elynx-tree (empty) → 0.0.1
raw patch · 31 files changed
+3484/−0 lines, 31 filesdep +QuickCheckdep +basedep +bytestring
Dependencies added: QuickCheck, base, bytestring, containers, elynx-tools, elynx-tree, hspec, hspec-megaparsec, lifted-async, math-functions, megaparsec, mwc-random, optparse-applicative, parallel, primitive, quickcheck-instances, statistics, transformers, vector
Files
- ChangeLog.md +10/−0
- LICENSE +674/−0
- README.md +417/−0
- elynx-tree.cabal +102/−0
- src/ELynx/Data/Tree/Bipartition.hs +231/−0
- src/ELynx/Data/Tree/BranchSupportTree.hs +64/−0
- src/ELynx/Data/Tree/Distance.hs +124/−0
- src/ELynx/Data/Tree/EvoTree.hs +43/−0
- src/ELynx/Data/Tree/MeasurableTree.hs +98/−0
- src/ELynx/Data/Tree/NamedTree.hs +23/−0
- src/ELynx/Data/Tree/PhyloTree.hs +89/−0
- src/ELynx/Data/Tree/SumStat.hs +57/−0
- src/ELynx/Data/Tree/Tree.hs +143/−0
- src/ELynx/Distribution/BirthDeath.hs +84/−0
- src/ELynx/Distribution/BirthDeathCritical.hs +76/−0
- src/ELynx/Distribution/BirthDeathCriticalNoTime.hs +73/−0
- src/ELynx/Distribution/BirthDeathNearlyCritical.hs +89/−0
- src/ELynx/Distribution/CoalescentContinuous.hs +26/−0
- src/ELynx/Distribution/TimeOfOrigin.hs +84/−0
- src/ELynx/Distribution/TimeOfOriginNearCritical.hs +84/−0
- src/ELynx/Distribution/Types.hs +27/−0
- src/ELynx/Export/Tree/Newick.hs +62/−0
- src/ELynx/Import/Tree/Newick.hs +110/−0
- src/ELynx/Simulate/Coalescent.hs +62/−0
- src/ELynx/Simulate/PointProcess.hs +233/−0
- test/ELynx/Data/Tree/BipartitionSpec.hs +79/−0
- test/ELynx/Data/Tree/DistanceSpec.hs +99/−0
- test/ELynx/Data/Tree/TreeSpec.hs +66/−0
- test/ELynx/Export/Tree/NewickSpec.hs +39/−0
- test/ELynx/Import/Tree/NewickSpec.hs +115/−0
- test/Spec.hs +1/−0
+ ChangeLog.md view
@@ -0,0 +1,10 @@++# Table of Contents++1. [Changelog for ELynx](#org9916021)+++<a id="org9916021"></a>++# Changelog for ELynx+
+ LICENSE view
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Of course, your program's commands+might be different; for a GUI interface, you would use an "about box".++ You should also get your employer (if you work as a programmer) or school,+if any, to sign a "copyright disclaimer" for the program, if necessary.+For more information on this, and how to apply and follow the GNU GPL, see+<https://www.gnu.org/licenses/>.++ The GNU General Public License does not permit incorporating your program+into proprietary programs. If your program is a subroutine library, you+may consider it more useful to permit linking proprietary applications with+the library. If this is what you want to do, use the GNU Lesser General+Public License instead of this License. But first, please read+<https://www.gnu.org/licenses/why-not-lgpl.html>.
+ README.md view
@@ -0,0 +1,417 @@+++# The ELynx Suite++Version: 0.0.1.+Reproducible evolution made easy.++The ELynx Suite is a Haskell library and a tool set for computational biology.+The goal of the ELynx Suite is reproducible research. Evolutionary sequences and+phylogenetic trees can be read, viewed, modified and simulated. Exact+specification of all options is necessary, and nothing is assumed about the data+(e.g., the type of code). The command line with all arguments is consistently,+and automatically logged. The work overhead in the beginning usually pays off in+the end.++The Elynx Suite consists of three library packages and two executables providing+a range of sub commands.++The library packages are:++- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments;+- **elynx-tree:** Handle phylogenetic trees;+- **elynx-tools:** Tools for the provided executables;++The executables are:++- **SLynx:** Analyze, modify, and simulate evolutionary sequences (FASTA format);+- **TLynx:** Analyze, modify, and simulate phylogenetic trees (Newick format).++**ELynx is still under development. We happily receive comments, ideas, feature+requests, or pull requests!**+++# Installation++ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/).++1. Install Stack with your package manager, or directly from the web+ page.+ + curl -sSL https://get.haskellstack.org/ | sh++2. Clone the ELynx repository.+ + git clone clone https://github.com/dschrempf/elynx++3. Navigate to the newly created `elynx` folder and build the binaries.+ This will take a while.+ + stack build++4. Run a binary from within the project directory. For example,+ + stack exec tlynx -- --help++5. If needed, install the binaries.+ + stack install+ + The binaries are installed into `~/.local/bin/` which has to be added [PATH](https://en.wikipedia.org/wiki/PATH_(variable)).+ Then, they can be used directly.+++# SLynx++Handle evolutionary sequences.++ slynx --help++ ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September+ 9, 2019, at 10:48 am, UTC.+ + Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] COMMAND+ Analyze, and simulate multi sequence alignments.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info+ Debug (default: Info)+ -o,--output-file-basename NAME+ Specify base name of output file+ + Available commands:+ concatenate + examine If data is a multi sequence alignment, additionally+ analyze columns.+ filter-rows + filter-columns + simulate + sub-sample Create a given number of multi sequence alignments,+ each of which containing a given number of random+ sites drawn from the original multi sequence+ alignment.+ translate + + File formats:+ - FASTA+ + Alphabet types:+ - DNA (nucleotides)+ - DNAX (nucleotides; including gaps)+ - DNAI (nucleotides; including gaps, and IUPAC codes)+ - Protein (amino acids)+ - ProteinX (amino acids; including gaps)+ - ProteinS (amino acids; including gaps, and translation stops)+ - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)+ + The ELynx Suite.+ A Haskell library and a tool set for computational biology. The goal of the+ ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic+ trees can be read, viewed, modified and simulated. Exact specification of all+ options is necessary, and nothing is assumed about the data (e.g., the type of+ code). The command line with all arguments is consistently, and automatically+ logged. The work overhead in the beginning usually pays off in the end.+ slynx Analyze, modify, and simulate evolutionary sequences.+ tlynx Analyze, modify, and simulate phylogenetic trees.+++## Concatenate++Concatenate multi sequence alignments.++ slynx concatenate --help++ Concatenate sequences found in input files.+ + Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -h,--help Show this help text+++## Examine++Examine sequence with `slynx examine`.++ slynx examine --help++ Examine sequences.+ + Usage: slynx examine (-a|--alphabet NAME) [INPUT-FILE] [--per-site]+ If data is a multi sequence alignment, additionally analyze columns.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --per-site Report per site summary statistics+ -h,--help Show this help text+++## Filter++Filter sequences with `filer-rows`.++ slynx filter-rows --help++ Filter rows (or sequences) found in input files.+ + Usage: slynx filter-rows (-a|--alphabet NAME) [INPUT-FILE]+ [--longer-than LENGTH] [--shorter-than LENGTH]+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --longer-than LENGTH Only keep sequences longer than LENGTH+ --shorter-than LENGTH Only keep sequences shorter than LENGTH+ -h,--help Show this help text++Filter columns of multi sequence alignments with `filter-columns`.++ slynx filter-columns --help++ Filter columns of multi-sequence alignments.+ + Usage: slynx filter-columns (-a|--alphabet NAME) [INPUT-FILE]+ [--standard-chars DOUBLE]+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ --standard-chars DOUBLE Keep columns with a proportion standard (non-IUPAC)+ characters larger than DOUBLE in [0,1]+ -h,--help Show this help text+++## Simulate++Simulate sequences with `slynx simulate`.++ slynx simulate --help++ Simulate multi sequence alignments.+ + Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]+ [-m|--mixture-model MODEL] [-e|--edm-file NAME]+ [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]+ [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]+ (-l|--length NUMBER) [-S|--seed [INT]]+ + Available options:+ -t,--tree-file Name Read trees from file NAME+ -s,--substitution-model MODEL+ Set the phylogenetic substitution model; available+ models are shown below (mutually exclusive with -m+ option)+ -m,--mixture-model MODEL Set the phylogenetic mixture model; available models+ are shown below (mutually exclusive with -s option)+ -e,--edm-file NAME Empirical distribution model file NAME in Phylobayes+ format+ -w,--mixture-model-weights "[DOUBLE,DOUBLE,...]"+ Weights of mixture model components+ -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)+ -h,--help Show this help text+ + Substitution models:+ -s "MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}"+ Supported DNA models: JC, HKY.