,
- 0.0233824,
- 0.0551124,
- 0.0201268,
- 0.0884267,
- 0.051789,
- 0.0177494,
- 0.000835994,
- 0.00221142
- ],
- [ 0.0143603,
- 0.0036047,
- 0.000411253,
- 0.00108887,
- 0.0196479,
- 0.00187385,
- 0.000991664,
- 0.285685,
- 0.00213672,
- 0.317288,
- 0.150556,
- 0.00155703,
- 0.00122034,
- 0.0028111,
- 0.00194519,
- 0.00344669,
- 0.0196686,
- 0.167294,
- 0.000843478,
- 0.00356936
- ],
- [ 0.150577,
- 0.00957632,
- 0.0227565,
- 0.0358641,
- 0.0104881,
- 0.0285062,
- 0.0171219,
- 0.0577109,
- 0.0276149,
- 0.0531781,
- 0.0298859,
- 0.0514957,
- 0.0243637,
- 0.0354202,
- 0.0272841,
- 0.132633,
- 0.169554,
- 0.104387,
- 0.00219421,
- 0.00938724
- ],
- [ 0.277615,
- 0.0280749,
- 0.00194439,
- 0.00537302,
- 0.0070772,
- 0.0234861,
- 0.0012257,
- 0.0949678,
- 0.00308357,
- 0.0474515,
- 0.0189616,
- 0.0034483,
- 0.0134815,
- 0.00374076,
- 0.00354151,
- 0.0423818,
- 0.0932708,
- 0.326207,
- 0.000963513,
- 0.00370386
- ],
- [ 0.205879,
- 0.00249091,
- 0.075426,
- 0.161651,
- 0.00210732,
- 0.0463391,
- 0.0159993,
- 0.00515537,
- 0.0913036,
- 0.0166911,
- 0.00536596,
- 0.0366042,
- 0.00849072,
- 0.0973331,
- 0.0696431,
- 0.088244,
- 0.0501877,
- 0.0172747,
- 0.000776174,
- 0.0030381
- ],
- [ 0.0704473,
- 0.00149732,
- 0.187469,
- 0.208434,
- 0.0013217,
- 0.0409359,
- 0.0247326,
- 0.00339884,
- 0.0739754,
- 0.00761491,
- 0.00270559,
- 0.0965448,
- 0.00673196,
- 0.0820493,
- 0.0355811,
- 0.0832004,
- 0.0610002,
- 0.00788473,
- 0.000646918,
- 0.00382803
- ],
- [ 0.108767,
- 0.00735776,
- 0.0100122,
- 0.0249269,
- 0.015562,
- 0.0114116,
- 0.00730171,
- 0.0923916,
- 0.0138538,
- 0.112308,
- 0.0251594,
- 0.00831075,
- 0.259979,
- 0.0187962,
- 0.0142911,
- 0.0329858,
- 0.0608007,
- 0.162244,
- 0.0049709,
- 0.00857003
- ],
- [ 0.109878,
- 0.0295589,
- 0.000867374,
- 0.00267084,
- 0.028604,
- 0.0101436,
- 0.00159952,
- 0.171472,
- 0.0015037,
- 0.241889,
- 0.0488425,
- 0.00201796,
- 0.00631863,
- 0.00393786,
- 0.00336164,
- 0.0148413,
- 0.0393773,
- 0.273667,
- 0.00359303,
- 0.00585493
- ],
- [ 0.058736,
- 0.00692528,
- 0.0144651,
- 0.0412403,
- 0.0154694,
- 0.015436,
- 0.0243546,
- 0.0388984,
- 0.0996366,
- 0.207192,
- 0.103832,
- 0.0289715,
- 0.00833815,
- 0.108218,
- 0.0976056,
- 0.0350037,
- 0.0432645,
- 0.0338957,
- 0.00652556,
- 0.0119916
- ],
- [ 0.0642736,
- 0.00525071,
- 0.144305,
- 0.153274,
- 0.0286093,
- 0.0265312,
- 0.0545105,
- 0.0231701,
- 0.0452879,
- 0.058794,
- 0.0192273,
- 0.071063,
- 0.0146855,
- 0.066931,
- 0.0405954,
- 0.054046,
- 0.043602,
- 0.0350962,
- 0.00655203,
- 0.0441953
- ],
- [ 0.00487716,
- 0.00503139,
- 0.00209095,
- 0.00192293,
- 0.0983777,
- 0.00615619,
- 0.00725617,
- 0.00400789,
- 0.000993075,
- 0.0277171,
- 0.00537714,
- 0.00145717,
- 0.0029039,
- 0.00350461,
- 0.0112195,
- 0.00329284,
- 0.00295187,
- 0.00708726,
- 0.724652,
- 0.0791231
- ],
- [ 0.0552756,
- 0.0115894,
- 0.00846155,
- 0.0432312,
- 0.00961795,
- 0.0074182,
- 0.0218432,
- 0.0843826,
- 0.163327,
- 0.0631707,
- 0.0228359,
- 0.0221225,
- 0.00652522,
- 0.0639538,
- 0.146077,
- 0.0387464,
- 0.100713,
- 0.118118,
- 0.00298298,
- 0.00960875
- ],
- [ 0.00449551,
- 0.00619902,
- 0.000890609,
- 0.000674178,
- 0.400884,
- 0.0013356,
- 0.0223834,
- 0.00805107,
- 0.00105813,
- 0.0341606,
- 0.00701178,
- 0.00318917,
- 0.00130624,
- 0.00157564,
- 0.00181707,
- 0.00502515,
- 0.00337803,
- 0.00946203,
- 0.0345278,
- 0.452575
- ],
- [ 0.0505469,
- 0.00768183,
- 0.0101983,
- 0.0470721,
- 0.0160596,
- 0.00517598,
- 0.0176387,
- 0.169463,
- 0.0497501,
- 0.209444,
- 0.0474166,
- 0.0132404,
- 0.00844474,
- 0.053753,
- 0.051076,
- 0.0149657,
- 0.03846,
- 0.172926,
- 0.00437246,
- 0.0123139
- ],
- [ 0.0749936,
- 0.0124353,
- 0.0203869,
- 0.0100161,
- 0.0038092,
- 0.0270453,
- 0.00581932,
- 0.00743392,
- 0.014732,
- 0.00838354,
- 0.00640172,
- 0.0530316,
- 0.0176075,
- 0.0096947,
- 0.0117746,
- 0.3482,
- 0.348235,
- 0.0157071,
- 0.00137596,
- 0.00291601
- ],
- [ 0.0569785,
- 0.00176591,
- 0.102737,
- 0.106157,
- 0.00132179,
- 0.0360979,
- 0.034465,
- 0.00311879,
- 0.185459,
- 0.00858711,
- 0.00431374,
- 0.139374,
- 0.00855798,
- 0.0898676,
- 0.101042,
- 0.0669467,
- 0.0422839,
- 0.00552428,
- 0.000686497,
- 0.00471478
- ],
- [ 0.0746973,
- 0.00394557,
- 0.0423454,
- 0.0906599,
- 0.00363883,
- 0.0183504,
- 0.0229406,
- 0.0156166,
- 0.12297,
- 0.0167059,
- 0.00901115,
- 0.0672502,
- 0.0127747,
- 0.0811334,
- 0.0755385,
- 0.132886,
- 0.170553,
- 0.0324157,
- 0.00152093,
- 0.00504616
- ],
- [ 0.17313,
- 0.00938612,
- 0.0203504,
- 0.0387504,
- 0.00448721,
- 0.0867075,
- 0.0227177,
- 0.00492238,
- 0.125544,
- 0.0156727,
- 0.00787132,
- 0.0400476,
- 0.0180405,
- 0.0680443,
- 0.133335,
- 0.142136,
- 0.0670614,
- 0.0136107,
- 0.00287027,
- 0.00531475
- ],
- [ 0.00751784,
- 0.00212117,
- 0.000341917,
- 0.000667876,
- 0.0310677,
- 0.000466913,
- 0.000898937,
- 0.320302,
- 0.00103903,
- 0.384419,
- 0.0335748,
- 0.000602706,
- 0.00243131,
- 0.00137426,
- 0.00152778,
- 0.00115498,
- 0.00552329,
- 0.199295,
- 0.00172716,
- 0.00394622
- ],
- [ 0.113459,
- 0.0281671,
- 0.0268294,
- 0.0283293,
- 0.0928796,
- 0.0494616,
- 0.0733971,
- 0.0152335,
- 0.0176739,
- 0.037425,
- 0.0140126,
- 0.0539481,
- 0.0259048,
- 0.0303861,
- 0.0259068,
- 0.121621,
- 0.0621544,
- 0.0350518,
- 0.0240853,
- 0.124074
- ],
- [ 0.0810974,
- 0.00899714,
- 0.0930492,
- 0.0372909,
- 0.002713,
- 0.0907986,
- 0.0275326,
- 0.00533957,
- 0.0362449,
- 0.00831441,
- 0.00615441,
- 0.177093,
- 0.0120848,
- 0.0316411,
- 0.025247,
- 0.233557,
- 0.106302,
- 0.00814021,
- 0.000950692,
- 0.00745168
- ],
- [ 0.00757098,
- 0.00716117,
- 0.00049456,
- 0.000891326,
- 0.297029,
- 0.00155605,
- 0.00342729,
- 0.0711141,
- 0.00107067,
- 0.416918,
- 0.0635143,
- 0.000864035,
- 0.00349893,
- 0.00251506,
- 0.00186372,
- 0.00271598,
- 0.00424124,
- 0.041488,
- 0.0202374,
- 0.0518279
- ],
- [ 0.086899,
- 0.00542266,
- 0.0274343,
- 0.117345,
- 0.00568342,
- 0.0162895,
- 0.0386176,
- 0.0182492,
- 0.149526,
- 0.048245,
- 0.0150062,
- 0.0265186,
- 0.00577334,
- 0.159013,
- 0.149227,
- 0.0416278,
- 0.0492401,
- 0.0283951,
- 0.00272523,
- 0.00876225
- ],
- [ 0.0501736,
- 0.0113806,
- 0.00768113,
- 0.0191841,
- 0.0119036,
- 0.00521331,
- 0.00988204,
- 0.203482,
- 0.0206446,
- 0.0870652,
- 0.036001,
- 0.0197961,
- 0.0061624,
- 0.0180415,
- 0.0178215,
- 0.0399964,
- 0.162255,
- 0.262373,
- 0.00172457,
- 0.00921833
- ],
- [ 0.177098,
- 0.00357587,
- 0.0740854,
- 0.0713923,
- 0.00385864,
- 0.211235,
- 0.0161904,
- 0.0040472,
- 0.0370753,
- 0.00826202,
- 0.00369757,
- 0.0494737,
- 0.0543871,
- 0.0396583,
- 0.0340392,
- 0.140615,
- 0.0532238,
- 0.0108131,
- 0.00212448,
- 0.00514764
- ],
- [ 0.242384,
- 0.0115188,
- 0.00720908,
- 0.00544261,
- 0.00229719,
- 0.593273,
- 0.00205723,
- 0.00208173,
- 0.00287156,
- 0.00491,
- 0.00271204,
- 0.00899551,
- 0.00763059,
- 0.00285962,
- 0.00600369,
- 0.0738385,
- 0.0108329,
- 0.00968775,
- 0.00178961,
- 0.00160391
- ],
- [ 0.032912,
- 0.00319267,
- 0.143899,
- 0.0532755,
- 0.00166462,
- 0.463509,
- 0.0175283,
- 0.000876108,
- 0.0317056,
- 0.00297349,
- 0.0012156,
- 0.131603,
- 0.00688601,
- 0.0251373,
- 0.0184844,
- 0.0491059,
- 0.00984294,
- 0.00239178,
- 0.0008917,
- 0.00290456
- ],
- [ 0.0388306,
- 0.00489943,
- 0.0491655,
- 0.0413874,
- 0.00170354,
- 0.345044,
- 0.0421499,
- 0.00103798,
- 0.123725,
- 0.00726049,
- 0.00335164,
- 0.119727,
- 0.00562115,
- 0.0664068,
- 0.0881106,
- 0.0460192,
- 0.00791813,
- 0.0020819,
- 0.00195492,
- 0.00360516
- ],
- [ 0.0373301,
- 0.00916334,
- 0.0396965,
- 0.0362168,
- 0.0144959,
- 0.0269081,
- 0.220512,
- 0.00638711,
- 0.0634517,
- 0.0225147,
- 0.00718608,
- 0.152708,
- 0.00995802,
- 0.108449,
- 0.0882553,
- 0.0609295,
- 0.0332848,
- 0.0105312,
- 0.00429315,
- 0.047729
- ],
- [ 0.0171508,
- 0.00565843,
- 0.00111564,
- 0.00268175,
- 0.0490847,
- 0.00219974,
- 0.00370226,
- 0.116938,
- 0.00407925,
- 0.500942,
- 0.1832,
- 0.00280387,
- 0.00400697,
- 0.0115255,
- 0.00613355,
- 0.00539456,
- 0.0140434,
- 0.0579479,
- 0.00419195,
- 0.00719895
- ],
- [ 0.0238117,
- 0.00329378,
- 0.370777,
- 0.0831676,
- 0.0022275,
- 0.053433,
- 0.0290274,
- 0.00288609,
- 0.0258098,
- 0.00370314,
- 0.00159506,
- 0.259554,
- 0.00668902,
- 0.0201877,
- 0.0117854,
- 0.0626213,
- 0.0278627,
- 0.00464381,
- 0.000688992,
- 0.0062349
- ],
- [ 0.209736,
- 0.0105937,
- 0.0311812,
- 0.0613839,
- 0.00991105,
- 0.0855144,
- 0.0226071,
- 0.0296058,
- 0.0455281,
- 0.0792591,
- 0.0306389,
- 0.019447,
- 0.0213982,
- 0.0610672,
- 0.0588191,
- 0.0820738,
- 0.0527883,
- 0.0722389,
- 0.00513,
- 0.0110785
- ],
- [ 0.0295833,
- 0.00588894,
- 0.00852018,
- 0.0296344,
- 0.00323424,
- 0.0154495,
- 0.02992,
- 0.00752729,
- 0.317117,
- 0.0212988,
- 0.00874154,
- 0.0312424,
- 0.00843308,
- 0.0831654,
- 0.323587,
- 0.0294177,
- 0.0283085,
- 0.0100345,
- 0.00257807,
- 0.00631797
- ],
- [ 0.0937098,
- 0.00289961,
- 0.0255803,
- 0.0577481,
- 0.0140839,
- 0.0182984,
- 0.0300827,
- 0.0312422,
- 0.0867966,
- 0.067914,
- 0.01767,
- 0.0206426,
- 0.213942,
- 0.0611154,
- 0.0902988,
- 0.0526724,
- 0.0464314,
- 0.0509513,
- 0.00365078,
- 0.01427
- ],
- [ 0.419507,
- 0.0176715,
- 0.00719436,
- 0.00880545,
- 0.00285112,
- 0.0865515,
- 0.00330323,
- 0.00419601,
- 0.00503365,
- 0.0048203,
- 0.00393323,
- 0.012443,
- 0.0192167,
- 0.00750218,
- 0.00609116,
- 0.295973,
- 0.0660748,
- 0.0253174,
- 0.000942289,
- 0.00257126
- ],
- [ 0.0368106,
- 0.0124259,
- 0.0102859,
- 0.0343205,
- 0.0759532,
- 0.00772969,
- 0.0938663,
- 0.0458547,
- 0.0701169,
- 0.133403,
- 0.031916,
- 0.0265402,
- 0.00749485,
- 0.0673302,
- 0.10388,
- 0.0271625,
- 0.0353789,
- 0.0485031,
- 0.0254607,
- 0.105568
- ],
- [ 0.0665479,
- 0.00185956,
- 0.183575,
- 0.149215,
- 0.00127224,
- 0.0634659,
- 0.019684,
- 0.00262142,
- 0.0655694,
- 0.00750609,
- 0.00151282,
- 0.0699101,
- 0.182105,
- 0.0446839,
- 0.0292035,
- 0.075452,
- 0.0278833,
- 0.00484561,
- 0.000723776,
- 0.00236318
- ],
- [ 0.16002,
- 0.00397537,
- 0.019682,
- 0.0286161,
- 0.00458768,
- 0.0326662,
- 0.0114325,
- 0.00722291,
- 0.0232558,
- 0.0202542,
- 0.00379358,
- 0.0142832,
- 0.460797,
- 0.0260458,
- 0.0217875,
- 0.0913633,
- 0.0427326,
- 0.0227118,
- 0.0012566,
- 0.0035159
- ],
- [ 0.0843584,
- 0.00129715,
- 0.0847585,
- 0.260552,
- 0.00143564,
- 0.0191268,
- 0.0174708,
- 0.00556223,
- 0.144172,
- 0.014456,
- 0.00550323,
- 0.0336163,
- 0.00724868,
- 0.160704,
- 0.0742581,
- 0.0323411,
- 0.0355032,
- 0.0136662,
- 0.000760206,
- 0.00320994
- ],
- [ 0.152149,
- 0.000925399,
- 0.116471,
- 0.220438,
- 0.00150071,
- 0.0172039,
- 0.0095692,
- 0.00747151,
- 0.0529323,
- 0.0148756,
- 0.00356173,
- 0.0157411,
- 0.217335,
- 0.0489135,
- 0.0171707,
- 0.044102,
- 0.0323715,
- 0.023915,
- 0.000908902,
- 0.00244332
- ]
- ]
-
--- | Weights of C50 model.
-c50Weights :: [Double]
-c50Weights =
- [ 0.00509464,
- 0.00753314,
- 0.0595801,
- 0.0100458,
- 0.0109109,
- 0.0427412,
- 0.00632106,
- 0.0192362,
- 0.0119168,
- 0.0154209,
- 0.0148037,
- 0.014293,
- 0.0164064,
- 0.0272538,
- 0.0178737,
- 0.0125183,
- 0.00698661,
- 0.0140027,
- 0.0140399,
- 0.0109043,
- 0.011579,
- 0.0138661,
- 0.0377329,
- 0.0118586,
- 0.0356688,
- 0.0161327,
- 0.0200601,
- 0.0133087,
- 0.0357641,
- 0.0119353,
- 0.0241183,
- 0.0243098,
- 0.0178039,
- 0.0200988,
- 0.00579569,
- 0.0397441,
- 0.0240799,
- 0.00868054,
- 0.0239822,
- 0.042803,
- 0.0335193,
- 0.00636191,
- 0.0547546,
- 0.00544598,
- 0.0354219,
- 0.0120158,
- 0.0047506,
- 0.036392,
- 0.0270346,
- 0.00709747
- ]
-
--- | Stationary distribution of C60 model.
-c60StatDists :: [StationaryDistribution]
-c60StatDists =
- map
- V.fromList
- [ [ 0.153436,
- 0.00473066,
- 0.0546757,
- 0.0529324,
- 0.00355543,
- 0.110378,
- 0.017448,
- 0.00503439,
- 0.0603929,
- 0.0130294,
- 0.00755506,
- 0.0796727,
- 0.0249524,
- 0.0514333,
- 0.0444389,
- 0.202963,
- 0.0957668,
- 0.0101809,
- 0.00144445,
- 0.00598003
- ],
- [ 0.0281985,
- 0.00195035,
- 0.00915493,
- 0.038853,
- 0.00159193,
- 0.00840283,
- 0.0155385,
- 0.0107873,
- 0.347604,
- 0.0217787,
- 0.0109905,
- 0.0312955,
- 0.00715399,
- 0.0939884,
- 0.303106,
- 0.0197479,
- 0.0328352,
- 0.0135303,
- 0.000920999,
- 0.0025714
- ],
- [ 0.00836807,
- 0.00204339,
- 0.000222837,
- 0.000473154,
- 0.0123984,
- 0.000482575,
- 0.000518999,
- 0.376845,
- 0.000629617,
- 0.260833,
- 0.0315701,
- 0.000612345,
- 0.000959592,
- 0.000949869,
- 0.000731977,
- 0.000974638,
- 0.00499908,
- 0.293808,
- 0.000865776,
- 0.00171323
- ],
- [ 0.222723,
- 0.164029,
- 0.000799759,
- 0.00272808,
- 0.0228667,
- 0.0202703,
- 0.00371839,
- 0.0455406,
- 0.00228329,
- 0.088335,
- 0.0348095,
- 0.00612065,
- 0.00354716,
- 0.00510519,
- 0.00648461,
- 0.085004,
- 0.101285,
- 0.169858,
- 0.00484248,
- 0.00965
- ],
- [ 0.041214,
- 0.0204716,
- 0.00174344,
- 0.00372634,
- 0.2239,
- 0.00691075,
- 0.0180294,
- 0.115428,
- 0.00429003,
- 0.169356,
- 0.0414067,
- 0.00510677,
- 0.00584164,
- 0.00575385,
- 0.00676271,
- 0.0149106,
- 0.0239548,
- 0.120034,
- 0.0332237,
- 0.137935
- ],
- [ 0.048055,
- 0.00378018,
- 0.208461,
- 0.185518,
- 0.0196001,
- 0.0191402,
- 0.0872162,
- 0.00946854,
- 0.0375741,
- 0.0277341,
- 0.00883084,
- 0.0940629,
- 0.00812678,
- 0.0747677,
- 0.0308438,
- 0.0439681,
- 0.0324589,
- 0.0181769,
- 0.00346657,
- 0.03875
- ],
- [ 0.00628487,
- 0.00730276,
- 0.000532415,
- 0.000974149,
- 0.397455,
- 0.00195782,
- 0.0102225,
- 0.0180592,
- 0.00162059,
- 0.117906,
- 0.0234722,
- 0.00303425,
- 0.00201656,
- 0.00344091,
- 0.00262469,
- 0.00569033,
- 0.00370918,
- 0.0152754,
- 0.0598639,
- 0.318557
- ],
- [ 0.181501,
- 0.420563,
- 0.00251455,
- 0.000708814,
- 0.00689764,
- 0.0461854,
- 0.00143746,
- 0.00417455,
- 0.000647425,
- 0.00983105,
- 0.00416114,
- 0.0148485,
- 0.00387672,
- 0.0014097,
- 0.00268454,
- 0.186454,
- 0.068719,
- 0.0345742,
- 0.00270835,
- 0.0061033
- ],
- [ 0.0600741,
- 0.00707198,
- 0.0170572,
- 0.0127487,
- 0.114091,
- 0.0343564,
- 0.0305859,
- 0.0204571,
- 0.0212367,
- 0.0994551,
- 0.0318166,
- 0.0134869,
- 0.0297628,
- 0.014247,
- 0.0367643,
- 0.0505793,
- 0.0339368,
- 0.0217422,
- 0.231281,
- 0.119249
- ],
- [ 0.0708395,
- 0.0131641,
- 0.0324483,
- 0.0508264,
- 0.059436,
- 0.0183309,
- 0.0567273,
- 0.0650369,
- 0.0343618,
- 0.128226,
- 0.0390363,
- 0.0416822,
- 0.0135608,
- 0.0494875,
- 0.0474098,
- 0.0551343,
- 0.064226,
- 0.078961,
- 0.0137118,
- 0.0673934
- ],
- [ 0.0617689,
- 0.000719984,
- 0.343023,
- 0.379251,
- 0.000981419,
- 0.0284659,
- 0.00795921,
- 0.00169996,
- 0.0216077,
- 0.00399453,
- 0.00197343,
- 0.0303082,
- 0.0174791,
- 0.0307856,
- 0.00763329,
- 0.0337832,
- 0.0203427,
- 0.00589923,
- 0.000613027,
- 0.00171028
- ],
- [ 0.042156,
- 0.00444503,
- 0.0164385,
- 0.0531949,
- 0.00867283,
- 0.0134711,
- 0.0177765,
- 0.0267728,
- 0.132374,
- 0.196724,
- 0.118283,
- 0.0286981,
- 0.00518379,
- 0.139369,
- 0.104207,
- 0.0255853,
- 0.0333292,
- 0.0217067,
- 0.00458523,
- 0.00702815
- ],
- [ 0.281481,
- 0.0258338,
- 0.00643857,
- 0.0115046,
- 0.00504817,
- 0.0270055,
- 0.00546297,
- 0.0188216,
- 0.00987128,
- 0.0190993,
- 0.015872,
- 0.0172868,
- 0.012951,
- 0.0133102,
- 0.0100367,
- 0.188681,
- 0.24271,
- 0.0837524,
- 0.00122746,
- 0.00360529
- ],
- [ 0.276919,
- 0.0318293,
- 0.00116725,
- 0.00247525,
- 0.00708439,
- 0.0199647,
- 0.000517086,
- 0.0983109,
- 0.00162322,
- 0.0489264,
- 0.0173415,
- 0.00213153,
- 0.00701797,
- 0.00182163,
- 0.0017227,
- 0.0336349,
- 0.0814141,
- 0.362092,
- 0.000711814,
- 0.00329423
- ],
- [ 0.15778,
- 0.00533181,
- 0.064829,
- 0.0913587,
- 0.00250478,
- 0.090621,
- 0.053381,
- 0.00291716,
- 0.0782149,
- 0.0156226,
- 0.0045759,
- 0.0570403,
- 0.00670778,
- 0.106537,
- 0.111214,
- 0.092931,
- 0.0393123,
- 0.00850409,
- 0.00285758,
- 0.00775903
- ],
- [ 0.0593735,
- 0.00153322,
- 0.218948,
- 0.181942,
- 0.00108383,
- 0.0813707,
- 0.0220478,
- 0.00209936,
- 0.0750172,
- 0.00561913,
- 0.00218717,
- 0.115118,
- 0.0109737,
- 0.0688752,
- 0.0354741,
- 0.0726449,
- 0.0380238,
- 0.00426697,
- 0.000734646,
- 0.00266649
- ],
- [ 0.0978066,
- 0.00641384,
- 0.0120781,
- 0.0291283,
- 0.0198964,
- 0.0128913,
- 0.0128037,
- 0.0723904,
- 0.0245631,
- 0.127944,
- 0.0303267,
- 0.0101844,
- 0.272352,
- 0.0307876,
- 0.0265576,
- 0.0350549,
- 0.0484557,
- 0.115203,
- 0.00468425,
- 0.0104774
- ],
- [ 0.0124023,
- 0.00418857,
- 0.000603732,
- 0.0012524,
- 0.0610615,
- 0.00113068,
- 0.00135421,
- 0.234417,
- 0.00167182,
- 0.455056,
- 0.0667308,
- 0.00092391,
- 0.00370762,
- 0.00329574,
- 0.00306804,
- 0.00194209,
- 0.00676129,
- 0.129048,
- 0.00389372,
- 0.00749118
- ],
- [ 0.0794231,
- 0.00199195,
- 0.0587236,
- 0.12469,
- 0.001287,
- 0.0325432,
- 0.0238605,
- 0.00362772,
- 0.21476,
- 0.0097988,
- 0.00418462,
- 0.0662793,
- 0.014241,
- 0.114388,
- 0.129474,
- 0.0615807,
- 0.0477334,
- 0.00781872,
- 0.000652537,
- 0.00294202
- ],
- [ 0.0248149,
- 0.00278397,
- 0.427883,
- 0.143239,
- 0.00146804,
- 0.0643968,
- 0.0185737,
- 0.00225069,
- 0.0179274,
- 0.00345586,
- 0.00157145,
- 0.188892,
- 0.0073768,
- 0.0210778,
- 0.00835529,
- 0.0377003,
- 0.0187768,
- 0.00460727,
- 0.000589186,
- 0.00426027
- ],
- [ 0.00170034,
- 0.00290594,
- 0.00107115,
- 0.00117317,
- 0.0513377,
- 0.00355796,
- 0.00276305,
- 0.00122912,
- 0.00042738,
- 0.0127421,
- 0.00256713,
- 0.00042229,
- 0.00135367,
- 0.00164242,
- 0.00606743,
- 0.00118717,
- 0.00140331,
- 0.00331373,
- 0.864044,
- 0.0390913
- ],
- [ 0.0468361,
- 0.00599541,
- 0.0185616,
- 0.0705436,
- 0.00801772,
- 0.00454353,
- 0.0152063,
- 0.155061,
- 0.0866248,
- 0.0824253,
- 0.0245854,
- 0.0205604,
- 0.00814856,
- 0.0557031,
- 0.0639797,
- 0.0237026,
- 0.0962054,
- 0.204749,
- 0.00183687,
- 0.00671317
- ],
- [ 0.0258765,
- 0.0142504,
- 0.0107037,
- 0.010565,
- 0.187643,
- 0.0073065,
- 0.141108,
- 0.0114778,
- 0.0119179,
- 0.0407992,
- 0.0098799,
- 0.0298384,
- 0.00512288,
- 0.0158529,
- 0.0201097,
- 0.02757,
- 0.0170765,
- 0.0187502,
- 0.0405125,
- 0.353639
- ],
- [ 0.0296285,
- 0.00900465,
- 0.000885102,
- 0.00330465,
- 0.0408798,
- 0.00279695,
- 0.00507015,
- 0.25834,
- 0.00466909,
- 0.266809,
- 0.0770825,
- 0.00349444,
- 0.00269182,
- 0.00554811,
- 0.00464003,
- 0.00685381,
- 0.0322266,
- 0.22719,
- 0.00355061,
- 0.0153353
- ],
- [ 0.0555726,
- 0.00974186,
- 0.014039,
- 0.00694432,
- 0.00344967,
- 0.0157957,
- 0.00416313,
- 0.00698265,
- 0.0139225,
- 0.00752712,
- 0.00587627,
- 0.0409064,
- 0.0119733,
- 0.00687277,
- 0.00984479,
- 0.348247,
- 0.421366,
- 0.0131119,
- 0.00100615,
- 0.00265768
- ],
- [ 0.0682671,
- 0.0141433,
- 0.0360279,
- 0.0497415,
- 0.0803376,
- 0.0268697,
- 0.112767,
- 0.0132647,
- 0.0482609,
- 0.0544494,
- 0.0170034,
- 0.0530661,
- 0.019195,
- 0.0612274,
- 0.0615207,
- 0.067184,
- 0.0443996,
- 0.0267714,
- 0.0199958,
- 0.125507
- ],
- [ 0.0792619,
- 0.00495033,
- 0.0436646,
- 0.0829639,
- 0.00491311,
- 0.0183429,
- 0.0233169,
- 0.0249427,
- 0.0932578,
- 0.0221483,
- 0.0120893,
- 0.0635289,
- 0.012636,
- 0.0666365,
- 0.0638377,
- 0.133485,
- 0.191675,
- 0.0503102,
- 0.00180401,
- 0.00623531
- ],
- [ 0.0731759,
- 0.0123459,
- 0.0110007,
- 0.0349943,
- 0.00931488,
- 0.0224509,
- 0.0386903,
- 0.0246226,
- 0.178334,
- 0.0508307,
- 0.0185741,
- 0.0324201,
- 0.0148723,
- 0.0858952,
- 0.210534,
- 0.0603181,
- 0.0649575,
- 0.038504,
- 0.00510464,
- 0.0130597
- ],
- [ 0.0878403,
- 0.0171147,
- 0.00328039,
- 0.0101466,
- 0.0191954,
- 0.00870909,
- 0.00549022,
- 0.198776,
- 0.00820969,
- 0.175646,
- 0.0417233,
- 0.00608012,
- 0.0111284,
- 0.0109832,
- 0.0110332,
- 0.0209863,
- 0.0697719,
- 0.28252,
- 0.0031744,
- 0.00819055
- ],
- [ 0.0990216,
- 0.0108996,
- 0.0118798,
- 0.0279,
- 0.0214442,
- 0.024025,
- 0.0123445,
- 0.0776565,
- 0.0322818,
- 0.235451,
- 0.120767,
- 0.021115,
- 0.00756555,
- 0.0557711,
- 0.0349352,
- 0.052417,
- 0.0649785,
- 0.0771067,
- 0.00470758,
- 0.00773287
- ],
- [ 0.0601641,
- 0.0315067,
- 0.0337189,
- 0.00598395,
- 0.00695259,
- 0.0543081,
- 0.0531524,
- 0.00706508,
- 0.0139598,
- 0.00706981,
- 0.00882987,
- 0.278352,
- 0.00758343,
- 0.0210646,
- 0.0161995,
- 0.28298,
- 0.0860317,
- 0.0100954,
- 0.00149666,
- 0.0134849
- ],
- [ 0.00497817,
- 0.00529787,
- 0.000531537,
- 0.000763055,
- 0.335112,
- 0.00150513,
- 0.00415752,
- 0.0443829,
- 0.00116151,
- 0.441742,
- 0.0602807,
- 0.000701221,
- 0.00278477,
- 0.00240899,
- 0.00184123,
- 0.00257958,
- 0.00302885,
- 0.0237677,
- 0.0171303,
- 0.0458456
- ],
- [ 0.0251997,
- 0.00970995,
- 0.00410123,
- 0.0262572,
- 0.0429092,
- 0.00380673,
- 0.0431939,
- 0.0974043,
- 0.0824313,
- 0.24472,
- 0.0539323,
- 0.0142032,
- 0.00526585,
- 0.0620071,
- 0.111447,
- 0.00960931,
- 0.0251183,
- 0.0783303,
- 0.0146572,
- 0.0456965
- ],
- [ 0.0230362,
- 0.00485801,
- 0.000626444,
- 0.00157626,
- 0.0072127,
- 0.00115653,
- 0.000889924,
- 0.39529,
- 0.00146635,
- 0.0576537,
- 0.0140987,
- 0.00135344,
- 0.00201779,
- 0.000987005,
- 0.00147487,
- 0.00287702,
- 0.0205581,
- 0.460366,
- 0.000547769,
- 0.00195391
- ],
- [ 0.140878,
- 0.00322137,
- 0.0285077,
- 0.0423839,
- 0.00412311,
- 0.0299558,
- 0.0131321,
- 0.00669145,
- 0.0383782,
- 0.019512,
- 0.00362769,
- 0.0171298,
- 0.438347,
- 0.0320632,
- 0.0297808,
- 0.08514,
- 0.0422766,
- 0.0198195,
- 0.00132369,
- 0.00370876
- ],
- [ 0.444249,
- 0.0235405,
- 0.0057193,
- 0.00648899,
- 0.00244132,
- 0.0822688,
- 0.00255057,
- 0.00336151,
- 0.00380971,
- 0.00409901,
- 0.00286831,
- 0.0102305,
- 0.0162891,
- 0.00559976,
- 0.00502166,
- 0.299997,
- 0.0559665,
- 0.0226608,
- 0.000773543,
- 0.00206398
- ],
- [ 0.0898718,
- 0.00441315,
- 0.0129167,
- 0.0058957,
- 0.000807357,
- 0.808756,
- 0.00165179,
- 0.000433928,
- 0.0033939,
- 0.00155645,
- 0.000425342,
- 0.0130068,
- 0.00341281,
- 0.00238065,
- 0.00709583,
- 0.0362877,
- 0.00328875,
- 0.00202896,
- 0.00152239,
- 0.000853745
- ],
- [ 0.055084,
- 0.00358249,
- 0.12738,
- 0.0655885,
- 0.0040375,
- 0.0637608,
- 0.0404883,
- 0.00755742,
- 0.0867683,
- 0.0136305,
- 0.00816842,
- 0.187783,
- 0.0110682,
- 0.0527969,
- 0.0472254,
- 0.126338,
- 0.0752544,
- 0.0102728,
- 0.00135637,
- 0.011859
- ],
- [ 0.0117681,
- 0.00703883,
- 0.0144712,
- 0.0110901,
- 0.0338266,
- 0.00496266,
- 0.433719,
- 0.0061337,
- 0.0137929,
- 0.0298795,
- 0.00762376,
- 0.0844145,
- 0.00813461,
- 0.103834,
- 0.0442559,
- 0.0140571,
- 0.0108277,
- 0.00837578,
- 0.00806831,
- 0.143725
- ],
- [ 0.0159286,
- 0.00805199,
- 0.00109669,
- 0.00213242,
- 0.0743651,
- 0.00250864,
- 0.00491921,
- 0.0501544,
- 0.00355994,
- 0.530763,
- 0.216009,
- 0.00326926,
- 0.00452474,
- 0.0134552,
- 0.00480987,
- 0.00669222,
- 0.0119092,
- 0.0281012,
- 0.00709281,
- 0.0106565
- ],
- [ 0.0195973,
- 0.0034539,
- 0.309985,
- 0.0250778,
- 0.00197065,
- 0.0627529,
- 0.0295961,
- 0.00326504,
- 0.0240964,
- 0.00282469,
- 0.000842506,
- 0.32891,
- 0.00490628,
- 0.0116197,
- 0.0105143,
- 0.106498,
- 0.0438054,
- 0.0040302,
- 0.000633396,
- 0.0056198
- ],
- [ 0.0833804,
- 0.00819811,
- 0.0686821,
- 0.0227415,
- 0.00241326,
- 0.0982292,
- 0.00739549,
- 0.00174712,
- 0.0129342,
- 0.00396531,
- 0.0019558,
- 0.0969824,
- 0.0355924,
- 0.0121521,
- 0.0125871,
- 0.311561,
- 0.211337,
- 0.00471386,
- 0.0016329,
- 0.00179911
- ],
- [ 0.0181409,
- 0.00851436,
- 0.00333335,
- 0.00965319,
- 0.00354269,
- 0.0224553,
- 0.0375239,
- 0.00350905,
- 0.320807,
- 0.0149147,
- 0.00460989,
- 0.0233205,
- 0.00871975,
- 0.0526694,
- 0.412966,
- 0.0262309,
- 0.0131791,
- 0.00447465,
- 0.0034767,
- 0.00795882
- ],
- [ 0.249423,
- 0.0122863,
- 0.0169234,
- 0.0370491,
- 0.00773609,
- 0.0347468,
- 0.00870696,
- 0.0595718,
- 0.0177065,
- 0.0451065,
- 0.0204556,
- 0.016412,
- 0.0686404,
- 0.0228502,
- 0.0185482,
- 0.0889296,
- 0.0986017,
- 0.167252,
- 0.00286039,
- 0.00619385
- ],
- [ 0.141974,
- 0.00688567,
- 0.0537452,
- 0.040754,
- 0.00402861,
- 0.398811,
- 0.0152896,
- 0.00166276,
- 0.0314274,
- 0.00923483,
- 0.00554255,
- 0.0576297,
- 0.0180329,
- 0.028624,
- 0.0373946,
- 0.112373,
- 0.0242478,
- 0.00484629,
- 0.00259091,
- 0.00490542
- ],
- [ 0.0178903,
- 0.0290304,
- 0.00310543,
- 0.00405034,
- 0.0238913,
- 0.010048,
- 0.12527,
- 0.0016708,
- 0.023334,
- 0.0722357,
- 0.0116142,
- 0.0155854,
- 0.000993842,
- 0.105182,
- 0.195884,
- 0.0181676,
- 0.018626,
- 0.0113865,
- 0.226055,
- 0.0859787
- ],
- [ 0.145476,
- 0.00141863,
- 0.129425,
- 0.247135,
- 0.00175521,
- 0.0319651,
- 0.0130426,
- 0.00585254,
- 0.0818154,
- 0.0123593,
- 0.00441789,
- 0.040042,
- 0.0151136,
- 0.0906469,
- 0.0420979,
- 0.0656688,
- 0.0511289,
- 0.0169401,
- 0.000773144,
- 0.00292584
- ],
- [ 0.0169799,
