diff --git a/elynx-markov.cabal b/elynx-markov.cabal --- a/elynx-markov.cabal +++ b/elynx-markov.cabal @@ -1,9 +1,9 @@ cabal-version: 2.2 name: elynx-markov -version: 0.5.1.0 +version: 0.5.1.1 license: GPL-3.0-or-later license-file: LICENSE -copyright: Dominik Schrempf (2020) +copyright: Dominik Schrempf (2021) maintainer: dominik.schrempf@gmail.com author: Dominik Schrempf homepage: https://github.com/dschrempf/elynx#readme @@ -53,11 +53,11 @@ base >=4.7 && <5, bytestring >=0.10.12.0, containers >=0.6.2.1, - elynx-seq >=0.5.1.0, + elynx-seq >=0.5.1.1, hmatrix >=0.20.2, integration >=0.2.1, math-functions >=0.3.4.2, - mwc-random >=0.14.0.0, + mwc-random >=0.15.0.1, primitive >=0.7.1.0, statistics >=0.15.2.0, vector >=0.12.3.0 @@ -81,10 +81,10 @@ base >=4.7 && <5, containers >=0.6.2.1, elynx-markov -any, - elynx-tools >=0.5.1.0, + elynx-tools >=0.5.1.1, hmatrix >=0.20.2, hspec >=2.7.10, - mwc-random >=0.14.0.0, + mwc-random >=0.15.0.1, vector >=0.12.3.0 benchmark markov-bench diff --git a/src/ELynx/Data/MarkovProcess/AminoAcid.hs b/src/ELynx/Data/MarkovProcess/AminoAcid.hs --- a/src/ELynx/Data/MarkovProcess/AminoAcid.hs +++ b/src/ELynx/Data/MarkovProcess/AminoAcid.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.AminoAcid -- Description : Amino acid rate matrices such as LG --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/CXXModels.hs b/src/ELynx/Data/MarkovProcess/CXXModels.hs --- a/src/ELynx/Data/MarkovProcess/CXXModels.hs +++ b/src/ELynx/Data/MarkovProcess/CXXModels.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.CXXModels -- Description : C10 to C60 models --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/CXXModelsData.hs b/src/ELynx/Data/MarkovProcess/CXXModelsData.hs --- a/src/ELynx/Data/MarkovProcess/CXXModelsData.hs +++ b/src/ELynx/Data/MarkovProcess/CXXModelsData.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.CXXModelsData -- Description : Stationary distributions and weights --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs b/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs --- a/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs +++ b/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.GammaRateHeterogeneity -- Description : Discrete gamma rate heterogeneity --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/MixtureModel.hs b/src/ELynx/Data/MarkovProcess/MixtureModel.hs --- a/src/ELynx/Data/MarkovProcess/MixtureModel.hs +++ b/src/ELynx/Data/MarkovProcess/MixtureModel.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.MixtureModel -- Description : Mixture models are a set of substitution models with weights --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/Nucleotide.hs b/src/ELynx/Data/MarkovProcess/Nucleotide.hs --- a/src/ELynx/Data/MarkovProcess/Nucleotide.hs +++ b/src/ELynx/Data/MarkovProcess/Nucleotide.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.Nucleotide -- Description : Substitution models using nucleotides --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/PhyloModel.hs b/src/ELynx/Data/MarkovProcess/PhyloModel.hs --- a/src/ELynx/Data/MarkovProcess/PhyloModel.hs +++ b/src/ELynx/Data/MarkovProcess/PhyloModel.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.PhyloModel -- Description : Phylogenetic model --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/RateMatrix.hs b/src/ELynx/Data/MarkovProcess/RateMatrix.hs --- a/src/ELynx/Data/MarkovProcess/RateMatrix.hs +++ b/src/ELynx/Data/MarkovProcess/RateMatrix.hs @@ -2,7 +2,7 @@ -- | -- Description : Rate matrix helper functions --- Copyright : (c) Dominik Schrempf 2017 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPLv3 -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs b/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs --- a/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs +++ b/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.SubstitutionModel -- Description : Data type describing substitution model --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com 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 @@ -3,7 +3,7 @@ -- | -- Module : ELynx.Import.MarkovProcess.EDMModelPhylobayes -- Description : Import stationary distributions from Phylobayes format --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs b/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs --- a/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs +++ b/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Import.MarkovProcess.SiteprofilesPhylobayes -- Description : Import site profiles in Phylobayes format --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com 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 @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Simulate.MarkovProcess -- Description : Markov process helpers --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com 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 @@ -2,7 +2,7 @@ -- | -- Description : Work with transition probability matrices on rooted trees --- Copyright : (c) Dominik Schrempf 2017 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPLv3 -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs --- a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs +++ b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs @@ -1,6 +1,6 @@ -- | -- Module : ELynx.Data.MarkovProcess.AminoAcidSpec --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs --- a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs +++ b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs @@ -1,6 +1,6 @@ -- | -- Module : ELynx.Data.MarkovProcess.NucleotideSpec --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs b/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs --- a/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs +++ b/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs @@ -1,7 +1,7 @@ -- | -- Module : ELynx.Data.MarkovProcess.RateMatrixSpec -- Description : Unit tests for rate matrices --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs --- a/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs +++ b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs @@ -1,6 +1,6 @@ -- | -- Module : ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com diff --git a/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs --- a/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs +++ b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs @@ -1,6 +1,6 @@ -- | -- Module : ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com 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 @@ -1,6 +1,6 @@ -- | -- Module : ELynx.Simulate.MarkovProcessAlongTreeSpec --- Copyright : (c) Dominik Schrempf 2020 +-- Copyright : (c) Dominik Schrempf 2021 -- License : GPL-3.0-or-later -- -- Maintainer : dominik.schrempf@gmail.com @@ -34,7 +34,7 @@ nullTree = Node 0 [] nullStateTree :: Tree State -nullStateTree = fmap (const 0) nullTree +nullStateTree = fmap (const 2) nullTree -- uniformStationaryDistribution :: Int -> Vector R -- uniformStationaryDistribution n = fromList $ replicate n (1.0 / fromIntegral n)