+ For example,+ -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}+ Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom.+ MODEL-Custom means that only the exchangeabilities of MODEL are used,+ and a custom stationary distribution is provided.+ For example,+ -s LG-Custom{...}+ + Mixture models:+ -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2)"+ For example,+ -m "MIXTURE(JC,HKY[6.0]{0.3,0.2,0.2,0.3})"+ Mixture weights have to be provided with the -w option.+ + Special mixture models:+ -m CXX+ where XX is 10, 20, 30, 40, 50, or 60; CXX models, Quang et al., 2008.+ -m "EDM(EXCHANGEABILITIES)"+ Arbitrary empirical distribution mixture (EDM) models.+ Stationary distributions have to be provided with the -e option.+ For example,+ LG exchangeabilities with stationary distributions given in FILE.+ -m "EDM(LG-Custom)" -e FILE+ For special mixture models, mixture weights are optional.+++## Sub-sample++Sub-sample columns from multi sequence alignments.++ slynx sub-sample --help++ Usage: slynx sub-sample (-a|--alphabet NAME) [INPUT-FILE]+ (-n|--number-of-sites INT)+ (-m|--number-of-alignments INT) [-S|--seed [INT]]+ Create a given number of multi sequence alignments, each of which containing a+ given number of random sites drawn from the original multi sequence alignment.+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -n,--number-of-sites INT Number of sites randomly drawn with replacement+ -m,--number-of-alignments INT+ Number of multi sequence alignments to be created+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text+++## Translate++Translate sequences.++ slynx translate --help++ Translate from DNA to Protein or DNAX to ProteinX.+ + Usage: slynx translate (-a|--alphabet NAME) [INPUT-FILE]+ (-r|--reading-frame INT) (-u|--universal-code CODE)+ + Available options:+ -a,--alphabet NAME Specify alphabet type NAME+ INPUT-FILE Read sequences from INPUT-FILE+ -r,--reading-frame INT Reading frame [0|1|2].+ -u,--universal-code CODE universal code; one of: Standard,+ VertebrateMitochondrial.+ -h,--help Show this help text+++# TLynx++Handle phylogenetic trees in Newick format.++ tlynx --help++ ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September+ 9, 2019, at 10:48 am, UTC.+ + Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] COMMAND+ Compare, examine, and simulate phylogenetic trees.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info+ Debug (default: Info)+ -o,--output-file-basename NAME+ Specify base name of output file+ + Available commands:+ compare + examine + simulate Simulate reconstructed trees using the point process.+ See Gernhard, T. (2008). The conditioned+ reconstructed process. Journal of Theoretical+ Biology, 253(4), 769–778.+ http://doi.org/10.1016/j.jtbi.2008.04.005+ + File formats:+ - Newick+ + The ELynx Suite.+ A Haskell library and a tool set for computational biology. The goal of the+ ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic+ trees can be read, viewed, modified and simulated. Exact specification of all+ options is necessary, and nothing is assumed about the data (e.g., the type of+ code). The command line with all arguments is consistently, and automatically+ logged. The work overhead in the beginning usually pays off in the end.+ slynx Analyze, modify, and simulate evolutionary sequences.+ tlynx Analyze, modify, and simulate phylogenetic trees.+++## Compare++Compute distances between phylogenetic trees.++ tlynx compare --help++ Compute distances between phylogenetic trees.+ + Usage: tlynx compare (-d|--distance MEASURE) [-s|--summary-statistics]+ [INPUT-FILES]+ + Available options:+ -d,--distance MEASURE Type of distance to calculate (available distance+ measures are listed below)+ -s,--summary-statistics Report summary statistics only+ INPUT-FILES Read tree(s) from INPUT-FILES; if more files are+ given, one tree is expected per file+ -h,--help Show this help text+ + Available distance measures:+ Symmetric distance: -d symmetric+ Incompatible split distance: -d incompatible-split[VAL]+ Collapse branches with support less than VAL before distance calculation;+ in this way, only well supported difference contribute to the distance measure.+++## Examine++Compute summary statistics of phylogenetic trees.++ tlynx examine --help++ Compute summary statistics of phylogenetic trees.+ + Usage: tlynx examine [INPUT-FILE]+ + Available options:+ INPUT-FILE Read trees from INPUT-FILE+ -h,--help Show this help text+++## Simulate++Simulate phylogenetic trees using birth and death processes.++ tlynx simulate --help++ Simulate phylogenetic trees using birth and death processes.+ + Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE]+ [-M|--condition-on-mrca] [-l|--lambda DOUBLE]+ [-m|--mu DOUBLE] [-r|--rho DOUBLE] [-u|--sub-sample]+ [-s|--summary-statistics] [-S|--seed [INT]]+ Simulate reconstructed trees using the point process. See Gernhard, T. (2008).+ The conditioned reconstructed process. Journal of Theoretical Biology, 253(4),+ 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005+ + Available options:+ -t,--nTrees INT Number of trees (default: 10)+ -n,--nLeaves INT Number of leaves per tree (default: 5)+ -H,--height DOUBLE Fix tree height (no default)+ -M,--condition-on-mrca Do not condition on height of origin but on height of+ MRCA+ -l,--lambda DOUBLE Birth rate lambda (default: 1.0)+ -m,--mu DOUBLE Death rate mu (default: 0.9)+ -r,--rho DOUBLE Sampling probability rho (default: 1.0)+ -u,--sub-sample Perform sub-sampling; see below.+ -s,--summary-statistics Only output number of children for each branch+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text+ + Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate.+ Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character.+ Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again.+++# ELynx++Documentation of the library can be found on Hackage.+
+ elynx-tree.cabal view
@@ -0,0 +1,102 @@+cabal-version: 1.12+name: elynx-tree+version: 0.0.1+license: GPL-3+license-file: LICENSE+copyright: Dominik Schrempf (2019)+maintainer: dominik.schrempf@gmail.com+author: Dominik Schrempf+homepage: https://github.com/dschrempf/elynx#readme+bug-reports: https://github.com/dschrempf/elynx/issues+synopsis: Handle phylogenetic trees+description:+ Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.+category: Bioinformatics+build-type: Simple+extra-source-files:+ README.md+ ChangeLog.md++source-repository head+ type: git+ location: https://github.com/dschrempf/elynx++library+ exposed-modules:+ ELynx.Data.Tree.Bipartition+ ELynx.Data.Tree.BranchSupportTree+ ELynx.Data.Tree.Distance+ ELynx.Data.Tree.EvoTree+ ELynx.Data.Tree.MeasurableTree+ ELynx.Data.Tree.NamedTree+ ELynx.Data.Tree.PhyloTree+ ELynx.Data.Tree.SumStat+ ELynx.Data.Tree.Tree+ ELynx.Distribution.BirthDeath+ ELynx.Distribution.BirthDeathCritical+ ELynx.Distribution.BirthDeathCriticalNoTime+ ELynx.Distribution.BirthDeathNearlyCritical+ ELynx.Distribution.CoalescentContinuous+ ELynx.Distribution.TimeOfOrigin+ ELynx.Distribution.TimeOfOriginNearCritical+ ELynx.Distribution.Types+ ELynx.Export.Tree.Newick+ ELynx.Import.Tree.Newick+ ELynx.Simulate.Coalescent+ ELynx.Simulate.PointProcess+ hs-source-dirs: src+ other-modules:+ Paths_elynx_tree+ default-language: Haskell2010+ ghc-options: -Wall+ build-depends:+ QuickCheck >=2.13.2 && <2.14,+ base >=4.12.0.0 && <4.13,+ bytestring >=0.10.8.2 && <0.11,+ containers >=0.6.0.1 && <0.7,+ elynx-tools >=0.0.1 && <0.1,+ lifted-async >=0.10.0.4 && <0.11,+ math-functions >=0.3.1.0 && <0.4,+ megaparsec >=7.0.5 && <7.1,+ mwc-random >=0.14.0.0 && <0.15,+ optparse-applicative >=0.14.3.0 && <0.15,+ parallel >=3.2.2.0 && <3.3,+ primitive >=0.6.4.0 && <0.7,+ quickcheck-instances >=0.3.22 && <0.4,+ statistics >=0.15.0.0 && <0.16,+ transformers >=0.5.6.2 && <0.6,+ vector >=0.12.0.3 && <0.13++test-suite tree-test+ type: exitcode-stdio-1.0+ main-is: Spec.hs+ hs-source-dirs: test+ other-modules:+ ELynx.Data.Tree.BipartitionSpec+ ELynx.Data.Tree.DistanceSpec+ ELynx.Data.Tree.TreeSpec+ ELynx.Export.Tree.NewickSpec+ ELynx.Import.Tree.NewickSpec+ Paths_elynx_tree+ default-language: Haskell2010+ ghc-options: -Wall -eventlog -threaded -rtsopts -with-rtsopts=-N+ build-depends:+ QuickCheck >=2.13.2 && <2.14,+ base >=4.12.0.0 && <4.13,+ bytestring >=0.10.8.2 && <0.11,+ containers >=0.6.0.1 && <0.7,+ elynx-tools >=0.0.1 && <0.1,+ elynx-tree -any,+ hspec >=2.7.1 && <2.8,+ hspec-megaparsec >=2.0.1 && <2.1,+ lifted-async >=0.10.0.4 && <0.11,+ math-functions >=0.3.1.0 && <0.4,+ megaparsec >=7.0.5 && <7.1,+ mwc-random >=0.14.0.0 && <0.15,+ optparse-applicative >=0.14.3.0 && <0.15,+ parallel >=3.2.2.0 && <3.3,+ primitive >=0.6.4.0 && <0.7,+ quickcheck-instances >=0.3.22 && <0.4,+ statistics >=0.15.0.0 && <0.16,+ transformers >=0.5.6.2 && <0.6,+ vector >=0.12.0.3 && <0.13
