elynx-markov 0.5.1.0 → 0.5.1.1
raw patch · 20 files changed
+26/−26 lines, 20 filesdep ~elynx-seqdep ~elynx-toolsdep ~mwc-randomPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: elynx-seq, elynx-tools, mwc-random
API changes (from Hackage documentation)
Files
- elynx-markov.cabal +6/−6
- src/ELynx/Data/MarkovProcess/AminoAcid.hs +1/−1
- src/ELynx/Data/MarkovProcess/CXXModels.hs +1/−1
- src/ELynx/Data/MarkovProcess/CXXModelsData.hs +1/−1
- src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs +1/−1
- src/ELynx/Data/MarkovProcess/MixtureModel.hs +1/−1
- src/ELynx/Data/MarkovProcess/Nucleotide.hs +1/−1
- src/ELynx/Data/MarkovProcess/PhyloModel.hs +1/−1
- src/ELynx/Data/MarkovProcess/RateMatrix.hs +1/−1
- src/ELynx/Data/MarkovProcess/SubstitutionModel.hs +1/−1
- src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs +1/−1
- src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs +1/−1
- src/ELynx/Simulate/MarkovProcess.hs +1/−1
- src/ELynx/Simulate/MarkovProcessAlongTree.hs +1/−1
- test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs +1/−1
- test/ELynx/Data/MarkovProcess/NucleotideSpec.hs +1/−1
- test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs +1/−1
- test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs +1/−1
- test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs +1/−1
- test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs +2/−2
elynx-markov.cabal view
@@ -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
src/ELynx/Data/MarkovProcess/AminoAcid.hs view
@@ -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
src/ELynx/Data/MarkovProcess/CXXModels.hs view
@@ -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
src/ELynx/Data/MarkovProcess/CXXModelsData.hs view
@@ -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
src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs view
@@ -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
src/ELynx/Data/MarkovProcess/MixtureModel.hs view
@@ -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
src/ELynx/Data/MarkovProcess/Nucleotide.hs view
@@ -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
src/ELynx/Data/MarkovProcess/PhyloModel.hs view
@@ -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
src/ELynx/Data/MarkovProcess/RateMatrix.hs view
@@ -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
src/ELynx/Data/MarkovProcess/SubstitutionModel.hs view
@@ -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
src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs view
@@ -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
src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs view
@@ -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
src/ELynx/Simulate/MarkovProcess.hs view
@@ -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
src/ELynx/Simulate/MarkovProcessAlongTree.hs view
@@ -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
test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs view
@@ -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
test/ELynx/Data/MarkovProcess/NucleotideSpec.hs view
@@ -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
test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs view
@@ -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
test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs view
@@ -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
test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs view
@@ -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
test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs view
@@ -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)