- 0.00220872,
- 0.104366,
- 0.037638,
- 0.000678059,
- 0.540447,
- 0.0181137,
- 0.000745968,
- 0.0508618,
- 0.0021147,
- 0.000947377,
- 0.131805,
- 0.00387544,
- 0.026935,
- 0.0242347,
- 0.029703,
- 0.00458362,
- 0.00158917,
- 0.000603189,
- 0.00157041
- ],
- [ 0.0402646,
- 0.00393887,
- 0.0293968,
- 0.160352,
- 0.00411534,
- 0.012926,
- 0.0617968,
- 0.00984913,
- 0.14488,
- 0.0354919,
- 0.0124819,
- 0.0323829,
- 0.00433742,
- 0.249701,
- 0.115202,
- 0.0243247,
- 0.0305645,
- 0.0156027,
- 0.00266766,
- 0.00972278
- ],
- [ 0.225691,
- 0.00433901,
- 0.0637125,
- 0.115483,
- 0.00274401,
- 0.0867335,
- 0.0131067,
- 0.00850862,
- 0.0660469,
- 0.0193314,
- 0.00648772,
- 0.0244309,
- 0.0611149,
- 0.0578159,
- 0.0523417,
- 0.107088,
- 0.0507677,
- 0.0299883,
- 0.00136959,
- 0.00289829
- ],
- [ 0.00331642,
- 0.00518907,
- 0.000826647,
- 0.000513413,
- 0.380176,
- 0.00104328,
- 0.0278451,
- 0.00418953,
- 0.000714992,
- 0.0111212,
- 0.00236218,
- 0.00308302,
- 0.000836508,
- 0.00110249,
- 0.00153108,
- 0.00358767,
- 0.00236089,
- 0.00607663,
- 0.0333347,
- 0.510789
- ],
- [ 0.199501,
- 0.058459,
- 0.00949551,
- 0.0125535,
- 0.0634434,
- 0.0939787,
- 0.0341857,
- 0.014021,
- 0.0118723,
- 0.0449388,
- 0.0246991,
- 0.0392255,
- 0.0145385,
- 0.0254265,
- 0.0236079,
- 0.166392,
- 0.0533159,
- 0.0367303,
- 0.0129803,
- 0.0606346
- ],
- [ 0.0319449,
- 0.00660403,
- 0.0378075,
- 0.0279488,
- 0.0108916,
- 0.0365541,
- 0.208864,
- 0.00475423,
- 0.0868665,
- 0.0156546,
- 0.00432533,
- 0.208471,
- 0.00608996,
- 0.0766373,
- 0.101167,
- 0.0577657,
- 0.0302051,
- 0.00605852,
- 0.00260019,
- 0.0387897
- ],
- [ 0.07768,
- 0.0140093,
- 0.00806517,
- 0.0112622,
- 0.0173585,
- 0.0136868,
- 0.013373,
- 0.123964,
- 0.0129145,
- 0.0724671,
- 0.0420745,
- 0.0403217,
- 0.0117084,
- 0.0179996,
- 0.0142519,
- 0.0922724,
- 0.23169,
- 0.167914,
- 0.00281536,
- 0.0141727
- ],
- [ 0.118366,
- 0.00356248,
- 0.0495595,
- 0.153759,
- 0.00686657,
- 0.0194993,
- 0.0229373,
- 0.0302661,
- 0.0982304,
- 0.0571251,
- 0.0171727,
- 0.0259525,
- 0.0175153,
- 0.120492,
- 0.0805193,
- 0.0486588,
- 0.0635796,
- 0.0553336,
- 0.00230083,
- 0.00830274
- ],
- [ 0.052856,
- 0.000862588,
- 0.209276,
- 0.402419,
- 0.00126507,
- 0.0155838,
- 0.0124149,
- 0.00548648,
- 0.0497017,
- 0.00902565,
- 0.00423571,
- 0.0264744,
- 0.00631856,
- 0.121241,
- 0.0193569,
- 0.0197263,
- 0.0235464,
- 0.0159764,
- 0.000838161,
- 0.00339487
- ],
- [ 0.0344366,
- 0.0020986,
- 0.113901,
- 0.054178,
- 0.00315576,
- 0.336164,
- 0.0461777,
- 0.000346342,
- 0.0667553,
- 0.00483557,
- 0.00197045,
- 0.163672,
- 0.00403698,
- 0.0605414,
- 0.0426222,
- 0.0481173,
- 0.00891481,
- 0.00201106,
- 0.00065101,
- 0.00541456
- ],
- [ 0.115309,
- 0.00149624,
- 0.175552,
- 0.174941,
- 0.00157002,
- 0.0394181,
- 0.0132402,
- 0.0056913,
- 0.0433118,
- 0.010141,
- 0.00303321,
- 0.0458477,
- 0.16658,
- 0.0366731,
- 0.0151279,
- 0.0871536,
- 0.0468261,
- 0.0141932,
- 0.00075157,
- 0.00314327
- ],
- [ 0.386515,
- 0.0218928,
- 0.00223668,
- 0.00313878,
- 0.00392814,
- 0.369435,
- 0.00146729,
- 0.00853761,
- 0.00188405,
- 0.0127257,
- 0.00805817,
- 0.00304205,
- 0.0158688,
- 0.00214647,
- 0.00375793,
- 0.0808877,
- 0.0305196,
- 0.0410635,
- 0.000992288,
- 0.00190203
- ],
- [ 0.0146571,
- 0.00243179,
- 0.000521057,
- 0.00148744,
- 0.00916375,
- 0.00209533,
- 0.00101819,
- 0.19139,
- 0.00228984,
- 0.44328,
- 0.221743,
- 0.00129983,
- 0.000768515,
- 0.00493628,
- 0.00288413,
- 0.00272515,
- 0.0170997,
- 0.0778557,
- 0.000877938,
- 0.0014756
- ]
- ]
-
--- | Weights of C60 model.
-c60Weights :: [Double]
-c60Weights =
- [ 0.0169699,
- 0.0211683,
- 0.0276589,
- 0.0065676,
- 0.0141221,
- 0.00687748,
- 0.014691,
- 0.00672258,
- 0.00183967,
- 0.0102547,
- 0.0230896,
- 0.0057941,
- 0.0125395,
- 0.0204526,
- 0.00706296,
- 0.0117983,
- 0.00683347,
- 0.0433776,
- 0.0318279,
- 0.0222546,
- 0.0102265,
- 0.0150546,
- 0.013416,
- 0.0148552,
- 0.0239112,
- 0.0128776,
- 0.0222319,
- 0.0247445,
- 0.0214275,
- 0.0115002,
- 0.00760174,
- 0.0130259,
- 0.0093702,
- 0.0467194,
- 0.044194,
- 0.0322263,
- 0.0403,
- 0.0150234,
- 0.010459,
- 0.0214742,
- 0.0154958,
- 0.010179,
- 0.022798,
- 0.0123205,
- 0.00667776,
- 0.000415008,
- 0.0344385,
- 0.0113663,
- 0.0127143,
- 0.0124324,
- 0.0262124,
- 0.0064995,
- 0.0103203,
- 0.0142464,
- 0.02156,
- 0.0199151,
- 0.00389642,
- 0.0113449,
- 0.0128596,
- 0.0117657
- ]
diff --git a/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs b/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs
+++ /dev/null
@@ -1,125 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.GammaRateHeterogeneity
--- Description : Discrete gamma rate heterogeneity
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Thu Feb 28 14:09:11 2019.
---
--- At the moment, a mixture model is used to emulate gamma rate heterogeneity. This
--- does not come with huge run time increases when simulating data. For inference
--- however, it would make a lot of sense to reuse the Eigendecomposition for all
--- rate heterogeneity components though.
-module ELynx.Data.MarkovProcess.GammaRateHeterogeneity
- ( summarizeGammaRateHeterogeneity,
- expand,
- )
-where
-
-import qualified Data.ByteString.Lazy.Char8 as BL
-import qualified Data.Vector as V
-import qualified ELynx.Data.MarkovProcess.MixtureModel as M
-import qualified ELynx.Data.MarkovProcess.PhyloModel as P
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-import Numeric.Integration.TanhSinh
-import Statistics.Distribution
-import Statistics.Distribution.Gamma
-import Prelude hiding (repeat)
-
--- | Short summary of gamma rate heterogeneity parameters.
-summarizeGammaRateHeterogeneity :: Int -> Double -> [BL.ByteString]
-summarizeGammaRateHeterogeneity n alpha =
- map
- BL.pack
- [ "Discrete gamma rate heterogeneity.",
- "Number of categories: " ++ show n,
- "Shape parameter of gamma distribution: " ++ show alpha,
- "Rates: " ++ show (getMeans n alpha)
- ]
-
--- | For a given number of rate categories, a gamma shape parameter alpha and a
--- substitution model, compute the scaled substitution models corresponding to
--- the gamma rates.
-expand :: Int -> Double -> P.PhyloModel -> P.PhyloModel
-expand n alpha (P.SubstitutionModel sm) =
- P.MixtureModel $ expandSubstitutionModel n alpha sm
-expand n alpha (P.MixtureModel mm) =
- P.MixtureModel $ expandMixtureModel n alpha mm
-
-getName :: Int -> Double -> String
-getName n alpha =
- " with discrete gamma rate heterogeneity; "
- ++ show n
- ++ " categories; "
- ++ "shape parameter "
- ++ show alpha
-
-splitSubstitutionModel ::
- Int -> Double -> S.SubstitutionModel -> V.Vector S.SubstitutionModel
-splitSubstitutionModel n alpha sm = renamedSMs
- where
- means = getMeans n alpha
- scaledSMs = V.map (`S.scale` sm) means
- names = V.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
- renamedSMs = V.zipWith S.appendName names scaledSMs
-
-expandSubstitutionModel ::
- Int -> Double -> S.SubstitutionModel -> M.MixtureModel
-expandSubstitutionModel n alpha sm = M.fromSubstitutionModels name ws sms
- where
- name = S.name sm <> getName n alpha
- ws = V.replicate n 1.0
- sms = splitSubstitutionModel n alpha sm
-
-expandMixtureModel :: Int -> Double -> M.MixtureModel -> M.MixtureModel
-expandMixtureModel n alpha mm = M.concatenate name renamedMMs
- where
- name = M.name mm <> getName n alpha
- means = getMeans n alpha
- scaledMMs = V.map (`M.scale` mm) means
- names = V.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
- renamedMMs = V.zipWith M.appendNameComponents names scaledMMs
-
--- For a given number of rate categories 'n' and a shape parameter 'alpha' (the
--- rate or scale is set such that the mean is 1.0), return a list of rates that
--- represent the respective categories. Use the mean rate for each category.
-getMeans :: Int -> Double -> V.Vector Double
-getMeans n alpha
- | n <= 0 = error "getMeans: Number of rate categories is zero or negative."
- | otherwise = means <> pure lastMean
- where
- gamma = gammaDistr alpha (1.0 / alpha)
- quantiles =
- [quantile gamma (fromIntegral i / fromIntegral n) | i <- [0 .. n]]
- -- Calculate the mean rate. Multiplication with the number of rate
- -- categories 'n' is necessary because in each n-quantile the
- -- probability mass is 1/n.
- meanFunc x = fromIntegral n * x * density gamma x
- -- Only calculate the first (n-1) categories with normal integration.
- means =
- V.fromList
- [ integralAToB meanFunc (quantiles !! i) (quantiles !! (i + 1))
- | i <- [0 .. n - 2]
- ]
- -- The last category has to be calculated with an improper integration.
- lastMean = integralAToInf meanFunc (quantiles !! (n - 1))
-
-eps :: Double
-eps = 1e-8
-
--- The integration method to use
-method :: (Double -> Double) -> Double -> Double -> [Result]
-method = parSimpson
-
--- Helper function for a normal integral from 'a' to 'b'.
-integralAToB :: (Double -> Double) -> Double -> Double -> Double
-integralAToB f a b = result . absolute eps $ method f a b
-
--- Helper function for an improper integral from 'a' to infinity.
-integralAToInf :: (Double -> Double) -> Double -> Double
-integralAToInf f a =
- (result . absolute eps $ nonNegative method f) - integralAToB f 0 a
diff --git a/src/ELynx/Data/MarkovProcess/MixtureModel.hs b/src/ELynx/Data/MarkovProcess/MixtureModel.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/MixtureModel.hs
+++ /dev/null
@@ -1,118 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.MixtureModel
--- Description : Mixture models are a set of substitution models with weights
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Jan 29 19:17:40 2019.
---
--- To be imported qualified.
-module ELynx.Data.MarkovProcess.MixtureModel
- ( -- * Types
- Weight,
- Component (weight, substModel),
- MixtureModel (name, alphabet, components),
-
- -- * Getters
- getWeights,
- getSubstitutionModels,
-
- -- * Building mixture models
- fromSubstitutionModels,
-
- -- * Transformations
- concatenate,
- scale,
- normalize,
- appendNameComponents,
- )
-where
-
-import qualified Data.Vector as V
-import ELynx.Data.Alphabet.Alphabet hiding (all)
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-import Prelude
-
--- | Mixture model component weight.
-type Weight = Double
-
--- | A mixture model component has a weight and a substitution model.
-data Component = Component
- { weight :: Weight,
- substModel :: S.SubstitutionModel
- }
- deriving (Show, Read)
-
--- | A mixture model with its components.
-data MixtureModel = MixtureModel
- { -- | Name
- name :: S.Name,
- alphabet :: Alphabet,
- components :: V.Vector Component
- }
- deriving (Show, Read)
-
--- | Get weights.
-getWeights :: MixtureModel -> V.Vector Weight
-getWeights = V.map weight . components
-
--- | Get substitution models.
-getSubstitutionModels :: MixtureModel -> V.Vector S.SubstitutionModel
-getSubstitutionModels = V.map substModel . components
-
--- | Create a mixture model from a list of substitution models.
-fromSubstitutionModels :: S.Name -> V.Vector Weight -> V.Vector S.SubstitutionModel -> MixtureModel
-fromSubstitutionModels n ws sms
- | null ws = error "fromSubstitutionModels: No weights given."
- | length ws /= length sms = error "fromSubstitutionModels: Number of weights and substitution models does not match."
- | not $ allEqual alphs = error "fromSubstitutionModels: alphabets of substitution models are not equal."
- | otherwise = MixtureModel n (V.head alphs) comps
- where
- comps = V.zipWith Component ws sms
- alphs = V.map S.alphabet sms
- allEqual xs
- | V.null xs = True
- | otherwise = V.all (== V.head xs) xs
-
--- | Concatenate mixture models.
-concatenate :: S.Name -> V.Vector MixtureModel -> MixtureModel
-concatenate n mms = fromSubstitutionModels n ws sms
- where
- comps = V.concatMap components mms
- ws = V.map weight comps
- sms = V.map substModel comps
-
-scaleComponent :: Double -> Component -> Component
-scaleComponent s c = c {substModel = s'} where s' = S.scale s $ substModel c
-
--- | Scale all substitution models of the mixture model.
-scale :: Double -> MixtureModel -> MixtureModel
-scale s m = m {components = cs'}
- where
- cs = components m
- cs' = V.map (scaleComponent s) cs
-
--- | Globally normalize a mixture model so that on average one event happens per
--- unit time.
-normalize :: MixtureModel -> MixtureModel
-normalize mm = scale (1 / c) mm
- where
- c = sum $ V.zipWith (*) weights scales
- weights = getWeights mm
- scales = V.map S.totalRate $ getSubstitutionModels mm
-
-appendNameComponent :: S.Name -> Component -> Component
-appendNameComponent n c = c {substModel = s'}
- where
- s' = S.appendName n $ substModel c
-
--- | Append byte string to all substitution models of mixture model.
-appendNameComponents :: S.Name -> MixtureModel -> MixtureModel
-appendNameComponents n m = m {components = cs'}
- where
- cs = components m
- cs' = V.map (appendNameComponent n) cs
diff --git a/src/ELynx/Data/MarkovProcess/Nucleotide.hs b/src/ELynx/Data/MarkovProcess/Nucleotide.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/Nucleotide.hs
+++ /dev/null
@@ -1,104 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.Nucleotide
--- Description : Substitution models using nucleotides
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Thu Jan 24 08:33:26 2019.
---
--- XXX: Maybe rename to something like /DNA substitution models/. Nucleotide ~
--- Alphabet; DNA ~ Character.
---
--- The order of nucleotides is A, C, G, T; see 'ELynx.Data.Character.Nucleotide'.
---
--- For the different DNA substitution models, please see
--- https://en.wikipedia.org/wiki/Models_of_DNA_evolution
-module ELynx.Data.MarkovProcess.Nucleotide
- ( jc,
- f81,
- hky,
- gtr4,
- )
-where
-
-import qualified Data.Vector.Storable as V
-import ELynx.Data.Alphabet.Alphabet
-import ELynx.Data.MarkovProcess.RateMatrix
-import ELynx.Data.MarkovProcess.SubstitutionModel
-import Numeric.LinearAlgebra hiding (normalize)
-
--- XXX: Another idea of structuring the code. This would probably be cleaner in
--- the long run.
-
--- data PhyloModel = MixtureModel | SubstitutionModel
-
---
--- I think it could simply be:
--- data PhyloModel = [(Weight, SubstitutionModel)]
---
-
--- data MixtureModel = [(Weight, SubstitutionModel)]
-
--- data SubstitutionModel = SMDNA DNASubstitutionModel | SMAA AASubstitutionModel
-
--- data DNASubstitutionModel = JC | HKY Double StationaryDistribution
-
--- data AASubstitutionModel = LG | ...
-
-n :: Int
--- n = length (alphabet :: [Nucleotide])
--- Hard code this here. Reduces model dependencies, and number of nucleotides
--- will not change.
-n = 4
-
--- | JC model matrix.
-jcExch :: ExchangeabilityMatrix
-jcExch =
- (n >< n)
- [ 0.0,
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 0.0,
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 0.0,
- 1.0,
- 1.0,
- 1.0,
- 1.0,
- 0.0
- ]
-
-uniformVec :: Vector Double
-uniformVec = V.replicate n (1 / fromIntegral n)
-
--- | JC substitution model.
-jc :: SubstitutionModel
-jc = substitutionModel DNA "JC" [] uniformVec jcExch
-
--- | F81 substitution model.
-f81 :: StationaryDistribution -> SubstitutionModel
-f81 d = substitutionModel DNA "F81" [] d jcExch
-
-hkyExch :: Double -> ExchangeabilityMatrix
-hkyExch k =
- (n >< n)
- [0.0, 1.0, k, 1.0, 1.0, 0.0, 1.0, k, k, 1.0, 0.0, 1.0, 1.0, k, 1.0, 0.0]
-
--- | HKY substitution model.
-hky :: Double -> StationaryDistribution -> SubstitutionModel
-hky k d = substitutionModel DNA "HKY" [k] d e where e = hkyExch k
-
--- | HKY substitution model.
-gtr4 :: [Double] -> StationaryDistribution -> SubstitutionModel
-gtr4 es d = substitutionModel DNA "GTR" es d e
- where
- e = exchFromListUpper n es
diff --git a/src/ELynx/Data/MarkovProcess/PhyloModel.hs b/src/ELynx/Data/MarkovProcess/PhyloModel.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/PhyloModel.hs
+++ /dev/null
@@ -1,36 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.PhyloModel
--- Description : Phylogenetic model
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Fri Feb 1 12:43:06 2019.
---
--- A phylogenetic model is a complete description of the evolutionary process. At
--- the moment, it is either a mixture model or a plain substitution model, but more
--- complicated models may be added in the future.
---
--- To be imported qualified.
-module ELynx.Data.MarkovProcess.PhyloModel
- ( PhyloModel (..),
- getAlphabet,
- )
-where
-
-import ELynx.Data.Alphabet.Alphabet
-import qualified ELynx.Data.MarkovProcess.MixtureModel as M
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-
--- | A phylogenetic model is a mixture model or a substitution model. More
--- complicated models may be added.
-data PhyloModel = MixtureModel M.MixtureModel | SubstitutionModel S.SubstitutionModel
- deriving (Show, Read)
-
--- | Extract code from phylogenetic model.
-getAlphabet :: PhyloModel -> Alphabet
-getAlphabet (MixtureModel mm) = M.alphabet mm
-getAlphabet (SubstitutionModel sm) = S.alphabet sm
diff --git a/src/ELynx/Data/MarkovProcess/RateMatrix.hs b/src/ELynx/Data/MarkovProcess/RateMatrix.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/RateMatrix.hs
+++ /dev/null
@@ -1,225 +0,0 @@
-{-# LANGUAGE FlexibleContexts #-}
-
--- |
--- Description : Rate matrix helper functions
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPLv3
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : non-portable (not tested)
---
--- Some helper functions that come handy when working with rate matrices of
--- continuous-time discrete-state Markov processes.
---
--- * Changelog
---
--- To be imported qualified.
-module ELynx.Data.MarkovProcess.RateMatrix
- ( RateMatrix,
- ExchangeabilityMatrix,
- StationaryDistribution,
- isValid,
- normalizeSD,
- totalRate,
- totalRateWith,
- normalize,
- normalizeWith,
- setDiagonal,
- toExchangeabilityMatrix,
- fromExchangeabilityMatrix,
- getStationaryDistribution,
- exchFromListLower,
- exchFromListUpper,
- )
-where
-
-import qualified Data.Vector.Storable as V
-import Numeric.LinearAlgebra hiding (normalize)
-import Numeric.SpecFunctions
-import Prelude hiding ((<>))
-
--- | A rate matrix is just a real matrix.
-type RateMatrix = Matrix R
-
--- | A matrix of exchangeabilities, we have q = e * pi, where q is a rate
--- matrix, e is the exchangeability matrix and pi is the diagonal matrix
--- containing the stationary frequency distribution.
-type ExchangeabilityMatrix = Matrix R
-
--- | Stationary distribution of a rate matrix.
-type StationaryDistribution = Vector R
-
-epsRelaxed :: Double
-epsRelaxed = 1e-5
-
--- | True if distribution sums to 1.0.
-isValid :: StationaryDistribution -> Bool
-isValid d = epsRelaxed > abs (norm_1 d - 1.0)
-
--- | Normalize a stationary distribution so that the elements sum to 1.0.
-normalizeSD :: StationaryDistribution -> StationaryDistribution
-normalizeSD d = d / scalar (norm_1 d)
-
-matrixSetDiagToZero :: Matrix R -> Matrix R
-matrixSetDiagToZero m = m - diag (takeDiag m)
-{-# INLINE matrixSetDiagToZero #-}
-
--- | Get average number of substitutions per unit time.
-totalRateWith :: StationaryDistribution -> RateMatrix -> Double
-totalRateWith d m = norm_1 $ d <# matrixSetDiagToZero m
-
--- | Get average number of substitutions per unit time.
-totalRate :: RateMatrix -> Double
-totalRate m = totalRateWith (getStationaryDistribution m) m
-
--- | Normalizes a Markov process generator such that one event happens per unit
--- time. Calculates stationary distribution from rate matrix.
-normalize :: RateMatrix -> RateMatrix
-normalize m = normalizeWith (getStationaryDistribution m) m
-
--- | Normalizes a Markov process generator such that one event happens per unit
--- time. Faster, but stationary distribution has to be given.
-normalizeWith :: StationaryDistribution -> RateMatrix -> RateMatrix
-normalizeWith d m = scale (1.0 / totalRateWith d m) m
-
--- | Set the diagonal entries of a matrix such that the rows sum to 0.
-setDiagonal :: RateMatrix -> RateMatrix
-setDiagonal m = diagZeroes - diag (fromList rowSums)
- where
- diagZeroes = matrixSetDiagToZero m
- rowSums = map norm_1 $ toRows diagZeroes
-
--- | Extract the exchangeability matrix from a rate matrix.
-toExchangeabilityMatrix ::
- RateMatrix -> StationaryDistribution -> ExchangeabilityMatrix
-toExchangeabilityMatrix m f = m <> diag oneOverF
- where
- oneOverF = cmap (1.0 /) f
-
--- | Convert exchangeability matrix to rate matrix.
-fromExchangeabilityMatrix ::
- ExchangeabilityMatrix -> StationaryDistribution -> RateMatrix
-fromExchangeabilityMatrix em d = setDiagonal $ em <> diag d
-
-eps :: Double
-eps = 1e-12
-
-normalizeSumVec :: V.Vector Double -> V.Vector Double
-normalizeSumVec v = V.map (/ s) v
- where
- s = V.sum v
-{-# INLINE normalizeSumVec #-}
-
--- | Get stationary distribution from 'RateMatrix'. Involves eigendecomposition.
--- If the given matrix does not satisfy the required properties of transition
--- rate matrices and no eigenvector with an eigenvalue nearly equal to 0 is
--- found, an error is thrown. Is there an easier way to calculate the stationary
--- distribution or a better way to handle errors (of course I could use the
--- Maybe monad, but then the error report is just delayed to the calling
--- function)?
-getStationaryDistribution :: RateMatrix -> StationaryDistribution
-getStationaryDistribution m =
- if eps > abs (magnitude (eVals ! i))
- then normalizeSumVec distReal
- else error "getStationaryDistribution: Could not retrieve stationary distribution."
- where
- (eVals, eVecs) = eig (tr m)
- i = minIndex eVals
- distComplex = toColumns eVecs !! i
- distReal = cmap realPart distComplex
-
--- The next functions tackle the somewhat trivial, but not easily solvable
--- problem of converting a triangular matrix (excluding the diagonal) given as a
--- list into a symmetric matrix. The diagonal entries are set to zero.
-
--- Lower triangular matrix. This is how the exchangeabilities are specified in
--- PAML. Conversion from matrix indices (i,j) to list index k.
---
--- (i,j) k
---
--- (0,0) -
--- (1,0) 0 (1,1) -
--- (2,0) 1 (2,1) 2 (2,2) -
--- (3,0) 3 (3,1) 4 (3,2) 5 (3,3) -
--- (4,0) 6 (4,1) 7 (4,2) 8 (4,3) 9 (4,4) -
--- .
--- .
--- .
---
--- k = (i choose 2) + j.
-ijToKLower :: Int -> Int -> Int
-ijToKLower i j
- | i > j = round (i `choose` 2) + j
- | otherwise = error "ijToKLower: not defined for upper triangular matrix."
-
--- Upper triangular matrix. Conversion from matrix indices (i,j) to list index
--- k. Matrix is square of size n.
---
--- (i,j) k
---
--- (0,0) - (0,1) 0 (0,2) 1 (0,3) 2 (0,4) 3 ...
--- (1,1) - (1,2) n-1 (1,3) n (1,4) n+1
--- (2,2) - (2,3) 2n-3 (2,4) 2n-2
--- (3,3) - (3,4) 3n-6
--- (4,4) -
--- ...
---
--- k = i*(n-2) - (i choose 2) + (j - 1)
-ijToKUpper :: Int -> Int -> Int -> Int
-ijToKUpper n i j
- | i < j = i * (n - 2) - round (i `choose` 2) + j - 1
- | otherwise = error "ijToKUpper: not defined for lower triangular matrix."
-
--- The function is a little weird because HMatrix uses Double indices for Matrix
--- Double builders.
-fromListBuilderLower :: RealFrac a => [a] -> a -> a -> a
-fromListBuilderLower es i j
- | i > j = es !! ijToKLower iI jI
- | i == j = 0.0
- | i < j = es !! ijToKLower jI iI
- | otherwise =
- error
- "Float indices could not be compared during matrix creation."
- where
- iI = round i :: Int
- jI = round j :: Int
-
--- The function is a little weird because HMatrix uses Double indices for Matrix
--- Double builders.
-fromListBuilderUpper :: RealFrac a => Int -> [a] -> a -> a -> a
-fromListBuilderUpper n es i j
- | i < j = es !! ijToKUpper n iI jI
- | i == j = 0.0
- | i > j = es !! ijToKUpper n jI iI
- | otherwise =
- error
- "Float indices could not be compared during matrix creation."
- where
- iI = round i :: Int
- jI = round j :: Int
-
-checkEs :: RealFrac a => Int -> [a] -> [a]
-checkEs n es
- | length es == nExp = es
- | otherwise = error eStr
- where
- nExp = round (n `choose` 2)
- eStr =
- unlines
- [ "exchFromListlower: the number of exchangeabilities does not match the matrix size",
- "matrix size: " ++ show n,
- "expected number of exchangeabilities: " ++ show nExp,
- "received number of exchangeabilities: " ++ show (length es)
- ]
-
--- | Build exchangeability matrix from list denoting lower triangular matrix,
--- and excluding diagonal. This is how the exchangeabilities are specified in
--- PAML.