+ src/ELynx/Data/Tree/Bipartition.hs view
@@ -0,0 +1,231 @@+{- |+Module : ELynx.Data.Tree.Bipartition+Description : Bipartitions on trees+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Aug 30 15:28:17 2019.++'Bipartition's are weird in that+> Bipartition x y == Bipartition y x+is True.++Also,+> Bipartition x y > Bipartition y x+is False, even when @x > y@.++That's why we have to make sure that for+> Bipartition x y+we always have @x >= y@.++-}++module ELynx.Data.Tree.Bipartition+ ( -- * The 'Bipartition' data type.+ Bipartition ()+ , bp+ , bpmap+ -- * Working with 'Bipartition's.+ , bipartitions+ , bipartitionToBranch+ , bipartitionsCombined+ ) where++-- import Data.List+import qualified Data.Map as M+import Data.Maybe+import qualified Data.Set as S+import Data.Tree++import ELynx.Data.Tree.Tree++-- | Bipartitions with 'S.Set's, since order of elements within the leaf sets+-- is not important. Also the order of the two leaf sets of the bipartition is+-- not important (see 'Eq' instance definition).+newtype Bipartition a = Bipartition (S.Set a, S.Set a)+ deriving (Show, Read)++-- instance Show a => Show (Bipartition a) where+-- show (Bipartition (x, y)) = "(" ++ showSet x ++ "|" ++ showSet y ++ ")"+-- where showSet s = intercalate "," $ map show $ S.toList s++-- | Create a bipartition from two 'S.Set's.+bp :: Ord a => S.Set a -> S.Set a -> Bipartition a+bp x y = if x >= y+ then Bipartition (x, y)+ else Bipartition (y, x)++-- | Create a bipartition from two 'S.Set's.+bpWith :: (Ord a, Ord b) => (a -> b) -> S.Set a -> S.Set a -> Bipartition b+bpWith f x y = bpmap f $ bp x y++instance (Eq a) => Eq (Bipartition a) where+ Bipartition x == Bipartition y = x == y++instance (Ord a) => Ord (Bipartition a) where+ Bipartition x `compare` Bipartition y = x `compare` y++-- | Map a function over all elements in the 'Bipartition's.+bpmap :: (Ord a, Ord b) => (a -> b) -> Bipartition a -> Bipartition b+bpmap f (Bipartition (x, y)) = bp (S.map f x) (S.map f y)++-- | Each node of a tree is root of a subtree. Get the leaves of the subtree of+-- each node.+leavesTree :: (Ord a) => Tree a -> Tree (S.Set a)+leavesTree (Node l []) = Node (S.singleton l) []+leavesTree (Node _ xs) = Node (S.unions $ map rootLabel xs') xs'+ where xs' = map leavesTree xs++-- | Loop through each tree in a forest to report the complementary leaf sets.+subForestGetLeafSets :: (Ord a)+ => S.Set a -- ^ Complementary leaf set at the stem+ -> Tree (S.Set a) -- ^ Tree with leaf set nodes+ -> [S.Set a]+subForestGetLeafSets lvsS t = lvsOthers+ where+ xs = subForest t+ nChildren = length xs+ lvsChildren = map rootLabel xs+ lvsOtherChildren = [ S.unions $ lvsS+ : take i lvsChildren ++ drop (i+1) lvsChildren+ | i <- [0 .. (nChildren - 1)] ]+ lvsOthers = map (S.union lvsS) lvsOtherChildren+++-- | Get all bipartitions.+bipartitions :: Ord a => Tree a -> S.Set (Bipartition a)+bipartitions t = if S.size (S.fromList lvs) == length lvs+ then bipartitionsUnsafe t+ else error "bipartitions: The tree contains duplicate leaves."+ where lvs = leaves t++-- | See 'bipartitions', but do not check if leaves are unique.+bipartitionsUnsafe :: Ord a => Tree a -> S.Set (Bipartition a)+bipartitionsUnsafe (Node _ [] ) = S.empty+-- If the root stem is split by degree two nodes, just go on since the root stem+-- does not induce any bipartitions.+bipartitionsUnsafe (Node _ [x]) = bipartitionsUnsafe x+-- We have rose trees, so we need to through the list of children and combine+-- each of them with the rest.+bipartitionsUnsafe t =+ S.unions [ bipartitions' lvs x+ | (lvs, x) <- zip lvsOthers (subForest lvsTree) ]+ where+ lvsTree = leavesTree t+ lvsOthers = subForestGetLeafSets S.empty lvsTree++bipartitions' :: Ord a => S.Set a -> Tree (S.Set a) -> S.Set (Bipartition a)+bipartitions' lvsStem t@(Node lvs xs)+ | S.null lvsStem = error "bipartitions': no complementing leaf set."+ -- Leaf; return a singleton map; bipartition with the leaf and the rest of the tree.+ | null xs = S.singleton $ bp lvsStem lvs+ -- For degree two nodes, pass the creation of the set on.+ | length xs == 1 = bipartitions' lvsStem (head xs)+ -- We have rose trees, so we need to through the list of children and combine+ -- each of them with the rest. Also, we use up the possible branch information+ -- 'br' and start afresh with 'mempty'.+ | otherwise = S.unions $ S.singleton (bp lvsStem lvs) : zipWith bipartitions' lvsOthers xs+ where+ lvsOthers = subForestGetLeafSets lvsStem t++-- | Each branch on a 'Tree' defines a unique 'Bipartition' of leaves. Convert a+-- tree into a 'M.Map' from each 'Bipartition' to the branch inducing the+-- respective 'Bipartition'. The information about the branch is extracted from+-- the nodes with a given function. If the tree has degree two nodes, the branch+-- values are combined; a unity element is required, and so we need the 'Monoid'+-- type class constraint. Checks if leaves are unique.+bipartitionToBranch :: (Ord a, Ord b, Monoid c)+ => (a -> b) -- ^ Value to compare on+ -> (a -> c) -- ^ Convert node to branch length+ -> Tree a -- ^ Tree to dissect+ -> M.Map (Bipartition b) c+bipartitionToBranch f g t = if S.size (S.fromList lvs) == length lvs+ then bipartitionToBranchUnsafe f g t+ else error "bipartitionToBranch: The tree contains duplicate leaves."+ where lvs = leaves t++-- | See 'bipartitionToBranch', but does not check if leaves are unique.+bipartitionToBranchUnsafe :: (Ord a, Ord b, Monoid c)+ => (a -> b) -- ^ Value to compare on+ -> (a -> c) -- ^ Convert node to branch length+ -> Tree a -- ^ Tree to dissect+ -> M.Map (Bipartition b) c+bipartitionToBranchUnsafe _ _ (Node _ [] ) = M.empty+-- If the root stem is split by degree two nodes, just go on and ignore the+-- branch information, because the stem does not induce any bipartition+-- anyways..+bipartitionToBranchUnsafe f g (Node _ [x]) = bipartitionToBranchUnsafe f g x+-- We have rose trees, so we need to through the list of children and combine+-- each of them with the rest.+bipartitionToBranchUnsafe f g t =+ M.unionsWith (<>) [ bipartitionToBranch' lvs mempty f g x+ | (lvs, x) <- zip lvsOthers (subForest nodeAndLeavesTrees) ]+ where+ lvsTree = leavesTree t+ nodeAndLeavesTrees = fromJust $ merge t lvsTree+ lvsOthers = subForestGetLeafSets S.empty lvsTree++-- We need information about the nodes, and also about the leaves of the induced+-- sub trees. Hence, we need a somewhat complicated node type @(a, S.Set a)@.+bipartitionToBranch' :: (Ord a, Ord b, Monoid c)+ => S.Set a -- ^ Complementary set of leaves+ -- towards the stem+ -> c -- ^ Maybe we have to pass along some+ -- information from above (degree two+ -- nodes)+ -> (a -> b) -- ^ Extract value to compare on+ -> (a -> c) -- ^ Extract information about branch+ -- from node+ -> Tree (a, S.Set a) -- ^ Tree containing nodes and sub+ -- tree leaf sets+ -> M.Map (Bipartition b) c+bipartitionToBranch' lvsStem br f g t@(Node l xs )+ | S.null lvsStem = error "bipartitionToBranch': no complementing leaf set."+ -- Leaf; return a singleton map; bipartition with the leaf and the rest of the tree.+ | null xs = M.singleton (bpWith f lvsStem lvsThisNode) (br <> g label)+ -- Pass the creation of the map entry on, but extend the branch.+ | length xs == 1 = bipartitionToBranch' lvsStem (br <> g label) f g (head xs)+ -- We have rose trees, so we need to through the list of children and combine+ -- each of them with the rest. Also, we use up the possible branch information+ -- 'br' and start afresh with 'mempty'.+ | otherwise = M.insert (bpWith f lvsStem lvsThisNode) (br <> g label)+ $ M.unions [ bipartitionToBranch' lvs mempty f g x+ | (lvs, x) <- zip lvsOthers xs ]+ where+ label = fst l+ lvsThisNode = snd l+ lvsOthers = subForestGetLeafSets lvsStem $ fmap snd t++-- | Get all bipartitions, but combine leaves from multifurcations. This is+-- useful to find incompatible splits. See+-- 'ELynx.Data.Tree.Distance.incompatibleSplitsDistance'. Assume that a root+-- node with three children is actually not a multifurcation (because then we+-- would have no induced bypartitions), but rather corresponds to an unrooted+-- tree.+bipartitionsCombined :: (Ord a, Show a) => Tree a -> S.Set (Bipartition a)+bipartitionsCombined t@(Node _ xs)+ | null xs = S.empty+ | length xs == 1 = bipartitionsCombined (head xs)+ -- One big multifurcation does not induce any bipartitions.+ | length xs > 3 = S.empty+ | otherwise = res+ where+ res = S.unions [ bipartitionsCombined' lvs x+ | (lvs, x) <- zip lvsOthers (subForest lvsTree) ]+ lvsTree = leavesTree t+ lvsOthers = subForestGetLeafSets S.empty lvsTree++bipartitionsCombined' :: Ord a => S.Set a -> Tree (S.Set a) -> S.Set (Bipartition a)+bipartitionsCombined' lvsStem t@(Node lvs xs)+ | S.null lvsStem = error "bipartitionsCombined': no complementing leaf set."+ | null xs = S.singleton $ bp lvsStem lvs+ | length xs == 1 = bipartitionsCombined' lvsStem (head xs)+ | length xs == 2 = S.unions $+ S.singleton (bp lvsStem lvs) : zipWith bipartitionsCombined' lvsOthers xs+ | otherwise = S.singleton $ bp lvsStem lvs+ where+ lvsOthers = subForestGetLeafSets lvsStem t
