elynx-markov 0.6.1.1 → 0.7.0.1

raw patch · 23 files changed

+151/−144 lines, 23 filesdep +randomdep −primitivePVP ok

version bump matches the API change (PVP)

Dependencies added: random

Dependencies removed: primitive

API changes (from Hackage documentation)

Files

• ChangeLog.md +8/−1
• README.md +7/−8
• bench/Bench.hs +1/−1
• elynx-markov.cabal +66/−64
• src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs +1/−1
• src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs +1/−1
• src/ELynx/MarkovProcess/AminoAcid.hs +1/−1
• src/ELynx/MarkovProcess/CXXModels.hs +1/−1
• src/ELynx/MarkovProcess/CXXModelsData.hs +1/−1
• src/ELynx/MarkovProcess/GammaRateHeterogeneity.hs +1/−1
• src/ELynx/MarkovProcess/MixtureModel.hs +1/−1
• src/ELynx/MarkovProcess/Nucleotide.hs +1/−1
• src/ELynx/MarkovProcess/PhyloModel.hs +1/−1
• src/ELynx/MarkovProcess/RateMatrix.hs +5/−5
• src/ELynx/MarkovProcess/SubstitutionModel.hs +1/−1
• src/ELynx/Simulate/MarkovProcess.hs +9/−9
• src/ELynx/Simulate/MarkovProcessAlongTree.hs +36/−37
• test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs +1/−1
• test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs +1/−1
• test/ELynx/MarkovProcess/AminoAcidSpec.hs +1/−1
• test/ELynx/MarkovProcess/NucleotideSpec.hs +1/−1
• test/ELynx/MarkovProcess/RateMatrixSpec.hs +1/−1
• test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs +4/−4

@@ -5,9 +5,16 @@ ## Unreleased changes  +## Version 0.7.0.1++-   Random 1.2: Parallel functions now require an \`IOGenM\` random number+    generator.+-   Fix splitting of the random number generator.++ ## Version 0.6.1.1 --   Remove plotting functionality (gnuplot incompatible with ghc921).+-   Remove plotting functionality (gnuplot incompatible with ghc922). -   Read files strictly. -   Refactor; flatten model hierarchy. 

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.6.1.1.+Version: 0.7.0.0. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -74,9 +74,9 @@     # OR: slynx --help      Up to date-    ELynx Suite version 0.6.1.1.+    ELynx Suite version 0.7.0.0.     Developed by Dominik Schrempf.-    Compiled on February 22, 2022, at 15:10 pm, UTC.+    Compiled on July 10, 2022, at 08:48 am, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                  [-f|--force] [--no-elynx-file] COMMAND@@ -144,16 +144,16 @@     # OR: slynx simulate --help      Up to date-    ELynx Suite version 0.6.1.1.+    ELynx Suite version 0.7.0.0.     Developed by Dominik Schrempf.-    Compiled on February 22, 2022, at 15:10 pm, UTC.+    Compiled on July 10, 2022, at 08:48 am, 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,...]"]                           [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]-                          (-l|--length NUMBER) [-S|--seed [INT]]+                          (-l|--length NUMBER) [-S|--seed INT]       Simulate multi sequence alignments.          Available options:@@ -175,8 +175,7 @@       -g,--gamma-rate-heterogeneity "(NCAT,SHAPE)"                                Number of gamma rate categories and shape parameter       -l,--length NUMBER       Set alignment length to NUMBER-      -S,--seed [INT]          Seed for random number generator; list of 32 bit-                               integers with up to 256 elements (default: random)+      -S,--seed INT            Seed for random number generator (default: random)       -h,--help                Show this help text          Substitution models:

@@ -1,7 +1,7 @@ -- | -- Module      :  Main -- Description :  Benchmark Markov process along tree--- Copyright   :  (c) 2021 Dominik Schrempf+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,55 +1,55 @@-cabal-version:  3.0-name:           elynx-markov-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 <https://github.com/dschrempf/elynx>.-category:       Bioinformatics-homepage:       https://github.com/dschrempf/elynx#readme-bug-reports:    https://github.com/dschrempf/elynx/issues-author:         Dominik Schrempf-maintainer:     dominik.schrempf@gmail.com-copyright:      Dominik Schrempf (2021)-license:        GPL-3.0-or-later-license-file:   LICENSE-build-type:     Simple+cabal-version:      3.0+name:               elynx-markov+version:            0.7.0.1+synopsis:           Simulate molecular sequences along trees+description:+  Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. +category:           Bioinformatics+homepage:           https://github.com/dschrempf/elynx#readme+bug-reports:        https://github.com/dschrempf/elynx/issues+author:             Dominik Schrempf+maintainer:         dominik.schrempf@gmail.com+copyright:          2021 Dominik Schrempf+license:            GPL-3.0-or-later+license-file:       LICENSE+build-type:         Simple extra-source-files:-    README.md-    ChangeLog.md-    data/EDMDistsIQTREE.nex-    data/EDMDistsPhylobayes.txt-    data/HSSPMany.siteprofiles-    data/HSSPSingle.siteprofiles+  ChangeLog.md+  data/EDMDistsIQTREE.nex+  data/EDMDistsPhylobayes.txt+  data/HSSPMany.siteprofiles+  data/HSSPSingle.siteprofiles+  README.md  source-repository head-  type: git+  type:     git   location: https://github.com/dschrempf/elynx  library   exposed-modules:-      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-      ELynx.Simulate.MarkovProcessAlongTree-  other-modules:-      Paths_elynx_markov-  autogen-modules:-      Paths_elynx_markov-  hs-source-dirs: src-  ghc-options: -Wall -Wunused-packages+    ELynx.Import.MarkovProcess.EDMModelPhylobayes+    ELynx.Import.MarkovProcess.SiteprofilesPhylobayes+    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.Simulate.MarkovProcess+    ELynx.Simulate.MarkovProcessAlongTree++  other-modules:    Paths_elynx_markov+  autogen-modules:  Paths_elynx_markov+  hs-source-dirs:   src+  ghc-options:      -Wall -Wunused-packages   build-depends:-      async+    , async     , attoparsec-    , base >=4.7 && <5+    , base            >=4.7 && <5     , bytestring     , containers     , elynx-seq@@ -57,45 +57,47 @@     , integration     , math-functions     , mwc-random-    , primitive+    , random     , statistics     , vector+   default-language: Haskell2010  test-suite markov-test-  type: exitcode-stdio-1.0-  main-is: Spec.hs+  type:             exitcode-stdio-1.0+  main-is:          Spec.hs   other-modules:-      ELynx.MarkovProcess.AminoAcidSpec-      ELynx.MarkovProcess.NucleotideSpec-      ELynx.MarkovProcess.RateMatrixSpec-      ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec-      ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec-      ELynx.Simulate.MarkovProcessAlongTreeSpec-      Paths_elynx_markov-  autogen-modules:-      Paths_elynx_markov-  hs-source-dirs: test-  ghc-options: -Wall -Wunused-packages+    ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec+    ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec+    ELynx.MarkovProcess.AminoAcidSpec+    ELynx.MarkovProcess.NucleotideSpec+    ELynx.MarkovProcess.RateMatrixSpec+    ELynx.Simulate.MarkovProcessAlongTreeSpec+    Paths_elynx_markov++  autogen-modules:  Paths_elynx_markov+  hs-source-dirs:   test+  ghc-options:      -Wall -Wunused-packages   build-depends:-      base >=4.7 && <5+    , base          >=4.7 && <5     , containers     , elynx-markov     , elynx-tools     , hmatrix     , hspec-    , mwc-random+    , random     , vector+   default-language: Haskell2010  benchmark markov-bench-  type:            exitcode-stdio-1.0-  main-is:         Bench.hs+  type:             exitcode-stdio-1.0+  main-is:          Bench.hs+   -- other-modules:   -- autogen-modules:   -- ghc-options:-  hs-source-dirs:  bench-  ghc-options: -Wall -Wunused-packages-  build-depends:-      base+  hs-source-dirs:   bench+  ghc-options:      -Wall -Wunused-packages+  build-depends:    base   default-language: Haskell2010