-exchFromListLower :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
-exchFromListLower n es = build (n, n) (fromListBuilderLower (checkEs n es))
-
--- | Build exchangeability matrix from list denoting upper triangular matrix,
--- and excluding diagonal.
-exchFromListUpper :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
-exchFromListUpper n es = build (n, n) (fromListBuilderUpper n (checkEs n es))
diff --git a/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs b/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs
deleted file mode 100644
--- a/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs
+++ /dev/null
@@ -1,124 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.SubstitutionModel
--- Description : Data type describing substitution model
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Jan 29 19:10:46 2019.
---
--- To be imported qualified.
-module ELynx.Data.MarkovProcess.SubstitutionModel
- ( -- * Types
- Name,
- Params,
- SubstitutionModel,
-
- -- * Accessors
- alphabet,
- name,
- params,
- stationaryDistribution,
- exchangeabilityMatrix,
- rateMatrix,
- totalRate,
-
- -- * Building substitution models
- substitutionModel,
-
- -- * Transformations
- scale,
- normalize,
- appendName,
- )
-where
-
-import qualified Data.Vector.Storable as V
-import ELynx.Data.Alphabet.Alphabet
-import qualified ELynx.Data.MarkovProcess.RateMatrix as R
-import qualified Numeric.LinearAlgebra as LinAlg
-
--- | Name of substitution model; abstracted and subject to change.
-type Name = String
-
--- | Parameters of substitution model. May be the empty list.
-type Params = [Double]
-
--- XXX: Use a proper data type. For example:
--- data SubstitutionModelAA = LG | WAG | LG-Custom dist | ...
--- data SubstitutionModelNuc = JC | HKY p1 p2 ... | GTR p1 p2 ...
---
--- I thought about this a lot, and it seems easier like it is at the moment.
--- Since the data types are abstracted anyways, not much harm can be done. Of
--- course, conflicting substitution models can be declared, or duplicate ones
--- with different names, but well...
-
--- | Complete definition of a substitution model. Create instances with
--- 'substitutionModel'. A substitution model has an alphabet, a name, and a list
--- of parameters (e.g., the kappa value for the HKY model). Further, the
--- transition rate matrix is defined by a stationary distribution and a set of
--- exchangeabilities.
-data SubstitutionModel = SubstitutionModel
- { -- | Alphabet
- alphabet :: Alphabet,
- -- | Name
- name :: Name,
- -- | List of parameters
- params :: Params,
- -- | Stationary distribution
- stationaryDistribution :: R.StationaryDistribution,
- -- | Exchangeability matrix
- exchangeabilityMatrix :: R.ExchangeabilityMatrix
- }
- deriving (Show, Read)
-
--- | Calculate rate matrix from substitution model.
-rateMatrix :: SubstitutionModel -> R.RateMatrix
-rateMatrix sm =
- R.fromExchangeabilityMatrix
- (exchangeabilityMatrix sm)
- (stationaryDistribution sm)
-
--- | Get scale of substitution model.
-totalRate :: SubstitutionModel -> Double
-totalRate sm = R.totalRate (rateMatrix sm)
-
-normalizeSumVec :: V.Vector Double -> V.Vector Double
-normalizeSumVec v = V.map (/ s) v
- where
- s = V.sum v
-{-# INLINE normalizeSumVec #-}
-
--- | Create normalized 'SubstitutionModel'. See 'normalize'.
-substitutionModel ::
- Alphabet ->
- Name ->
- Params ->
- R.StationaryDistribution ->
- R.ExchangeabilityMatrix ->
- SubstitutionModel
-substitutionModel c n ps d e =
- if R.isValid d
- then normalize $ SubstitutionModel c n ps (normalizeSumVec d) e
- else
- error $
- "substitionModel: Stationary distribution does not sum to 1.0: "
- ++ show d
-
--- | Scale the rate of a substitution model by given factor.
-scale :: Double -> SubstitutionModel -> SubstitutionModel
-scale r sm = sm {exchangeabilityMatrix = em'}
- where
- em' = LinAlg.scale r $ exchangeabilityMatrix sm
-
--- | Normalize a substitution model, so that, on average, one substitution
--- happens per unit time.
-normalize :: SubstitutionModel -> SubstitutionModel
-normalize sm = scale (1.0 / r) sm where r = totalRate sm
-
--- | Abbend to name.
-appendName :: Name -> SubstitutionModel -> SubstitutionModel
-appendName n sm = sm {name = n'} where n' = name sm <> n
diff --git a/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs b/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs
--- a/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs
+++ b/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs
@@ -23,7 +23,7 @@
import qualified Data.Attoparsec.ByteString.Char8 as AC
import qualified Data.ByteString.Lazy.Char8 as BL
import qualified Data.Vector.Storable as V
-import ELynx.Data.MarkovProcess.MixtureModel
+import ELynx.MarkovProcess.MixtureModel
-- | An empirical mixture model component has a weight and a stationary
-- distribution.
diff --git a/src/ELynx/MarkovProcess/AminoAcid.hs b/src/ELynx/MarkovProcess/AminoAcid.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/AminoAcid.hs
@@ -0,0 +1,647 @@
+-- |
+-- Module : ELynx.MarkovProcess.AminoAcid
+-- Description : Amino acid rate matrices such as LG
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Jan 29 09:29:19 2019.
+--
+-- The order of amino acids is alphabetic.
+module ELynx.MarkovProcess.AminoAcid
+ ( -- * Amino acid substitution models
+ lg,
+ lgCustom,
+ wag,
+ wagCustom,
+ poisson,
+ poissonCustom,
+ gtr20,
+
+ -- * Convenience functions
+ alphaToPamlVec,
+ pamlToAlphaVec,
+ )
+where
+
+import Data.ByteString.Internal (c2w)
+import Data.Maybe (fromMaybe)
+import qualified Data.Vector.Storable as V
+import Data.Word (Word8)
+import ELynx.Alphabet.Alphabet
+import ELynx.MarkovProcess.RateMatrix
+import ELynx.MarkovProcess.SubstitutionModel
+import Numeric.LinearAlgebra
+
+n :: Int
+n = 20
+
+-- Some matrices have to be converted from PAML order to alphabetical order. See
+-- 'pamlToAlphaVec' and 'pamlToAlphaMat'.
+
+-- Amno acids in alphabetical order.
+aaAlphaOrder :: V.Vector Word8
+aaAlphaOrder =
+ V.map
+ c2w
+ $ V.fromList
+ [ 'A',
+ 'C',
+ 'D',
+ 'E',
+ 'F',
+ 'G',
+ 'H',
+ 'I',
+ 'K',
+ 'L',
+ 'M',
+ 'N',
+ 'P',
+ 'Q',
+ 'R',
+ 'S',
+ 'T',
+ 'V',
+ 'W',
+ 'Y'
+ ]
+
+-- Amino acids in PAML oder.
+aaPamlOrder :: V.Vector Word8
+aaPamlOrder =
+ V.map
+ c2w
+ $ V.fromList
+ [ 'A',
+ 'R',
+ 'N',
+ 'D',
+ 'C',
+ 'Q',
+ 'E',
+ 'G',
+ 'H',
+ 'I',
+ 'L',
+ 'K',
+ 'M',
+ 'F',
+ 'P',
+ 'S',
+ 'T',
+ 'W',
+ 'Y',
+ 'V'
+ ]
+
+alphaIndexToPamlIndex :: Int -> Int
+alphaIndexToPamlIndex i =
+ fromMaybe
+ (error $ "Could not convert index " ++ show i ++ ".")
+ (V.elemIndex aa aaPamlOrder)
+ where
+ aa = aaAlphaOrder V.! i
+
+pamlIndexToAlphaIndex :: Int -> Int
+pamlIndexToAlphaIndex i =
+ fromMaybe
+ (error $ "Could not convert index " ++ show i ++ ".")
+ (V.elemIndex aa aaAlphaOrder)
+ where
+ aa = aaPamlOrder V.! i
+
+-- | Convert an amino acid vector in PAML order to a vector in alphabetical order.
+pamlToAlphaVec :: Vector R -> Vector R
+pamlToAlphaVec v = build n (\i -> v ! alphaIndexToPamlIndex (round i))
+
+-- | Convert an amino acid vector in alphabetical order to a vector in PAML order.
+alphaToPamlVec :: Vector R -> Vector R
+alphaToPamlVec v = build n (\i -> v ! pamlIndexToAlphaIndex (round i))
+
+-- Convert an amino acid matrix in PAML order to a matrix in alphabetical order.
+pamlToAlphaMat :: Matrix R -> Matrix R
+pamlToAlphaMat m =
+ build
+ (n, n)
+ ( \i j -> m ! alphaIndexToPamlIndex (round i) ! alphaIndexToPamlIndex (round j)
+ )
+
+-- Lower triangular matrix of LG exchangeabilities in PAML order and in form of
+-- a list.
+lgExchRawPaml :: [Double]
+lgExchRawPaml =
+ [ 0.425093,
+ 0.276818,
+ 0.751878,
+ 0.395144,
+ 0.123954,
+ 5.076149,
+ 2.489084,
+ 0.534551,
+ 0.528768,
+ 0.062556,
+ 0.969894,
+ 2.807908,
+ 1.695752,
+ 0.523386,
+ 0.084808,
+ 1.038545,
+ 0.363970,
+ 0.541712,
+ 5.243870,
+ 0.003499,
+ 4.128591,
+ 2.066040,
+ 0.390192,
+ 1.437645,
+ 0.844926,
+ 0.569265,
+ 0.267959,
+ 0.348847,
+ 0.358858,
+ 2.426601,
+ 4.509238,
+ 0.927114,
+ 0.640543,
+ 4.813505,
+ 0.423881,
+ 0.311484,
+ 0.149830,
+ 0.126991,
+ 0.191503,
+ 0.010690,
+ 0.320627,
+ 0.072854,
+ 0.044265,
+ 0.008705,
+ 0.108882,
+ 0.395337,
+ 0.301848,
+ 0.068427,
+ 0.015076,
+ 0.594007,
+ 0.582457,
+ 0.069673,
+ 0.044261,
+ 0.366317,
+ 4.145067,
+ 0.536518,
+ 6.326067,
+ 2.145078,
+ 0.282959,
+ 0.013266,
+ 3.234294,
+ 1.807177,
+ 0.296636,
+ 0.697264,
+ 0.159069,
+ 0.137500,
+ 1.124035,
+ 0.484133,
+ 0.371004,
+ 0.025548,
+ 0.893680,
+ 1.672569,
+ 0.173735,
+ 0.139538,
+ 0.442472,
+ 4.273607,
+ 6.312358,
+ 0.656604,
+ 0.253701,
+ 0.052722,
+ 0.089525,
+ 0.017416,
+ 1.105251,
+ 0.035855,
+ 0.018811,
+ 0.089586,
+ 0.682139,
+ 1.112727,
+ 2.592692,
+ 0.023918,
+ 1.798853,
+ 1.177651,
+ 0.332533,
+ 0.161787,
+ 0.394456,
+ 0.075382,
+ 0.624294,
+ 0.419409,
+ 0.196961,
+ 0.508851,
+ 0.078281,
+ 0.249060,
+ 0.390322,
+ 0.099849,
+ 0.094464,
+ 4.727182,
+ 0.858151,
+ 4.008358,
+ 1.240275,
+ 2.784478,
+ 1.223828,
+ 0.611973,
+ 1.739990,
+ 0.990012,
+ 0.064105,
+ 0.182287,
+ 0.748683,
+ 0.346960,
+ 0.361819,
+ 1.338132,
+ 2.139501,
+ 0.578987,
+ 2.000679,
+ 0.425860,
+ 1.143480,
+ 1.080136,
+ 0.604545,
+ 0.129836,
+ 0.584262,
+ 1.033739,
+ 0.302936,
+ 1.136863,
+ 2.020366,
+ 0.165001,
+ 0.571468,
+ 6.472279,
+ 0.180717,
+ 0.593607,
+ 0.045376,
+ 0.029890,
+ 0.670128,
+ 0.236199,
+ 0.077852,
+ 0.268491,
+ 0.597054,
+ 0.111660,
+ 0.619632,
+ 0.049906,
+ 0.696175,
+ 2.457121,
+ 0.095131,
+ 0.248862,
+ 0.140825,
+ 0.218959,
+ 0.314440,
+ 0.612025,
+ 0.135107,
+ 1.165532,
+ 0.257336,
+ 0.120037,
+ 0.054679,
+ 5.306834,
+ 0.232523,
+ 0.299648,
+ 0.131932,
+ 0.481306,
+ 7.803902,
+ 0.089613,
+ 0.400547,
+ 0.245841,
+ 3.151815,
+ 2.547870,
+ 0.170887,
+ 0.083688,
+ 0.037967,
+ 1.959291,
+ 0.210332,
+ 0.245034,
+ 0.076701,
+ 0.119013,
+ 10.649107,
+ 1.702745,
+ 0.185202,
+ 1.898718,
+ 0.654683,
+ 0.296501,
+ 0.098369,
+ 2.188158,
+ 0.189510,
+ 0.249313
+ ]
+
+-- Exchangeabilities of LG model in alphabetical order.
+lgExch :: ExchangeabilityMatrix
+lgExch = pamlToAlphaMat $ exchFromListLower n lgExchRawPaml
+
+normalizeSumVec :: Vector Double -> Vector Double
+normalizeSumVec v = V.map (/ s) v
+ where
+ s = V.sum v
+{-# INLINE normalizeSumVec #-}
+
+-- Stationary distribution in PAML order.
+lgStatDistPaml :: StationaryDistribution
+lgStatDistPaml =
+ normalizeSumVec $
+ fromList
+ [ 0.079066,
+ 0.055941,
+ 0.041977,
+ 0.053052,
+ 0.012937,
+ 0.040767,
+ 0.071586,
+ 0.057337,
+ 0.022355,
+ 0.062157,
+ 0.099081,
+ 0.064600,
+ 0.022951,
+ 0.042302,
+ 0.044040,
+ 0.061197,
+ 0.053287,
+ 0.012066,
+ 0.034155,
+ 0.069147
+ ]
+
+-- Stationary distribution of LG model in alphabetical order.
+lgStatDist :: StationaryDistribution
+lgStatDist = pamlToAlphaVec lgStatDistPaml
+
+-- | LG substitution model.
+lg :: SubstitutionModel
+lg = substitutionModel Protein "LG" [] lgStatDist lgExch
+
+-- | LG substitution model with maybe a name and a custom stationary distribution.
+lgCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+lgCustom mnm d = substitutionModel Protein nm [] d lgExch
+ where
+ nm = fromMaybe "LG-Custom" mnm
+
+-- WAG exchangeability list in PAML order.
+wagExchRawPaml :: [Double]
+wagExchRawPaml =
+ [ 55.15710,
+ 50.98480,
+ 63.53460,
+ 73.89980,
+ 14.73040,
+ 542.94200,
+ 102.70400,
+ 52.81910,
+ 26.52560,
+ 3.02949,
+ 90.85980,
+ 303.55000,
+ 154.36400,
+ 61.67830,
+ 9.88179,
+ 158.28500,
+ 43.91570,
+ 94.71980,
+ 617.41600,
+ 2.13520,
+ 546.94700,
+ 141.67200,
+ 58.46650,
+ 112.55600,
+ 86.55840,
+ 30.66740,
+ 33.00520,
+ 56.77170,
+ 31.69540,
+ 213.71500,
+ 395.62900,
+ 93.06760,
+ 24.89720,
+ 429.41100,
+ 57.00250,
+ 24.94100,
+ 19.33350,
+ 18.69790,
+ 55.42360,
+ 3.94370,
+ 17.01350,
+ 11.39170,
+ 12.73950,
+ 3.04501,
+ 13.81900,
+ 39.79150,
+ 49.76710,
+ 13.15280,
+ 8.48047,
+ 38.42870,
+ 86.94890,
+ 15.42630,
+ 6.13037,
+ 49.94620,
+ 317.09700,
+ 90.62650,
+ 535.14200,
+ 301.20100,
+ 47.98550,
+ 7.40339,
+ 389.49000,
+ 258.44300,
+ 37.35580,
+ 89.04320,
+ 32.38320,
+ 25.75550,
+ 89.34960,
+ 68.31620,
+ 19.82210,
+ 10.37540,
+ 39.04820,
+ 154.52600,
+ 31.51240,
+ 17.41000,
+ 40.41410,
+ 425.74600,
+ 485.40200,
+ 93.42760,
+ 21.04940,
+ 10.27110,
+ 9.61621,
+ 4.67304,
+ 39.80200,
+ 9.99208,
+ 8.11339,
+ 4.99310,
+ 67.93710,
+ 105.94700,
+ 211.51700,
+ 8.88360,
+ 119.06300,
+ 143.85500,
+ 67.94890,
+ 19.50810,
+ 42.39840,
+ 10.94040,
+ 93.33720,
+ 68.23550,
+ 24.35700,
+ 69.61980,
+ 9.99288,
+ 41.58440,
+ 55.68960,
+ 17.13290,
+ 16.14440,
+ 337.07900,
+ 122.41900,
+ 397.42300,
+ 107.17600,
+ 140.76600,
+ 102.88700,
+ 70.49390,
+ 134.18200,
+ 74.01690,
+ 31.94400,
+ 34.47390,
+ 96.71300,
+ 49.39050,
+ 54.59310,
+ 161.32800,
+ 212.11100,
+ 55.44130,
+ 203.00600,
+ 37.48660,
+ 51.29840,
+ 85.79280,
+ 82.27650,
+ 22.58330,
+ 47.33070,
+ 145.81600,
+ 32.66220,
+ 138.69800,
+ 151.61200,
+ 17.19030,
+ 79.53840,
+ 437.80200,
+ 11.31330,
+ 116.39200,
+ 7.19167,
+ 12.97670,
+ 71.70700,
+ 21.57370,
+ 15.65570,
+ 33.69830,
+ 26.25690,
+ 21.24830,
+ 66.53090,
+ 13.75050,
+ 51.57060,
+ 152.96400,
+ 13.94050,
+ 52.37420,
+ 11.08640,
+ 24.07350,
+ 38.15330,
+ 108.60000,
+ 32.57110,
+ 54.38330,
+ 22.77100,
+ 19.63030,
+ 10.36040,
+ 387.34400,
+ 42.01700,
+ 39.86180,
+ 13.32640,
+ 42.84370,
+ 645.42800,
+ 21.60460,
+ 78.69930,
+ 29.11480,
+ 248.53900,
+ 200.60100,
+ 25.18490,
+ 19.62460,
+ 15.23350,
+ 100.21400,
+ 30.12810,
+ 58.87310,
+ 18.72470,
+ 11.83580,
+ 782.13000,
+ 180.03400,
+ 30.54340,
+ 205.84500,
+ 64.98920,
+ 31.48870,
+ 23.27390,
+ 138.82300,
+ 36.53690,
+ 31.47300
+ ]
+
+-- WAG exchangeability matrix n alphabetical order.
+wagExch :: ExchangeabilityMatrix
+wagExch = pamlToAlphaMat $ exchFromListLower n wagExchRawPaml
+
+-- WAG stationary distribution in PAML order.
+wagStatDistPaml :: StationaryDistribution
+wagStatDistPaml =
+ normalizeSumVec $
+ fromList
+ [ 0.0866279,
+ 0.043972,
+ 0.0390894,
+ 0.0570451,
+ 0.0193078,
+ 0.0367281,
+ 0.0580589,
+ 0.0832518,
+ 0.0244313,
+ 0.048466,
+ 0.086209,
+ 0.0620286,
+ 0.0195027,
+ 0.0384319,
+ 0.0457631,
+ 0.0695179,
+ 0.0610127,
+ 0.0143859,
+ 0.0352742,
+ 0.0708957
+ ]
+
+-- WAG stationary distribution in alphabetical order.
+wagStatDist :: StationaryDistribution
+wagStatDist = pamlToAlphaVec wagStatDistPaml
+
+-- | LG substitution model.
+wag :: SubstitutionModel
+wag = substitutionModel Protein "WAG" [] wagStatDist wagExch
+
+-- | LG substitution model with maybe a name and a custom stationary distribution.
+wagCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+wagCustom mnm d = substitutionModel Protein nm [] d wagExch
+ where
+ nm = fromMaybe "WAG-Custom" mnm
+
+matrixSetDiagToZero :: Matrix R -> Matrix R
+matrixSetDiagToZero m = m - diag (takeDiag m)
+{-# INLINE matrixSetDiagToZero #-}
+
+uniformExch :: ExchangeabilityMatrix
+uniformExch = matrixSetDiagToZero $ matrix n $ replicate (n * n) 1.0
+
+poissonExch :: ExchangeabilityMatrix
+poissonExch = uniformExch
+
+uniformVec :: Vector Double
+uniformVec = V.replicate n (1 / fromIntegral n)
+
+-- | Poisson substitution model.
+poisson :: SubstitutionModel
+poisson = substitutionModel Protein "Poisson" [] uniformVec poissonExch
+
+-- | Poisson substitution model with maybe a name and a custom stationary distribution.
+poissonCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+poissonCustom mnm d = substitutionModel Protein nm [] d poissonExch
+ where
+ nm = fromMaybe "Poisson-Custom" mnm
+
+-- | General time reversible (GTR) substitution model for amino acids.
+gtr20 :: [Double] -> StationaryDistribution -> SubstitutionModel
+gtr20 es d = substitutionModel Protein "GTR" es d e
+ where
+ e = exchFromListUpper n es
diff --git a/src/ELynx/MarkovProcess/CXXModels.hs b/src/ELynx/MarkovProcess/CXXModels.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/CXXModels.hs
@@ -0,0 +1,146 @@
+-- |
+-- Module : ELynx.MarkovProcess.CXXModels
+-- Description : C10 to C60 models
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Feb 26 16:44:33 2019.
+--
+-- Quang, BL. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
+-- phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
+--
+-- XXX: For now, I only provide Poisson exchangeabilities.
+module ELynx.MarkovProcess.CXXModels
+ ( cxx,
+ )
+where
+
+import qualified Data.Vector as V
+import ELynx.MarkovProcess.AminoAcid
+import ELynx.MarkovProcess.CXXModelsData
+import qualified ELynx.MarkovProcess.MixtureModel as M
+import ELynx.MarkovProcess.RateMatrix
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
+
+-- | Create CXX model with given number of components and probably with custom
+-- weights.
+cxx :: Int -> Maybe [M.Weight] -> M.MixtureModel
+cxx 10 (Just ws) = c10CustomWeights ws
+cxx 20 (Just ws) = c20CustomWeights ws
+cxx 30 (Just ws) = c30CustomWeights ws
+cxx 40 (Just ws) = c40CustomWeights ws
+cxx 50 (Just ws) = c50CustomWeights ws
+cxx 60 (Just ws) = c60CustomWeights ws
+cxx 10 Nothing = c10
+cxx 20 Nothing = c20
+cxx 30 Nothing = c30
+cxx 40 Nothing = c40
+cxx 50 Nothing = c50
+cxx 60 Nothing = c60
+cxx n _ =
+ error $ "cxx: cannot create CXX model with " ++ show n ++ " components."
+
+-- | C10 model.
+c10 :: M.MixtureModel
+c10 = cxxFromStatDistsAndWeights c10Weights c10StatDists
+
+-- | C20 model.
+c20 :: M.MixtureModel
+c20 = cxxFromStatDistsAndWeights c20Weights c20StatDists
+
+-- | C30 model.
+c30 :: M.MixtureModel
+c30 = cxxFromStatDistsAndWeights c30Weights c30StatDists
+
+-- | C40 model.
+c40 :: M.MixtureModel
+c40 = cxxFromStatDistsAndWeights c40Weights c40StatDists
+
+-- | C50 model.
+c50 :: M.MixtureModel
+c50 = cxxFromStatDistsAndWeights c50Weights c50StatDists
+
+-- | C60 model.
+c60 :: M.MixtureModel
+c60 = cxxFromStatDistsAndWeights c60Weights c60StatDists
+
+-- | C10 model with custom weights.
+c10CustomWeights :: [M.Weight] -> M.MixtureModel
+c10CustomWeights ws
+ | length ws == 10 = cxxFromStatDistsAndWeights ws c10StatDists
+ | otherwise = error "Number of weights does not match C10 model."
+
+-- | C20 model with custom weights.
+c20CustomWeights :: [M.Weight] -> M.MixtureModel
+c20CustomWeights ws
+ | length ws == 20 = cxxFromStatDistsAndWeights ws c20StatDists
+ | otherwise = error "Number of weights does not match C20 model."
+
+-- | C30 model with custom weights.
+c30CustomWeights :: [M.Weight] -> M.MixtureModel
+c30CustomWeights ws
+ | length ws == 30 = cxxFromStatDistsAndWeights ws c30StatDists
+ | otherwise = error "Number of weights does not match C30 model."
+
+-- | C40 model with custom weights.
+c40CustomWeights :: [M.Weight] -> M.MixtureModel
+c40CustomWeights ws
+ | length ws == 40 = cxxFromStatDistsAndWeights ws c40StatDists
+ | otherwise = error "Number of weights does not match C40 model."
+
+-- | C50 model with custom weights.
+c50CustomWeights :: [M.Weight] -> M.MixtureModel
+c50CustomWeights ws
+ | length ws == 50 = cxxFromStatDistsAndWeights ws c50StatDists
+ | otherwise = error "Number of weights does not match C50 model."
+
+-- | C60 model with custom weights.
+c60CustomWeights :: [M.Weight] -> M.MixtureModel
+c60CustomWeights ws
+ | length ws == 60 = cxxFromStatDistsAndWeights ws c60StatDists
+ | otherwise = error "Number of weights does not match C60 model."
+
+cxxName :: Int -> String
+cxxName nComps = 'C' : show nComps
+
+componentName :: Int -> Int -> String
+componentName nComps comp = cxxName nComps ++ "; component " ++ show comp
+
+-- Keep in mind, that when using different exchangeabilities, I have to decide
+-- about global or local normalization.
+cxxSubstitutionModelFromStatDist ::
+ Int -> Int -> StationaryDistribution -> S.SubstitutionModel
+cxxSubstitutionModelFromStatDist nComps comp d =
+ poissonCustom
+ (Just name)
+ (normalizeSD d)
+ where
+ name = componentName nComps comp
+
+cxxSubstitutionModelsFromStatDists ::
+ [StationaryDistribution] -> [S.SubstitutionModel]
+cxxSubstitutionModelsFromStatDists ds =
+ zipWith
+ (cxxSubstitutionModelFromStatDist nComp)
+ [1 ..]
+ ds
+ where
+ nComp = length ds
+
+-- XXX: The use of `Data.List.NonEmpty.fromList` is daring, but since this
+-- function is not exported and only applied to predefined non-empty lists, it
+-- should be OK.
+cxxFromStatDistsAndWeights ::
+ [M.Weight] -> [StationaryDistribution] -> M.MixtureModel
+cxxFromStatDistsAndWeights ws ds =
+ M.fromSubstitutionModels
+ (cxxName n)
+ (V.fromList ws)
+ sms
+ where
+ n = length ds
+ sms = V.fromList $ cxxSubstitutionModelsFromStatDists ds
diff --git a/src/ELynx/MarkovProcess/CXXModelsData.hs b/src/ELynx/MarkovProcess/CXXModelsData.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/CXXModelsData.hs
@@ -0,0 +1,4724 @@
+-- |
+-- Module : ELynx.MarkovProcess.CXXModelsData
+-- Description : Stationary distributions and weights
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Feb 26 17:17:35 2019.
+--
+-- Quang, BL. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
+-- phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
+module ELynx.MarkovProcess.CXXModelsData
+ ( c10StatDists,
+ c10Weights,
+ c20StatDists,
+ c20Weights,
+ c30StatDists,
+ c30Weights,
+ c40StatDists,
+ c40Weights,
+ c50StatDists,
+ c50Weights,
+ c60StatDists,
+ c60Weights,
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import ELynx.MarkovProcess.RateMatrix
+
+-- | Stationary distribution of C10 model.
+c10StatDists :: [StationaryDistribution]
+c10StatDists =
+ map
+ V.fromList
+ [ [ 0.408257,
+ 0.0349388,
+ 0.00698709,
+ 0.00978467,
+ 0.00616043,
+ 0.122161,
+ 0.00391518,
+ 0.0125784,
+ 0.00596702,
+ 0.0158339,
+ 0.00813132,
+ 0.00962854,
+ 0.0394156,
+ 0.00752797,
+ 0.0081783,
+ 0.168245,
+ 0.0658133,
+ 0.0604427,
+ 0.00187516,
+ 0.00415797
+ ],
+ [ 0.102776,
+ 0.0149663,
+ 0.0155944,
+ 0.0419667,
+ 0.0180729,
+ 0.0138806,
+ 0.0158865,
+ 0.106608,
+ 0.0436344,
+ 0.113194,
+ 0.04378,
+ 0.0213272,
+ 0.0223251,
+ 0.0440685,
+ 0.0418664,
+ 0.0529608,
+ 0.108174,
+ 0.160665,
+ 0.00451472,
+ 0.0137374
+ ],
+ [ 0.0351766,
+ 0.00787065,
+ 0.000676874,
+ 0.00196868,
+ 0.0126221,
+ 0.00224206,
+ 0.00128783,
+ 0.351582,
+ 0.00188565,
+ 0.127818,
+ 0.0242632,
+ 0.00165915,
+ 0.00297716,
+ 0.00165596,
+ 0.00196786,
+ 0.00499981,
+ 0.0255378,
+ 0.388864,
+ 0.00119078,
+ 0.00375393
+ ],
+ [ 0.0408514,
+ 0.00376029,
+ 0.233381,
+ 0.0901239,
+ 0.00251082,
+ 0.115833,
+ 0.0373197,
+ 0.00255236,
+ 0.0485017,
+ 0.00521646,
+ 0.00225718,
+ 0.218565,
+ 0.0108334,
+ 0.0380451,
+ 0.0269887,
+ 0.0804527,
+ 0.030288,
+ 0.00444811,
+ 0.00108153,
+ 0.00698909
+ ],
+ [ 0.0185493,
+ 0.00704165,
+ 0.000977506,
+ 0.00248916,
+ 0.073333,
+ 0.00289529,
+ 0.0040104,
+ 0.163242,
+ 0.00435709,
+ 0.444308,
+ 0.120282,
+ 0.00248957,
+ 0.00488276,
+ 0.00835394,
+ 0.00623624,
+ 0.00516424,
+ 0.0131807,
+ 0.0968581,
+ 0.00687598,
+ 0.0144734
+ ],
+ [ 0.110675,
+ 0.00148349,
+ 0.163644,
+ 0.263846,
+ 0.00232568,
+ 0.0325228,
+ 0.0163804,
+ 0.00683349,
+ 0.0677158,
+ 0.014068,
+ 0.00489881,
+ 0.0405186,
+ 0.0298982,
+ 0.0877962,
+ 0.035219,
+ 0.0562888,
+ 0.0426922,
+ 0.0181079,
+ 0.0010339,
+ 0.00405223
+ ],
+ [ 0.0522658,
+ 0.0143325,
+ 0.0297745,
+ 0.0388387,
+ 0.0624033,
+ 0.0228101,
+ 0.155164,
+ 0.0187406,
+ 0.0439469,
+ 0.065378,
+ 0.0207189,
+ 0.0714837,
+ 0.0145475,
+ 0.073654,
+ 0.0668295,
+ 0.0549018,
+ 0.037014,
+ 0.0267512,
+ 0.0193757,
+ 0.111069
+ ],
+ [ 0.0116587,
+ 0.0105341,
+ 0.00217425,
+ 0.00242511,
+ 0.365099,
+ 0.00347091,
+ 0.0366787,
+ 0.0187185,
+ 0.00266947,
+ 0.067649,
+ 0.0143535,
+ 0.00640111,
+ 0.00311599,
+ 0.00402037,
+ 0.00509901,
+ 0.00948485,
+ 0.00737139,
+ 0.0206341,
+ 0.0509565,
+ 0.357486
+ ],
+ [ 0.0627196,
+ 0.00526629,
+ 0.0236193,
+ 0.0686285,
+ 0.00391818,
+ 0.0256175,
+ 0.0332612,
+ 0.0128968,
+ 0.227084,
+ 0.0305628,
+ 0.0124037,
+ 0.0428629,
+ 0.0140441,
+ 0.109811,
+ 0.203878,
+ 0.0483152,
+ 0.0463378,
+ 0.0197063,
+ 0.00251435,
+ 0.00655211
+ ],
+ [ 0.114552,
+ 0.00985495,
+ 0.0416192,
+ 0.0364908,
+ 0.0046606,
+ 0.0503818,
+ 0.0165233,
+ 0.00929495,
+ 0.0423027,
+ 0.0139154,
+ 0.00822408,
+ 0.0750615,
+ 0.0379222,
+ 0.0339625,
+ 0.0324009,
+ 0.261065,
+ 0.184583,
+ 0.0195769,
+ 0.0017549,
+ 0.00585383
+ ]
+ ]
+
+-- | Weights of C10 model.
+c10Weights :: [Double]
+c10Weights =
+ [ 0.119134,
+ 0.0874372,
+ 0.103711,
+ 0.0922585,
+ 0.107049,
+ 0.132995,
+ 0.0538028,
+ 0.0691986,
+ 0.131994,
+ 0.10242
+ ]
+
+-- | Stationary distribution of C20 model.