+ src/ELynx/Data/Tree/BranchSupportTree.hs view
@@ -0,0 +1,64 @@+{- |+Module : ELynx.Data.Tree.BranchSupportTree+Description : Node label with branch support+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jun 13 14:06:45 2019.++-}++module ELynx.Data.Tree.BranchSupportTree+ ( BranchSupport+ , BranchSupportLabel (..)+ , normalize+ , collapse+ ) where++import Data.List+import Data.Maybe+import Data.Tree++-- XXX : This is probably the preferred way.+-- data BranchSupport =+-- BSNothing+-- | BSInt Int+-- | BSDouble Double+-- deriving (Num)++-- | At the moment, just use 'Double'. It would be preferable to use a wrapper+-- data type that can handle 'Int' or 'Double'.+type BranchSupport = Maybe Double++-- | A label that supports branch support values.+class BranchSupportLabel a where+ -- | For now, branch support is a Double, but one could also think about+ -- bootstrap values, which are integers.+ getBranchSupport :: a -> BranchSupport+ setBranchSupport :: BranchSupport -> a -> a++apply :: BranchSupportLabel a => (Double -> Double) -> a -> a+apply f l = setBranchSupport (f <$> s) l+ where s = getBranchSupport l++-- | Normalize branch support values. The maximum branch support value will be+-- set to 1.0.+normalize :: BranchSupportLabel a => Tree a -> Tree a+normalize t = if isNothing m then t else fmap (apply (/ fromJust m)) t+ where m = maximum $ fmap getBranchSupport t++accept :: Double -> Maybe Double -> Bool+accept _ Nothing = True+accept thresh (Just s) = s > thresh++-- | Collapse branches with support lower than given value. Note, branch length+-- is ignored at the moment.+collapse :: BranchSupportLabel a => Double -> Tree a -> Tree a+collapse _ n@(Node _ []) = n+collapse thresh (Node l xs) = Node l $ map (collapse thresh) (highS ++ lowSubForest)+ where (highS, lowS) = partition (accept thresh . getBranchSupport . rootLabel) xs+ lowSubForest = concatMap subForest lowS
+ src/ELynx/Data/Tree/Distance.hs view
@@ -0,0 +1,124 @@+{- |+Module : ELynx.Data.Tree.Distance+Description : Compute distances between trees+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jun 13 17:15:54 2019.++Various distance functions for phylogenetic trees (and binary trees in general).+All trees are assumed to be UNROOTED.++-}++module ELynx.Data.Tree.Distance+ ( symmetricDistance+ , symmetricDistanceWith+ , incompatibleSplitsDistance+ , incompatibleSplitsDistanceWith+ , computePairwiseDistances+ , computeAdjacentDistances+ , branchScoreDistance+ , branchScoreDistanceWith+ ) where++import Data.List+import qualified Data.Map as M+import Data.Monoid+import qualified Data.Set as S+import Data.Tree++import ELynx.Data.Tree.Bipartition+import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.NamedTree++-- -- Difference between two 'Set's, see 'Set.difference'. Do not compare elements+-- -- directly but apply a function beforehand.+-- differenceWith :: (Ord a, Ord b) => (a -> b) -> Set.Set a -> Set.Set a -> Set.Set a+-- differenceWith f xs ys = Set.filter (\e -> f e `Set.notMember` ys') xs+-- where ys' = Set.map f ys++-- -- Symmetric difference between two 'Set's. Do not compare elements directly but+-- -- apply a function beforehand.+-- symmetricDifferenceWith :: (Ord a, Ord b) => (a -> b) -> Set.Set a -> Set.Set a -> Set.Set a+-- symmetricDifferenceWith f xs ys = xsNotInYs `Set.union` ysNotInXs+-- where+-- xsNotInYs = differenceWith f xs ys+-- ysNotInXs = differenceWith f ys xs++-- Symmetric difference between two 'Set's.+symmetricDifferenceS :: Ord a => S.Set a -> S.Set a -> S.Set a+symmetricDifferenceS xs ys = S.difference xs ys `S.union` S.difference ys xs++-- -- Symmetric difference between two 'Map's.+-- symmetricDifferenceM :: Ord k => M.Map k a -> M.Map k a -> M.Map k a+-- symmetricDifferenceM x y = M.difference x y `M.union` M.difference y x++-- | Symmetric (Robinson-Foulds) distance between two trees. Before comparing+-- the leaf labels, apply a given function. This is useful, for example, to+-- compare the labels of 'Named' trees on their names only. The tree is assumed+-- to be UNROOTED!+--+-- XXX: Comparing a list of trees with this function recomputes bipartitions.+symmetricDistanceWith :: (Ord b) => (a -> b) -> Tree a -> Tree a -> Int+symmetricDistanceWith f t1 t2 = length $ symmetricDifferenceS (bs t1) (bs t2)+ where bs t = bipartitions $ fmap f t++-- | See 'symmetricDistanceWith', but with 'id' for comparisons.+symmetricDistance :: Ord a => Tree a -> Tree a -> Int+symmetricDistance = symmetricDistanceWith id++-- | Number of incompatible splits. Similar to 'symmetricDistanceWith' but+-- merges multifurcations.+--+-- XXX: Comparing a list of trees with this function recomputes bipartitions.+incompatibleSplitsDistanceWith :: (Ord b, Show b) => (a -> b) -> Tree a -> Tree a -> Int+incompatibleSplitsDistanceWith f t1 t2 = length $ symmetricDifferenceS (ms t1) (ms t2)+ where ms t = bipartitionsCombined $ fmap f t++-- | See 'incompatibleSplitsDistanceWith', use 'id' for comparisons.+incompatibleSplitsDistance :: (Ord a, Show a) => Tree a -> Tree a -> Int+incompatibleSplitsDistance = incompatibleSplitsDistanceWith id++-- | Compute branch score distance between two trees. Before comparing the leaf+-- labels, apply a function. This is useful, for example, to compare the labels+-- of 'Named' trees on their names only. The branch information which is+-- compared to compute the distance is extracted from the nodes with a given+-- function. Assumes that the trees are UNROOTED.+--+-- XXX: Comparing a list of trees with this function recomputes bipartitions.+branchScoreDistanceWith :: (Ord a, Ord b, Floating c)+ => (a -> b) -- ^ Label to compare on+ -> (a -> c) -- ^ Branch information (e.g., length)+ -- associated with a node+ -> Tree a -> Tree a -> c+branchScoreDistanceWith f g t1 t2 = sqrt dsSquared+ where bs = bipartitionToBranch f (Sum . g)+ dBs = M.map getSum $ M.unionWith (-) (bs t1) (bs t2)+ dsSquared = foldl' (\acc e -> acc + e*e) 0 dBs++-- | See 'branchScoreDistanceWith', use 'id' for comparisons.+branchScoreDistance :: (Ord a, Measurable a, Named a) => Tree a -> Tree a -> Double+branchScoreDistance = branchScoreDistanceWith getName getLen++-- | Compute pairwise distances of a list of input trees. Use given distance+-- measure. Returns a triple, the first two elements are the indices of the+-- compared trees, the third is the distance.+computePairwiseDistances :: (a -> a -> b) -- ^ Distance function+ -> [a] -- ^ Input trees+ -> [(Int, Int, b)] -- ^ (index i, index j, distance i j)+computePairwiseDistances dist trs = [ (i, j, dist x y)+ | (i:is, x:xs) <- zip (tails [0..]) (tails trs)+ , (j, y) <- zip is xs ]++-- | Compute distances between adjacent pairs of a list of input trees. Use+-- given distance measure.+computeAdjacentDistances :: (Tree a -> Tree a -> b) -- ^ Distance function+ -> [Tree a] -- ^ Input trees+ -> [b]+computeAdjacentDistances dist trs = [ dist x y | (x, y) <- zip trs (tail trs) ]+
+ src/ELynx/Data/Tree/EvoTree.hs view
@@ -0,0 +1,43 @@+{- |+Module : ELynx.Data.Tree.EvoTree+Description : Evolutionary nodes+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 14:19:26 2019.++XXX: This module is not used.++-}++module ELynx.Data.Tree.EvoTree+ ( EvoLabel (..)+ ) where++-- | An evolutionary label has some information about where the corresponding+-- node is on the tree, and if the node is 'extant', 'extinct', 'internal', or+-- 'external'. The latter two could also be determined from the tree. This could+-- be species, genes or individuals; probably more.+class EvoLabel n where+ extant :: n -> Bool+ extinct :: n -> Bool++ internal :: n -> Bool+ internal n = not $ extant n || extinct n+ external :: n -> Bool+ external = not . internal++-- -- | Glue branches together, so that one new tree emerges. It's root node is+-- -- new, the sub-forest has to be given (a list of trees).+-- glue :: (NodeType c)+-- => PhyloLabel a b c -- ^ New root node.+-- -> [PhyloTree a b c] -- ^ Sub-forest.+-- -> PhyloTree a b c+-- glue s@(PhyloLabel _ _ n) ts+-- | extant n = error "Root node cannot be of type 'Exant'."+-- | extinct n = error "Root node cannot be of type 'Extinct'."+-- | otherwise = Node s ts
+ src/ELynx/Data/Tree/MeasurableTree.hs view