@@ -3,7 +3,7 @@ -- | -- Module      :  ELynx.Import.MarkovProcess.EDMModelPhylobayes -- Description :  Import stationary distributions from Phylobayes format--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.Import.MarkovProcess.SiteprofilesPhylobayes -- Description :  Import site profiles in Phylobayes format--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.AminoAcid -- Description :  Amino acid rate matrices such as LG--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.CXXModels -- Description :  C10 to C60 models--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.CXXModelsData -- Description :  Stationary distributions and weights--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.GammaRateHeterogeneity -- Description :  Discrete gamma rate heterogeneity--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.MixtureModel -- Description :  Mixture models are a set of substitution models with weights--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.Nucleotide -- Description :  Substitution models using nucleotides--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.PhyloModel -- Description :  Phylogenetic model--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -2,7 +2,7 @@  -- | -- Description :  Rate matrix helper functions--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPLv3 -- -- Maintainer  :  dominik.schrempf@gmail.com@@ -179,8 +179,8 @@   | i == j = 0.0   | i < j = es !! ijToKLower jI iI   | otherwise =-    error-      "Float indices could not be compared during matrix creation."+      error+        "Float indices could not be compared during matrix creation."   where     iI = round i :: Int     jI = round j :: Int@@ -193,8 +193,8 @@   | i == j = 0.0   | i > j = es !! ijToKUpper n jI iI   | otherwise =-    error-      "Float indices could not be compared during matrix creation."+      error+        "Float indices could not be compared during matrix creation."   where     iI = round i :: Int     jI = round j :: Int

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.SubstitutionModel -- Description :  Data type describing substitution model--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.Simulate.MarkovProcess -- Description :  Markov process helpers--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com@@ -17,11 +17,10 @@   ) where -import Control.Monad.Primitive import ELynx.MarkovProcess.RateMatrix import Numeric.LinearAlgebra-import System.Random.MWC import System.Random.MWC.Distributions+import System.Random.Stateful  -- | A probability matrix, P_ij(t) = Pr (X_t = j | X_0 = i). type ProbMatrix = Matrix R@@ -33,19 +32,20 @@ -- another in a specific time (branch length). probMatrix :: RateMatrix -> Double -> ProbMatrix probMatrix q t-  | t == 0 =-    if rows q == cols q-      then ident (rows q)-      else error "probMatrix: Matrix is not square."+  | n /= m = error "probMatrix: Matrix is not square."+  | t == 0 = ident n   | t < 0 = error "probMatrix: Time is negative."   | otherwise = expm $ scale t q+  where+    n = rows q+    m = cols q  -- | Move from a given state to a new one according to a transition probability -- matrix . -- -- This function is the bottleneck of the simulator and takes up most of the -- computation time.-jump :: (PrimMonad m) => State -> ProbMatrix -> Gen (PrimState m) -> m State+jump :: StatefulGen g m => State -> ProbMatrix -> g -> m State jump i p = categorical (p ! i)  -- XXX: Maybe for later, use condensed tables.@@ -55,7 +55,7 @@ -- -- Do not generate table for each jump. ----- jump :: (PrimMonad m) => State -> ProbMatrix -> Gen (PrimState m) -> m State+-- jump :: StatefulGen g m => State -> ProbMatrix -> g -> m State -- jump i p = genFromTable table --   where --     ws = toList $ p ! i