+c20StatDists :: [StationaryDistribution]
+c20StatDists =
+ map
+ V.fromList
+ [ [ 0.0862413,
+ 0.0130505,
+ 0.0329909,
+ 0.0184527,
+ 0.00441553,
+ 0.0366905,
+ 0.0108013,
+ 0.00979071,
+ 0.0220195,
+ 0.0112826,
+ 0.00878215,
+ 0.0791293,
+ 0.0189273,
+ 0.0169047,
+ 0.0171944,
+ 0.317815,
+ 0.27117,
+ 0.0179753,
+ 0.00153173,
+ 0.00483429
+ ],
+ [ 0.203558,
+ 0.0348667,
+ 0.00316561,
+ 0.00708594,
+ 0.0112429,
+ 0.0195236,
+ 0.0024392,
+ 0.115257,
+ 0.00423808,
+ 0.0789777,
+ 0.0309187,
+ 0.00770524,
+ 0.0164189,
+ 0.00640441,
+ 0.00509808,
+ 0.0496777,
+ 0.111895,
+ 0.284906,
+ 0.00177626,
+ 0.00484482
+ ],
+ [ 0.0211547,
+ 0.00481886,
+ 0.000549287,
+ 0.00145396,
+ 0.0128252,
+ 0.00114309,
+ 0.00113464,
+ 0.392846,
+ 0.00135799,
+ 0.125064,
+ 0.0209789,
+ 0.0012755,
+ 0.00202472,
+ 0.00123288,
+ 0.00149462,
+ 0.00262407,
+ 0.0171914,
+ 0.386068,
+ 0.00115911,
+ 0.0036028
+ ],
+ [ 0.0376904,
+ 0.00640738,
+ 0.0109469,
+ 0.0358365,
+ 0.00363498,
+ 0.0191107,
+ 0.0329514,
+ 0.0101712,
+ 0.289763,
+ 0.0237496,
+ 0.00965289,
+ 0.0365411,
+ 0.0105337,
+ 0.0893564,
+ 0.28852,
+ 0.0356314,
+ 0.0355927,
+ 0.0144622,
+ 0.00279252,
+ 0.00665572
+ ],
+ [ 0.00845978,
+ 0.0084909,
+ 0.00244879,
+ 0.00250555,
+ 0.342046,
+ 0.00242771,
+ 0.0433214,
+ 0.0097713,
+ 0.0026741,
+ 0.0380507,
+ 0.00807248,
+ 0.00725259,
+ 0.00214187,
+ 0.00427815,
+ 0.00535899,
+ 0.00804189,
+ 0.00553221,
+ 0.012141,
+ 0.049484,
+ 0.4375
+ ],
+ [ 0.17599,
+ 0.00175587,
+ 0.130126,
+ 0.218217,
+ 0.0025277,
+ 0.0409535,
+ 0.0130708,
+ 0.00856221,
+ 0.0542946,
+ 0.0159531,
+ 0.00540458,
+ 0.0332846,
+ 0.037102,
+ 0.0707184,
+ 0.0290429,
+ 0.0793481,
+ 0.0540083,
+ 0.0249553,
+ 0.00105921,
+ 0.00362591
+ ],
+ [ 0.16344,
+ 0.00886599,
+ 0.0374273,
+ 0.0220612,
+ 0.00306413,
+ 0.529672,
+ 0.00900061,
+ 0.00175694,
+ 0.0167118,
+ 0.00611563,
+ 0.00293908,
+ 0.0438702,
+ 0.0126458,
+ 0.0137555,
+ 0.0195541,
+ 0.0829343,
+ 0.0142836,
+ 0.00579857,
+ 0.00286407,
+ 0.00323983
+ ],
+ [ 0.0917469,
+ 0.0284015,
+ 0.0133819,
+ 0.0196876,
+ 0.0998479,
+ 0.0249899,
+ 0.0449766,
+ 0.0583556,
+ 0.0164916,
+ 0.115501,
+ 0.0395995,
+ 0.0290699,
+ 0.0209916,
+ 0.0255085,
+ 0.0265853,
+ 0.0736483,
+ 0.0661518,
+ 0.0831856,
+ 0.0246464,
+ 0.0972327
+ ],
+ [ 0.0646701,
+ 0.00771176,
+ 0.0168734,
+ 0.0544978,
+ 0.0219148,
+ 0.0148894,
+ 0.0313852,
+ 0.0505983,
+ 0.0907931,
+ 0.184428,
+ 0.077484,
+ 0.0228907,
+ 0.0105004,
+ 0.0996415,
+ 0.0988016,
+ 0.0321196,
+ 0.0411766,
+ 0.0505824,
+ 0.0084303,
+ 0.0206106
+ ],
+ [ 0.0135994,
+ 0.010009,
+ 0.00079517,
+ 0.00180118,
+ 0.264097,
+ 0.00267946,
+ 0.00724019,
+ 0.0814027,
+ 0.00251581,
+ 0.366142,
+ 0.0734965,
+ 0.00184694,
+ 0.00389941,
+ 0.00464208,
+ 0.00434084,
+ 0.00436688,
+ 0.00752485,
+ 0.0573473,
+ 0.0261565,
+ 0.0660971
+ ],
+ [ 0.147804,
+ 0.00488258,
+ 0.0534743,
+ 0.0727246,
+ 0.00299039,
+ 0.0907726,
+ 0.0262289,
+ 0.00357811,
+ 0.105166,
+ 0.0126777,
+ 0.00596218,
+ 0.072663,
+ 0.0156558,
+ 0.0757166,
+ 0.0842845,
+ 0.14599,
+ 0.0634877,
+ 0.00927198,
+ 0.00159285,
+ 0.00507607
+ ],
+ [ 0.0186377,
+ 0.00549689,
+ 0.00083297,
+ 0.00202485,
+ 0.0385383,
+ 0.00217135,
+ 0.0023666,
+ 0.202081,
+ 0.00291207,
+ 0.437038,
+ 0.124186,
+ 0.00198652,
+ 0.00406723,
+ 0.00658901,
+ 0.00420552,
+ 0.00461774,
+ 0.0149904,
+ 0.118938,
+ 0.00268717,
+ 0.00563241
+ ],
+ [ 0.0477624,
+ 0.00757917,
+ 0.0141349,
+ 0.0462688,
+ 0.0130691,
+ 0.00523279,
+ 0.0165352,
+ 0.17415,
+ 0.0577575,
+ 0.112125,
+ 0.0330288,
+ 0.0209574,
+ 0.0124375,
+ 0.0429297,
+ 0.0505743,
+ 0.0264989,
+ 0.0951755,
+ 0.20937,
+ 0.00316605,
+ 0.0112466
+ ],
+ [ 0.416419,
+ 0.0406938,
+ 0.00451317,
+ 0.00632298,
+ 0.00484384,
+ 0.0946185,
+ 0.00310574,
+ 0.00764432,
+ 0.00389418,
+ 0.00998854,
+ 0.00693232,
+ 0.00917014,
+ 0.0187841,
+ 0.00613205,
+ 0.00561008,
+ 0.236077,
+ 0.0746275,
+ 0.0459225,
+ 0.00121726,
+ 0.00348258
+ ],
+ [ 0.0402296,
+ 0.0124783,
+ 0.0365524,
+ 0.0372197,
+ 0.0459095,
+ 0.0233618,
+ 0.210831,
+ 0.00934787,
+ 0.0482411,
+ 0.0360561,
+ 0.010029,
+ 0.103665,
+ 0.0098504,
+ 0.0826558,
+ 0.0735203,
+ 0.0533383,
+ 0.0310209,
+ 0.015248,
+ 0.0140077,
+ 0.106438
+ ],
+ [ 0.0323453,
+ 0.00359763,
+ 0.24315,
+ 0.0710274,
+ 0.00244293,
+ 0.101607,
+ 0.0366225,
+ 0.00314108,
+ 0.0470129,
+ 0.00519805,
+ 0.00240287,
+ 0.252045,
+ 0.00948378,
+ 0.0330831,
+ 0.0236283,
+ 0.0848355,
+ 0.0359083,
+ 0.00487046,
+ 0.000873093,
+ 0.00672477
+ ],
+ [ 0.147626,
+ 0.00323272,
+ 0.0403052,
+ 0.0576893,
+ 0.00471772,
+ 0.0330851,
+ 0.0146393,
+ 0.0108267,
+ 0.0451351,
+ 0.0256201,
+ 0.00586514,
+ 0.0211973,
+ 0.347371,
+ 0.0371554,
+ 0.0334507,
+ 0.0892065,
+ 0.0485899,
+ 0.0282336,
+ 0.00163587,
+ 0.00441772
+ ],
+ [ 0.103145,
+ 0.00617625,
+ 0.0386402,
+ 0.0923369,
+ 0.00676664,
+ 0.0202338,
+ 0.0246762,
+ 0.0376904,
+ 0.0921699,
+ 0.0376284,
+ 0.0161883,
+ 0.0435172,
+ 0.0128302,
+ 0.0786603,
+ 0.0717748,
+ 0.095145,
+ 0.137857,
+ 0.0740454,
+ 0.00221447,
+ 0.00830416
+ ],
+ [ 0.0837543,
+ 0.00207351,
+ 0.0804871,
+ 0.194776,
+ 0.00230634,
+ 0.022903,
+ 0.0268459,
+ 0.00740798,
+ 0.145929,
+ 0.019025,
+ 0.00673952,
+ 0.0518811,
+ 0.0085616,
+ 0.14565,
+ 0.0899383,
+ 0.045574,
+ 0.0451081,
+ 0.0150303,
+ 0.00107713,
+ 0.00493253
+ ],
+ [ 0.0578736,
+ 0.00111308,
+ 0.294674,
+ 0.34021,
+ 0.00170349,
+ 0.0293911,
+ 0.0139817,
+ 0.00305257,
+ 0.0363365,
+ 0.00626119,
+ 0.0027296,
+ 0.0491422,
+ 0.0156106,
+ 0.059825,
+ 0.0138314,
+ 0.0358045,
+ 0.0249942,
+ 0.00876742,
+ 0.000866434,
+ 0.0038313
+ ]
+ ]
+
+-- | Weights of C20 model.
+c20Weights :: [Double]
+c20Weights =
+ [ 0.0559911,
+ 0.0514825,
+ 0.0812922,
+ 0.0721977,
+ 0.0556719,
+ 0.0331003,
+ 0.0589502,
+ 0.0263757,
+ 0.0307584,
+ 0.0376701,
+ 0.0303058,
+ 0.0808776,
+ 0.0263349,
+ 0.0579101,
+ 0.0371248,
+ 0.0586868,
+ 0.0561479,
+ 0.0349811,
+ 0.0544937,
+ 0.0596472
+ ]
+
+-- | Stationary distribution of C30 model.
+c30StatDists :: [StationaryDistribution]
+c30StatDists =
+ map
+ V.fromList
+ [ [ 0.110045,
+ 0.00190472,
+ 0.159541,
+ 0.109896,
+ 0.00166295,
+ 0.0684302,
+ 0.0137951,
+ 0.00262831,
+ 0.0358554,
+ 0.00733965,
+ 0.00247064,
+ 0.0640338,
+ 0.166936,
+ 0.0310187,
+ 0.0171295,
+ 0.138179,
+ 0.0568343,
+ 0.00823656,
+ 0.000466112,
+ 0.00359702
+ ],
+ [ 0.0874125,
+ 0.00498264,
+ 0.032612,
+ 0.0951701,
+ 0.00489966,
+ 0.0144043,
+ 0.0210627,
+ 0.0399884,
+ 0.11472,
+ 0.0301585,
+ 0.0126489,
+ 0.0382152,
+ 0.0137397,
+ 0.0798169,
+ 0.080632,
+ 0.087377,
+ 0.155862,
+ 0.0793881,
+ 0.00151228,
+ 0.00539745
+ ],
+ [ 0.0225477,
+ 0.00500182,
+ 0.000595928,
+ 0.00150305,
+ 0.0089216,
+ 0.0011571,
+ 0.000937432,
+ 0.394469,
+ 0.00136009,
+ 0.0889573,
+ 0.0189103,
+ 0.00130346,
+ 0.0018312,
+ 0.00114366,
+ 0.00149005,
+ 0.00283364,
+ 0.0189813,
+ 0.425056,
+ 0.000669375,
+ 0.00233037
+ ],
+ [ 0.0602158,
+ 0.000952546,
+ 0.290008,
+ 0.361087,
+ 0.00146256,
+ 0.0281926,
+ 0.0130501,
+ 0.00305162,
+ 0.0352705,
+ 0.00604019,
+ 0.00274606,
+ 0.0414988,
+ 0.0127175,
+ 0.0621611,
+ 0.0136833,
+ 0.0318109,
+ 0.022528,
+ 0.00932584,
+ 0.000794803,
+ 0.00340246
+ ],
+ [ 0.0101224,
+ 0.00859894,
+ 0.000637919,
+ 0.00112496,
+ 0.278538,
+ 0.00240852,
+ 0.00477534,
+ 0.0701153,
+ 0.00167485,
+ 0.413591,
+ 0.0744863,
+ 0.00129289,
+ 0.00404666,
+ 0.00350286,
+ 0.00283449,
+ 0.00370872,
+ 0.00523793,
+ 0.040886,
+ 0.0200223,
+ 0.0523939
+ ],
+ [ 0.133583,
+ 0.00105145,
+ 0.112578,
+ 0.209957,
+ 0.00167936,
+ 0.0207552,
+ 0.012133,
+ 0.00735265,
+ 0.0771772,
+ 0.0133278,
+ 0.00305717,
+ 0.0213892,
+ 0.18902,
+ 0.0565844,
+ 0.028479,
+ 0.0484054,
+ 0.0373318,
+ 0.0225174,
+ 0.000926699,
+ 0.00269464
+ ],
+ [ 0.0408277,
+ 0.0153918,
+ 0.00306349,
+ 0.00660109,
+ 0.157505,
+ 0.00581131,
+ 0.0245212,
+ 0.148751,
+ 0.00759232,
+ 0.16378,
+ 0.0385527,
+ 0.00804649,
+ 0.00583522,
+ 0.0102922,
+ 0.0124492,
+ 0.0151579,
+ 0.033222,
+ 0.154771,
+ 0.0264937,
+ 0.121334
+ ],
+ [ 0.246906,
+ 0.103941,
+ 0.00274183,
+ 0.00549448,
+ 0.0251776,
+ 0.0373263,
+ 0.00857523,
+ 0.0292404,
+ 0.00561231,
+ 0.0535091,
+ 0.0302246,
+ 0.016893,
+ 0.00780989,
+ 0.0103988,
+ 0.0106279,
+ 0.164235,
+ 0.123989,
+ 0.0955868,
+ 0.00531559,
+ 0.0163954
+ ],
+ [ 0.0549429,
+ 0.0099281,
+ 0.00929153,
+ 0.0417085,
+ 0.024386,
+ 0.0105564,
+ 0.0363512,
+ 0.0569585,
+ 0.115252,
+ 0.168183,
+ 0.0592328,
+ 0.0202958,
+ 0.00830554,
+ 0.0906036,
+ 0.130543,
+ 0.0283779,
+ 0.0412594,
+ 0.0592101,
+ 0.00963554,
+ 0.024978
+ ],
+ [ 0.0462773,
+ 0.0172727,
+ 0.0182504,
+ 0.0224266,
+ 0.133632,
+ 0.0160971,
+ 0.135785,
+ 0.0164967,
+ 0.0239396,
+ 0.0598936,
+ 0.0164507,
+ 0.0412365,
+ 0.0117413,
+ 0.0348991,
+ 0.0362984,
+ 0.0454156,
+ 0.0304388,
+ 0.0253979,
+ 0.0330338,
+ 0.235016
+ ],
+ [ 0.047438,
+ 0.00823324,
+ 0.0112117,
+ 0.0388101,
+ 0.0116644,
+ 0.00559986,
+ 0.0149157,
+ 0.183217,
+ 0.0467851,
+ 0.110069,
+ 0.0356444,
+ 0.0222454,
+ 0.0100245,
+ 0.0374051,
+ 0.041018,
+ 0.0317171,
+ 0.111435,
+ 0.219931,
+ 0.00266856,
+ 0.00996601
+ ],
+ [ 0.0213608,
+ 0.00610249,
+ 0.00129412,
+ 0.00362973,
+ 0.0371808,
+ 0.0030017,
+ 0.00384259,
+ 0.130947,
+ 0.00545678,
+ 0.456699,
+ 0.194784,
+ 0.0039879,
+ 0.00407473,
+ 0.0139566,
+ 0.00699762,
+ 0.00769915,
+ 0.0198019,
+ 0.0693208,
+ 0.00340864,
+ 0.00645457
+ ],
+ [ 0.0919632,
+ 0.0117031,
+ 0.0306717,
+ 0.0171908,
+ 0.00415894,
+ 0.0370685,
+ 0.0100793,
+ 0.00931237,
+ 0.0205386,
+ 0.0097241,
+ 0.00757673,
+ 0.0764682,
+ 0.0179686,
+ 0.016006,
+ 0.0160005,
+ 0.325447,
+ 0.274438,
+ 0.0178218,
+ 0.00138874,
+ 0.00447397
+ ],
+ [ 0.464925,
+ 0.0233329,
+ 0.00507317,
+ 0.00579942,
+ 0.00255882,
+ 0.149524,
+ 0.00232984,
+ 0.00433612,
+ 0.00285254,
+ 0.00559955,
+ 0.00393132,
+ 0.00753048,
+ 0.0186467,
+ 0.00435713,
+ 0.00430132,
+ 0.215019,
+ 0.047703,
+ 0.0292668,
+ 0.00090381,
+ 0.00200872
+ ],
+ [ 0.205133,
+ 0.00209159,
+ 0.107098,
+ 0.198973,
+ 0.00182351,
+ 0.0487574,
+ 0.0127143,
+ 0.00581247,
+ 0.0667787,
+ 0.0133472,
+ 0.00437834,
+ 0.0339418,
+ 0.0110998,
+ 0.0822742,
+ 0.0439661,
+ 0.0873962,
+ 0.0519782,
+ 0.0193174,
+ 0.00073616,
+ 0.00238214
+ ],
+ [ 0.026369,
+ 0.00394624,
+ 0.311772,
+ 0.0694354,
+ 0.00233519,
+ 0.0799842,
+ 0.0309615,
+ 0.00275212,
+ 0.0288631,
+ 0.00385797,
+ 0.00183637,
+ 0.272716,
+ 0.00624576,
+ 0.0218979,
+ 0.0133614,
+ 0.0798729,
+ 0.0324143,
+ 0.00427053,
+ 0.000722966,
+ 0.00638577
+ ],
+ [ 0.15265,
+ 0.00402153,
+ 0.0237392,
+ 0.0377949,
+ 0.00585844,
+ 0.0306214,
+ 0.014193,
+ 0.0123318,
+ 0.0375543,
+ 0.0290062,
+ 0.00644732,
+ 0.016823,
+ 0.38645,
+ 0.0341734,
+ 0.0332784,
+ 0.0880336,
+ 0.0489543,
+ 0.0313553,
+ 0.00182526,
+ 0.00488778
+ ],
+ [ 0.00802476,
+ 0.00234121,
+ 0.000338596,
+ 0.000781895,
+ 0.0311968,
+ 0.000540383,
+ 0.00100264,
+ 0.317706,
+ 0.00125983,
+ 0.373789,
+ 0.0488212,
+ 0.00063274,
+ 0.00206875,
+ 0.00155079,
+ 0.00174086,
+ 0.00120951,
+ 0.00656968,
+ 0.19446,
+ 0.00163092,
+ 0.00433436
+ ],
+ [ 0.059995,
+ 0.0016885,
+ 0.0889731,
+ 0.0962701,
+ 0.00118007,
+ 0.0588796,
+ 0.0327277,
+ 0.00214673,
+ 0.182586,
+ 0.00708764,
+ 0.00339794,
+ 0.133492,
+ 0.0141408,
+ 0.0864856,
+ 0.100054,
+ 0.0779002,
+ 0.0448817,
+ 0.00422414,
+ 0.000624903,
+ 0.00326411
+ ],
+ [ 0.0393521,
+ 0.00990719,
+ 0.0431198,
+ 0.039464,
+ 0.0188681,
+ 0.0282866,
+ 0.209572,
+ 0.00761014,
+ 0.0596434,
+ 0.025834,
+ 0.00845867,
+ 0.142548,
+ 0.00968405,
+ 0.101979,
+ 0.0838171,
+ 0.0624999,
+ 0.0347088,
+ 0.0127686,
+ 0.00546458,
+ 0.0564145
+ ],
+ [ 0.00727155,
+ 0.00678525,
+ 0.00276038,
+ 0.00250694,
+ 0.127148,
+ 0.00808347,
+ 0.0113218,
+ 0.00566096,
+ 0.00177351,
+ 0.03942,
+ 0.00798661,
+ 0.00197568,
+ 0.00410981,
+ 0.00433393,
+ 0.0140999,
+ 0.00522444,
+ 0.00430223,
+ 0.00942264,
+ 0.627357,
+ 0.108456
+ ],
+ [ 0.090707,
+ 0.00636999,
+ 0.0745873,
+ 0.0386802,
+ 0.00288592,
+ 0.475005,
+ 0.016809,
+ 0.00147211,
+ 0.0343856,
+ 0.00551498,
+ 0.00246921,
+ 0.0860678,
+ 0.0112151,
+ 0.0259377,
+ 0.0290062,
+ 0.073111,
+ 0.0153706,
+ 0.00392819,
+ 0.00229148,
+ 0.00418607
+ ],
+ [ 0.00552919,
+ 0.00721059,
+ 0.00114134,
+ 0.000968304,
+ 0.374409,
+ 0.0016071,
+ 0.0325831,
+ 0.00829184,
+ 0.00138494,
+ 0.0353678,
+ 0.00744868,
+ 0.00460866,
+ 0.00133746,
+ 0.00226922,
+ 0.00246263,
+ 0.00574027,
+ 0.00372796,
+ 0.00988026,
+ 0.0330334,
+ 0.460998
+ ],
+ [ 0.244326,
+ 0.027388,
+ 0.00315909,
+ 0.00767156,
+ 0.00606194,
+ 0.019609,
+ 0.00201894,
+ 0.101744,
+ 0.00454923,
+ 0.0468424,
+ 0.0201286,
+ 0.00624227,
+ 0.0185219,
+ 0.0053594,
+ 0.00453866,
+ 0.0497754,
+ 0.11708,
+ 0.310493,
+ 0.000957725,
+ 0.00353337
+ ],
+ [ 0.0863111,
+ 0.00244198,
+ 0.0600903,
+ 0.20361,
+ 0.00293931,
+ 0.0175221,
+ 0.0245245,
+ 0.0105994,
+ 0.148579,
+ 0.027121,
+ 0.00958244,
+ 0.0313963,
+ 0.00682768,
+ 0.167235,
+ 0.0984812,
+ 0.03478,
+ 0.0408211,
+ 0.0202271,
+ 0.00140013,
+ 0.00551054
+ ],
+ [ 0.0643926,
+ 0.00231659,
+ 0.162821,
+ 0.17627,
+ 0.00430667,
+ 0.0297139,
+ 0.0303504,
+ 0.0088163,
+ 0.072714,
+ 0.0148017,
+ 0.00567484,
+ 0.103121,
+ 0.00992703,
+ 0.0752535,
+ 0.0369049,
+ 0.0926434,
+ 0.083313,
+ 0.0161551,
+ 0.00112371,
+ 0.00938015
+ ],
+ [ 0.173668,
+ 0.00835966,
+ 0.0285985,
+ 0.0483894,
+ 0.0058274,
+ 0.0781901,
+ 0.0266135,
+ 0.00686419,
+ 0.0964012,
+ 0.0219499,
+ 0.0112303,
+ 0.0520405,
+ 0.0169661,
+ 0.0722447,
+ 0.0943629,
+ 0.15478,
+ 0.0751702,
+ 0.0172524,
+ 0.00287745,
+ 0.00821304
+ ],
+ [ 0.0347857,
+ 0.00627549,
+ 0.00923552,
+ 0.0323568,
+ 0.00343035,
+ 0.0170288,
+ 0.0306439,
+ 0.00919323,
+ 0.302085,
+ 0.0224429,
+ 0.00937208,
+ 0.0314157,
+ 0.0104447,
+ 0.0861073,
+ 0.307598,
+ 0.0326883,
+ 0.0328713,
+ 0.0130832,
+ 0.00252449,
+ 0.00641713
+ ],
+ [ 0.108774,
+ 0.0247877,
+ 0.00158232,
+ 0.00417699,
+ 0.0316523,
+ 0.0134703,
+ 0.00247658,
+ 0.164346,
+ 0.00270004,
+ 0.233715,
+ 0.0539213,
+ 0.00326798,
+ 0.0154887,
+ 0.0057932,
+ 0.0051781,
+ 0.0188188,
+ 0.0474912,
+ 0.251283,
+ 0.00376565,
+ 0.00731064
+ ],
+ [ 0.110101,
+ 0.00726998,
+ 0.0579269,
+ 0.0828181,
+ 0.0269154,
+ 0.0314463,
+ 0.0308557,
+ 0.0530866,
+ 0.029386,
+ 0.109679,
+ 0.0458729,
+ 0.0435099,
+ 0.0296431,
+ 0.0615197,
+ 0.0324325,
+ 0.0715888,
+ 0.0685882,
+ 0.0754042,
+ 0.00623241,
+ 0.0257238
+ ]
+ ]
+
+-- | Weights of C30 model.
+c30Weights :: [Double]
+c30Weights =
+ [ 0.00957833,
+ 0.0248476,
+ 0.0636309,
+ 0.0537939,
+ 0.0295886,
+ 0.0117588,
+ 0.0132013,
+ 0.0236869,
+ 0.0261688,
+ 0.0239822,
+ 0.0257101,
+ 0.0465072,
+ 0.0546795,
+ 0.0536085,
+ 0.0270623,
+ 0.0403914,
+ 0.0474213,
+ 0.0458816,
+ 0.0214037,
+ 0.0290386,
+ 0.0123392,
+ 0.056935,
+ 0.0419688,
+ 0.0339027,
+ 0.0388777,
+ 0.0196344,
+ 0.0233086,
+ 0.0622723,
+ 0.0184803,
+ 0.0203395
+ ]
+
+-- | Stationary distribution of C40 model.