@@ -0,0 +1,98 @@+{- |+Module : ELynx.Data.Tree.MeasurableTree+Description : Functions on trees with branch lengths+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 14:16:34 2019.++-}+++module ELynx.Data.Tree.MeasurableTree+ ( Measurable (..)+ , distancesRootLeaves+ , averageDistanceRootLeaves+ , height+ , lengthenRoot+ , shortenRoot+ , summarize+ , totalBranchLength+ , normalize+ , prune+ ) where++import qualified Data.ByteString.Lazy.Char8 as L+import Data.Foldable+import Data.Tree++import ELynx.Data.Tree.Tree++-- | A 'Node' label with measurable and modifiable branch length to the parent.+class Measurable a where+ -- | Length of attached branch.+ getLen :: a -> Double+ -- | Set attached branch length.+ setLen :: Double -> a -> a++ -- | Elongate branch length.+ lengthen :: Double -> a -> a+ lengthen dl l = setLen (dl + getLen l) l++ -- | Shorten branch length.+ shorten :: Double -> a -> a+ shorten dl = lengthen (-dl)++-- | Distances from the root of a tree to its leaves.+distancesRootLeaves :: (Measurable a) => Tree a -> [Double]+distancesRootLeaves (Node l []) = [getLen l]+distancesRootLeaves (Node l f ) = concatMap (map (+ getLen l) . distancesRootLeaves) f++-- | Average distance from the root of a tree to its leaves.+averageDistanceRootLeaves :: (Measurable a) => Tree a -> Double+averageDistanceRootLeaves tr = sum ds / fromIntegral n+ where ds = distancesRootLeaves tr+ n = length ds++-- | Height of a tree. Returns 0 if the tree is empty.+height :: (Measurable a) => Tree a -> Double+height = maximum . distancesRootLeaves++-- | Lengthen the distance between root and origin.+lengthenRoot :: (Measurable a) => Double -> Tree a -> Tree a+lengthenRoot dl (Node lbl chs) = Node (lengthen dl lbl) chs++-- | Lengthen the distance between root and origin.+shortenRoot :: (Measurable a) => Double -> Tree a -> Tree a+shortenRoot dl = lengthenRoot (-dl)++-- | Summarize a tree with measureable branch lengths.+summarize :: (Measurable a) => Tree a -> L.ByteString+summarize t = L.unlines $ map L.pack+ [ "Leaves: " ++ show n ++ "."+ , "Height: " ++ show h ++ "."+ , "Average distance root to leaves: " ++ show h' ++ "."+ , "Total branch length: " ++ show b ++ "." ]+ where n = length . leaves $ t+ h = height t+ b = totalBranchLength t+ h' = sum (distancesRootLeaves t) / fromIntegral n++-- | Total branch length of a tree.+totalBranchLength :: (Measurable a) => Tree a -> Double+totalBranchLength = foldl' (\acc n -> acc + getLen n) 0++-- | Normalize tree so that sum of branch lengths is 1.0.+normalize :: (Measurable a) => Tree a -> Tree a+normalize t = fmap (\n -> setLen (getLen n / s) n) t+ where s = totalBranchLength t++-- | Prune degree 2 nodes. Add branch lengths but forget pruned node label. See+-- 'pruneWith'.+prune :: (Measurable a) => Tree a -> Tree a+prune = pruneWith f+ where f da pa = lengthen (getLen pa) da
+ src/ELynx/Data/Tree/NamedTree.hs view
@@ -0,0 +1,23 @@+{- |+Module : ELynx.Data.Tree.NamedTree+Description : Trees with named nodes+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 24 20:09:20 2019.++-}++module ELynx.Data.Tree.NamedTree+ ( Named (..)+ ) where++import qualified Data.ByteString.Lazy.Char8 as L++-- | Data types with names.+class Named a where+ getName :: a -> L.ByteString
+ src/ELynx/Data/Tree/PhyloTree.hs view
@@ -0,0 +1,89 @@+{-# LANGUAGE FlexibleInstances #-}++{- |+Module : ELynx.Data.Tree.PhyloTree+Description : Phylogenetic trees+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 16:08:54 2019.++Phylogenetic nodes have a branch length and a label.++The easiest label type is 'Int': 'PhyloIntLabel'.++Also, the 'L.ByteString' label is needed often: 'PhyloByteStringLabel'.++XXX: This is all too complicated. Maybe I should just define a standard tree object like+> data PhyloTree a = Tree (PhyloLabel a)+and that's it. Forget about type classes like Measurable, Named and so on.++-}+++module ELynx.Data.Tree.PhyloTree+ ( PhyloLabel (..)+ , PhyloIntLabel+ , PhyloByteStringLabel+ , removeBrLen+ ) where++import qualified Data.ByteString.Lazy.Builder as L+import qualified Data.ByteString.Lazy.Char8 as L+import Data.Function+import Data.Tree+import Test.QuickCheck++import ELynx.Data.Tree.BranchSupportTree+import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.NamedTree++-- | A primitive label type for phylogenetic trees with a name, possibly a+-- branch support value, and a 'Double' branch length.+data PhyloLabel a = PhyloLabel { pLabel :: a+ , pBrSup :: Maybe Double+ , pBrLen :: Double }+ deriving (Read, Show, Eq)++instance Ord a => Ord (PhyloLabel a) where+ compare = compare `on` pLabel++instance Measurable (PhyloLabel a) where+ getLen = pBrLen+ setLen l (PhyloLabel lbl s _)+ | l >= 0 = PhyloLabel lbl s l+ | otherwise = error "Branch lengths cannot be negative."++instance BranchSupportLabel (PhyloLabel a) where+ getBranchSupport = pBrSup+ setBranchSupport Nothing l = l {pBrSup = Nothing}+ setBranchSupport (Just s) l+ | s > 0 = l {pBrSup = Just s}+ | otherwise = error "Branch support cannot be negative."++instance Arbitrary a => Arbitrary (PhyloLabel a) where+ arbitrary = PhyloLabel+ <$> arbitrary+ <*> (Just <$> choose (0, 100))+ <*> choose (0, 10)++-- | Tree node with 'Int' label.+type PhyloIntLabel = PhyloLabel Int++instance Named PhyloIntLabel where+ getName = L.toLazyByteString . L.intDec . pLabel++-- | Tree node with 'L.ByteString' label. Important for parsing+-- 'ELynx.Import.Tree.Newick' files.+type PhyloByteStringLabel = PhyloLabel L.ByteString++instance Named PhyloByteStringLabel where+ getName = pLabel++-- | Remove branch lengths from tree.+removeBrLen :: Tree (PhyloLabel a) -> Tree a+removeBrLen = fmap pLabel
+ src/ELynx/Data/Tree/SumStat.hs view
@@ -0,0 +1,57 @@+{- |+Module : ELynx.Data.Tree.SumStat+Description : Summary statistics for phylogenetic trees+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu May 17 14:05:45 2018.++-}++module ELynx.Data.Tree.SumStat+ ( BrLnNChildren+ , NChildSumStat+ , toNChildSumStat+ , formatNChildSumStat+ ) where++import qualified Data.ByteString.Builder as L+import qualified Data.ByteString.Lazy.Char8 as L+import Data.Monoid ((<>))+import Data.Tree+import ELynx.Data.Tree.MeasurableTree++-- This may be too specific, but I only change it if necessary. E.g., use types+-- a (for node labels) and b (for branch lengths).++-- | Pair of branch length with number of extant children.+type BrLnNChildren = (Double, Int)++-- | Possible summary statistic of phylogenetic trees. A list of tuples+-- (BranchLength, NumberOfExtantChildrenBelowThisBranch).+type NChildSumStat = [BrLnNChildren]++-- | Format the summary statistics in the following form:+-- @+-- nLeaves1 branchLength1+-- nLeaves2 branchLength2+-- ....+formatNChildSumStat :: NChildSumStat -> L.ByteString+formatNChildSumStat s = L.toLazyByteString . mconcat $ map formatNChildSumStatLine s++formatNChildSumStatLine :: BrLnNChildren -> L.Builder+formatNChildSumStatLine (l, n) = L.intDec n+ <> L.char8 ' '+ <> L.doubleDec l+ <> L.char8 '\n'++-- | Compute NChilSumStat for a phylogenetic tree.+toNChildSumStat :: Measurable a => Tree a -> NChildSumStat+toNChildSumStat (Node lbl []) = [(getLen lbl, 1)]+toNChildSumStat (Node lbl ts) = (getLen lbl, sumCh) : concat nChSS+ where nChSS = map toNChildSumStat ts+ sumCh = sum $ map (snd . head) nChSS
+ src/ELynx/Data/Tree/Tree.hs view
@@ -0,0 +1,143 @@+{- |+Module : ELynx.Data.Tree.Tree+Description : Functions related to phylogenetic trees+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 09:57:29 2019.++Comment about nomenclature:++- In "Data.Tree", a 'Tree' is defined as++@+data Tree a = Node {+ rootLabel :: a, -- ^ label value+ subForest :: Forest a -- ^ zero or more child trees+ }+@++This means, that the word 'Node' is reserved for the constructor of a tree, and+that a 'Node' has a label and a children. The terms 'Node' and /label/ are not+to be confused.++- Branches have /lengths/. For example, a branch length can be a distances or a+ time.++NOTE: Trees in this library are all rooted. Unrooted trees can be treated with a+rooted data structure equally well. However, in these cases, some functions have+no meaning. For example, functions measuring the distance from the root to the+leaves (the height of a rooted tree).++NOTE: Try fgl or alga. Use functional graph library for unrooted trees see also+the book /Haskell high performance programming from Thomasson/, p. 344.++-}+++module ELynx.Data.Tree.Tree+ ( singleton+ , degree+ , leaves+ , subTree+ , subSample+ , nSubSamples+ , pruneWith+ , merge+ , tZipWith+ ) where++import Control.Monad+import Control.Monad.Primitive+import Data.Maybe+import qualified Data.Sequence as Seq+import qualified Data.Set as Set+import Data.Traversable+import Data.Tree+import System.Random.MWC++import ELynx.Tools.Random++-- | The simplest tree. Usually an extant leaf.+singleton :: a -> Tree a+singleton l = Node l []++-- | The degree of the root node of a tree.