@@ -2,7 +2,7 @@  -- | --   Description :  Work with transition probability matrices on rooted trees---   Copyright   :  (c) Dominik Schrempf 2021+--   Copyright   :  2021 Dominik Schrempf --   License     :  GPLv3 -- --   Maintainer  :  dominik.schrempf@gmail.com@@ -30,14 +30,12 @@ import Control.Concurrent import Control.Concurrent.Async import Control.Monad-import Control.Monad.Primitive import Data.Tree import qualified Data.Vector as V-import Data.Word (Word32) import ELynx.MarkovProcess.RateMatrix import ELynx.Simulate.MarkovProcess-import System.Random.MWC-import System.Random.MWC.Distributions (categorical)+import System.Random.MWC.Distributions+import System.Random.Stateful  -- XXX @performace. The horizontal concatenation might be slow. If so, -- 'concatenateSeqs' or 'concatenateAlignments' can be used, which directly@@ -55,10 +53,10 @@ toProbTree q = fmap (probMatrix q)  getRootStates ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   StationaryDistribution ->-  Gen (PrimState m) ->+  g ->   m [State] getRootStates n d g = replicateM n $ categorical d g @@ -69,12 +67,12 @@ -- XXX: Improve performance. Use vectors, not lists. I am actually not sure if -- this improves performance... simulateAndFlatten ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   StationaryDistribution ->   ExchangeabilityMatrix ->   Tree Double ->-  Gen (PrimState m) ->+  g ->   m [[State]] simulateAndFlatten n d e t g = do   let q = fromExchangeabilityMatrix e d@@ -86,10 +84,10 @@ -- Recursively jump down the branches to the leafs. Forget states at internal -- nodes. simulateAndFlatten' ::-  (PrimMonad m) =>+  StatefulGen g m =>   [State] ->   Tree ProbMatrix ->-  Gen (PrimState m) ->+  g ->   m [[State]] simulateAndFlatten' is (Node p f) g = do   is' <- mapM (\i -> jump i p g) is@@ -99,15 +97,17 @@  -- | See 'simulateAndFlatten', parallel version. simulateAndFlattenPar ::+  RandomGen g =>   Int ->   StationaryDistribution ->   ExchangeabilityMatrix ->   Tree Double ->-  GenIO ->+  IOGenM g ->   IO [[State]] simulateAndFlattenPar n d e t g = do   c <- getNumCapabilities-  gs <- splitGen c g+  rs <- replicateM c $ splitGenM g+  gs <- mapM newIOGenM rs   let chunks = getChunks c n       q = fromExchangeabilityMatrix e d       pt = toProbTree q t@@ -126,12 +126,12 @@ -- internal nodes. The result is a tree with the list of simulated states as -- node labels. simulate ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   StationaryDistribution ->   ExchangeabilityMatrix ->   Tree Double ->-  Gen (PrimState m) ->+  g ->   m (Tree [State]) simulate n d e t g = do   let q = fromExchangeabilityMatrix e d@@ -142,10 +142,10 @@ -- This is the heart of the simulation. Take a tree and a list of root states. -- Recursively jump down the branches to the leafs. simulate' ::-  (PrimMonad m) =>+  StatefulGen g m =>   [State] ->   Tree ProbMatrix ->-  Gen (PrimState m) ->+  g ->   m (Tree [State]) simulate' is (Node p f) g = do   is' <- mapM (\i -> jump i p g) is@@ -159,11 +159,11 @@   fmap (\a -> V.map (`probMatrix` a) qs)  getComponentsAndRootStates ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   V.Vector Double ->   V.Vector StationaryDistribution ->-  Gen (PrimState m) ->+  g ->   m ([Int], [State]) getComponentsAndRootStates n ws ds g = do   cs <- replicateM n $ categorical ws g@@ -174,13 +174,13 @@ -- corresponding weights. Forget states at internal nodes. See also -- 'simulateAndFlatten'. simulateAndFlattenMixtureModel ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   V.Vector Double ->   V.Vector StationaryDistribution ->   V.Vector ExchangeabilityMatrix ->   Tree Double ->-  Gen (PrimState m) ->+  g ->   -- | (IndicesOfComponents, [SimulatedSequenceForEachTip])   m ([Int], [[State]]) simulateAndFlattenMixtureModel n ws ds es t g = do@@ -191,11 +191,11 @@   return (cs, ss)  simulateAndFlattenMixtureModel' ::-  (PrimMonad m) =>+  StatefulGen g m =>   [State] ->   [Int] ->   Tree (V.Vector ProbMatrix) ->-  Gen (PrimState m) ->+  g ->   m [[State]] simulateAndFlattenMixtureModel' is cs (Node ps f) g = do   is' <- sequence [jump i (ps V.! c) g | (i, c) <- zip is cs]@@ -212,28 +212,27 @@     r = n `mod` c     ns = replicate r (n' + 1) ++ replicate (c - r) n' -splitGen :: PrimMonad m => Int -> Gen (PrimState m) -> m [Gen (PrimState m)]-splitGen n gen-  | n <= 0 = return []-  | otherwise = do-    seeds :: [V.Vector Word32] <- replicateM (n -1) $ uniformVector gen 256-    fmap (gen :) (mapM initialize seeds)--parComp :: Int -> (Int -> GenIO -> IO b) -> GenIO -> IO [b]+-- NOTE: We could move away from IO here, but moving away from 'mapConcurrently'+-- requires benchmarks. I am just not sure if it makes sense to spend more time+-- on this since the parallelization itself is a bit weird. Like so, we walk+-- along separate trees in each process.+parComp :: RandomGen g => Int -> (Int -> IOGenM g -> IO b) -> IOGenM g -> IO [b] parComp num fun gen = do   ncap <- getNumCapabilities   let chunks = getChunks ncap num-  gs <- splitGen ncap gen+  rs <- replicateM ncap $ splitGenM gen+  gs <- mapM newIOGenM rs   mapConcurrently (uncurry fun) (zip chunks gs)  -- | See 'simulateAndFlattenMixtureModel', parallel version. simulateAndFlattenMixtureModelPar ::+  RandomGen g =>   Int ->   V.Vector Double ->   V.Vector StationaryDistribution ->   V.Vector ExchangeabilityMatrix ->   Tree Double ->-  GenIO ->+  IOGenM g ->   IO ([Int], [[State]]) simulateAndFlattenMixtureModelPar n ws ds es t g = do   let qs = V.zipWith fromExchangeabilityMatrix es ds@@ -256,13 +255,13 @@ -- corresponding weights. Keep states at internal nodes. See also -- 'simulate'. simulateMixtureModel ::-  PrimMonad m =>+  StatefulGen g m =>   Int ->   V.Vector Double ->   V.Vector StationaryDistribution ->   V.Vector ExchangeabilityMatrix ->   Tree Double ->-  Gen (PrimState m) ->+  g ->   m (Tree [State]) simulateMixtureModel n ws ds es t g = do   let qs = V.zipWith fromExchangeabilityMatrix es ds@@ -273,11 +272,11 @@ -- See 'simulateAlongProbTree', only we have a number of mixture components. The -- starting states and the components for each site have to be provided. simulateMixtureModel' ::-  (PrimMonad m) =>+  StatefulGen g m =>   [State] ->   [Int] ->   Tree (V.Vector ProbMatrix) ->-  Gen (PrimState m) ->+  g ->   m (Tree [State]) simulateMixtureModel' is cs (Node ps f) g = do   is' <- sequence [jump i (ps V.! c) g | (i, c) <- zip is cs]