+c40StatDists :: [StationaryDistribution]
+c40StatDists =
+ map
+ V.fromList
+ [ [ 0.066026,
+ 0.00565867,
+ 0.105447,
+ 0.0440361,
+ 0.00131048,
+ 0.0711239,
+ 0.0168195,
+ 0.00390887,
+ 0.036669,
+ 0.0055316,
+ 0.00374124,
+ 0.159982,
+ 0.0176359,
+ 0.0273928,
+ 0.0231862,
+ 0.249769,
+ 0.150708,
+ 0.0065529,
+ 0.000672321,
+ 0.00382902
+ ],
+ [ 0.0232377,
+ 0.00379875,
+ 0.353209,
+ 0.0739378,
+ 0.00240321,
+ 0.0576668,
+ 0.0315867,
+ 0.00310928,
+ 0.0259363,
+ 0.00387116,
+ 0.00173556,
+ 0.275965,
+ 0.00631169,
+ 0.0197339,
+ 0.0122683,
+ 0.0657068,
+ 0.0270484,
+ 0.00475317,
+ 0.000760289,
+ 0.00696025
+ ],
+ [ 0.0166487,
+ 0.00366657,
+ 0.000565145,
+ 0.00133563,
+ 0.00827757,
+ 0.000889475,
+ 0.000823185,
+ 0.412937,
+ 0.00119041,
+ 0.0884689,
+ 0.0186055,
+ 0.00126222,
+ 0.001403,
+ 0.00106698,
+ 0.00125948,
+ 0.00213394,
+ 0.0162167,
+ 0.420686,
+ 0.000608205,
+ 0.00195532
+ ],
+ [ 0.239474,
+ 0.0283812,
+ 0.00447417,
+ 0.010553,
+ 0.00559911,
+ 0.013511,
+ 0.00389298,
+ 0.0765957,
+ 0.0071093,
+ 0.0358495,
+ 0.0199496,
+ 0.0120537,
+ 0.0114266,
+ 0.00865589,
+ 0.00729013,
+ 0.0847799,
+ 0.179728,
+ 0.245468,
+ 0.0009838,
+ 0.00422407
+ ],
+ [ 0.119461,
+ 0.0150527,
+ 0.0134273,
+ 0.0192173,
+ 0.0550467,
+ 0.0337676,
+ 0.0214746,
+ 0.0579002,
+ 0.0147261,
+ 0.144631,
+ 0.0561243,
+ 0.0294552,
+ 0.0631355,
+ 0.0301538,
+ 0.0233256,
+ 0.0925267,
+ 0.083123,
+ 0.0811758,
+ 0.0131636,
+ 0.0331118
+ ],
+ [ 0.0567044,
+ 0.00089248,
+ 0.29555,
+ 0.379515,
+ 0.00129723,
+ 0.023047,
+ 0.0118361,
+ 0.0031182,
+ 0.0314206,
+ 0.00601375,
+ 0.00285841,
+ 0.0364734,
+ 0.0124746,
+ 0.0609517,
+ 0.0117359,
+ 0.0300335,
+ 0.0227051,
+ 0.00946396,
+ 0.000773876,
+ 0.00313438
+ ],
+ [ 0.0179027,
+ 0.016076,
+ 0.000887041,
+ 0.00231821,
+ 0.334486,
+ 0.00398298,
+ 0.0127293,
+ 0.0404651,
+ 0.00279947,
+ 0.167614,
+ 0.0424172,
+ 0.00356977,
+ 0.00201151,
+ 0.00453955,
+ 0.00409671,
+ 0.00758416,
+ 0.00682273,
+ 0.0326045,
+ 0.0518381,
+ 0.245254
+ ],
+ [ 0.271217,
+ 0.200383,
+ 0.0021017,
+ 0.002323,
+ 0.020299,
+ 0.0502501,
+ 0.0053728,
+ 0.0150685,
+ 0.00206463,
+ 0.0330003,
+ 0.0154811,
+ 0.0141045,
+ 0.0045351,
+ 0.00482641,
+ 0.00564808,
+ 0.17642,
+ 0.0839578,
+ 0.0741934,
+ 0.00462652,
+ 0.0141271
+ ],
+ [ 0.0894737,
+ 0.00455383,
+ 0.0272183,
+ 0.127508,
+ 0.00565902,
+ 0.0115686,
+ 0.0215746,
+ 0.0469424,
+ 0.138205,
+ 0.0512035,
+ 0.0147657,
+ 0.0190192,
+ 0.00955465,
+ 0.116809,
+ 0.104003,
+ 0.0383954,
+ 0.0836653,
+ 0.0819556,
+ 0.00170794,
+ 0.00621813
+ ],
+ [ 0.0495441,
+ 0.0182506,
+ 0.0143641,
+ 0.0215379,
+ 0.141805,
+ 0.01402,
+ 0.110854,
+ 0.0247066,
+ 0.0258142,
+ 0.0700288,
+ 0.0188272,
+ 0.0315864,
+ 0.0112101,
+ 0.0316504,
+ 0.0375346,
+ 0.0456094,
+ 0.0361428,
+ 0.0369178,
+ 0.0371985,
+ 0.222397
+ ],
+ [ 0.170431,
+ 0.000974733,
+ 0.109856,
+ 0.253646,
+ 0.00133213,
+ 0.0249846,
+ 0.010139,
+ 0.00587494,
+ 0.0903324,
+ 0.0116526,
+ 0.00365127,
+ 0.0271109,
+ 0.0293614,
+ 0.09173,
+ 0.0415784,
+ 0.0561766,
+ 0.0479046,
+ 0.02033,
+ 0.000669682,
+ 0.00226373
+ ],
+ [ 0.0162725,
+ 0.00506141,
+ 0.00101821,
+ 0.00251413,
+ 0.0376246,
+ 0.00219354,
+ 0.00299143,
+ 0.132817,
+ 0.00401204,
+ 0.490444,
+ 0.192993,
+ 0.00218762,
+ 0.00343332,
+ 0.0104414,
+ 0.00548261,
+ 0.00401221,
+ 0.0127074,
+ 0.064772,
+ 0.00321076,
+ 0.00581006
+ ],
+ [ 0.0823766,
+ 0.00656943,
+ 0.0311745,
+ 0.0675531,
+ 0.00647179,
+ 0.0178962,
+ 0.0251144,
+ 0.0291162,
+ 0.0982302,
+ 0.0287904,
+ 0.0168023,
+ 0.059839,
+ 0.0114045,
+ 0.0686451,
+ 0.0734226,
+ 0.1303,
+ 0.182037,
+ 0.0540271,
+ 0.00227246,
+ 0.00795733
+ ],
+ [ 0.359497,
+ 0.0251417,
+ 0.00314844,
+ 0.00649627,
+ 0.00920205,
+ 0.119468,
+ 0.00229704,
+ 0.0458767,
+ 0.00501688,
+ 0.0468054,
+ 0.0215569,
+ 0.00334215,
+ 0.0443916,
+ 0.00490143,
+ 0.00724072,
+ 0.0465271,
+ 0.0477755,
+ 0.194216,
+ 0.00245402,
+ 0.00464504
+ ],
+ [ 0.201558,
+ 0.00323653,
+ 0.095415,
+ 0.153491,
+ 0.00256433,
+ 0.0667292,
+ 0.0155219,
+ 0.00677408,
+ 0.0547323,
+ 0.0165114,
+ 0.0060163,
+ 0.0425386,
+ 0.00919706,
+ 0.0772011,
+ 0.0430162,
+ 0.118598,
+ 0.0625473,
+ 0.0202798,
+ 0.000956551,
+ 0.003115
+ ],
+ [ 0.104273,
+ 0.00224501,
+ 0.242407,
+ 0.177482,
+ 0.00125703,
+ 0.169782,
+ 0.0132649,
+ 0.00189295,
+ 0.0220652,
+ 0.00425426,
+ 0.00164412,
+ 0.0621646,
+ 0.0317042,
+ 0.0356499,
+ 0.0147062,
+ 0.0778636,
+ 0.0288516,
+ 0.00602502,
+ 0.00069309,
+ 0.00177419
+ ],
+ [ 0.0781183,
+ 0.0194449,
+ 0.00415417,
+ 0.0116634,
+ 0.0262794,
+ 0.0111524,
+ 0.00635894,
+ 0.135453,
+ 0.00937298,
+ 0.245757,
+ 0.108778,
+ 0.015927,
+ 0.0055294,
+ 0.0240152,
+ 0.0111498,
+ 0.0408519,
+ 0.0860514,
+ 0.148276,
+ 0.00315476,
+ 0.00851085
+ ],
+ [ 0.0856592,
+ 0.0136073,
+ 0.0135062,
+ 0.00786026,
+ 0.0047153,
+ 0.0245401,
+ 0.00553791,
+ 0.0100592,
+ 0.0127319,
+ 0.0103344,
+ 0.00806758,
+ 0.0441923,
+ 0.0175274,
+ 0.00925906,
+ 0.0101233,
+ 0.340648,
+ 0.357329,
+ 0.019367,
+ 0.00142431,
+ 0.00350998
+ ],
+ [ 0.0674595,
+ 0.00216342,
+ 0.0662588,
+ 0.0865501,
+ 0.00182127,
+ 0.0368557,
+ 0.0381149,
+ 0.00332388,
+ 0.189974,
+ 0.009384,
+ 0.00394874,
+ 0.116311,
+ 0.0151208,
+ 0.093936,
+ 0.116173,
+ 0.0842204,
+ 0.0565954,
+ 0.00645142,
+ 0.00071873,
+ 0.00461894
+ ],
+ [ 0.0572262,
+ 0.00153015,
+ 0.179393,
+ 0.199226,
+ 0.00137018,
+ 0.0316472,
+ 0.0291392,
+ 0.00458046,
+ 0.101562,
+ 0.010074,
+ 0.00402046,
+ 0.108388,
+ 0.00636741,
+ 0.0903669,
+ 0.0494724,
+ 0.0621143,
+ 0.0496102,
+ 0.00859413,
+ 0.000666929,
+ 0.00464976
+ ],
+ [ 0.00360202,
+ 0.00454848,
+ 0.00208716,
+ 0.00178577,
+ 0.0855715,
+ 0.00563916,
+ 0.00649688,
+ 0.00292929,
+ 0.00104198,
+ 0.0232635,
+ 0.00445923,
+ 0.00134555,
+ 0.0024992,
+ 0.00327181,
+ 0.0102713,
+ 0.00306718,
+ 0.00259003,
+ 0.00586684,
+ 0.761782,
+ 0.067881
+ ],
+ [ 0.203202,
+ 0.00981316,
+ 0.0135012,
+ 0.00838182,
+ 0.00196196,
+ 0.618489,
+ 0.00277479,
+ 0.00118285,
+ 0.00445989,
+ 0.00398268,
+ 0.00206318,
+ 0.0143744,
+ 0.00858704,
+ 0.00445146,
+ 0.00838957,
+ 0.073992,
+ 0.0108922,
+ 0.00607691,
+ 0.00186061,
+ 0.00156387
+ ],
+ [ 0.00508988,
+ 0.00617765,
+ 0.00161262,
+ 0.00120404,
+ 0.356313,
+ 0.00163342,
+ 0.0393461,
+ 0.00590888,
+ 0.00137137,
+ 0.0249344,
+ 0.00497952,
+ 0.0057093,
+ 0.00141364,
+ 0.00246931,
+ 0.00287408,
+ 0.00595277,
+ 0.00365368,
+ 0.00819341,
+ 0.0357987,
+ 0.485365
+ ],
+ [ 0.0403336,
+ 0.00815495,
+ 0.00982186,
+ 0.0375407,
+ 0.0119141,
+ 0.00479344,
+ 0.0176736,
+ 0.189342,
+ 0.0607377,
+ 0.105186,
+ 0.03056,
+ 0.0216052,
+ 0.00775506,
+ 0.0383639,
+ 0.0540186,
+ 0.025711,
+ 0.100991,
+ 0.221091,
+ 0.002878,
+ 0.0115277
+ ],
+ [ 0.0790086,
+ 0.00249479,
+ 0.0546012,
+ 0.199788,
+ 0.00237734,
+ 0.0192656,
+ 0.02707,
+ 0.00756675,
+ 0.155311,
+ 0.0254542,
+ 0.00980244,
+ 0.0309384,
+ 0.00566407,
+ 0.184338,
+ 0.106544,
+ 0.0332371,
+ 0.0359575,
+ 0.0145306,
+ 0.00116828,
+ 0.00488208
+ ],
+ [ 0.0722241,
+ 0.00647553,
+ 0.119488,
+ 0.134589,
+ 0.0348233,
+ 0.0287815,
+ 0.0699011,
+ 0.0173589,
+ 0.0490342,
+ 0.051987,
+ 0.0154411,
+ 0.067893,
+ 0.0145597,
+ 0.070897,
+ 0.0489728,
+ 0.058958,
+ 0.0425973,
+ 0.0317884,
+ 0.00879138,
+ 0.0554387
+ ],
+ [ 0.108584,
+ 0.00125026,
+ 0.152967,
+ 0.166485,
+ 0.00145535,
+ 0.0336098,
+ 0.0134902,
+ 0.00388218,
+ 0.0576227,
+ 0.00898614,
+ 0.0024339,
+ 0.0441956,
+ 0.19901,
+ 0.0405398,
+ 0.020645,
+ 0.084675,
+ 0.0454715,
+ 0.0113416,
+ 0.000590283,
+ 0.00276502
+ ],
+ [ 0.0309526,
+ 0.0065594,
+ 0.00823521,
+ 0.0291974,
+ 0.00368916,
+ 0.0154206,
+ 0.0310385,
+ 0.00982516,
+ 0.306263,
+ 0.02379,
+ 0.00970717,
+ 0.0301337,
+ 0.00950291,
+ 0.0832608,
+ 0.319589,
+ 0.0295285,
+ 0.0303052,
+ 0.0133037,
+ 0.00281253,
+ 0.00688506
+ ],
+ [ 0.00989537,
+ 0.00282767,
+ 0.000374823,
+ 0.00091821,
+ 0.0298607,
+ 0.000699707,
+ 0.00104195,
+ 0.311504,
+ 0.00139605,
+ 0.375039,
+ 0.0474451,
+ 0.000730793,
+ 0.00252963,
+ 0.0017337,
+ 0.00196045,
+ 0.0014628,
+ 0.0075739,
+ 0.1973,
+ 0.00167998,
+ 0.00402599
+ ],
+ [ 0.116321,
+ 0.00347923,
+ 0.0731918,
+ 0.138088,
+ 0.00941177,
+ 0.0193193,
+ 0.0160241,
+ 0.0712243,
+ 0.035512,
+ 0.0771474,
+ 0.0242841,
+ 0.0250164,
+ 0.0508927,
+ 0.0586677,
+ 0.0273321,
+ 0.047556,
+ 0.0726552,
+ 0.123571,
+ 0.00268927,
+ 0.0076166
+ ],
+ [ 0.128522,
+ 0.0172929,
+ 0.040275,
+ 0.0250692,
+ 0.0199118,
+ 0.112703,
+ 0.0606981,
+ 0.010935,
+ 0.028875,
+ 0.0258416,
+ 0.0167593,
+ 0.117984,
+ 0.0180675,
+ 0.0439706,
+ 0.0373073,
+ 0.174149,
+ 0.0648968,
+ 0.0182067,
+ 0.0063575,
+ 0.0321772
+ ],
+ [ 0.0372287,
+ 0.014494,
+ 0.00237032,
+ 0.00485851,
+ 0.146377,
+ 0.00464339,
+ 0.0186795,
+ 0.182046,
+ 0.00581985,
+ 0.17801,
+ 0.0371334,
+ 0.00533773,
+ 0.00485386,
+ 0.00790971,
+ 0.0094528,
+ 0.0103571,
+ 0.0284162,
+ 0.184992,
+ 0.0211294,
+ 0.0958905
+ ],
+ [ 0.0535644,
+ 0.00962562,
+ 0.0113537,
+ 0.0391699,
+ 0.0264214,
+ 0.0120279,
+ 0.0384888,
+ 0.0522748,
+ 0.0996038,
+ 0.189239,
+ 0.0712219,
+ 0.0239173,
+ 0.00837206,
+ 0.0928585,
+ 0.11598,
+ 0.0299114,
+ 0.0389485,
+ 0.0500948,
+ 0.0104232,
+ 0.026503
+ ],
+ [ 0.133242,
+ 0.0246514,
+ 0.00127392,
+ 0.00404615,
+ 0.0156995,
+ 0.00891392,
+ 0.00158647,
+ 0.197128,
+ 0.00237132,
+ 0.125129,
+ 0.0286947,
+ 0.0022705,
+ 0.0118846,
+ 0.00308435,
+ 0.00331477,
+ 0.0171462,
+ 0.0563298,
+ 0.356621,
+ 0.00173418,
+ 0.00487784
+ ],
+ [ 0.149866,
+ 0.00354374,
+ 0.0280355,
+ 0.0435381,
+ 0.00475339,
+ 0.0311113,
+ 0.0140626,
+ 0.0101953,
+ 0.0393125,
+ 0.0251434,
+ 0.00515483,
+ 0.0176453,
+ 0.39238,
+ 0.0348151,
+ 0.0326607,
+ 0.0874497,
+ 0.0473307,
+ 0.0271597,
+ 0.00152152,
+ 0.00432083
+ ],
+ [ 0.421437,
+ 0.018761,
+ 0.00733051,
+ 0.00868378,
+ 0.00271561,
+ 0.0902333,
+ 0.0030262,
+ 0.00393628,
+ 0.00515087,
+ 0.00471933,
+ 0.00383066,
+ 0.012159,
+ 0.020894,
+ 0.00727486,
+ 0.0061426,
+ 0.290119,
+ 0.0651922,
+ 0.0252211,
+ 0.000810824,
+ 0.00236228
+ ],
+ [ 0.177071,
+ 0.00783489,
+ 0.02265,
+ 0.0509767,
+ 0.00405142,
+ 0.089739,
+ 0.0220667,
+ 0.00595198,
+ 0.125769,
+ 0.020537,
+ 0.00929825,
+ 0.0311657,
+ 0.0264088,
+ 0.0752471,
+ 0.133278,
+ 0.116959,
+ 0.0565567,
+ 0.0165087,
+ 0.00299471,
+ 0.00493467
+ ],
+ [ 0.0293984,
+ 0.00317291,
+ 0.109971,
+ 0.046427,
+ 0.00150396,
+ 0.422242,
+ 0.0272495,
+ 0.000799733,
+ 0.0622314,
+ 0.00376343,
+ 0.00166571,
+ 0.148362,
+ 0.00564818,
+ 0.0388688,
+ 0.0370902,
+ 0.0472252,
+ 0.0086569,
+ 0.00203639,
+ 0.000917602,
+ 0.00276931
+ ],
+ [ 0.0265779,
+ 0.0101369,
+ 0.0280314,
+ 0.0269057,
+ 0.0276961,
+ 0.0173377,
+ 0.281513,
+ 0.0064647,
+ 0.0474749,
+ 0.026821,
+ 0.00723753,
+ 0.13186,
+ 0.0083015,
+ 0.0989711,
+ 0.0791105,
+ 0.0426277,
+ 0.0259043,
+ 0.0100147,
+ 0.00785289,
+ 0.0891598
+ ],
+ [ 0.00960965,
+ 0.00773017,
+ 0.000633186,
+ 0.00104719,
+ 0.263017,
+ 0.00202274,
+ 0.00390014,
+ 0.0733098,
+ 0.00149315,
+ 0.445169,
+ 0.0732575,
+ 0.00131044,
+ 0.00427681,
+ 0.00338994,
+ 0.00271362,
+ 0.00361174,
+ 0.00579284,
+ 0.0425173,
+ 0.0181276,
+ 0.0370698
+ ]
+ ]
+
+-- | Weights of C40 model.
+c40Weights :: [Double]
+c40Weights =
+ [ 0.0223854,
+ 0.0338892,
+ 0.0577169,
+ 0.0252416,
+ 0.0108608,
+ 0.0462374,
+ 0.0102293,
+ 0.0147524,
+ 0.0143161,
+ 0.0182303,
+ 0.0204025,
+ 0.0425505,
+ 0.0248627,
+ 0.0105893,
+ 0.0188239,
+ 0.00866634,
+ 0.0148496,
+ 0.0343037,
+ 0.0225335,
+ 0.0174069,
+ 0.0112208,
+ 0.0443532,
+ 0.0392573,
+ 0.0196757,
+ 0.028769,
+ 0.0114441,
+ 0.0112339,
+ 0.0582694,
+ 0.0444272,
+ 0.0112011,
+ 0.0145176,
+ 0.0114629,
+ 0.0239628,
+ 0.0266266,
+ 0.0481201,
+ 0.0371147,
+ 0.0160477,
+ 0.0237249,
+ 0.0235226,
+ 0.0261998
+ ]
+
+-- | Stationary distribution of C50 model.
+c50StatDists :: [StationaryDistribution]
+c50StatDists =
+ map
+ V.fromList
+ [ [ 0.115682,
+ 0.00212412,
+ 0.125699,
+ 0.0919063,
+ 0.0016175,
+ 0.0391977,
+ 0.0108596,
+ 0.00344834,
+ 0.0344439,
+ 0.0125587,
+ 0.00467132,
+ 0.0530851,
+ 0.206661,
+ 0.0264814,
+ 0.0147638,
+ 0.154493,
+ 0.0841319,
+ 0.0134754,
+ 0.000392551,
+ 0.00430762
+ ],
+ [ 0.0983768,
+ 0.00160659,
+ 0.0456633,
+ 0.0935028,
+ 0.00112009,
+ 0.0251388,
+ 0.0191777,
+ 0.00367483,
+ 0.151407,
+ 0.0115555,
+ 0.00258422,
+ 0.0266318,
+ 0.229718,
+ 0.0694385,
+ 0.0855866,
+ 0.0696565,
+ 0.0498854,
+ 0.0123983,
+ 0.00069296,
+ 0.00218381
+ ],
+ [ 0.0214598,
+ 0.00446298,
+ 0.000555089,
+ 0.00135258,
+ 0.00855351,
+ 0.00112246,
+ 0.000813505,
+ 0.399631,
+ 0.00128242,
+ 0.0868331,
+ 0.0170323,
+ 0.00117488,
+ 0.00183519,
+ 0.00101872,
+ 0.00142423,
+ 0.00233511,
+ 0.0161891,
+ 0.430205,
+ 0.00061736,
+ 0.00210206
+ ],
+ [ 0.117155,
+ 0.032654,
+ 0.00620066,
+ 0.00998032,
+ 0.0657132,
+ 0.0333659,
+ 0.0134621,
+ 0.0557335,
+ 0.00794829,
+ 0.199356,
+ 0.0938018,
+ 0.0221831,
+ 0.0115415,
+ 0.0204903,
+ 0.0146873,
+ 0.0842555,
+ 0.0920314,
+ 0.0798031,
+ 0.0127314,
+ 0.0269048
+ ],
+ [ 0.0371284,
+ 0.0131607,
+ 0.00255462,
+ 0.00465054,
+ 0.156922,
+ 0.00416133,
+ 0.019977,
+ 0.178808,
+ 0.00498614,
+ 0.165159,
+ 0.0352649,
+ 0.0057612,
+ 0.00512406,
+ 0.00679862,
+ 0.00826841,
+ 0.0102949,
+ 0.0275498,
+ 0.181807,
+ 0.0221255,
+ 0.109498
+ ],
+ [ 0.0540087,
+ 0.000836323,
+ 0.306245,
+ 0.38187,
+ 0.00111469,
+ 0.0245756,
+ 0.0116353,
+ 0.00254509,
+ 0.030937,
+ 0.00536416,
+ 0.00256903,
+ 0.0359123,
+ 0.0122515,
+ 0.0586791,
+ 0.0115134,
+ 0.0277199,
+ 0.020314,
+ 0.00828799,
+ 0.000720693,
+ 0.00290032
+ ],
+ [ 0.0404572,
+ 0.028652,
+ 0.00495693,
+ 0.0068813,
+ 0.242849,
+ 0.0103569,
+ 0.0318377,
+ 0.0329142,
+ 0.0105561,
+ 0.143431,
+ 0.0485779,
+ 0.0105988,
+ 0.00489299,
+ 0.0118557,
+ 0.0126873,
+ 0.0229136,
+ 0.0212457,
+ 0.0349069,
+ 0.0593874,
+ 0.220042
+ ],
+ [ 0.319667,
+ 0.138968,
+ 0.00144847,
+ 0.00200138,
+ 0.00997903,
+ 0.0503464,
+ 0.00296588,
+ 0.0182219,
+ 0.00202126,
+ 0.0260477,
+ 0.0136422,
+ 0.00936868,
+ 0.00591365,
+ 0.00358722,
+ 0.00435407,
+ 0.1656,
+ 0.118413,
+ 0.0996664,
+ 0.00164228,
+ 0.00614589
+ ],
+ [ 0.0977328,
+ 0.00251083,
+ 0.0724816,
+ 0.197027,
+ 0.00556062,
+ 0.0117997,
+ 0.0154288,
+ 0.0563751,
+ 0.0613631,
+ 0.047368,
+ 0.0159721,
+ 0.0241106,
+ 0.0149,
+ 0.0909736,
+ 0.034432,
+ 0.0408092,
+ 0.0929289,
+ 0.111482,
+ 0.00122744,
+ 0.00551621
+ ],
+ [ 0.0195453,
+ 0.0107627,
+ 0.0127492,
+ 0.011794,
+ 0.14032,
+ 0.0061666,
+ 0.215761,
+ 0.00826718,
+ 0.0118897,
+ 0.0328258,
+ 0.00664433,
+ 0.0423533,
+ 0.00528472,
+ 0.0258824,
+ 0.024497,
+ 0.0203711,
+ 0.0124449,
+ 0.0133889,
+ 0.0330587,
+ 0.345993
+ ],
+ [ 0.185338,
+ 0.00185224,
+ 0.161345,
+ 0.234878,
+ 0.00192286,
+ 0.054278,
+ 0.0109591,
+ 0.00550122,
+ 0.0382027,
+ 0.00925008,
+ 0.00343293,
+ 0.033406,
+ 0.0233824,
+ 0.0551124,
+ 0.0201268,
+ 0.0884267,
+ 0.051789,
+ 0.0177494,
+ 0.000835994,
+ 0.00221142
+ ],
+ [ 0.0143603,
+ 0.0036047,
+ 0.000411253,
+ 0.00108887,
+ 0.0196479,
+ 0.00187385,
+ 0.000991664,
+ 0.285685,
+ 0.00213672,
+ 0.317288,
+ 0.150556,
+ 0.00155703,
+ 0.00122034,
+ 0.0028111,
+ 0.00194519,
+ 0.00344669,
+ 0.0196686,
+ 0.167294,
+ 0.000843478,
+ 0.00356936
+ ],
+ [ 0.150577,
+ 0.00957632,
+ 0.0227565,
+ 0.0358641,
+ 0.0104881,
+ 0.0285062,
+ 0.0171219,
+ 0.0577109,
+ 0.0276149,
+ 0.0531781,
+ 0.0298859,
+ 0.0514957,
+ 0.0243637,
+ 0.0354202,
+ 0.0272841,
+ 0.132633,
+ 0.169554,
+ 0.104387,
+ 0.00219421,
+ 0.00938724
+ ],
+ [ 0.277615,
+ 0.0280749,
+ 0.00194439,
+ 0.00537302,
+ 0.0070772,
+ 0.0234861,
+ 0.0012257,
+ 0.0949678,
+ 0.00308357,
+ 0.0474515,
+ 0.0189616,
+ 0.0034483,
+ 0.0134815,
+ 0.00374076,
+ 0.00354151,
+ 0.0423818,
+ 0.0932708,
+ 0.326207,
+ 0.000963513,
+ 0.00370386
+ ],
+ [ 0.205879,
+ 0.00249091,
+ 0.075426,
+ 0.161651,
+ 0.00210732,
+ 0.0463391,
+ 0.0159993,
+ 0.00515537,
+ 0.0913036,
+ 0.0166911,
+ 0.00536596,
+ 0.0366042,
+ 0.00849072,
+ 0.0973331,
+ 0.0696431,
+ 0.088244,
+ 0.0501877,
+ 0.0172747,
+ 0.000776174,
+ 0.0030381
+ ],
+ [ 0.0704473,
+ 0.00149732,
+ 0.187469,
+ 0.208434,
+ 0.0013217,
+ 0.0409359,
+ 0.0247326,
+ 0.00339884,
+ 0.0739754,
+ 0.00761491,
+ 0.00270559,
+ 0.0965448,
+ 0.00673196,
+ 0.0820493,
+ 0.0355811,
+ 0.0832004,
+ 0.0610002,
+ 0.00788473,
+ 0.000646918,
+ 0.00382803
+ ],
+ [ 0.108767,
+ 0.00735776,
+ 0.0100122,
+ 0.0249269,
+ 0.015562,
+ 0.0114116,
+ 0.00730171,
+ 0.0923916,
+ 0.0138538,
+ 0.112308,
+ 0.0251594,
+ 0.00831075,
+ 0.259979,
+ 0.0187962,
+ 0.0142911,
+ 0.0329858,
+ 0.0608007,
+ 0.162244,
+ 0.0049709,
+ 0.00857003
+ ],
+ [ 0.109878,
+ 0.0295589,
+ 0.000867374,
+ 0.00267084,
+ 0.028604,
+ 0.0101436,
+ 0.00159952,
+ 0.171472,
+ 0.0015037,
+ 0.241889,
+ 0.0488425,
+ 0.00201796,
+ 0.00631863,
+ 0.00393786,
+ 0.00336164,
+ 0.0148413,
+ 0.0393773,
+ 0.273667,
+ 0.00359303,
+ 0.00585493
+ ],
+ [ 0.058736,
+ 0.00692528,
+ 0.0144651,
+ 0.0412403,
+ 0.0154694,
+ 0.015436,
+ 0.0243546,
+ 0.0388984,
+ 0.0996366,
+ 0.207192,
+ 0.103832,
+ 0.0289715,
+ 0.00833815,
+ 0.108218,
+ 0.0976056,
+ 0.0350037,
+ 0.0432645,
+ 0.0338957,
+ 0.00652556,
+ 0.0119916
+ ],
+ [ 0.0642736,
+ 0.00525071,
+ 0.144305,
+ 0.153274,
+ 0.0286093,
+ 0.0265312,
+ 0.0545105,
+ 0.0231701,
+ 0.0452879,
+ 0.058794,
+ 0.0192273,
+ 0.071063,
+ 0.0146855,
+ 0.066931,
+ 0.0405954,
+ 0.054046,
+ 0.043602,
+ 0.0350962,
+ 0.00655203,
+ 0.0441953
+ ],
+ [ 0.00487716,
+ 0.00503139,
+ 0.00209095,
+ 0.00192293,
+ 0.0983777,
+ 0.00615619,
+ 0.00725617,
+ 0.00400789,
+ 0.000993075,
+ 0.0277171,
+ 0.00537714,
+ 0.00145717,
+ 0.0029039,
+ 0.00350461,
+ 0.0112195,
+ 0.00329284,
+ 0.00295187,
+ 0.00708726,
+ 0.724652,
+ 0.0791231
+ ],
+ [ 0.0552756,
+ 0.0115894,
+ 0.00846155,
+ 0.0432312,
+ 0.00961795,
+ 0.0074182,
+ 0.0218432,
+ 0.0843826,
+ 0.163327,
+ 0.0631707,
+ 0.0228359,
+ 0.0221225,
+ 0.00652522,
+ 0.0639538,
+ 0.146077,
+ 0.0387464,
+ 0.100713,
+ 0.118118,
+ 0.00298298,
+ 0.00960875
+ ],
+ [ 0.00449551,
+ 0.00619902,
+ 0.000890609,
+ 0.000674178,
+ 0.400884,
+ 0.0013356,
+ 0.0223834,
+ 0.00805107,
+ 0.00105813,
+ 0.0341606,
+ 0.00701178,
+ 0.00318917,
+ 0.00130624,
+ 0.00157564,
+ 0.00181707,
+ 0.00502515,
+ 0.00337803,
+ 0.00946203,
+ 0.0345278,
+ 0.452575
+ ],
+ [ 0.0505469,
+ 0.00768183,
+ 0.0101983,
+ 0.0470721,
+ 0.0160596,
+ 0.00517598,
+ 0.0176387,
+ 0.169463,
+ 0.0497501,
+ 0.209444,
+ 0.0474166,
+ 0.0132404,
+ 0.00844474,
+ 0.053753,
+ 0.051076,
+ 0.0149657,
+ 0.03846,
+ 0.172926,
+ 0.00437246,
+ 0.0123139
+ ],
+ [ 0.0749936,
+ 0.0124353,
+ 0.0203869,
+ 0.0100161,
+ 0.0038092,
+ 0.0270453,
+ 0.00581932,
+ 0.00743392,
+ 0.014732,
+ 0.00838354,
+ 0.00640172,
+ 0.0530316,
+ 0.0176075,
+ 0.0096947,
+ 0.0117746,
+ 0.3482,
+ 0.348235,
+ 0.0157071,
+ 0.00137596,
+ 0.00291601
+ ],
+ [ 0.0569785,
+ 0.00176591,
+ 0.102737,
+ 0.106157,
+ 0.00132179,
+ 0.0360979,
+ 0.034465,
+ 0.00311879,
+ 0.185459,
+ 0.00858711,
+ 0.00431374,
+ 0.139374,
+ 0.00855798,
+ 0.0898676,
+ 0.101042,
+ 0.0669467,
+ 0.0422839,
+ 0.00552428,
+ 0.000686497,
+ 0.00471478
+ ],
+ [ 0.0746973,
+ 0.00394557,
+ 0.0423454,
+ 0.0906599,
+ 0.00363883,
+ 0.0183504,
+ 0.0229406,
+ 0.0156166,
+ 0.12297,
+ 0.0167059,
+ 0.00901115,
+ 0.0672502,
+ 0.0127747,
+ 0.0811334,
+ 0.0755385,
+ 0.132886,
+ 0.170553,
+ 0.0324157,
+ 0.00152093,
+ 0.00504616
+ ],
+ [ 0.17313,
+ 0.00938612,
+ 0.0203504,
+ 0.0387504,
+ 0.00448721,
+ 0.0867075,
+ 0.0227177,
+ 0.00492238,
+ 0.125544,
+ 0.0156727,
+ 0.00787132,
+ 0.0400476,
+ 0.0180405,
+ 0.0680443,
+ 0.133335,
+ 0.142136,
+ 0.0670614,
+ 0.0136107,
+ 0.00287027,
+ 0.00531475
+ ],
+ [ 0.00751784,
+ 0.00212117,
+ 0.000341917,
+ 0.000667876,
+ 0.0310677,
+ 0.000466913,
+ 0.000898937,
+ 0.320302,
+ 0.00103903,
+ 0.384419,
+ 0.0335748,
+ 0.000602706,
+ 0.00243131,
+ 0.00137426,
+ 0.00152778,
+ 0.00115498,
+ 0.00552329,
+ 0.199295,
+ 0.00172716,
+ 0.00394622
+ ],
+ [ 0.113459,
+ 0.0281671,
+ 0.0268294,
+ 0.0283293,
+ 0.0928796,
+ 0.0494616,
+ 0.0733971,
+ 0.0152335,
+ 0.0176739,
+ 0.037425,
+ 0.0140126,
+ 0.0539481,
+ 0.0259048,
+ 0.0303861,
+ 0.0259068,
+ 0.121621,
+ 0.0621544,
+ 0.0350518,
+ 0.0240853,
+ 0.124074
+ ],
+ [ 0.0810974,
+ 0.00899714,
+ 0.0930492,
+ 0.0372909,
+ 0.002713,
+ 0.0907986,
+ 0.0275326,
+ 0.00533957,
+ 0.0362449,
+ 0.00831441,
+ 0.00615441,
+ 0.177093,
+ 0.0120848,
+ 0.0316411,
+ 0.025247,
+ 0.233557,
+ 0.106302,
+ 0.00814021,
+ 0.000950692,
+ 0.00745168
+ ],
+ [ 0.00757098,
+ 0.00716117,
+ 0.00049456,
+ 0.000891326,
+ 0.297029,
+ 0.00155605,
+ 0.00342729,
+ 0.0711141,
+ 0.00107067,
+ 0.416918,
+ 0.0635143,
+ 0.000864035,
+ 0.00349893,
+ 0.00251506,
+ 0.00186372,
+ 0.00271598,
+ 0.00424124,
+ 0.041488,
+ 0.0202374,
+ 0.0518279
+ ],
+ [ 0.086899,
+ 0.00542266,
+ 0.0274343,
+ 0.117345,
+ 0.00568342,
+ 0.0162895,
+ 0.0386176,
+ 0.0182492,
+ 0.149526,
+ 0.048245,
+ 0.0150062,
+ 0.0265186,
+ 0.00577334,
+ 0.159013,
+ 0.149227,
+ 0.0416278,
+ 0.0492401,
+ 0.0283951,
+ 0.00272523,
+ 0.00876225
+ ],
+ [ 0.0501736,
+ 0.0113806,
+ 0.00768113,
+ 0.0191841,
+ 0.0119036,
+ 0.00521331,
+ 0.00988204,
+ 0.203482,
+ 0.0206446,
+ 0.0870652,
+ 0.036001,
+ 0.0197961,
+ 0.0061624,
+ 0.0180415,
+ 0.0178215,
+ 0.0399964,
+ 0.162255,
+ 0.262373,
+ 0.00172457,
+ 0.00921833
+ ],
+ [ 0.177098,
+ 0.00357587,
+ 0.0740854,
+ 0.0713923,
+ 0.00385864,
+ 0.211235,
+ 0.0161904,
+ 0.0040472,
+ 0.0370753,
+ 0.00826202,
+ 0.00369757,
+ 0.0494737,
+ 0.0543871,
+ 0.0396583,
+ 0.0340392,
+ 0.140615,
+ 0.0532238,
+ 0.0108131,
+ 0.00212448,
+ 0.00514764
+ ],
+ [ 0.242384,
+ 0.0115188,
+ 0.00720908,
+ 0.00544261,
+ 0.00229719,
+ 0.593273,
+ 0.00205723,
+ 0.00208173,
+ 0.00287156,
+ 0.00491,
+ 0.00271204,
+ 0.00899551,
+ 0.00763059,
+ 0.00285962,
+ 0.00600369,
+ 0.0738385,
+ 0.0108329,
+ 0.00968775,
+ 0.00178961,
+ 0.00160391
+ ],
+ [ 0.032912,
+ 0.00319267,
+ 0.143899,
+ 0.0532755,
+ 0.00166462,
+ 0.463509,
+ 0.0175283,
+ 0.000876108,
+ 0.0317056,
+ 0.00297349,
+ 0.0012156,
+ 0.131603,
+ 0.00688601,
+ 0.0251373,
+ 0.0184844,
+ 0.0491059,
+ 0.00984294,
+ 0.00239178,
+ 0.0008917,
+ 0.00290456
+ ],
+ [ 0.0388306,
+ 0.00489943,
+ 0.0491655,
+ 0.0413874,
+ 0.00170354,
+ 0.345044,
+ 0.0421499,
+ 0.00103798,
+ 0.123725,
+ 0.00726049,
+ 0.00335164,
+ 0.119727,
+ 0.00562115,
+ 0.0664068,
+ 0.0881106,
+ 0.0460192,
+ 0.00791813,
+ 0.0020819,
+ 0.00195492,
+ 0.00360516
+ ],
+ [ 0.0373301,
+ 0.00916334,
+ 0.0396965,
+ 0.0362168,
+ 0.0144959,
+ 0.0269081,
+ 0.220512,
+ 0.00638711,
+ 0.0634517,
+ 0.0225147,
+ 0.00718608,
+ 0.152708,
+ 0.00995802,
+ 0.108449,
+ 0.0882553,
+ 0.0609295,
+ 0.0332848,
+ 0.0105312,
+ 0.00429315,
+ 0.047729
+ ],
+ [ 0.0171508,
+ 0.00565843,
+ 0.00111564,
+ 0.00268175,
+ 0.0490847,
+ 0.00219974,
+ 0.00370226,
+ 0.116938,
+ 0.00407925,
+ 0.500942,
+ 0.1832,
+ 0.00280387,
+ 0.00400697,
+ 0.0115255,
+ 0.00613355,
+ 0.00539456,
+ 0.0140434,
+ 0.0579479,
+ 0.00419195,
+ 0.00719895
+ ],
+ [ 0.0238117,
+ 0.00329378,
+ 0.370777,
+ 0.0831676,
+ 0.0022275,
+ 0.053433,
+ 0.0290274,
+ 0.00288609,
+ 0.0258098,
+ 0.00370314,
+ 0.00159506,
+ 0.259554,
+ 0.00668902,
+ 0.0201877,
+ 0.0117854,
+ 0.0626213,
+ 0.0278627,
+ 0.00464381,
+ 0.000688992,
+ 0.0062349
+ ],
+ [ 0.209736,
+ 0.0105937,
+ 0.0311812,
+ 0.0613839,
+ 0.00991105,
+ 0.0855144,
+ 0.0226071,
+ 0.0296058,
+ 0.0455281,
+ 0.0792591,
+ 0.0306389,
+ 0.019447,
+ 0.0213982,
+ 0.0610672,
+ 0.0588191,
+ 0.0820738,
+ 0.0527883,
+ 0.0722389,
+ 0.00513,
+ 0.0110785
+ ],
+ [ 0.0295833,
+ 0.00588894,
+ 0.00852018,
+ 0.0296344,
+ 0.00323424,
+ 0.0154495,
+ 0.02992,
+ 0.00752729,
+ 0.317117,
+ 0.0212988,
+ 0.00874154,
+ 0.0312424,
+ 0.00843308,
+ 0.0831654,
+ 0.323587,
+ 0.0294177,
+ 0.0283085,
+ 0.0100345,
+ 0.00257807,
+ 0.00631797
+ ],
+ [ 0.0937098,
+ 0.00289961,
+ 0.0255803,
+ 0.0577481,
+ 0.0140839,
+ 0.0182984,
+ 0.0300827,
+ 0.0312422,
+ 0.0867966,
+ 0.067914,
+ 0.01767,
+ 0.0206426,
+ 0.213942,
+ 0.0611154,
+ 0.0902988,
+ 0.0526724,
+ 0.0464314,
+ 0.0509513,
+ 0.00365078,
+ 0.01427
+ ],
+ [ 0.419507,
+ 0.0176715,
+ 0.00719436,
+ 0.00880545,
+ 0.00285112,
+ 0.0865515,
+ 0.00330323,
+ 0.00419601,
+ 0.00503365,
+ 0.0048203,
+ 0.00393323,
+ 0.012443,
+ 0.0192167,
+ 0.00750218,
+ 0.00609116,
+ 0.295973,
+ 0.0660748,
+ 0.0253174,
+ 0.000942289,
+ 0.00257126
+ ],
+ [ 0.0368106,
+ 0.0124259,
+ 0.0102859,
+ 0.0343205,
+ 0.0759532,
+ 0.00772969,
+ 0.0938663,
+ 0.0458547,
+ 0.0701169,
+ 0.133403,
+ 0.031916,
+ 0.0265402,
+ 0.00749485,
+ 0.0673302,
+ 0.10388,
+ 0.0271625,
+ 0.0353789,
+ 0.0485031,
+ 0.0254607,
+ 0.105568
+ ],
+ [ 0.0665479,
+ 0.00185956,
+ 0.183575,
+ 0.149215,
+ 0.00127224,
+ 0.0634659,
+ 0.019684,
+ 0.00262142,
+ 0.0655694,
+ 0.00750609,
+ 0.00151282,
+ 0.0699101,
+ 0.182105,
+ 0.0446839,
+ 0.0292035,
+ 0.075452,
+ 0.0278833,
+ 0.00484561,
+ 0.000723776,
+ 0.00236318
+ ],
+ [ 0.16002,
+ 0.00397537,
+ 0.019682,
+ 0.0286161,
+ 0.00458768,
+ 0.0326662,
+ 0.0114325,
+ 0.00722291,
+ 0.0232558,
+ 0.0202542,
+ 0.00379358,
+ 0.0142832,
+ 0.460797,
+ 0.0260458,
+ 0.0217875,
+ 0.0913633,
+ 0.0427326,
+ 0.0227118,
+ 0.0012566,
+ 0.0035159
+ ],
+ [ 0.0843584,
+ 0.00129715,
+ 0.0847585,
+ 0.260552,
+ 0.00143564,
+ 0.0191268,
+ 0.0174708,
+ 0.00556223,
+ 0.144172,
+ 0.014456,
+ 0.00550323,
+ 0.0336163,
+ 0.00724868,
+ 0.160704,
+ 0.0742581,
+ 0.0323411,
+ 0.0355032,
+ 0.0136662,
+ 0.000760206,
+ 0.00320994
+ ],
+ [ 0.152149,
+ 0.000925399,
+ 0.116471,
+ 0.220438,
+ 0.00150071,
+ 0.0172039,
+ 0.0095692,
+ 0.00747151,
+ 0.0529323,
+ 0.0148756,
+ 0.00356173,
+ 0.0157411,
+ 0.217335,
+ 0.0489135,
+ 0.0171707,
+ 0.044102,
+ 0.0323715,
+ 0.023915,
+ 0.000908902,
+ 0.00244332
+ ]
+ ]
+
+-- | Weights of C50 model.