+degree :: Tree a -> Int+degree = (+ 1) . length . subForest++-- | Get leaves of tree.+leaves :: Tree a -> [a]+leaves (Node l []) = [l]+leaves (Node _ f) = concatMap leaves f++-- -- | Check if ancestor and daughters of first tree are a subset of the ancestor+-- -- and daughters of the second tree. Useful to test if, e.g., speciations agree.+-- rootNodesAgreeWith :: (Ord c) => (a -> c) -> Tree a -> (b -> c) -> Tree b -> Bool+-- rootNodesAgreeWith f s g t =+-- f (rootLabel s) == g (rootLabel t) &&+-- S.fromList sDs `S.isSubsetOf` S.fromList tDs+-- where sDs = map (f . rootLabel) (subForest s)+-- tDs = map (g . rootLabel) (subForest t)++-- | Get subtree of 'Tree' with nodes satisfying predicate. Return 'Nothing', if+-- no leaf satisfies predicate. At the moment: recursively, for each child, take+-- the child if any leaf in the child satisfies the predicate.+subTree :: (a -> Bool) -> Tree a -> Maybe (Tree a)+subTree p leaf@(Node lbl [])+ | p lbl = Just leaf+ | otherwise = Nothing+subTree p (Node lbl chs) = if null subTrees+ then Nothing+ else Just $ Node lbl subTrees+ where subTrees = mapMaybe (subTree p) chs++-- XXX: If module gets too big, move the sampling functions into their own+-- module.+-- | Extract a random sub tree with N leaves of a tree with M leaves, where M>N+-- (otherwise error). The complete list of leaves (names are assumed to be+-- unique) has to be provided as a 'Seq.Seq', and a 'Seq.Set', so that we have+-- fast sub-sampling as well as lookup and don't have to recompute them when+-- many sub-samples are requested.+subSample :: (PrimMonad m, Ord a)+ => Seq.Seq a -> Int -> Tree a -> Gen (PrimState m) -> m (Maybe (Tree a))+subSample lvs n tree g+ | Seq.length lvs < n = error "Given list of leaves is shorter than requested number of leaves."+ | otherwise = do+ sampledLs <- sample lvs n g+ let ls = Set.fromList sampledLs+ return $ subTree (`Set.member` ls) tree++-- | See 'subSample', but n times.+nSubSamples :: (PrimMonad m, Ord a)+ => Int -> Seq.Seq a -> Int -> Tree a -> Gen (PrimState m) -> m [Maybe (Tree a)]+nSubSamples nS lvs nL tree g = replicateM nS $ subSample lvs nL tree g++-- | Prune degree 2 inner nodes. The information stored in a pruned node can be+-- used to change the daughter node. To discard this information, use,+-- @pruneWith const tree@, otherwise @pruneWith (\daughter parent -> combined)+-- tree@.+pruneWith :: (a -> a -> a) -> Tree a -> Tree a+pruneWith _ n@(Node _ []) = n+pruneWith f (Node paLbl [ch]) = let lbl = f (rootLabel ch) paLbl+ in pruneWith f $ Node lbl (subForest ch)+pruneWith f (Node paLbl chs) = Node paLbl (map (pruneWith f) chs)++-- | Merge two trees with the same topology. Returns 'Nothing' if the topologies are different.+merge :: Tree a -> Tree b -> Maybe (Tree (a, b))+merge (Node l xs) (Node r ys) =+ if length xs == length ys+ -- I am proud of that :)).+ then zipWithM merge xs ys >>= Just . Node (l, r)+ else Nothing++-- | Apply a function with different effect on each node to a 'Traversable'.+-- Based on https://stackoverflow.com/a/41523456.+tZipWith :: Traversable t => (a -> b -> c) -> [a] -> t b -> Maybe (t c)+tZipWith f xs = sequenceA . snd . mapAccumL pair xs+ where pair [] _ = ([], Nothing)+ pair (y:ys) z = (ys, Just (f y z))
+ src/ELynx/Distribution/BirthDeath.hs view
@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.BirthDeath+ Description : Birth and death distribution+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the values of the point process such that it corresponds to+reconstructed trees under the birth and death process.++-}++module ELynx.Distribution.BirthDeath+ ( BirthDeathDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the values of the point process such that it corresponds to+-- a reconstructed tree of the birth and death process.+data BirthDeathDistribution = BDD+ { bddTOr :: Time -- ^ Time to origin of the tree.+ , bddLa :: Rate -- ^ Birth rate.+ , bddMu :: Rate -- ^ Death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution BirthDeathDistribution where+ cumulative = cumulative++-- | Cumulative distribution function Eq. (3).+cumulative :: BirthDeathDistribution -> Time -> Double+cumulative (BDD t l m) x+ | x <= 0 = 0+ | x > t = 1+ | otherwise = t1 * t2+ where d = l - m+ t1 = (1.0 - exp (-d*x)) / (l - m*exp(-d*x))+ t2 = (l - m*exp(-d*t)) / (1.0 - exp(-d*t))++instance D.ContDistr BirthDeathDistribution where+ density = density+ quantile = quantile++-- | Density function Eq. (2).+density :: BirthDeathDistribution -> Time -> Double+density (BDD t l m) x+ | x < 0 = 0+ | x > t = 0+ | otherwise = d**2 * t1 * t2+ where d = l - m+ t1 = exp (-d*x) / ((l - m*exp(-d*x))**2)+ t2 = (l - m*exp(-d*t)) / (1.0 - exp(-d*t))++-- | Inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: BirthDeathDistribution -> Double -> Time+quantile (BDD t l m) p+ | p >= 0 && p <= 1 = res+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1] range. Got: " ++ show p ++ "."+ where d = l - m+ t2 = (l - m*exp(-d*t)) / (1.0 - exp(-d*t))+ res = (-1.0/d) * log ((1.0 - p*l/t2)/(1.0 - p*m/t2))++instance D.ContGen BirthDeathDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/BirthDeathCritical.hs view
@@ -0,0 +1,76 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.BirthDeathCritical+ Description : Birth and death distribution+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the values of the point process such that it corresponds to+reconstructed trees under the birth and death process; critical birth and death+process with lambda=mu.++-}++module ELynx.Distribution.BirthDeathCritical+ ( BirthDeathCriticalDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the values of the point process such that it corresponds to+-- a reconstructed tree of the birth and death process.+data BirthDeathCriticalDistribution = BDCD+ { bdcdTOr :: Time -- ^ Time to origin of the tree.+ , bdcdLa :: Rate -- ^ Birth and death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution BirthDeathCriticalDistribution where+ cumulative = cumulative++-- | Cumulative distribution function section 2.1.2, second formula.+cumulative :: BirthDeathCriticalDistribution -> Time -> Double+cumulative (BDCD t l) x+ | x <= 0 = 0+ | x > t = 1+ | otherwise = x / (1.0 + l * x) * (1.0 + l * t) / t++instance D.ContDistr BirthDeathCriticalDistribution where+ density = density+ quantile = quantile++-- | Density function section 2.1.2, first formula.+density :: BirthDeathCriticalDistribution -> Time -> Double+density (BDCD t l) x+ | x < 0 = 0+ | x > t = 0+ | otherwise = (1.0 + l * t) / (t * (1.0 + l * x)**2)++-- | Inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: BirthDeathCriticalDistribution -> Double -> Time+quantile (BDCD t l) p+ | p >= 0 && p <= 1 = res+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1] range. Got: " ++ show p ++ "."+ where res = p * t / (1 + l*t - l*p*t)++instance D.ContGen BirthDeathCriticalDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/BirthDeathCriticalNoTime.hs view
@@ -0,0 +1,73 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.BirthDeathCriticalNoTime+ Description : Birth and death distribution+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the values of the point process such that it corresponds to+reconstructed trees under the birth and death process; critical birth and death+process with lambda=mu.++-}++module ELynx.Distribution.BirthDeathCriticalNoTime+ ( BirthDeathCriticalNoTimeDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the values of the point process such that it corresponds to+-- a reconstructed tree of the birth and death process.+newtype BirthDeathCriticalNoTimeDistribution = BDCNTD+ { bdcntdLa :: Rate -- ^ Birth and death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution BirthDeathCriticalNoTimeDistribution where+ cumulative = cumulative++-- | Cumulative distribution function section 2.1.2, second formula.+cumulative :: BirthDeathCriticalNoTimeDistribution -> Time -> Double+cumulative (BDCNTD l) x+ | x <= 0 = 0+ | otherwise = x * l / (1.0 + x * l)++instance D.ContDistr BirthDeathCriticalNoTimeDistribution where+ density = density+ quantile = quantile++-- | Density function section 2.1.2, first formula; t cancels out because it is+-- expected to be much larger than 1.0; because t \in [0, \infty].+density :: BirthDeathCriticalNoTimeDistribution -> Time -> Double+density (BDCNTD l) x+ | x < 0 = 0+ | otherwise = l / ((1.0 + x * l)**2)++-- | Inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: BirthDeathCriticalNoTimeDistribution -> Double -> Time+quantile (BDCNTD l) p+ | p >= 0 && p <= 1 = p / (l - l*p)+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1]. Got: " ++ show p ++ "."++instance D.ContGen BirthDeathCriticalNoTimeDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/BirthDeathNearlyCritical.hs view