@@ -1,6 +1,6 @@ -- | -- Module      :  ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,6 +1,6 @@ -- | -- Module      :  ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,6 +1,6 @@ -- | -- Module      :  ELynx.MarkovProcess.AminoAcidSpec--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,6 +1,6 @@ -- | -- Module      :  ELynx.MarkovProcess.NucleotideSpec--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,7 +1,7 @@ -- | -- Module      :  ELynx.MarkovProcess.RateMatrixSpec -- Description :  Unit tests for rate matrices--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com

@@ -1,6 +1,6 @@ -- | -- Module      :  ELynx.Simulate.MarkovProcessAlongTreeSpec--- Copyright   :  (c) Dominik Schrempf 2021+-- Copyright   :  2021 Dominik Schrempf -- License     :  GPL-3.0-or-later -- -- Maintainer  :  dominik.schrempf@gmail.com@@ -18,7 +18,7 @@ import qualified ELynx.MarkovProcess.SubstitutionModel as S import ELynx.Simulate.MarkovProcess import ELynx.Simulate.MarkovProcessAlongTree-import System.Random.MWC+import System.Random.Stateful import Test.Hspec  -- sampleNewickText :: T.Text@@ -42,11 +42,11 @@ spec :: Spec spec = describe "simulateNSitesAlongTree" $ do   it "simulates one site along an easy tree" $ do-    gen <- create+    gen <- newIOGenM $ mkStdGen 0     tr <- simulate 1 d e nullTree gen     fmap head tr `shouldBe` nullStateTree   it "simulates some sites along a harder tree" $ do-    gen <- create+    gen <- newIOGenM $ mkStdGen 0     tr <- simulate 10 d e testTree gen     (length . rootLabel $ tr) `shouldBe` 10   where