+c50Weights :: [Double]
+c50Weights =
+ [ 0.00509464,
+ 0.00753314,
+ 0.0595801,
+ 0.0100458,
+ 0.0109109,
+ 0.0427412,
+ 0.00632106,
+ 0.0192362,
+ 0.0119168,
+ 0.0154209,
+ 0.0148037,
+ 0.014293,
+ 0.0164064,
+ 0.0272538,
+ 0.0178737,
+ 0.0125183,
+ 0.00698661,
+ 0.0140027,
+ 0.0140399,
+ 0.0109043,
+ 0.011579,
+ 0.0138661,
+ 0.0377329,
+ 0.0118586,
+ 0.0356688,
+ 0.0161327,
+ 0.0200601,
+ 0.0133087,
+ 0.0357641,
+ 0.0119353,
+ 0.0241183,
+ 0.0243098,
+ 0.0178039,
+ 0.0200988,
+ 0.00579569,
+ 0.0397441,
+ 0.0240799,
+ 0.00868054,
+ 0.0239822,
+ 0.042803,
+ 0.0335193,
+ 0.00636191,
+ 0.0547546,
+ 0.00544598,
+ 0.0354219,
+ 0.0120158,
+ 0.0047506,
+ 0.036392,
+ 0.0270346,
+ 0.00709747
+ ]
+
+-- | Stationary distribution of C60 model.
+c60StatDists :: [StationaryDistribution]
+c60StatDists =
+ map
+ V.fromList
+ [ [ 0.153436,
+ 0.00473066,
+ 0.0546757,
+ 0.0529324,
+ 0.00355543,
+ 0.110378,
+ 0.017448,
+ 0.00503439,
+ 0.0603929,
+ 0.0130294,
+ 0.00755506,
+ 0.0796727,
+ 0.0249524,
+ 0.0514333,
+ 0.0444389,
+ 0.202963,
+ 0.0957668,
+ 0.0101809,
+ 0.00144445,
+ 0.00598003
+ ],
+ [ 0.0281985,
+ 0.00195035,
+ 0.00915493,
+ 0.038853,
+ 0.00159193,
+ 0.00840283,
+ 0.0155385,
+ 0.0107873,
+ 0.347604,
+ 0.0217787,
+ 0.0109905,
+ 0.0312955,
+ 0.00715399,
+ 0.0939884,
+ 0.303106,
+ 0.0197479,
+ 0.0328352,
+ 0.0135303,
+ 0.000920999,
+ 0.0025714
+ ],
+ [ 0.00836807,
+ 0.00204339,
+ 0.000222837,
+ 0.000473154,
+ 0.0123984,
+ 0.000482575,
+ 0.000518999,
+ 0.376845,
+ 0.000629617,
+ 0.260833,
+ 0.0315701,
+ 0.000612345,
+ 0.000959592,
+ 0.000949869,
+ 0.000731977,
+ 0.000974638,
+ 0.00499908,
+ 0.293808,
+ 0.000865776,
+ 0.00171323
+ ],
+ [ 0.222723,
+ 0.164029,
+ 0.000799759,
+ 0.00272808,
+ 0.0228667,
+ 0.0202703,
+ 0.00371839,
+ 0.0455406,
+ 0.00228329,
+ 0.088335,
+ 0.0348095,
+ 0.00612065,
+ 0.00354716,
+ 0.00510519,
+ 0.00648461,
+ 0.085004,
+ 0.101285,
+ 0.169858,
+ 0.00484248,
+ 0.00965
+ ],
+ [ 0.041214,
+ 0.0204716,
+ 0.00174344,
+ 0.00372634,
+ 0.2239,
+ 0.00691075,
+ 0.0180294,
+ 0.115428,
+ 0.00429003,
+ 0.169356,
+ 0.0414067,
+ 0.00510677,
+ 0.00584164,
+ 0.00575385,
+ 0.00676271,
+ 0.0149106,
+ 0.0239548,
+ 0.120034,
+ 0.0332237,
+ 0.137935
+ ],
+ [ 0.048055,
+ 0.00378018,
+ 0.208461,
+ 0.185518,
+ 0.0196001,
+ 0.0191402,
+ 0.0872162,
+ 0.00946854,
+ 0.0375741,
+ 0.0277341,
+ 0.00883084,
+ 0.0940629,
+ 0.00812678,
+ 0.0747677,
+ 0.0308438,
+ 0.0439681,
+ 0.0324589,
+ 0.0181769,
+ 0.00346657,
+ 0.03875
+ ],
+ [ 0.00628487,
+ 0.00730276,
+ 0.000532415,
+ 0.000974149,
+ 0.397455,
+ 0.00195782,
+ 0.0102225,
+ 0.0180592,
+ 0.00162059,
+ 0.117906,
+ 0.0234722,
+ 0.00303425,
+ 0.00201656,
+ 0.00344091,
+ 0.00262469,
+ 0.00569033,
+ 0.00370918,
+ 0.0152754,
+ 0.0598639,
+ 0.318557
+ ],
+ [ 0.181501,
+ 0.420563,
+ 0.00251455,
+ 0.000708814,
+ 0.00689764,
+ 0.0461854,
+ 0.00143746,
+ 0.00417455,
+ 0.000647425,
+ 0.00983105,
+ 0.00416114,
+ 0.0148485,
+ 0.00387672,
+ 0.0014097,
+ 0.00268454,
+ 0.186454,
+ 0.068719,
+ 0.0345742,
+ 0.00270835,
+ 0.0061033
+ ],
+ [ 0.0600741,
+ 0.00707198,
+ 0.0170572,
+ 0.0127487,
+ 0.114091,
+ 0.0343564,
+ 0.0305859,
+ 0.0204571,
+ 0.0212367,
+ 0.0994551,
+ 0.0318166,
+ 0.0134869,
+ 0.0297628,
+ 0.014247,
+ 0.0367643,
+ 0.0505793,
+ 0.0339368,
+ 0.0217422,
+ 0.231281,
+ 0.119249
+ ],
+ [ 0.0708395,
+ 0.0131641,
+ 0.0324483,
+ 0.0508264,
+ 0.059436,
+ 0.0183309,
+ 0.0567273,
+ 0.0650369,
+ 0.0343618,
+ 0.128226,
+ 0.0390363,
+ 0.0416822,
+ 0.0135608,
+ 0.0494875,
+ 0.0474098,
+ 0.0551343,
+ 0.064226,
+ 0.078961,
+ 0.0137118,
+ 0.0673934
+ ],
+ [ 0.0617689,
+ 0.000719984,
+ 0.343023,
+ 0.379251,
+ 0.000981419,
+ 0.0284659,
+ 0.00795921,
+ 0.00169996,
+ 0.0216077,
+ 0.00399453,
+ 0.00197343,
+ 0.0303082,
+ 0.0174791,
+ 0.0307856,
+ 0.00763329,
+ 0.0337832,
+ 0.0203427,
+ 0.00589923,
+ 0.000613027,
+ 0.00171028
+ ],
+ [ 0.042156,
+ 0.00444503,
+ 0.0164385,
+ 0.0531949,
+ 0.00867283,
+ 0.0134711,
+ 0.0177765,
+ 0.0267728,
+ 0.132374,
+ 0.196724,
+ 0.118283,
+ 0.0286981,
+ 0.00518379,
+ 0.139369,
+ 0.104207,
+ 0.0255853,
+ 0.0333292,
+ 0.0217067,
+ 0.00458523,
+ 0.00702815
+ ],
+ [ 0.281481,
+ 0.0258338,
+ 0.00643857,
+ 0.0115046,
+ 0.00504817,
+ 0.0270055,
+ 0.00546297,
+ 0.0188216,
+ 0.00987128,
+ 0.0190993,
+ 0.015872,
+ 0.0172868,
+ 0.012951,
+ 0.0133102,
+ 0.0100367,
+ 0.188681,
+ 0.24271,
+ 0.0837524,
+ 0.00122746,
+ 0.00360529
+ ],
+ [ 0.276919,
+ 0.0318293,
+ 0.00116725,
+ 0.00247525,
+ 0.00708439,
+ 0.0199647,
+ 0.000517086,
+ 0.0983109,
+ 0.00162322,
+ 0.0489264,
+ 0.0173415,
+ 0.00213153,
+ 0.00701797,
+ 0.00182163,
+ 0.0017227,
+ 0.0336349,
+ 0.0814141,
+ 0.362092,
+ 0.000711814,
+ 0.00329423
+ ],
+ [ 0.15778,
+ 0.00533181,
+ 0.064829,
+ 0.0913587,
+ 0.00250478,
+ 0.090621,
+ 0.053381,
+ 0.00291716,
+ 0.0782149,
+ 0.0156226,
+ 0.0045759,
+ 0.0570403,
+ 0.00670778,
+ 0.106537,
+ 0.111214,
+ 0.092931,
+ 0.0393123,
+ 0.00850409,
+ 0.00285758,
+ 0.00775903
+ ],
+ [ 0.0593735,
+ 0.00153322,
+ 0.218948,
+ 0.181942,
+ 0.00108383,
+ 0.0813707,
+ 0.0220478,
+ 0.00209936,
+ 0.0750172,
+ 0.00561913,
+ 0.00218717,
+ 0.115118,
+ 0.0109737,
+ 0.0688752,
+ 0.0354741,
+ 0.0726449,
+ 0.0380238,
+ 0.00426697,
+ 0.000734646,
+ 0.00266649
+ ],
+ [ 0.0978066,
+ 0.00641384,
+ 0.0120781,
+ 0.0291283,
+ 0.0198964,
+ 0.0128913,
+ 0.0128037,
+ 0.0723904,
+ 0.0245631,
+ 0.127944,
+ 0.0303267,
+ 0.0101844,
+ 0.272352,
+ 0.0307876,
+ 0.0265576,
+ 0.0350549,
+ 0.0484557,
+ 0.115203,
+ 0.00468425,
+ 0.0104774
+ ],
+ [ 0.0124023,
+ 0.00418857,
+ 0.000603732,
+ 0.0012524,
+ 0.0610615,
+ 0.00113068,
+ 0.00135421,
+ 0.234417,
+ 0.00167182,
+ 0.455056,
+ 0.0667308,
+ 0.00092391,
+ 0.00370762,
+ 0.00329574,
+ 0.00306804,
+ 0.00194209,
+ 0.00676129,
+ 0.129048,
+ 0.00389372,
+ 0.00749118
+ ],
+ [ 0.0794231,
+ 0.00199195,
+ 0.0587236,
+ 0.12469,
+ 0.001287,
+ 0.0325432,
+ 0.0238605,
+ 0.00362772,
+ 0.21476,
+ 0.0097988,
+ 0.00418462,
+ 0.0662793,
+ 0.014241,
+ 0.114388,
+ 0.129474,
+ 0.0615807,
+ 0.0477334,
+ 0.00781872,
+ 0.000652537,
+ 0.00294202
+ ],
+ [ 0.0248149,
+ 0.00278397,
+ 0.427883,
+ 0.143239,
+ 0.00146804,
+ 0.0643968,
+ 0.0185737,
+ 0.00225069,
+ 0.0179274,
+ 0.00345586,
+ 0.00157145,
+ 0.188892,
+ 0.0073768,
+ 0.0210778,
+ 0.00835529,
+ 0.0377003,
+ 0.0187768,
+ 0.00460727,
+ 0.000589186,
+ 0.00426027
+ ],
+ [ 0.00170034,
+ 0.00290594,
+ 0.00107115,
+ 0.00117317,
+ 0.0513377,
+ 0.00355796,
+ 0.00276305,
+ 0.00122912,
+ 0.00042738,
+ 0.0127421,
+ 0.00256713,
+ 0.00042229,
+ 0.00135367,
+ 0.00164242,
+ 0.00606743,
+ 0.00118717,
+ 0.00140331,
+ 0.00331373,
+ 0.864044,
+ 0.0390913
+ ],
+ [ 0.0468361,
+ 0.00599541,
+ 0.0185616,
+ 0.0705436,
+ 0.00801772,
+ 0.00454353,
+ 0.0152063,
+ 0.155061,
+ 0.0866248,
+ 0.0824253,
+ 0.0245854,
+ 0.0205604,
+ 0.00814856,
+ 0.0557031,
+ 0.0639797,
+ 0.0237026,
+ 0.0962054,
+ 0.204749,
+ 0.00183687,
+ 0.00671317
+ ],
+ [ 0.0258765,
+ 0.0142504,
+ 0.0107037,
+ 0.010565,
+ 0.187643,
+ 0.0073065,
+ 0.141108,
+ 0.0114778,
+ 0.0119179,
+ 0.0407992,
+ 0.0098799,
+ 0.0298384,
+ 0.00512288,
+ 0.0158529,
+ 0.0201097,
+ 0.02757,
+ 0.0170765,
+ 0.0187502,
+ 0.0405125,
+ 0.353639
+ ],
+ [ 0.0296285,
+ 0.00900465,
+ 0.000885102,
+ 0.00330465,
+ 0.0408798,
+ 0.00279695,
+ 0.00507015,
+ 0.25834,
+ 0.00466909,
+ 0.266809,
+ 0.0770825,
+ 0.00349444,
+ 0.00269182,
+ 0.00554811,
+ 0.00464003,
+ 0.00685381,
+ 0.0322266,
+ 0.22719,
+ 0.00355061,
+ 0.0153353
+ ],
+ [ 0.0555726,
+ 0.00974186,
+ 0.014039,
+ 0.00694432,
+ 0.00344967,
+ 0.0157957,
+ 0.00416313,
+ 0.00698265,
+ 0.0139225,
+ 0.00752712,
+ 0.00587627,
+ 0.0409064,
+ 0.0119733,
+ 0.00687277,
+ 0.00984479,
+ 0.348247,
+ 0.421366,
+ 0.0131119,
+ 0.00100615,
+ 0.00265768
+ ],
+ [ 0.0682671,
+ 0.0141433,
+ 0.0360279,
+ 0.0497415,
+ 0.0803376,
+ 0.0268697,
+ 0.112767,
+ 0.0132647,
+ 0.0482609,
+ 0.0544494,
+ 0.0170034,
+ 0.0530661,
+ 0.019195,
+ 0.0612274,
+ 0.0615207,
+ 0.067184,
+ 0.0443996,
+ 0.0267714,
+ 0.0199958,
+ 0.125507
+ ],
+ [ 0.0792619,
+ 0.00495033,
+ 0.0436646,
+ 0.0829639,
+ 0.00491311,
+ 0.0183429,
+ 0.0233169,
+ 0.0249427,
+ 0.0932578,
+ 0.0221483,
+ 0.0120893,
+ 0.0635289,
+ 0.012636,
+ 0.0666365,
+ 0.0638377,
+ 0.133485,
+ 0.191675,
+ 0.0503102,
+ 0.00180401,
+ 0.00623531
+ ],
+ [ 0.0731759,
+ 0.0123459,
+ 0.0110007,
+ 0.0349943,
+ 0.00931488,
+ 0.0224509,
+ 0.0386903,
+ 0.0246226,
+ 0.178334,
+ 0.0508307,
+ 0.0185741,
+ 0.0324201,
+ 0.0148723,
+ 0.0858952,
+ 0.210534,
+ 0.0603181,
+ 0.0649575,
+ 0.038504,
+ 0.00510464,
+ 0.0130597
+ ],
+ [ 0.0878403,
+ 0.0171147,
+ 0.00328039,
+ 0.0101466,
+ 0.0191954,
+ 0.00870909,
+ 0.00549022,
+ 0.198776,
+ 0.00820969,
+ 0.175646,
+ 0.0417233,
+ 0.00608012,
+ 0.0111284,
+ 0.0109832,
+ 0.0110332,
+ 0.0209863,
+ 0.0697719,
+ 0.28252,
+ 0.0031744,
+ 0.00819055
+ ],
+ [ 0.0990216,
+ 0.0108996,
+ 0.0118798,
+ 0.0279,
+ 0.0214442,
+ 0.024025,
+ 0.0123445,
+ 0.0776565,
+ 0.0322818,
+ 0.235451,
+ 0.120767,
+ 0.021115,
+ 0.00756555,
+ 0.0557711,
+ 0.0349352,
+ 0.052417,
+ 0.0649785,
+ 0.0771067,
+ 0.00470758,
+ 0.00773287
+ ],
+ [ 0.0601641,
+ 0.0315067,
+ 0.0337189,
+ 0.00598395,
+ 0.00695259,
+ 0.0543081,
+ 0.0531524,
+ 0.00706508,
+ 0.0139598,
+ 0.00706981,
+ 0.00882987,
+ 0.278352,
+ 0.00758343,
+ 0.0210646,
+ 0.0161995,
+ 0.28298,
+ 0.0860317,
+ 0.0100954,
+ 0.00149666,
+ 0.0134849
+ ],
+ [ 0.00497817,
+ 0.00529787,
+ 0.000531537,
+ 0.000763055,
+ 0.335112,
+ 0.00150513,
+ 0.00415752,
+ 0.0443829,
+ 0.00116151,
+ 0.441742,
+ 0.0602807,
+ 0.000701221,
+ 0.00278477,
+ 0.00240899,
+ 0.00184123,
+ 0.00257958,
+ 0.00302885,
+ 0.0237677,
+ 0.0171303,
+ 0.0458456
+ ],
+ [ 0.0251997,
+ 0.00970995,
+ 0.00410123,
+ 0.0262572,
+ 0.0429092,
+ 0.00380673,
+ 0.0431939,
+ 0.0974043,
+ 0.0824313,
+ 0.24472,
+ 0.0539323,
+ 0.0142032,
+ 0.00526585,
+ 0.0620071,
+ 0.111447,
+ 0.00960931,
+ 0.0251183,
+ 0.0783303,
+ 0.0146572,
+ 0.0456965
+ ],
+ [ 0.0230362,
+ 0.00485801,
+ 0.000626444,
+ 0.00157626,
+ 0.0072127,
+ 0.00115653,
+ 0.000889924,
+ 0.39529,
+ 0.00146635,
+ 0.0576537,
+ 0.0140987,
+ 0.00135344,
+ 0.00201779,
+ 0.000987005,
+ 0.00147487,
+ 0.00287702,
+ 0.0205581,
+ 0.460366,
+ 0.000547769,
+ 0.00195391
+ ],
+ [ 0.140878,
+ 0.00322137,
+ 0.0285077,
+ 0.0423839,
+ 0.00412311,
+ 0.0299558,
+ 0.0131321,
+ 0.00669145,
+ 0.0383782,
+ 0.019512,
+ 0.00362769,
+ 0.0171298,
+ 0.438347,
+ 0.0320632,
+ 0.0297808,
+ 0.08514,
+ 0.0422766,
+ 0.0198195,
+ 0.00132369,
+ 0.00370876
+ ],
+ [ 0.444249,
+ 0.0235405,
+ 0.0057193,
+ 0.00648899,
+ 0.00244132,
+ 0.0822688,
+ 0.00255057,
+ 0.00336151,
+ 0.00380971,
+ 0.00409901,
+ 0.00286831,
+ 0.0102305,
+ 0.0162891,
+ 0.00559976,
+ 0.00502166,
+ 0.299997,
+ 0.0559665,
+ 0.0226608,
+ 0.000773543,
+ 0.00206398
+ ],
+ [ 0.0898718,
+ 0.00441315,
+ 0.0129167,
+ 0.0058957,
+ 0.000807357,
+ 0.808756,
+ 0.00165179,
+ 0.000433928,
+ 0.0033939,
+ 0.00155645,
+ 0.000425342,
+ 0.0130068,
+ 0.00341281,
+ 0.00238065,
+ 0.00709583,
+ 0.0362877,
+ 0.00328875,
+ 0.00202896,
+ 0.00152239,
+ 0.000853745
+ ],
+ [ 0.055084,
+ 0.00358249,
+ 0.12738,
+ 0.0655885,
+ 0.0040375,
+ 0.0637608,
+ 0.0404883,
+ 0.00755742,
+ 0.0867683,
+ 0.0136305,
+ 0.00816842,
+ 0.187783,
+ 0.0110682,
+ 0.0527969,
+ 0.0472254,
+ 0.126338,
+ 0.0752544,
+ 0.0102728,
+ 0.00135637,
+ 0.011859
+ ],
+ [ 0.0117681,
+ 0.00703883,
+ 0.0144712,
+ 0.0110901,
+ 0.0338266,
+ 0.00496266,
+ 0.433719,
+ 0.0061337,
+ 0.0137929,
+ 0.0298795,
+ 0.00762376,
+ 0.0844145,
+ 0.00813461,
+ 0.103834,
+ 0.0442559,
+ 0.0140571,
+ 0.0108277,
+ 0.00837578,
+ 0.00806831,
+ 0.143725
+ ],
+ [ 0.0159286,
+ 0.00805199,
+ 0.00109669,
+ 0.00213242,
+ 0.0743651,
+ 0.00250864,
+ 0.00491921,
+ 0.0501544,
+ 0.00355994,
+ 0.530763,
+ 0.216009,
+ 0.00326926,
+ 0.00452474,
+ 0.0134552,
+ 0.00480987,
+ 0.00669222,
+ 0.0119092,
+ 0.0281012,
+ 0.00709281,
+ 0.0106565
+ ],
+ [ 0.0195973,
+ 0.0034539,
+ 0.309985,
+ 0.0250778,
+ 0.00197065,
+ 0.0627529,
+ 0.0295961,
+ 0.00326504,
+ 0.0240964,
+ 0.00282469,
+ 0.000842506,
+ 0.32891,
+ 0.00490628,
+ 0.0116197,
+ 0.0105143,
+ 0.106498,
+ 0.0438054,
+ 0.0040302,
+ 0.000633396,
+ 0.0056198
+ ],
+ [ 0.0833804,
+ 0.00819811,
+ 0.0686821,
+ 0.0227415,
+ 0.00241326,
+ 0.0982292,
+ 0.00739549,
+ 0.00174712,
+ 0.0129342,
+ 0.00396531,
+ 0.0019558,
+ 0.0969824,
+ 0.0355924,
+ 0.0121521,
+ 0.0125871,
+ 0.311561,
+ 0.211337,
+ 0.00471386,
+ 0.0016329,
+ 0.00179911
+ ],
+ [ 0.0181409,
+ 0.00851436,
+ 0.00333335,
+ 0.00965319,
+ 0.00354269,
+ 0.0224553,
+ 0.0375239,
+ 0.00350905,
+ 0.320807,
+ 0.0149147,
+ 0.00460989,
+ 0.0233205,
+ 0.00871975,
+ 0.0526694,
+ 0.412966,
+ 0.0262309,
+ 0.0131791,
+ 0.00447465,
+ 0.0034767,
+ 0.00795882
+ ],
+ [ 0.249423,
+ 0.0122863,
+ 0.0169234,
+ 0.0370491,
+ 0.00773609,
+ 0.0347468,
+ 0.00870696,
+ 0.0595718,
+ 0.0177065,
+ 0.0451065,
+ 0.0204556,
+ 0.016412,
+ 0.0686404,
+ 0.0228502,
+ 0.0185482,
+ 0.0889296,
+ 0.0986017,
+ 0.167252,
+ 0.00286039,
+ 0.00619385
+ ],
+ [ 0.141974,
+ 0.00688567,
+ 0.0537452,
+ 0.040754,
+ 0.00402861,
+ 0.398811,
+ 0.0152896,
+ 0.00166276,
+ 0.0314274,
+ 0.00923483,
+ 0.00554255,
+ 0.0576297,
+ 0.0180329,
+ 0.028624,
+ 0.0373946,
+ 0.112373,
+ 0.0242478,
+ 0.00484629,
+ 0.00259091,
+ 0.00490542
+ ],
+ [ 0.0178903,
+ 0.0290304,
+ 0.00310543,
+ 0.00405034,
+ 0.0238913,
+ 0.010048,
+ 0.12527,
+ 0.0016708,
+ 0.023334,
+ 0.0722357,
+ 0.0116142,
+ 0.0155854,
+ 0.000993842,
+ 0.105182,
+ 0.195884,
+ 0.0181676,
+ 0.018626,
+ 0.0113865,
+ 0.226055,
+ 0.0859787
+ ],
+ [ 0.145476,
+ 0.00141863,
+ 0.129425,
+ 0.247135,
+ 0.00175521,
+ 0.0319651,
+ 0.0130426,
+ 0.00585254,
+ 0.0818154,
+ 0.0123593,
+ 0.00441789,
+ 0.040042,
+ 0.0151136,
+ 0.0906469,
+ 0.0420979,
+ 0.0656688,
+ 0.0511289,
+ 0.0169401,
+ 0.000773144,
+ 0.00292584
+ ],
+ [ 0.0169799,
+ 0.00220872,
+ 0.104366,
+ 0.037638,
+ 0.000678059,
+ 0.540447,
+ 0.0181137,
+ 0.000745968,
+ 0.0508618,
+ 0.0021147,
+ 0.000947377,
+ 0.131805,
+ 0.00387544,
+ 0.026935,
+ 0.0242347,
+ 0.029703,
+ 0.00458362,
+ 0.00158917,
+ 0.000603189,
+ 0.00157041
+ ],
+ [ 0.0402646,
+ 0.00393887,
+ 0.0293968,
+ 0.160352,
+ 0.00411534,
+ 0.012926,
+ 0.0617968,
+ 0.00984913,
+ 0.14488,
+ 0.0354919,
+ 0.0124819,
+ 0.0323829,
+ 0.00433742,
+ 0.249701,
+ 0.115202,
+ 0.0243247,
+ 0.0305645,
+ 0.0156027,
+ 0.00266766,
+ 0.00972278
+ ],
+ [ 0.225691,
+ 0.00433901,
+ 0.0637125,
+ 0.115483,
+ 0.00274401,
+ 0.0867335,
+ 0.0131067,
+ 0.00850862,
+ 0.0660469,
+ 0.0193314,
+ 0.00648772,
+ 0.0244309,
+ 0.0611149,
+ 0.0578159,
+ 0.0523417,
+ 0.107088,
+ 0.0507677,
+ 0.0299883,
+ 0.00136959,
+ 0.00289829
+ ],
+ [ 0.00331642,
+ 0.00518907,
+ 0.000826647,
+ 0.000513413,
+ 0.380176,
+ 0.00104328,
+ 0.0278451,
+ 0.00418953,
+ 0.000714992,
+ 0.0111212,
+ 0.00236218,
+ 0.00308302,
+ 0.000836508,
+ 0.00110249,
+ 0.00153108,
+ 0.00358767,
+ 0.00236089,
+ 0.00607663,
+ 0.0333347,
+ 0.510789
+ ],
+ [ 0.199501,
+ 0.058459,
+ 0.00949551,
+ 0.0125535,
+ 0.0634434,
+ 0.0939787,
+ 0.0341857,
+ 0.014021,
+ 0.0118723,
+ 0.0449388,
+ 0.0246991,
+ 0.0392255,
+ 0.0145385,
+ 0.0254265,
+ 0.0236079,
+ 0.166392,
+ 0.0533159,
+ 0.0367303,
+ 0.0129803,
+ 0.0606346
+ ],
+ [ 0.0319449,
+ 0.00660403,
+ 0.0378075,
+ 0.0279488,
+ 0.0108916,
+ 0.0365541,
+ 0.208864,
+ 0.00475423,
+ 0.0868665,
+ 0.0156546,
+ 0.00432533,
+ 0.208471,
+ 0.00608996,
+ 0.0766373,
+ 0.101167,
+ 0.0577657,
+ 0.0302051,
+ 0.00605852,
+ 0.00260019,
+ 0.0387897
+ ],
+ [ 0.07768,
+ 0.0140093,
+ 0.00806517,
+ 0.0112622,
+ 0.0173585,
+ 0.0136868,
+ 0.013373,
+ 0.123964,
+ 0.0129145,
+ 0.0724671,
+ 0.0420745,
+ 0.0403217,
+ 0.0117084,
+ 0.0179996,
+ 0.0142519,
+ 0.0922724,
+ 0.23169,
+ 0.167914,
+ 0.00281536,
+ 0.0141727
+ ],
+ [ 0.118366,
+ 0.00356248,
+ 0.0495595,
+ 0.153759,
+ 0.00686657,
+ 0.0194993,
+ 0.0229373,
+ 0.0302661,
+ 0.0982304,
+ 0.0571251,
+ 0.0171727,
+ 0.0259525,
+ 0.0175153,
+ 0.120492,
+ 0.0805193,
+ 0.0486588,
+ 0.0635796,
+ 0.0553336,
+ 0.00230083,
+ 0.00830274
+ ],
+ [ 0.052856,
+ 0.000862588,
+ 0.209276,
+ 0.402419,
+ 0.00126507,
+ 0.0155838,
+ 0.0124149,
+ 0.00548648,
+ 0.0497017,
+ 0.00902565,
+ 0.00423571,
+ 0.0264744,
+ 0.00631856,
+ 0.121241,
+ 0.0193569,
+ 0.0197263,
+ 0.0235464,
+ 0.0159764,
+ 0.000838161,
+ 0.00339487
+ ],
+ [ 0.0344366,
+ 0.0020986,
+ 0.113901,
+ 0.054178,
+ 0.00315576,
+ 0.336164,
+ 0.0461777,
+ 0.000346342,
+ 0.0667553,
+ 0.00483557,
+ 0.00197045,
+ 0.163672,
+ 0.00403698,
+ 0.0605414,
+ 0.0426222,
+ 0.0481173,
+ 0.00891481,
+ 0.00201106,
+ 0.00065101,
+ 0.00541456
+ ],
+ [ 0.115309,
+ 0.00149624,
+ 0.175552,
+ 0.174941,
+ 0.00157002,
+ 0.0394181,
+ 0.0132402,
+ 0.0056913,
+ 0.0433118,
+ 0.010141,
+ 0.00303321,
+ 0.0458477,
+ 0.16658,
+ 0.0366731,
+ 0.0151279,
+ 0.0871536,
+ 0.0468261,
+ 0.0141932,
+ 0.00075157,
+ 0.00314327
+ ],
+ [ 0.386515,
+ 0.0218928,
+ 0.00223668,
+ 0.00313878,
+ 0.00392814,
+ 0.369435,
+ 0.00146729,
+ 0.00853761,
+ 0.00188405,
+ 0.0127257,
+ 0.00805817,
+ 0.00304205,
+ 0.0158688,
+ 0.00214647,
+ 0.00375793,
+ 0.0808877,
+ 0.0305196,
+ 0.0410635,
+ 0.000992288,
+ 0.00190203
+ ],
+ [ 0.0146571,
+ 0.00243179,
+ 0.000521057,
+ 0.00148744,
+ 0.00916375,
+ 0.00209533,
+ 0.00101819,
+ 0.19139,
+ 0.00228984,
+ 0.44328,
+ 0.221743,
+ 0.00129983,
+ 0.000768515,
+ 0.00493628,
+ 0.00288413,
+ 0.00272515,
+ 0.0170997,
+ 0.0778557,
+ 0.000877938,
+ 0.0014756
+ ]
+ ]
+
+-- | Weights of C60 model.