@@ -0,0 +1,89 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.BirthDeathNearlyCritical+ Description : Birth and death distribution+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the values of the point process such that it corresponds to+reconstructed trees under the birth and death process; nearly critical birth and+death process with lambda~mu.++Basically, this is a Taylor expansion of Eq. (2) and Eq. (3).++-}++module ELynx.Distribution.BirthDeathNearlyCritical+ ( BirthDeathNearlyCriticalDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the values of the point process such that it corresponds to+-- a reconstructed tree of the birth and death process.+data BirthDeathNearlyCriticalDistribution = BDNCD+ { bdncdTOr :: Time -- ^ Time to origin of the tree.+ , bdncdLa :: Rate -- ^ Birth and death rate.+ , bdncdMu :: Rate -- ^ Birth and death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution BirthDeathNearlyCriticalDistribution where+ cumulative = cumulative++-- | Cumulative distribution function section 2.1.2, second formula.+cumulative :: BirthDeathNearlyCriticalDistribution -> Time -> Double+cumulative (BDNCD t l m) s+ | s <= 0 = 0+ | s > t = 1+ | otherwise = o0 + o1+ where o0 = s * (1.0 + t*l) / t / (1.0 + s*l)+ o1 = (-s*s + s*t) * (m - l) / (2.0*t * (1.0 + s*l)**2)++instance D.ContDistr BirthDeathNearlyCriticalDistribution where+ density = density+ quantile = quantile++-- | Density function section 2.1.2, first formula.+density :: BirthDeathNearlyCriticalDistribution -> Time -> Double+density (BDNCD t l m) s+ | s < 0 = 0+ | s > t = 0+ | otherwise = o0 + o1+ where+ o0 = (1.0 + t*l) / (t * (1.0 + s*l)**2)+ o1 = (-2.0*s + t - s*t*l) * (m - l) / (2.0*t * (1.0 + s*l)**3)++-- | Inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: BirthDeathNearlyCriticalDistribution -> Double -> Time+quantile (BDNCD t l m) p+ | p >= 0 && p <= 1 = res+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1] range. Got: " ++ show p ++ "."+ where+ den = l*(-3.0 + 2.0*t*(-1.0+p)*l)+m+ t1 = (2.0 + t*(l - 4.0*p*l + m)) / den+ t2Nom = 4.0 + t*(l*(4.0 + t*l + 8.0*p*(1.0 + t*l)) + 2.0*(2.0 + t*l - 4.0*p*(1.0 + t*l))*m + t*m*m)+ t2 = t2Nom / (den**2)+ res = 0.5 * (t1 + sqrt t2)++instance D.ContGen BirthDeathNearlyCriticalDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/CoalescentContinuous.hs view
@@ -0,0 +1,26 @@+{- |+Module : ELynx.Distribution.CoalescentContinuous+Description : Distribution of coalescent times+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Wed May 16 12:40:45 2018.++-}++module ELynx.Distribution.CoalescentContinuous+ ( coalescentDistributionCont+ ) where++import Numeric.SpecFunctions (choose)+import Statistics.Distribution.Exponential++-- | Distribution of the next coalescent event for a number of samples @n@. The+-- time is measured in units of effective number of population size.+coalescentDistributionCont :: Int -- ^ Sample size.+ -> ExponentialDistribution+coalescentDistributionCont n = exponential (choose n 2)
+ src/ELynx/Distribution/TimeOfOrigin.hs view
@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.TimeOfOrigin+ Description : Distribution of time of origin for birth and death trees+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the time of origin for birth and death trees. See corollary 3.3+in the paper cited above.++-}++module ELynx.Distribution.TimeOfOrigin+ ( TimeOfOriginDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the time of origin for a phylogenetic tree evolving under+-- the birth and death process and conditioned on observing n leaves today.+data TimeOfOriginDistribution = TOD+ { todTN :: Int -- ^ Number of leaves of the tree.+ , todLa :: Rate -- ^ Birth rate.+ , todMu :: Rate -- ^ Death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution TimeOfOriginDistribution where+ cumulative = cumulative++-- | Cumulative distribution function Corollary 3.3.+cumulative :: TimeOfOriginDistribution -> Time -> Double+cumulative (TOD n l m) x+ | x <= 0 = 0+ | otherwise = te ** fromIntegral n+ where d = l - m+ te = l * (1.0 - exp (-d*x)) / (l - m*exp(-d*x))++instance D.ContDistr TimeOfOriginDistribution where+ density = density+ quantile = quantile++-- | The density function Eq. (5).+density :: TimeOfOriginDistribution -> Time -> Double+density (TOD nn l m) x+ | x < 0 = 0+ | otherwise = n * l**n * d**2 * t1**(n-1.0) * ex / (t2**(n+1.0))+ where d = l - m+ n = fromIntegral nn+ ex = exp(-d*x)+ t1 = 1.0 - ex+ t2 = l - m*ex++-- | The inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: TimeOfOriginDistribution -> Double -> Time+quantile (TOD n' l m) p+ | p >= 0 && p <= 1 = -1.0/d * log(t1/t2)+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1] range. Got: " ++ show p ++ "."+ where d = l - m+ n = fromIntegral n'+ t1 = l*(1.0-p**(1.0/n))+ t2 = l - p**(1.0/n)*m++instance D.ContGen TimeOfOriginDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/TimeOfOriginNearCritical.hs view
@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE DeriveGeneric #-}++{- |+ Module : ELynx.Distribution.TimeOfOriginNearCritical+ Description : Distribution of time of origin for birth and death trees+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++Distribution of the time of origin for birth and death trees. See corollary 3.3+in the paper cited above.++-}++module ELynx.Distribution.TimeOfOriginNearCritical+ ( TimeOfOriginNearCriticalDistribution(..)+ , cumulative+ , density+ , quantile+ ) where++import Data.Data (Data, Typeable)+import GHC.Generics (Generic)+import qualified Statistics.Distribution as D++import ELynx.Distribution.Types++-- | Distribution of the time of origin for a phylogenetic tree evolving under+-- the birth and death process and conditioned on observing n leaves today.+data TimeOfOriginNearCriticalDistribution = TONCD+ { todTN :: Int -- ^ Number of leaves of the tree.+ , todLa :: Rate -- ^ Birth rate.+ , todMu :: Rate -- ^ Death rate.+ } deriving (Eq, Typeable, Data, Generic)++instance D.Distribution TimeOfOriginNearCriticalDistribution where+ cumulative = cumulative++-- | Cumulative distribution function; see Mathematica notebook.+cumulative :: TimeOfOriginNearCriticalDistribution -> Time -> Double+cumulative (TONCD n' l m) t+ | t <= 0 = 0+ | otherwise = t1 + t2+ where d = l - m+ n = fromIntegral n'+ t1 = (t*l/(1.0 + t*l)) ** n+ t2 = (n * t * t1) * d / (2.0 * (1.0 + t*l))++instance D.ContDistr TimeOfOriginNearCriticalDistribution where+ density = density+ quantile = quantile++-- | The density function Eq. (5).+density :: TimeOfOriginNearCriticalDistribution -> Time -> Double+density (TONCD n' l m) t+ | t < 0 = 0+ | otherwise = nom/den+ where n = fromIntegral n'+ nom = n * (t*l/(1+t*l))**n * (2+(3+n)*t*l - (1+n)*t*m)+ den = 2*t*(1+t*l)**2++-- | The inverted cumulative probability distribution 'cumulative'. See also+-- 'D.ContDistr'.+quantile :: TimeOfOriginNearCriticalDistribution -> Double -> Time+quantile (TONCD n' l m) p+ | p >= 0 && p <= 1 = t1 + t2nom/t2den+ | otherwise =+ error $ "PointProcess.quantile: p must be in [0,1] range. Got: " ++ show p ++ "."+ where n = fromIntegral n'+ t1 = - p**(1/n)/((-1+p**(1/n))*l)+ t2nom = p**(2/n)*(m-l)+ t2den = 2*(-1+p**(1/n))**2 * l**2++instance D.ContGen TimeOfOriginNearCriticalDistribution where+ genContVar = D.genContinuous
+ src/ELynx/Distribution/Types.hs view
@@ -0,0 +1,27 @@+{- |+Module : ELynx.Distribution.Types+Description : Data types for distributions on trees+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Wed May 16 12:21:57 2018.++-}+++module ELynx.Distribution.Types+ ( Time+ , Rate+ ) where++-- | Branch lengths are measured in time.+type Time = Double++-- | Birth or death rates.+type Rate = Double++
+ src/ELynx/Export/Tree/Newick.hs view
@@ -0,0 +1,62 @@+{- |+Module : ELynx.Export.Tree.Newick+Description : Export tree objects to Newick format+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 13:51:47 2019.++Parts of the code are from https://hackage.haskell.org/package/BiobaseNewick.++See nomenclature in 'ELynx.Data.Tree.Tree'.++-}++module ELynx.Export.Tree.Newick+ ( toNewick+ -- , toNewickPhyloIntTree+ -- , toNewickPhyloByteStringTree+ ) where++import qualified Data.ByteString.Lazy.Builder as L+import qualified Data.ByteString.Lazy.Char8 as L+import Data.List (intersperse)+-- import Data.Maybe+import Data.Tree++import ELynx.Data.Tree.BranchSupportTree+import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.NamedTree+-- import ELynx.Data.Tree.PhyloTree+import ELynx.Tools.ByteString (c2w)++-- | General conversion of a tree into a Newick 'L.Bytestring'. Use provided+-- functions to extract node labels and branch lengths builder objects. See also+-- Biobase.Newick.Export.+toNewick :: (Named a, Measurable a, BranchSupportLabel a) => Tree a -> L.ByteString+toNewick t =+ L.toLazyByteString $ go t <> L.word8 (c2w ';')+ where+ go (Node l []) = lbl l+ go (Node l ts) = L.word8 (c2w '(')+ <> mconcat (intersperse (L.word8 $ c2w ',') $ map go ts)+ <> L.word8 (c2w ')') <> brSup l+ <> lbl l+ lbl l = L.lazyByteString (getName l)+ <> L.word8 (c2w ':')+ <> L.doubleDec (getLen l)+ brSup l = maybe mempty L.doubleDec (getBranchSupport l)++-- -- | Convenience function for exporting trees with 'Int' labels and 'Double'+-- -- branch lengths.+-- toNewickPhyloIntTree :: Tree PhyloIntLabel -> L.ByteString+-- toNewickPhyloIntTree = toNewickWith (L.intDec . pLabel) (L.doubleDec . pBrLen)++-- -- | Convenience function for exporting trees with 'L.ByteString' labels and+-- -- 'Double' branch lengths.+-- toNewickPhyloByteStringTree :: Tree PhyloByteStringLabel -> L.ByteString+-- toNewickPhyloByteStringTree = toNewickWith (L.lazyByteString . pLabel) (L.doubleDec . pBrLen)