+c60Weights :: [Double]
+c60Weights =
+ [ 0.0169699,
+ 0.0211683,
+ 0.0276589,
+ 0.0065676,
+ 0.0141221,
+ 0.00687748,
+ 0.014691,
+ 0.00672258,
+ 0.00183967,
+ 0.0102547,
+ 0.0230896,
+ 0.0057941,
+ 0.0125395,
+ 0.0204526,
+ 0.00706296,
+ 0.0117983,
+ 0.00683347,
+ 0.0433776,
+ 0.0318279,
+ 0.0222546,
+ 0.0102265,
+ 0.0150546,
+ 0.013416,
+ 0.0148552,
+ 0.0239112,
+ 0.0128776,
+ 0.0222319,
+ 0.0247445,
+ 0.0214275,
+ 0.0115002,
+ 0.00760174,
+ 0.0130259,
+ 0.0093702,
+ 0.0467194,
+ 0.044194,
+ 0.0322263,
+ 0.0403,
+ 0.0150234,
+ 0.010459,
+ 0.0214742,
+ 0.0154958,
+ 0.010179,
+ 0.022798,
+ 0.0123205,
+ 0.00667776,
+ 0.000415008,
+ 0.0344385,
+ 0.0113663,
+ 0.0127143,
+ 0.0124324,
+ 0.0262124,
+ 0.0064995,
+ 0.0103203,
+ 0.0142464,
+ 0.02156,
+ 0.0199151,
+ 0.00389642,
+ 0.0113449,
+ 0.0128596,
+ 0.0117657
+ ]
diff --git a/src/ELynx/MarkovProcess/GammaRateHeterogeneity.hs b/src/ELynx/MarkovProcess/GammaRateHeterogeneity.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/GammaRateHeterogeneity.hs
@@ -0,0 +1,125 @@
+-- |
+-- Module : ELynx.MarkovProcess.GammaRateHeterogeneity
+-- Description : Discrete gamma rate heterogeneity
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Thu Feb 28 14:09:11 2019.
+--
+-- At the moment, a mixture model is used to emulate gamma rate heterogeneity. This
+-- does not come with huge run time increases when simulating data. For inference
+-- however, it would make a lot of sense to reuse the Eigendecomposition for all
+-- rate heterogeneity components though.
+module ELynx.MarkovProcess.GammaRateHeterogeneity
+ ( summarizeGammaRateHeterogeneity,
+ expand,
+ )
+where
+
+import qualified Data.ByteString.Lazy.Char8 as BL
+import qualified Data.Vector as V
+import qualified ELynx.MarkovProcess.MixtureModel as M
+import qualified ELynx.MarkovProcess.PhyloModel as P
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
+import Numeric.Integration.TanhSinh
+import Statistics.Distribution
+import Statistics.Distribution.Gamma
+import Prelude hiding (repeat)
+
+-- | Short summary of gamma rate heterogeneity parameters.
+summarizeGammaRateHeterogeneity :: Int -> Double -> [BL.ByteString]
+summarizeGammaRateHeterogeneity n alpha =
+ map
+ BL.pack
+ [ "Discrete gamma rate heterogeneity.",
+ "Number of categories: " ++ show n,
+ "Shape parameter of gamma distribution: " ++ show alpha,
+ "Rates: " ++ show (getMeans n alpha)
+ ]
+
+-- | For a given number of rate categories, a gamma shape parameter alpha and a
+-- substitution model, compute the scaled substitution models corresponding to
+-- the gamma rates.
+expand :: Int -> Double -> P.PhyloModel -> P.PhyloModel
+expand n alpha (P.SubstitutionModel sm) =
+ P.MixtureModel $ expandSubstitutionModel n alpha sm
+expand n alpha (P.MixtureModel mm) =
+ P.MixtureModel $ expandMixtureModel n alpha mm
+
+getName :: Int -> Double -> String
+getName n alpha =
+ " with discrete gamma rate heterogeneity; "
+ ++ show n
+ ++ " categories; "
+ ++ "shape parameter "
+ ++ show alpha
+
+splitSubstitutionModel ::
+ Int -> Double -> S.SubstitutionModel -> V.Vector S.SubstitutionModel
+splitSubstitutionModel n alpha sm = renamedSMs
+ where
+ means = getMeans n alpha
+ scaledSMs = V.map (`S.scale` sm) means
+ names = V.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
+ renamedSMs = V.zipWith S.appendName names scaledSMs
+
+expandSubstitutionModel ::
+ Int -> Double -> S.SubstitutionModel -> M.MixtureModel
+expandSubstitutionModel n alpha sm = M.fromSubstitutionModels name ws sms
+ where
+ name = S.name sm <> getName n alpha
+ ws = V.replicate n 1.0
+ sms = splitSubstitutionModel n alpha sm
+
+expandMixtureModel :: Int -> Double -> M.MixtureModel -> M.MixtureModel
+expandMixtureModel n alpha mm = M.concatenate name renamedMMs
+ where
+ name = M.name mm <> getName n alpha
+ means = getMeans n alpha
+ scaledMMs = V.map (`M.scale` mm) means
+ names = V.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
+ renamedMMs = V.zipWith M.appendNameComponents names scaledMMs
+
+-- For a given number of rate categories 'n' and a shape parameter 'alpha' (the
+-- rate or scale is set such that the mean is 1.0), return a list of rates that
+-- represent the respective categories. Use the mean rate for each category.
+getMeans :: Int -> Double -> V.Vector Double
+getMeans n alpha
+ | n <= 0 = error "getMeans: Number of rate categories is zero or negative."
+ | otherwise = means <> pure lastMean
+ where
+ gamma = gammaDistr alpha (1.0 / alpha)
+ quantiles =
+ [quantile gamma (fromIntegral i / fromIntegral n) | i <- [0 .. n]]
+ -- Calculate the mean rate. Multiplication with the number of rate
+ -- categories 'n' is necessary because in each n-quantile the
+ -- probability mass is 1/n.
+ meanFunc x = fromIntegral n * x * density gamma x
+ -- Only calculate the first (n-1) categories with normal integration.
+ means =
+ V.fromList
+ [ integralAToB meanFunc (quantiles !! i) (quantiles !! (i + 1))
+ | i <- [0 .. n - 2]
+ ]
+ -- The last category has to be calculated with an improper integration.
+ lastMean = integralAToInf meanFunc (quantiles !! (n - 1))
+
+eps :: Double
+eps = 1e-8
+
+-- The integration method to use
+method :: (Double -> Double) -> Double -> Double -> [Result]
+method = parSimpson
+
+-- Helper function for a normal integral from 'a' to 'b'.
+integralAToB :: (Double -> Double) -> Double -> Double -> Double
+integralAToB f a b = result . absolute eps $ method f a b
+
+-- Helper function for an improper integral from 'a' to infinity.
+integralAToInf :: (Double -> Double) -> Double -> Double
+integralAToInf f a =
+ (result . absolute eps $ nonNegative method f) - integralAToB f 0 a
diff --git a/src/ELynx/MarkovProcess/MixtureModel.hs b/src/ELynx/MarkovProcess/MixtureModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/MixtureModel.hs
@@ -0,0 +1,118 @@
+-- |
+-- Module : ELynx.MarkovProcess.MixtureModel
+-- Description : Mixture models are a set of substitution models with weights
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Jan 29 19:17:40 2019.
+--
+-- To be imported qualified.
+module ELynx.MarkovProcess.MixtureModel
+ ( -- * Types
+ Weight,
+ Component (weight, substModel),
+ MixtureModel (name, alphabet, components),
+
+ -- * Getters
+ getWeights,
+ getSubstitutionModels,
+
+ -- * Building mixture models
+ fromSubstitutionModels,
+
+ -- * Transformations
+ concatenate,
+ scale,
+ normalize,
+ appendNameComponents,
+ )
+where
+
+import qualified Data.Vector as V
+import ELynx.Alphabet.Alphabet hiding (all)
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
+import Prelude
+
+-- | Mixture model component weight.
+type Weight = Double
+
+-- | A mixture model component has a weight and a substitution model.
+data Component = Component
+ { weight :: Weight,
+ substModel :: S.SubstitutionModel
+ }
+ deriving (Show, Read)
+
+-- | A mixture model with its components.
+data MixtureModel = MixtureModel
+ { -- | Name
+ name :: S.Name,
+ alphabet :: Alphabet,
+ components :: V.Vector Component
+ }
+ deriving (Show, Read)
+
+-- | Get weights.
+getWeights :: MixtureModel -> V.Vector Weight
+getWeights = V.map weight . components
+
+-- | Get substitution models.
+getSubstitutionModels :: MixtureModel -> V.Vector S.SubstitutionModel
+getSubstitutionModels = V.map substModel . components
+
+-- | Create a mixture model from a list of substitution models.
+fromSubstitutionModels :: S.Name -> V.Vector Weight -> V.Vector S.SubstitutionModel -> MixtureModel
+fromSubstitutionModels n ws sms
+ | null ws = error "fromSubstitutionModels: No weights given."
+ | length ws /= length sms = error "fromSubstitutionModels: Number of weights and substitution models does not match."
+ | not $ allEqual alphs = error "fromSubstitutionModels: alphabets of substitution models are not equal."
+ | otherwise = MixtureModel n (V.head alphs) comps
+ where
+ comps = V.zipWith Component ws sms
+ alphs = V.map S.alphabet sms
+ allEqual xs
+ | V.null xs = True
+ | otherwise = V.all (== V.head xs) xs
+
+-- | Concatenate mixture models.
+concatenate :: S.Name -> V.Vector MixtureModel -> MixtureModel
+concatenate n mms = fromSubstitutionModels n ws sms
+ where
+ comps = V.concatMap components mms
+ ws = V.map weight comps
+ sms = V.map substModel comps
+
+scaleComponent :: Double -> Component -> Component
+scaleComponent s c = c {substModel = s'} where s' = S.scale s $ substModel c
+
+-- | Scale all substitution models of the mixture model.
+scale :: Double -> MixtureModel -> MixtureModel
+scale s m = m {components = cs'}
+ where
+ cs = components m
+ cs' = V.map (scaleComponent s) cs
+
+-- | Globally normalize a mixture model so that on average one event happens per
+-- unit time.
+normalize :: MixtureModel -> MixtureModel
+normalize mm = scale (1 / c) mm
+ where
+ c = sum $ V.zipWith (*) weights scales
+ weights = getWeights mm
+ scales = V.map S.totalRate $ getSubstitutionModels mm
+
+appendNameComponent :: S.Name -> Component -> Component
+appendNameComponent n c = c {substModel = s'}
+ where
+ s' = S.appendName n $ substModel c
+
+-- | Append byte string to all substitution models of mixture model.
+appendNameComponents :: S.Name -> MixtureModel -> MixtureModel
+appendNameComponents n m = m {components = cs'}
+ where
+ cs = components m
+ cs' = V.map (appendNameComponent n) cs
diff --git a/src/ELynx/MarkovProcess/Nucleotide.hs b/src/ELynx/MarkovProcess/Nucleotide.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/Nucleotide.hs
@@ -0,0 +1,104 @@
+-- |
+-- Module : ELynx.MarkovProcess.Nucleotide
+-- Description : Substitution models using nucleotides
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Thu Jan 24 08:33:26 2019.
+--
+-- XXX: Maybe rename to something like /DNA substitution models/. Nucleotide ~
+-- Alphabet; DNA ~ Character.
+--
+-- The order of nucleotides is A, C, G, T; see 'ELynx.Character.Nucleotide'.
+--
+-- For the different DNA substitution models, please see
+-- https://en.wikipedia.org/wiki/Models_of_DNA_evolution
+module ELynx.MarkovProcess.Nucleotide
+ ( jc,
+ f81,
+ hky,
+ gtr4,
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import ELynx.Alphabet.Alphabet
+import ELynx.MarkovProcess.RateMatrix
+import ELynx.MarkovProcess.SubstitutionModel
+import Numeric.LinearAlgebra hiding (normalize)
+
+-- XXX: Another idea of structuring the code. This would probably be cleaner in
+-- the long run.
+
+-- data PhyloModel = MixtureModel | SubstitutionModel
+
+--
+-- I think it could simply be:
+-- data PhyloModel = [(Weight, SubstitutionModel)]
+--
+
+-- data MixtureModel = [(Weight, SubstitutionModel)]
+
+-- data SubstitutionModel = SMDNA DNASubstitutionModel | SMAA AASubstitutionModel
+
+-- data DNASubstitutionModel = JC | HKY Double StationaryDistribution
+
+-- data AASubstitutionModel = LG | ...
+
+n :: Int
+-- n = length (alphabet :: [Nucleotide])
+-- Hard code this here. Reduces model dependencies, and number of nucleotides
+-- will not change.
+n = 4
+
+-- | JC model matrix.
+jcExch :: ExchangeabilityMatrix
+jcExch =
+ (n >< n)
+ [ 0.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 0.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 0.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 1.0,
+ 0.0
+ ]
+
+uniformVec :: Vector Double
+uniformVec = V.replicate n (1 / fromIntegral n)
+
+-- | JC substitution model.
+jc :: SubstitutionModel
+jc = substitutionModel DNA "JC" [] uniformVec jcExch
+
+-- | F81 substitution model.
+f81 :: StationaryDistribution -> SubstitutionModel
+f81 d = substitutionModel DNA "F81" [] d jcExch
+
+hkyExch :: Double -> ExchangeabilityMatrix
+hkyExch k =
+ (n >< n)
+ [0.0, 1.0, k, 1.0, 1.0, 0.0, 1.0, k, k, 1.0, 0.0, 1.0, 1.0, k, 1.0, 0.0]
+
+-- | HKY substitution model.
+hky :: Double -> StationaryDistribution -> SubstitutionModel
+hky k d = substitutionModel DNA "HKY" [k] d e where e = hkyExch k
+
+-- | HKY substitution model.
+gtr4 :: [Double] -> StationaryDistribution -> SubstitutionModel
+gtr4 es d = substitutionModel DNA "GTR" es d e
+ where
+ e = exchFromListUpper n es
diff --git a/src/ELynx/MarkovProcess/PhyloModel.hs b/src/ELynx/MarkovProcess/PhyloModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/PhyloModel.hs
@@ -0,0 +1,36 @@
+-- |
+-- Module : ELynx.MarkovProcess.PhyloModel
+-- Description : Phylogenetic model
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Fri Feb 1 12:43:06 2019.
+--
+-- A phylogenetic model is a complete description of the evolutionary process. At
+-- the moment, it is either a mixture model or a plain substitution model, but more
+-- complicated models may be added in the future.
+--
+-- To be imported qualified.
+module ELynx.MarkovProcess.PhyloModel
+ ( PhyloModel (..),
+ getAlphabet,
+ )
+where
+
+import ELynx.Alphabet.Alphabet
+import qualified ELynx.MarkovProcess.MixtureModel as M
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
+
+-- | A phylogenetic model is a mixture model or a substitution model. More
+-- complicated models may be added.
+data PhyloModel = MixtureModel M.MixtureModel | SubstitutionModel S.SubstitutionModel
+ deriving (Show, Read)
+
+-- | Extract code from phylogenetic model.
+getAlphabet :: PhyloModel -> Alphabet
+getAlphabet (MixtureModel mm) = M.alphabet mm
+getAlphabet (SubstitutionModel sm) = S.alphabet sm
diff --git a/src/ELynx/MarkovProcess/RateMatrix.hs b/src/ELynx/MarkovProcess/RateMatrix.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/RateMatrix.hs
@@ -0,0 +1,225 @@
+{-# LANGUAGE FlexibleContexts #-}
+
+-- |
+-- Description : Rate matrix helper functions
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPLv3
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : non-portable (not tested)
+--
+-- Some helper functions that come handy when working with rate matrices of
+-- continuous-time discrete-state Markov processes.
+--
+-- * Changelog
+--
+-- To be imported qualified.
+module ELynx.MarkovProcess.RateMatrix
+ ( RateMatrix,
+ ExchangeabilityMatrix,
+ StationaryDistribution,
+ isValid,
+ normalizeSD,
+ totalRate,
+ totalRateWith,
+ normalize,
+ normalizeWith,
+ setDiagonal,
+ toExchangeabilityMatrix,
+ fromExchangeabilityMatrix,
+ getStationaryDistribution,
+ exchFromListLower,
+ exchFromListUpper,
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import Numeric.LinearAlgebra hiding (normalize)
+import Numeric.SpecFunctions
+import Prelude hiding ((<>))
+
+-- | A rate matrix is just a real matrix.
+type RateMatrix = Matrix R
+
+-- | A matrix of exchangeabilities, we have q = e * pi, where q is a rate
+-- matrix, e is the exchangeability matrix and pi is the diagonal matrix
+-- containing the stationary frequency distribution.
+type ExchangeabilityMatrix = Matrix R
+
+-- | Stationary distribution of a rate matrix.
+type StationaryDistribution = Vector R
+
+epsRelaxed :: Double
+epsRelaxed = 1e-5
+
+-- | True if distribution sums to 1.0.
+isValid :: StationaryDistribution -> Bool
+isValid d = epsRelaxed > abs (norm_1 d - 1.0)
+
+-- | Normalize a stationary distribution so that the elements sum to 1.0.
+normalizeSD :: StationaryDistribution -> StationaryDistribution
+normalizeSD d = d / scalar (norm_1 d)
+
+matrixSetDiagToZero :: Matrix R -> Matrix R
+matrixSetDiagToZero m = m - diag (takeDiag m)
+{-# INLINE matrixSetDiagToZero #-}
+
+-- | Get average number of substitutions per unit time.
+totalRateWith :: StationaryDistribution -> RateMatrix -> Double
+totalRateWith d m = norm_1 $ d <# matrixSetDiagToZero m
+
+-- | Get average number of substitutions per unit time.
+totalRate :: RateMatrix -> Double
+totalRate m = totalRateWith (getStationaryDistribution m) m
+
+-- | Normalizes a Markov process generator such that one event happens per unit
+-- time. Calculates stationary distribution from rate matrix.
+normalize :: RateMatrix -> RateMatrix
+normalize m = normalizeWith (getStationaryDistribution m) m
+
+-- | Normalizes a Markov process generator such that one event happens per unit
+-- time. Faster, but stationary distribution has to be given.
+normalizeWith :: StationaryDistribution -> RateMatrix -> RateMatrix
+normalizeWith d m = scale (1.0 / totalRateWith d m) m
+
+-- | Set the diagonal entries of a matrix such that the rows sum to 0.
+setDiagonal :: RateMatrix -> RateMatrix
+setDiagonal m = diagZeroes - diag (fromList rowSums)
+ where
+ diagZeroes = matrixSetDiagToZero m
+ rowSums = map norm_1 $ toRows diagZeroes
+
+-- | Extract the exchangeability matrix from a rate matrix.
+toExchangeabilityMatrix ::
+ RateMatrix -> StationaryDistribution -> ExchangeabilityMatrix
+toExchangeabilityMatrix m f = m <> diag oneOverF
+ where
+ oneOverF = cmap (1.0 /) f
+
+-- | Convert exchangeability matrix to rate matrix.
+fromExchangeabilityMatrix ::
+ ExchangeabilityMatrix -> StationaryDistribution -> RateMatrix
+fromExchangeabilityMatrix em d = setDiagonal $ em <> diag d
+
+eps :: Double
+eps = 1e-12
+
+normalizeSumVec :: V.Vector Double -> V.Vector Double
+normalizeSumVec v = V.map (/ s) v
+ where
+ s = V.sum v
+{-# INLINE normalizeSumVec #-}
+
+-- | Get stationary distribution from 'RateMatrix'. Involves eigendecomposition.
+-- If the given matrix does not satisfy the required properties of transition
+-- rate matrices and no eigenvector with an eigenvalue nearly equal to 0 is
+-- found, an error is thrown. Is there an easier way to calculate the stationary
+-- distribution or a better way to handle errors (of course I could use the
+-- Maybe monad, but then the error report is just delayed to the calling
+-- function)?
+getStationaryDistribution :: RateMatrix -> StationaryDistribution
+getStationaryDistribution m =
+ if eps > abs (magnitude (eVals ! i))
+ then normalizeSumVec distReal
+ else error "getStationaryDistribution: Could not retrieve stationary distribution."
+ where
+ (eVals, eVecs) = eig (tr m)
+ i = minIndex eVals
+ distComplex = toColumns eVecs !! i
+ distReal = cmap realPart distComplex
+
+-- The next functions tackle the somewhat trivial, but not easily solvable
+-- problem of converting a triangular matrix (excluding the diagonal) given as a
+-- list into a symmetric matrix. The diagonal entries are set to zero.
+
+-- Lower triangular matrix. This is how the exchangeabilities are specified in
+-- PAML. Conversion from matrix indices (i,j) to list index k.
+--
+-- (i,j) k
+--
+-- (0,0) -
+-- (1,0) 0 (1,1) -
+-- (2,0) 1 (2,1) 2 (2,2) -
+-- (3,0) 3 (3,1) 4 (3,2) 5 (3,3) -
+-- (4,0) 6 (4,1) 7 (4,2) 8 (4,3) 9 (4,4) -
+-- .
+-- .
+-- .
+--
+-- k = (i choose 2) + j.
+ijToKLower :: Int -> Int -> Int
+ijToKLower i j
+ | i > j = round (i `choose` 2) + j
+ | otherwise = error "ijToKLower: not defined for upper triangular matrix."
+
+-- Upper triangular matrix. Conversion from matrix indices (i,j) to list index
+-- k. Matrix is square of size n.
+--
+-- (i,j) k
+--
+-- (0,0) - (0,1) 0 (0,2) 1 (0,3) 2 (0,4) 3 ...
+-- (1,1) - (1,2) n-1 (1,3) n (1,4) n+1
+-- (2,2) - (2,3) 2n-3 (2,4) 2n-2
+-- (3,3) - (3,4) 3n-6
+-- (4,4) -
+-- ...
+--
+-- k = i*(n-2) - (i choose 2) + (j - 1)
+ijToKUpper :: Int -> Int -> Int -> Int
+ijToKUpper n i j
+ | i < j = i * (n - 2) - round (i `choose` 2) + j - 1
+ | otherwise = error "ijToKUpper: not defined for lower triangular matrix."
+
+-- The function is a little weird because HMatrix uses Double indices for Matrix
+-- Double builders.
+fromListBuilderLower :: RealFrac a => [a] -> a -> a -> a
+fromListBuilderLower es i j
+ | i > j = es !! ijToKLower iI jI
+ | i == j = 0.0
+ | i < j = es !! ijToKLower jI iI
+ | otherwise =
+ error
+ "Float indices could not be compared during matrix creation."
+ where
+ iI = round i :: Int
+ jI = round j :: Int
+
+-- The function is a little weird because HMatrix uses Double indices for Matrix
+-- Double builders.
+fromListBuilderUpper :: RealFrac a => Int -> [a] -> a -> a -> a
+fromListBuilderUpper n es i j
+ | i < j = es !! ijToKUpper n iI jI
+ | i == j = 0.0
+ | i > j = es !! ijToKUpper n jI iI
+ | otherwise =
+ error
+ "Float indices could not be compared during matrix creation."
+ where
+ iI = round i :: Int
+ jI = round j :: Int
+
+checkEs :: RealFrac a => Int -> [a] -> [a]
+checkEs n es
+ | length es == nExp = es
+ | otherwise = error eStr
+ where
+ nExp = round (n `choose` 2)
+ eStr =
+ unlines
+ [ "exchFromListlower: the number of exchangeabilities does not match the matrix size",
+ "matrix size: " ++ show n,
+ "expected number of exchangeabilities: " ++ show nExp,
+ "received number of exchangeabilities: " ++ show (length es)
+ ]
+
+-- | Build exchangeability matrix from list denoting lower triangular matrix,
+-- and excluding diagonal. This is how the exchangeabilities are specified in
+-- PAML.
+exchFromListLower :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
+exchFromListLower n es = build (n, n) (fromListBuilderLower (checkEs n es))
+
+-- | Build exchangeability matrix from list denoting upper triangular matrix,
+-- and excluding diagonal.
+exchFromListUpper :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
+exchFromListUpper n es = build (n, n) (fromListBuilderUpper n (checkEs n es))
diff --git a/src/ELynx/MarkovProcess/SubstitutionModel.hs b/src/ELynx/MarkovProcess/SubstitutionModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/MarkovProcess/SubstitutionModel.hs
@@ -0,0 +1,124 @@
+-- |
+-- Module : ELynx.MarkovProcess.SubstitutionModel
+-- Description : Data type describing substitution model
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Jan 29 19:10:46 2019.
+--
+-- To be imported qualified.
+module ELynx.MarkovProcess.SubstitutionModel
+ ( -- * Types
+ Name,
+ Params,
+ SubstitutionModel,
+
+ -- * Accessors
+ alphabet,
+ name,
+ params,
+ stationaryDistribution,
+ exchangeabilityMatrix,
+ rateMatrix,
+ totalRate,
+
+ -- * Building substitution models
+ substitutionModel,
+
+ -- * Transformations
+ scale,
+ normalize,
+ appendName,
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import ELynx.Alphabet.Alphabet
+import qualified ELynx.MarkovProcess.RateMatrix as R
+import qualified Numeric.LinearAlgebra as LinAlg
+
+-- | Name of substitution model; abstracted and subject to change.
+type Name = String
+
+-- | Parameters of substitution model. May be the empty list.
+type Params = [Double]
+
+-- XXX: Use a proper data type. For example:
+-- data SubstitutionModelAA = LG | WAG | LG-Custom dist | ...
+-- data SubstitutionModelNuc = JC | HKY p1 p2 ... | GTR p1 p2 ...
+--
+-- I thought about this a lot, and it seems easier like it is at the moment.
+-- Since the data types are abstracted anyways, not much harm can be done. Of
+-- course, conflicting substitution models can be declared, or duplicate ones
+-- with different names, but well...
+
+-- | Complete definition of a substitution model. Create instances with
+-- 'substitutionModel'. A substitution model has an alphabet, a name, and a list
+-- of parameters (e.g., the kappa value for the HKY model). Further, the
+-- transition rate matrix is defined by a stationary distribution and a set of
+-- exchangeabilities.
+data SubstitutionModel = SubstitutionModel
+ { -- | Alphabet
+ alphabet :: Alphabet,
+ -- | Name
+ name :: Name,
+ -- | List of parameters
+ params :: Params,
+ -- | Stationary distribution
+ stationaryDistribution :: R.StationaryDistribution,
+ -- | Exchangeability matrix
+ exchangeabilityMatrix :: R.ExchangeabilityMatrix
+ }
+ deriving (Show, Read)
+
+-- | Calculate rate matrix from substitution model.
+rateMatrix :: SubstitutionModel -> R.RateMatrix
+rateMatrix sm =
+ R.fromExchangeabilityMatrix
+ (exchangeabilityMatrix sm)
+ (stationaryDistribution sm)
+
+-- | Get scale of substitution model.
+totalRate :: SubstitutionModel -> Double
+totalRate sm = R.totalRate (rateMatrix sm)
+
+normalizeSumVec :: V.Vector Double -> V.Vector Double
+normalizeSumVec v = V.map (/ s) v
+ where
+ s = V.sum v
+{-# INLINE normalizeSumVec #-}
+
+-- | Create normalized 'SubstitutionModel'. See 'normalize'.
+substitutionModel ::
+ Alphabet ->
+ Name ->
+ Params ->
+ R.StationaryDistribution ->
+ R.ExchangeabilityMatrix ->
+ SubstitutionModel
+substitutionModel c n ps d e =
+ if R.isValid d
+ then normalize $ SubstitutionModel c n ps (normalizeSumVec d) e
+ else
+ error $
+ "substitionModel: Stationary distribution does not sum to 1.0: "
+ ++ show d
+
+-- | Scale the rate of a substitution model by given factor.
+scale :: Double -> SubstitutionModel -> SubstitutionModel
+scale r sm = sm {exchangeabilityMatrix = em'}
+ where
+ em' = LinAlg.scale r $ exchangeabilityMatrix sm
+
+-- | Normalize a substitution model, so that, on average, one substitution
+-- happens per unit time.
+normalize :: SubstitutionModel -> SubstitutionModel
+normalize sm = scale (1.0 / r) sm where r = totalRate sm
+
+-- | Abbend to name.
+appendName :: Name -> SubstitutionModel -> SubstitutionModel
+appendName n sm = sm {name = n'} where n' = name sm <> n
diff --git a/src/ELynx/Simulate/MarkovProcess.hs b/src/ELynx/Simulate/MarkovProcess.hs
--- a/src/ELynx/Simulate/MarkovProcess.hs
+++ b/src/ELynx/Simulate/MarkovProcess.hs
@@ -18,7 +18,7 @@
where
import Control.Monad.Primitive
-import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.MarkovProcess.RateMatrix
import Numeric.LinearAlgebra
import System.Random.MWC
import System.Random.MWC.Distributions
diff --git a/src/ELynx/Simulate/MarkovProcessAlongTree.hs b/src/ELynx/Simulate/MarkovProcessAlongTree.hs
--- a/src/ELynx/Simulate/MarkovProcessAlongTree.hs
+++ b/src/ELynx/Simulate/MarkovProcessAlongTree.hs
@@ -34,7 +34,7 @@
import Data.Tree
import qualified Data.Vector as V
import Data.Word (Word32)
-import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.MarkovProcess.RateMatrix
import ELynx.Simulate.MarkovProcess
import System.Random.MWC
import System.Random.MWC.Distributions (categorical)
diff --git a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
deleted file mode 100644
--- a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
+++ /dev/null
@@ -1,531 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.AminoAcidSpec
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Tue Jan 29 10:47:40 2019.
-module ELynx.Data.MarkovProcess.AminoAcidSpec
- ( spec,
- )
-where
-
-import qualified Data.Vector.Storable as V
-import ELynx.Data.MarkovProcess.AminoAcid
-import qualified ELynx.Data.MarkovProcess.RateMatrix as R
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-import ELynx.Tools.Equality
-import Numeric.LinearAlgebra
-import Test.Hspec
-
-normalizeSumVec :: Vector Double -> Vector Double
-normalizeSumVec v = V.map (/ s) v
- where
- s = V.sum v
-{-# INLINE normalizeSumVec #-}
-
-statDistLGPython :: R.StationaryDistribution
-statDistLGPython =
- normalizeSumVec $
- fromList
- [ 0.079066,
- 0.012937,
- 0.053052,
- 0.071586,
- 0.042302,
- 0.057337,
- 0.022355,
- 0.062157,
- 0.064600,
- 0.099081,
- 0.022951,
- 0.041977,
- 0.044040,
- 0.040767,
- 0.055941,
- 0.061197,
- 0.053287,
- 0.069147,
- 0.012066,
- 0.034155
- ]
-
-exchLGPython :: R.ExchangeabilityMatrix
-exchLGPython =
- fromLists
- [ [ 0.0000000e+00,
- 2.4890840e+00,
- 3.9514400e-01,
- 1.0385450e+00,
- 2.5370100e-01,
- 2.0660400e+00,
- 3.5885800e-01,
- 1.4983000e-01,
- 5.3651800e-01,
- 3.9533700e-01,
- 1.1240350e+00,
- 2.7681800e-01,
- 1.1776510e+00,
- 9.6989400e-01,
- 4.2509300e-01,
- 4.7271820e+00,
- 2.1395010e+00,
- 2.5478700e+00,
- 1.8071700e-01,
- 2.1895900e-01
- ],
- [ 2.4890840e+00,
- 0.0000000e+00,
- 6.2556000e-02,
- 3.4990000e-03,
- 1.1052510e+00,
- 5.6926500e-01,
- 6.4054300e-01,
- 3.2062700e-01,
- 1.3266000e-02,
- 5.9400700e-01,
- 8.9368000e-01,
- 5.2876800e-01,
- 7.5382000e-02,
- 8.4808000e-02,
- 5.3455100e-01,
- 2.7844780e+00,
- 1.1434800e+00,
- 1.9592910e+00,
- 6.7012800e-01,
- 1.1655320e+00
- ],
- [ 3.9514400e-01,
- 6.2556000e-02,
- 0.0000000e+00,
- 5.2438700e+00,
- 1.7416000e-02,
- 8.4492600e-01,
- 9.2711400e-01,
- 1.0690000e-02,
- 2.8295900e-01,
- 1.5076000e-02,
- 2.5548000e-02,
- 5.0761490e+00,
- 3.9445600e-01,
- 5.2338600e-01,
- 1.2395400e-01,
- 1.2402750e+00,
- 4.2586000e-01,
- 3.7967000e-02,
- 2.9890000e-02,
- 1.3510700e-01
- ],
- [ 1.0385450e+00,
- 3.4990000e-03,
- 5.2438700e+00,
- 0.0000000e+00,
- 1.8811000e-02,
- 3.4884700e-01,
- 4.2388100e-01,
- 4.4265000e-02,
- 1.8071770e+00,
- 6.9673000e-02,
- 1.7373500e-01,
- 5.4171200e-01,
- 4.1940900e-01,
- 4.1285910e+00,
- 3.6397000e-01,
- 6.1197300e-01,
- 6.0454500e-01,
- 2.4503400e-01,
- 7.7852000e-02,
- 1.2003700e-01
- ],
- [ 2.5370100e-01,
- 1.1052510e+00,
- 1.7416000e-02,
- 1.8811000e-02,
- 0.0000000e+00,
- 8.9586000e-02,
- 6.8213900e-01,
- 1.1127270e+00,
- 2.3918000e-02,
- 2.5926920e+00,
- 1.7988530e+00,
- 8.9525000e-02,
- 9.4464000e-02,
- 3.5855000e-02,
- 5.2722000e-02,
- 3.6181900e-01,
- 1.6500100e-01,
- 6.5468300e-01,
- 2.4571210e+00,
- 7.8039020e+00
- ],
- [ 2.0660400e+00,
- 5.6926500e-01,
- 8.4492600e-01,
- 3.4884700e-01,
- 8.9586000e-02,
- 0.0000000e+00,
- 3.1148400e-01,
- 8.7050000e-03,
- 2.9663600e-01,
- 4.4261000e-02,
- 1.3953800e-01,
- 1.4376450e+00,
- 1.9696100e-01,
- 2.6795900e-01,
- 3.9019200e-01,
- 1.7399900e+00,
- 1.2983600e-01,
- 7.6701000e-02,
- 2.6849100e-01,
- 5.4679000e-02
- ],
- [ 3.5885800e-01,
- 6.4054300e-01,
- 9.2711400e-01,
- 4.2388100e-01,
- 6.8213900e-01,
- 3.1148400e-01,
- 0.0000000e+00,
- 1.0888200e-01,
- 6.9726400e-01,
- 3.6631700e-01,
- 4.4247200e-01,
- 4.5092380e+00,
- 5.0885100e-01,
- 4.8135050e+00,
- 2.4266010e+00,
- 9.9001200e-01,
- 5.8426200e-01,
- 1.1901300e-01,
- 5.9705400e-01,
- 5.3068340e+00
- ],
- [ 1.4983000e-01,
- 3.2062700e-01,
- 1.0690000e-02,
- 4.4265000e-02,
- 1.1127270e+00,
- 8.7050000e-03,
- 1.0888200e-01,
- 0.0000000e+00,
- 1.5906900e-01,
- 4.1450670e+00,
- 4.2736070e+00,
- 1.9150300e-01,
- 7.8281000e-02,
- 7.2854000e-02,
- 1.2699100e-01,
- 6.4105000e-02,
- 1.0337390e+00,
- 1.0649107e+01,
- 1.1166000e-01,
- 2.3252300e-01
- ],
- [ 5.3651800e-01,
- 1.3266000e-02,
- 2.8295900e-01,
- 1.8071770e+00,
- 2.3918000e-02,
- 2.9663600e-01,
- 6.9726400e-01,
- 1.5906900e-01,
- 0.0000000e+00,
- 1.3750000e-01,
- 6.5660400e-01,
- 2.1450780e+00,
- 3.9032200e-01,
- 3.2342940e+00,
- 6.3260670e+00,
- 7.4868300e-01,
- 1.1368630e+00,
- 1.8520200e-01,
- 4.9906000e-02,
- 1.3193200e-01
- ],
- [ 3.9533700e-01,
- 5.9400700e-01,
- 1.5076000e-02,
- 6.9673000e-02,
- 2.5926920e+00,
- 4.4261000e-02,
- 3.6631700e-01,
- 4.1450670e+00,
- 1.3750000e-01,
- 0.0000000e+00,
- 6.3123580e+00,
- 6.8427000e-02,
- 2.4906000e-01,
- 5.8245700e-01,
- 3.0184800e-01,
- 1.8228700e-01,
- 3.0293600e-01,
- 1.7027450e+00,
- 6.1963200e-01,
- 2.9964800e-01
- ],
- [ 1.1240350e+00,
- 8.9368000e-01,
- 2.5548000e-02,
- 1.7373500e-01,
- 1.7988530e+00,
- 1.3953800e-01,
- 4.4247200e-01,
- 4.2736070e+00,
- 6.5660400e-01,
- 6.3123580e+00,
- 0.0000000e+00,
- 3.7100400e-01,
- 9.9849000e-02,
- 1.6725690e+00,
- 4.8413300e-01,
- 3.4696000e-01,
- 2.0203660e+00,
- 1.8987180e+00,
- 6.9617500e-01,
- 4.8130600e-01
- ],
- [ 2.7681800e-01,
- 5.2876800e-01,
- 5.0761490e+00,
- 5.4171200e-01,
- 8.9525000e-02,
- 1.4376450e+00,
- 4.5092380e+00,
- 1.9150300e-01,
- 2.1450780e+00,
- 6.8427000e-02,
- 3.7100400e-01,
- 0.0000000e+00,
- 1.6178700e-01,
- 1.6957520e+00,
- 7.5187800e-01,
- 4.0083580e+00,
- 2.0006790e+00,
- 8.3688000e-02,
- 4.5376000e-02,
- 6.1202500e-01
- ],
- [ 1.1776510e+00,
- 7.5382000e-02,
- 3.9445600e-01,
- 4.1940900e-01,
- 9.4464000e-02,
- 1.9696100e-01,
- 5.0885100e-01,
- 7.8281000e-02,
- 3.9032200e-01,
- 2.4906000e-01,
- 9.9849000e-02,
- 1.6178700e-01,
- 0.0000000e+00,
- 6.2429400e-01,
- 3.3253300e-01,
- 1.3381320e+00,
- 5.7146800e-01,
- 2.9650100e-01,
- 9.5131000e-02,
- 8.9613000e-02
- ],
- [ 9.6989400e-01,
- 8.4808000e-02,
- 5.2338600e-01,
- 4.1285910e+00,
- 3.5855000e-02,
- 2.6795900e-01,
- 4.8135050e+00,
- 7.2854000e-02,
- 3.2342940e+00,
- 5.8245700e-01,
- 1.6725690e+00,
- 1.6957520e+00,
- 6.2429400e-01,
- 0.0000000e+00,
- 2.8079080e+00,
- 1.2238280e+00,
- 1.0801360e+00,
- 2.1033200e-01,
- 2.3619900e-01,
- 2.5733600e-01
- ],
- [ 4.2509300e-01,
- 5.3455100e-01,
- 1.2395400e-01,
- 3.6397000e-01,
- 5.2722000e-02,
- 3.9019200e-01,
- 2.4266010e+00,
- 1.2699100e-01,
- 6.3260670e+00,
- 3.0184800e-01,
- 4.8413300e-01,
- 7.5187800e-01,
- 3.3253300e-01,
- 2.8079080e+00,
- 0.0000000e+00,
- 8.5815100e-01,
- 5.7898700e-01,
- 1.7088700e-01,
- 5.9360700e-01,
- 3.1444000e-01
- ],
- [ 4.7271820e+00,
- 2.7844780e+00,
- 1.2402750e+00,
- 6.1197300e-01,
- 3.6181900e-01,
- 1.7399900e+00,
- 9.9001200e-01,
- 6.4105000e-02,
- 7.4868300e-01,
- 1.8228700e-01,
- 3.4696000e-01,
- 4.0083580e+00,
- 1.3381320e+00,
- 1.2238280e+00,
- 8.5815100e-01,
- 0.0000000e+00,
- 6.4722790e+00,
- 9.8369000e-02,
- 2.4886200e-01,
- 4.0054700e-01
- ],
- [ 2.1395010e+00,
- 1.1434800e+00,
- 4.2586000e-01,
- 6.0454500e-01,
- 1.6500100e-01,
- 1.2983600e-01,
- 5.8426200e-01,
- 1.0337390e+00,
- 1.1368630e+00,
- 3.0293600e-01,
- 2.0203660e+00,
- 2.0006790e+00,
- 5.7146800e-01,
- 1.0801360e+00,
- 5.7898700e-01,
- 6.4722790e+00,
- 0.0000000e+00,
- 2.1881580e+00,
- 1.4082500e-01,
- 2.4584100e-01
- ],
- [ 2.5478700e+00,
- 1.9592910e+00,
- 3.7967000e-02,
- 2.4503400e-01,
- 6.5468300e-01,
- 7.6701000e-02,
- 1.1901300e-01,
- 1.0649107e+01,
- 1.8520200e-01,
- 1.7027450e+00,
- 1.8987180e+00,
- 8.3688000e-02,
- 2.9650100e-01,
- 2.1033200e-01,
- 1.7088700e-01,
- 9.8369000e-02,
- 2.1881580e+00,
- 0.0000000e+00,
- 1.8951000e-01,
- 2.4931300e-01
- ],
- [ 1.8071700e-01,
- 6.7012800e-01,
- 2.9890000e-02,
- 7.7852000e-02,
- 2.4571210e+00,
- 2.6849100e-01,
- 5.9705400e-01,
- 1.1166000e-01,
- 4.9906000e-02,
- 6.1963200e-01,
- 6.9617500e-01,
- 4.5376000e-02,
- 9.5131000e-02,
- 2.3619900e-01,
- 5.9360700e-01,
- 2.4886200e-01,
- 1.4082500e-01,
- 1.8951000e-01,
- 0.0000000e+00,
- 3.1518150e+00
- ],
- [ 2.1895900e-01,
- 1.1655320e+00,
- 1.3510700e-01,
- 1.2003700e-01,
- 7.8039020e+00,
- 5.4679000e-02,
- 5.3068340e+00,
- 2.3252300e-01,
- 1.3193200e-01,
- 2.9964800e-01,
- 4.8130600e-01,
- 6.1202500e-01,
- 8.9613000e-02,
- 2.5733600e-01,
- 3.1444000e-01,
- 4.0054700e-01,
- 2.4584100e-01,
- 2.4931300e-01,
- 3.1518150e+00,
- 0.0000000e+00
- ]
- ]
-
-statDistUniform :: R.StationaryDistribution
-statDistUniform = vector $ replicate 20 0.05
-
-statDistLG :: R.StationaryDistribution
-statDistLG = S.stationaryDistribution lg
-
-exchLG :: R.ExchangeabilityMatrix
-exchLG = S.exchangeabilityMatrix lg
-
-rmLG :: R.RateMatrix
-rmLG = S.rateMatrix lg
-
-spec :: Spec
-spec = do
- describe "statDistLG" $
- it "matches distribution from python library" $
- statDistLG
- `nearlyEqVec` statDistLGPython
- `shouldBe` True
- describe "exchLG" $
- it "matches exchangeability matrix from python library" $
- do
- exchLG `shouldSatisfy` nearlyEqMatWith 1e-4 exchLGPython
- exchLG `nearlyEqMat` rmLG `shouldBe` False
- describe "lg" $
- it "stationary distribution can be extracted" $
- nearlyEqVecWith 1e-4 (R.getStationaryDistribution rmLG) statDistLG
- `shouldBe` True
- describe "lgCustom" $
- it "stationary distribution can be recovered" $ do
- let f =
- R.getStationaryDistribution $
- S.rateMatrix $
- lgCustom
- Nothing
- statDistUniform
- f `nearlyEqVec` statDistUniform `shouldBe` True
- describe "poisson" $
- it "stationary distribution is uniform 1/20" $
- R.getStationaryDistribution (S.rateMatrix poisson)
- `nearlyEqVec` statDistUniform
- `shouldBe` True
- describe "poissonCustom" $
- it "stationary distribution can be recovered" $ do
- let f =
- R.getStationaryDistribution $
- S.rateMatrix $
- poissonCustom
- Nothing
- statDistLGPython
- f `nearlyEqVec` statDistLGPython `shouldBe` True
diff --git a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
deleted file mode 100644
--- a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
+++ /dev/null
@@ -1,35 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.NucleotideSpec
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Fri Jan 25 16:47:28 2019.
-module ELynx.Data.MarkovProcess.NucleotideSpec
- ( spec,
- )
-where
-
-import Data.Vector.Generic
-import ELynx.Data.MarkovProcess.Nucleotide
-import ELynx.Data.MarkovProcess.RateMatrix
-import ELynx.Data.MarkovProcess.SubstitutionModel
-import ELynx.Tools.Equality
-import Test.Hspec
-
-stationaryDist :: StationaryDistribution
-stationaryDist = fromList [0.2, 0.3, 0.3, 0.2]
-
-hkyModel :: SubstitutionModel
-hkyModel = hky 6.0 stationaryDist
-
-spec :: Spec
-spec =
- describe "getStationaryDistribution" $
- it "extracts the stationary distribution from a rate matrix" $
- do
- let sd = getStationaryDistribution (rateMatrix hkyModel)
- sd `nearlyEqVec` stationaryDist `shouldBe` True
diff --git a/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs b/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs
deleted file mode 100644
--- a/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs
+++ /dev/null
@@ -1,46 +0,0 @@
--- |
--- Module : ELynx.Data.MarkovProcess.RateMatrixSpec
--- Description : Unit tests for rate matrices
--- Copyright : (c) Dominik Schrempf 2021
--- License : GPL-3.0-or-later
---
--- Maintainer : dominik.schrempf@gmail.com
--- Stability : unstable
--- Portability : portable
---
--- Creation date: Fri Apr 17 15:18:02 2020.
-module ELynx.Data.MarkovProcess.RateMatrixSpec
- ( spec,
- )
-where
-
-import ELynx.Data.MarkovProcess.RateMatrix
- ( exchFromListLower,
- exchFromListUpper,
- )
-import Numeric.LinearAlgebra
-import Test.Hspec
-
-es :: [Double]
-es = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-
-exMLower :: Matrix R
-exMLower =
- (5 >< 5)
- [0, 1, 2, 4, 7, 1, 0, 3, 5, 8, 2, 3, 0, 6, 9, 4, 5, 6, 0, 10, 7, 8, 9, 10, 0]
-
-exMUpper :: Matrix R
-exMUpper =
- (5 >< 5)
- [0, 1, 2, 3, 4, 1, 0, 5, 6, 7, 2, 5, 0, 8, 9, 3, 6, 8, 0, 10, 4, 7, 9, 10, 0]
-
-spec :: Spec
-spec = do
- describe "exchFromListLower" $
- it "correctly converts to matrix from list" $
- exMLower
- `shouldBe` exchFromListLower 5 es
- describe "exchFromListUpper" $
- it "correctly converts to matrix from list" $
- exMUpper
- `shouldBe` exchFromListUpper 5 es
diff --git a/test/ELynx/MarkovProcess/AminoAcidSpec.hs b/test/ELynx/MarkovProcess/AminoAcidSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/MarkovProcess/AminoAcidSpec.hs
@@ -0,0 +1,531 @@
+-- |
+-- Module : ELynx.MarkovProcess.AminoAcidSpec
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Tue Jan 29 10:47:40 2019.
+module ELynx.MarkovProcess.AminoAcidSpec
+ ( spec,
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import ELynx.MarkovProcess.AminoAcid
+import qualified ELynx.MarkovProcess.RateMatrix as R
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
+import ELynx.Tools.Equality
+import Numeric.LinearAlgebra
+import Test.Hspec
+
+normalizeSumVec :: Vector Double -> Vector Double
+normalizeSumVec v = V.map (/ s) v
+ where
+ s = V.sum v
+{-# INLINE normalizeSumVec #-}
+
+statDistLGPython :: R.StationaryDistribution
+statDistLGPython =
+ normalizeSumVec $
+ fromList
+ [ 0.079066,
+ 0.012937,
+ 0.053052,
+ 0.071586,
+ 0.042302,
+ 0.057337,
+ 0.022355,
+ 0.062157,
+ 0.064600,
+ 0.099081,
+ 0.022951,
+ 0.041977,
+ 0.044040,
+ 0.040767,
+ 0.055941,
+ 0.061197,
+ 0.053287,
+ 0.069147,
+ 0.012066,
+ 0.034155
+ ]
+
+exchLGPython :: R.ExchangeabilityMatrix
+exchLGPython =
+ fromLists
+ [ [ 0.0000000e+00,
+ 2.4890840e+00,
+ 3.9514400e-01,
+ 1.0385450e+00,
+ 2.5370100e-01,
+ 2.0660400e+00,
+ 3.5885800e-01,
+ 1.4983000e-01,
+ 5.3651800e-01,
+ 3.9533700e-01,
+ 1.1240350e+00,
+ 2.7681800e-01,
+ 1.1776510e+00,
+ 9.6989400e-01,
+ 4.2509300e-01,
+ 4.7271820e+00,
+ 2.1395010e+00,
+ 2.5478700e+00,
+ 1.8071700e-01,
+ 2.1895900e-01
+ ],
+ [ 2.4890840e+00,
+ 0.0000000e+00,
+ 6.2556000e-02,
+ 3.4990000e-03,
+ 1.1052510e+00,
+ 5.6926500e-01,
+ 6.4054300e-01,
+ 3.2062700e-01,
+ 1.3266000e-02,
+ 5.9400700e-01,
+ 8.9368000e-01,
+ 5.2876800e-01,
+ 7.5382000e-02,
+ 8.4808000e-02,
+ 5.3455100e-01,
+ 2.7844780e+00,
+ 1.1434800e+00,
+ 1.9592910e+00,
+ 6.7012800e-01,
+ 1.1655320e+00
+ ],
+ [ 3.9514400e-01,
+ 6.2556000e-02,
+ 0.0000000e+00,
+ 5.2438700e+00,
+ 1.7416000e-02,
+ 8.4492600e-01,
+ 9.2711400e-01,
+ 1.0690000e-02,
+ 2.8295900e-01,
+ 1.5076000e-02,
+ 2.5548000e-02,
+ 5.0761490e+00,
+ 3.9445600e-01,
+ 5.2338600e-01,
+ 1.2395400e-01,
+ 1.2402750e+00,
+ 4.2586000e-01,
+ 3.7967000e-02,
+ 2.9890000e-02,
+ 1.3510700e-01
+ ],
+ [ 1.0385450e+00,
+ 3.4990000e-03,
+ 5.2438700e+00,
+ 0.0000000e+00,
+ 1.8811000e-02,
+ 3.4884700e-01,
+ 4.2388100e-01,
+ 4.4265000e-02,
+ 1.8071770e+00,
+ 6.9673000e-02,
+ 1.7373500e-01,
+ 5.4171200e-01,
+ 4.1940900e-01,
+ 4.1285910e+00,
+ 3.6397000e-01,
+ 6.1197300e-01,
+ 6.0454500e-01,
+ 2.4503400e-01,
+ 7.7852000e-02,
+ 1.2003700e-01
+ ],
+ [ 2.5370100e-01,
+ 1.1052510e+00,
+ 1.7416000e-02,
+ 1.8811000e-02,
+ 0.0000000e+00,
+ 8.9586000e-02,
+ 6.8213900e-01,
+ 1.1127270e+00,
+ 2.3918000e-02,
+ 2.5926920e+00,
+ 1.7988530e+00,
+ 8.9525000e-02,
+ 9.4464000e-02,
+ 3.5855000e-02,
+ 5.2722000e-02,
+ 3.6181900e-01,
+ 1.6500100e-01,
+ 6.5468300e-01,
+ 2.4571210e+00,
+ 7.8039020e+00
+ ],
+ [ 2.0660400e+00,
+ 5.6926500e-01,
+ 8.4492600e-01,
+ 3.4884700e-01,
+ 8.9586000e-02,
+ 0.0000000e+00,
+ 3.1148400e-01,
+ 8.7050000e-03,
+ 2.9663600e-01,
+ 4.4261000e-02,
+ 1.3953800e-01,
+ 1.4376450e+00,
+ 1.9696100e-01,
+ 2.6795900e-01,
+ 3.9019200e-01,
+ 1.7399900e+00,
+ 1.2983600e-01,
+ 7.6701000e-02,
+ 2.6849100e-01,
+ 5.4679000e-02
+ ],
+ [ 3.5885800e-01,
+ 6.4054300e-01,
+ 9.2711400e-01,
+ 4.2388100e-01,
+ 6.8213900e-01,
+ 3.1148400e-01,
+ 0.0000000e+00,
+ 1.0888200e-01,
+ 6.9726400e-01,
+ 3.6631700e-01,
+ 4.4247200e-01,
+ 4.5092380e+00,
+ 5.0885100e-01,
+ 4.8135050e+00,
+ 2.4266010e+00,
+ 9.9001200e-01,
+ 5.8426200e-01,
+ 1.1901300e-01,
+ 5.9705400e-01,
+ 5.3068340e+00
+ ],
+ [ 1.4983000e-01,
+ 3.2062700e-01,
+ 1.0690000e-02,
+ 4.4265000e-02,
+ 1.1127270e+00,
+ 8.7050000e-03,
+ 1.0888200e-01,
+ 0.0000000e+00,
+ 1.5906900e-01,
+ 4.1450670e+00,
+ 4.2736070e+00,
+ 1.9150300e-01,
+ 7.8281000e-02,
+ 7.2854000e-02,
+ 1.2699100e-01,
+ 6.4105000e-02,
+ 1.0337390e+00,
+ 1.0649107e+01,
+ 1.1166000e-01,
+ 2.3252300e-01
+ ],
+ [ 5.3651800e-01,
+ 1.3266000e-02,
+ 2.8295900e-01,
+ 1.8071770e+00,
+ 2.3918000e-02,
+ 2.9663600e-01,
+ 6.9726400e-01,
+ 1.5906900e-01,
+ 0.0000000e+00,
+ 1.3750000e-01,
+ 6.5660400e-01,
+ 2.1450780e+00,
+ 3.9032200e-01,
+ 3.2342940e+00,
+ 6.3260670e+00,
+ 7.4868300e-01,
+ 1.1368630e+00,
+ 1.8520200e-01,
+ 4.9906000e-02,
+ 1.3193200e-01
+ ],
+ [ 3.9533700e-01,
+ 5.9400700e-01,
+ 1.5076000e-02,
+ 6.9673000e-02,
+ 2.5926920e+00,
+ 4.4261000e-02,
+ 3.6631700e-01,
+ 4.1450670e+00,
+ 1.3750000e-01,
+ 0.0000000e+00,
+ 6.3123580e+00,
+ 6.8427000e-02,
+ 2.4906000e-01,
+ 5.8245700e-01,
+ 3.0184800e-01,
+ 1.8228700e-01,
+ 3.0293600e-01,
+ 1.7027450e+00,
+ 6.1963200e-01,
+ 2.9964800e-01
+ ],
+ [ 1.1240350e+00,
+ 8.9368000e-01,
+ 2.5548000e-02,
+ 1.7373500e-01,
+ 1.7988530e+00,
+ 1.3953800e-01,
+ 4.4247200e-01,
+ 4.2736070e+00,
+ 6.5660400e-01,
+ 6.3123580e+00,
+ 0.0000000e+00,
+ 3.7100400e-01,
+ 9.9849000e-02,
+ 1.6725690e+00,
+ 4.8413300e-01,
+ 3.4696000e-01,
+ 2.0203660e+00,
+ 1.8987180e+00,
+ 6.9617500e-01,
+ 4.8130600e-01
+ ],
+ [ 2.7681800e-01,
+ 5.2876800e-01,
+ 5.0761490e+00,
+ 5.4171200e-01,
+ 8.9525000e-02,
+ 1.4376450e+00,
+ 4.5092380e+00,
+ 1.9150300e-01,
+ 2.1450780e+00,
+ 6.8427000e-02,
+ 3.7100400e-01,
+ 0.0000000e+00,
+ 1.6178700e-01,
+ 1.6957520e+00,
+ 7.5187800e-01,
+ 4.0083580e+00,
+ 2.0006790e+00,
+ 8.3688000e-02,
+ 4.5376000e-02,
+ 6.1202500e-01
+ ],
+ [ 1.1776510e+00,
+ 7.5382000e-02,
+ 3.9445600e-01,
+ 4.1940900e-01,
+ 9.4464000e-02,
+ 1.9696100e-01,
+ 5.0885100e-01,
+ 7.8281000e-02,
+ 3.9032200e-01,
+ 2.4906000e-01,
+ 9.9849000e-02,
+ 1.6178700e-01,
+ 0.0000000e+00,
+ 6.2429400e-01,
+ 3.3253300e-01,
+ 1.3381320e+00,
+ 5.7146800e-01,
+ 2.9650100e-01,
+ 9.5131000e-02,
+ 8.9613000e-02
+ ],
+ [ 9.6989400e-01,
+ 8.4808000e-02,
+ 5.2338600e-01,
+ 4.1285910e+00,
+ 3.5855000e-02,
+ 2.6795900e-01,
+ 4.8135050e+00,
+ 7.2854000e-02,
+ 3.2342940e+00,
+ 5.8245700e-01,
+ 1.6725690e+00,
+ 1.6957520e+00,
+ 6.2429400e-01,
+ 0.0000000e+00,
+ 2.8079080e+00,
+ 1.2238280e+00,
+ 1.0801360e+00,
+ 2.1033200e-01,
+ 2.3619900e-01,
+ 2.5733600e-01
+ ],
+ [ 4.2509300e-01,
+ 5.3455100e-01,
+ 1.2395400e-01,
+ 3.6397000e-01,
+ 5.2722000e-02,
+ 3.9019200e-01,
+ 2.4266010e+00,
+ 1.2699100e-01,
+ 6.3260670e+00,
+ 3.0184800e-01,
+ 4.8413300e-01,
+ 7.5187800e-01,
+ 3.3253300e-01,
+ 2.8079080e+00,
+ 0.0000000e+00,
+ 8.5815100e-01,
+ 5.7898700e-01,
+ 1.7088700e-01,
+ 5.9360700e-01,
+ 3.1444000e-01
+ ],
+ [ 4.7271820e+00,
+ 2.7844780e+00,
+ 1.2402750e+00,
+ 6.1197300e-01,
+ 3.6181900e-01,
+ 1.7399900e+00,
+ 9.9001200e-01,
+ 6.4105000e-02,
+ 7.4868300e-01,
+ 1.8228700e-01,
+ 3.4696000e-01,
+ 4.0083580e+00,
+ 1.3381320e+00,
+ 1.2238280e+00,
+ 8.5815100e-01,
+ 0.0000000e+00,
+ 6.4722790e+00,
+ 9.8369000e-02,
+ 2.4886200e-01,
+ 4.0054700e-01
+ ],
+ [ 2.1395010e+00,
+ 1.1434800e+00,
+ 4.2586000e-01,
+ 6.0454500e-01,
+ 1.6500100e-01,
+ 1.2983600e-01,
+ 5.8426200e-01,
+ 1.0337390e+00,
+ 1.1368630e+00,
+ 3.0293600e-01,
+ 2.0203660e+00,
+ 2.0006790e+00,
+ 5.7146800e-01,
+ 1.0801360e+00,
+ 5.7898700e-01,
+ 6.4722790e+00,
+ 0.0000000e+00,
+ 2.1881580e+00,
+ 1.4082500e-01,
+ 2.4584100e-01
+ ],
+ [ 2.5478700e+00,
+ 1.9592910e+00,
+ 3.7967000e-02,
+ 2.4503400e-01,
+ 6.5468300e-01,
+ 7.6701000e-02,
+ 1.1901300e-01,
+ 1.0649107e+01,
+ 1.8520200e-01,
+ 1.7027450e+00,
+ 1.8987180e+00,
+ 8.3688000e-02,
+ 2.9650100e-01,
+ 2.1033200e-01,
+ 1.7088700e-01,
+ 9.8369000e-02,
+ 2.1881580e+00,
+ 0.0000000e+00,
+ 1.8951000e-01,
+ 2.4931300e-01
+ ],
+ [ 1.8071700e-01,
+ 6.7012800e-01,
+ 2.9890000e-02,
+ 7.7852000e-02,
+ 2.4571210e+00,
+ 2.6849100e-01,
+ 5.9705400e-01,
+ 1.1166000e-01,
+ 4.9906000e-02,
+ 6.1963200e-01,
+ 6.9617500e-01,
+ 4.5376000e-02,
+ 9.5131000e-02,
+ 2.3619900e-01,
+ 5.9360700e-01,
+ 2.4886200e-01,
+ 1.4082500e-01,
+ 1.8951000e-01,
+ 0.0000000e+00,
+ 3.1518150e+00
+ ],
+ [ 2.1895900e-01,
+ 1.1655320e+00,
+ 1.3510700e-01,
+ 1.2003700e-01,
+ 7.8039020e+00,
+ 5.4679000e-02,
+ 5.3068340e+00,
+ 2.3252300e-01,
+ 1.3193200e-01,
+ 2.9964800e-01,
+ 4.8130600e-01,
+ 6.1202500e-01,
+ 8.9613000e-02,
+ 2.5733600e-01,
+ 3.1444000e-01,
+ 4.0054700e-01,
+ 2.4584100e-01,
+ 2.4931300e-01,
+ 3.1518150e+00,
+ 0.0000000e+00
+ ]
+ ]
+
+statDistUniform :: R.StationaryDistribution
+statDistUniform = vector $ replicate 20 0.05
+
+statDistLG :: R.StationaryDistribution
+statDistLG = S.stationaryDistribution lg
+
+exchLG :: R.ExchangeabilityMatrix
+exchLG = S.exchangeabilityMatrix lg
+
+rmLG :: R.RateMatrix
+rmLG = S.rateMatrix lg
+
+spec :: Spec
+spec = do
+ describe "statDistLG" $
+ it "matches distribution from python library" $
+ statDistLG
+ `nearlyEqVec` statDistLGPython
+ `shouldBe` True
+ describe "exchLG" $
+ it "matches exchangeability matrix from python library" $
+ do
+ exchLG `shouldSatisfy` nearlyEqMatWith 1e-4 exchLGPython
+ exchLG `nearlyEqMat` rmLG `shouldBe` False
+ describe "lg" $
+ it "stationary distribution can be extracted" $
+ nearlyEqVecWith 1e-4 (R.getStationaryDistribution rmLG) statDistLG
+ `shouldBe` True
+ describe "lgCustom" $
+ it "stationary distribution can be recovered" $ do
+ let f =
+ R.getStationaryDistribution $
+ S.rateMatrix $
+ lgCustom
+ Nothing
+ statDistUniform
+ f `nearlyEqVec` statDistUniform `shouldBe` True
+ describe "poisson" $
+ it "stationary distribution is uniform 1/20" $
+ R.getStationaryDistribution (S.rateMatrix poisson)
+ `nearlyEqVec` statDistUniform
+ `shouldBe` True
+ describe "poissonCustom" $
+ it "stationary distribution can be recovered" $ do
+ let f =
+ R.getStationaryDistribution $
+ S.rateMatrix $
+ poissonCustom
+ Nothing
+ statDistLGPython
+ f `nearlyEqVec` statDistLGPython `shouldBe` True
diff --git a/test/ELynx/MarkovProcess/NucleotideSpec.hs b/test/ELynx/MarkovProcess/NucleotideSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/MarkovProcess/NucleotideSpec.hs
@@ -0,0 +1,35 @@
+-- |
+-- Module : ELynx.MarkovProcess.NucleotideSpec
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Fri Jan 25 16:47:28 2019.
+module ELynx.MarkovProcess.NucleotideSpec
+ ( spec,
+ )
+where
+
+import Data.Vector.Generic
+import ELynx.MarkovProcess.Nucleotide
+import ELynx.MarkovProcess.RateMatrix
+import ELynx.MarkovProcess.SubstitutionModel
+import ELynx.Tools.Equality
+import Test.Hspec
+
+stationaryDist :: StationaryDistribution
+stationaryDist = fromList [0.2, 0.3, 0.3, 0.2]
+
+hkyModel :: SubstitutionModel
+hkyModel = hky 6.0 stationaryDist
+
+spec :: Spec
+spec =
+ describe "getStationaryDistribution" $
+ it "extracts the stationary distribution from a rate matrix" $
+ do
+ let sd = getStationaryDistribution (rateMatrix hkyModel)
+ sd `nearlyEqVec` stationaryDist `shouldBe` True
diff --git a/test/ELynx/MarkovProcess/RateMatrixSpec.hs b/test/ELynx/MarkovProcess/RateMatrixSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/MarkovProcess/RateMatrixSpec.hs
@@ -0,0 +1,46 @@
+-- |
+-- Module : ELynx.MarkovProcess.RateMatrixSpec
+-- Description : Unit tests for rate matrices
+-- Copyright : (c) Dominik Schrempf 2021
+-- License : GPL-3.0-or-later
+--
+-- Maintainer : dominik.schrempf@gmail.com
+-- Stability : unstable
+-- Portability : portable
+--
+-- Creation date: Fri Apr 17 15:18:02 2020.
+module ELynx.MarkovProcess.RateMatrixSpec
+ ( spec,
+ )
+where
+
+import ELynx.MarkovProcess.RateMatrix
+ ( exchFromListLower,
+ exchFromListUpper,
+ )
+import Numeric.LinearAlgebra
+import Test.Hspec
+
+es :: [Double]
+es = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+
+exMLower :: Matrix R
+exMLower =
+ (5 >< 5)
+ [0, 1, 2, 4, 7, 1, 0, 3, 5, 8, 2, 3, 0, 6, 9, 4, 5, 6, 0, 10, 7, 8, 9, 10, 0]
+
+exMUpper :: Matrix R
+exMUpper =
+ (5 >< 5)
+ [0, 1, 2, 3, 4, 1, 0, 5, 6, 7, 2, 5, 0, 8, 9, 3, 6, 8, 0, 10, 4, 7, 9, 10, 0]
+
+spec :: Spec
+spec = do
+ describe "exchFromListLower" $
+ it "correctly converts to matrix from list" $
+ exMLower
+ `shouldBe` exchFromListLower 5 es
+ describe "exchFromListUpper" $
+ it "correctly converts to matrix from list" $
+ exMUpper
+ `shouldBe` exchFromListUpper 5 es
diff --git a/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs b/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs
--- a/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs
+++ b/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs
@@ -14,8 +14,8 @@
where
import Data.Tree
-import ELynx.Data.MarkovProcess.Nucleotide
-import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
+import ELynx.MarkovProcess.Nucleotide
+import qualified ELynx.MarkovProcess.SubstitutionModel as S
import ELynx.Simulate.MarkovProcess
import ELynx.Simulate.MarkovProcessAlongTree
import System.Random.MWC