+ src/ELynx/Import/Tree/Newick.hs view
@@ -0,0 +1,110 @@+{- |+Module : ELynx.Import.Tree.Newick+Description : Import Newick trees+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Jan 17 14:56:27 2019.++Code partly taken from Biobase.Newick.Import.++[Specifications](http://evolution.genetics.washington.edu/phylip/newicktree.html)++- In particular, no conversion from _ to (space) is done right now.++-}+++module ELynx.Import.Tree.Newick+ ( Parser+ , newick+ , manyNewick+ , forest+ , leaf+ , node+ , name+ , branchLength+ ) where++import qualified Data.ByteString.Lazy as L+import Data.Tree+import Data.Void+import Data.Word+import Text.Megaparsec+import Text.Megaparsec.Byte+import Text.Megaparsec.Byte.Lexer (decimal, float)++import ELynx.Data.Tree.PhyloTree+import ELynx.Tools.ByteString (c2w)++-- | Shortcut.+type Parser = Parsec Void L.ByteString++-- | Parse many Newick trees.+manyNewick :: Parser [Tree PhyloByteStringLabel]+manyNewick = some (newick <* space) <* eof <?> "manyNewick"++-- | Parse a Newick tree.+newick :: Parser (Tree PhyloByteStringLabel)+newick = tree <* char (c2w ';') <?> "newick"++tree :: Parser (Tree PhyloByteStringLabel)+tree = space *> (branched <|> leaf) <?> "tree"++branched :: Parser (Tree PhyloByteStringLabel)+branched = do+ f <- forest+ s <- branchSupport+ n <- node+ <?> "branched"+ let n' = n {pBrSup = s}+ return $ Node n' f++-- | A 'forest' is a set of trees separated by @,@ and enclosed by parentheses.+forest :: Parser [Tree PhyloByteStringLabel]+forest = do+ _ <- char (c2w '(')+ f <- tree `sepBy1` char (c2w ',')+ _ <- char (c2w ')')+ <?> "forest"+ return f++branchSupport :: Parser (Maybe Double)+branchSupport = optional $ try float <|> try decimalAsDouble++-- | A 'leaf' is a 'node' without children.+leaf :: Parser (Tree PhyloByteStringLabel)+leaf = do+ n <- node+ <?> "leaf"+ return $ Node n []++-- | A 'node' has a name and a 'branchLength'.+node :: Parser PhyloByteStringLabel+node = do+ n <- name+ b <- branchLength+ <?> "node"+ return $ PhyloLabel n Nothing b++checkNameCharacter :: Word8 -> Bool+checkNameCharacter c = c `notElem` map c2w " :;()[],"++-- | A name can be any string of printable characters except blanks, colons,+-- semicolons, parentheses, and square brackets (and commas).+name :: Parser L.ByteString+name = L.pack <$> many (satisfy checkNameCharacter) <?> "name"++-- | Branch lengths default to 0.+branchLength :: Parser Double+branchLength = char (c2w ':') *> branchLengthGiven <|> pure 0 <?> "branchLength"++branchLengthGiven :: Parser Double+branchLengthGiven = try float <|> decimalAsDouble++decimalAsDouble :: Parser Double+decimalAsDouble = fromIntegral <$> (decimal :: Parser Int)
+ src/ELynx/Simulate/Coalescent.hs view
@@ -0,0 +1,62 @@+{- |+Module : ELynx.Simulate.Coalescent+Description : Generate coalescent trees+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Wed May 16 13:13:11 2018.++-}+++module ELynx.Simulate.Coalescent+ ( simulate+ ) where++import Control.Monad.Primitive+import Data.Tree+import Statistics.Distribution+import System.Random.MWC++import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.PhyloTree+import ELynx.Data.Tree.Tree+import ELynx.Distribution.CoalescentContinuous++-- | Simulate a coalescent tree with @n@ leaves. The branch lengths are in units+-- of effective population size.+simulate :: (PrimMonad m)+ => Int -- ^ Number of leaves.+ -> Gen (PrimState m)+ -> m (Tree PhyloIntLabel)+simulate n = simulate' n 0 trs+ where trs = [ singleton (PhyloLabel i Nothing 0.0) | i <- [0..n-1] ]++simulate' :: (PrimMonad m)+ => Int+ -> Int+ -> [Tree PhyloIntLabel]+ -> Gen (PrimState m)+ -> m (Tree PhyloIntLabel)+simulate' n a trs g+ | n <= 0 = error "Cannot construct trees without leaves."+ | n == 1 && length trs /= 1 = error "Too many trees provided."+ | n == 1 && length trs == 1 = return $ head trs+ | otherwise =+ do+ -- Indices of the leaves to join will be i-1 and i.+ i <- uniformR (1, n-1) g+ -- The time of the coalescent event.+ t <- genContVar (coalescentDistributionCont n) g+ let trs' = map (lengthenRoot t) trs -- Move time 't' up on the tree.+ tl = trs' !! (i-1)+ tr = trs' !! i+ -- Join the two chosen trees.+ tm = Node (PhyloLabel a Nothing 0.0) [tl, tr]+ -- Take the trees on the left, the merged tree, and the trees on the right.+ trs'' = take (i-1) trs' ++ [tm] ++ drop (i+1) trs'+ simulate' (n-1) a trs'' g
+ src/ELynx/Simulate/PointProcess.hs view
@@ -0,0 +1,233 @@+{-# LANGUAGE BangPatterns #-}++{- |+ Module : ELynx.Simulate.PointProcess+ Description : Point process and functions+ Copyright : (c) Dominik Schrempf 2018+ License : GPL-3++ Maintainer : dominik.schrempf@gmail.com+ Stability : unstable+ Portability : portable++Creation date: Tue Feb 13 13:16:18 2018.++See Gernhard, T. (2008). The conditioned reconstructed process. Journal of+Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005.++The point process can be used to simulate reconstructed trees under the birth+and death process.++-}++module ELynx.Simulate.PointProcess+ ( PointProcess(..)+ , TimeSpec+ , simulate+ , toReconstructedTree+ , simulateReconstructedTree+ , simulateNReconstructedTrees+ ) where++import Control.Monad+import Control.Monad.Primitive+import Data.List (mapAccumL)+import Data.Tree+import qualified Statistics.Distribution as D (genContVar)+import System.Random.MWC++import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.PhyloTree+import ELynx.Data.Tree.Tree+import ELynx.Distribution.BirthDeath+import ELynx.Distribution.BirthDeathCritical+import ELynx.Distribution.BirthDeathCriticalNoTime+import ELynx.Distribution.BirthDeathNearlyCritical+import ELynx.Distribution.TimeOfOrigin+import ELynx.Distribution.TimeOfOriginNearCritical+import ELynx.Distribution.Types+import ELynx.Tools.Equality+import ELynx.Tools.List++epsNearCriticalPointProcess :: Double+epsNearCriticalPointProcess = 1e-5++epsNearCriticalTimeOfOrigin :: Double+epsNearCriticalTimeOfOrigin = 1e-8++-- | A __point process__ for \(n\) points and of age \(t_{or}\) is defined as+-- follows. Draw $n$ points on the horizontal axis at \(1,2,\ldots,n\). Pick+-- \(n-1\) points at locations \((i+1/2, s_i)\), \(i=1,2,\ldots,n-1\);+-- \(0 < s_i < t_{or}\). There is a bijection between (ranked) oriented trees+-- and the point process. Usually, a will be 'String' (or 'Int') and b will be+-- 'Double'.+data PointProcess a b = PointProcess+ { points :: ![a]+ , values :: ![b]+ , origin :: !b } deriving (Read, Show, Eq)++-- | If nothing, sample time of origin from respective distribution. If time is+-- given, we need to know if we condition on the time of origin, or the time of+-- the most recent common ancestor (MRCA).+type TimeSpec = Maybe (Time, Bool)++-- | Sample a point process using the 'BirthDeathDistribution'. The names of the+-- points will be integers.+simulate :: (PrimMonad m)+ => Int -- ^ Number of points (samples)+ -> TimeSpec -- ^ Time of origin or MRCA+ -> Rate -- ^ Birth rate+ -> Rate -- ^ Death rate+ -> Gen (PrimState m) -- ^ Generator (see 'System.Random.MWC')+ -> m (PointProcess Int Double)+-- No time of origin given. We also don't need to take care of the conditioning+-- (origin or MRCA).+simulate n Nothing l m g+ -- XXX. There is no formula for the over-critical process.+ | m > l = error "Time of origin distribution formula not available when mu > lambda. Please specify height for the moment."+ -- For the critical process, we have no idea about the time of origin, but can+ -- use a specially derived distribution.+ | m =~= l = do+ !vs <- replicateM (n-1) (D.genContVar (BDCNTD l) g)+ -- XXX: The length of the root branch will be 0.+ let t = maximum vs+ return $ PointProcess [0..(n-1)] vs t+ -- For the near critical process, we use a special distribution.+ | abs (m-l) <= epsNearCriticalTimeOfOrigin = do+ t <- D.genContVar (TONCD n l m) g+ simulate n (Just (t, False)) l m g+ -- For a sub-critical branching process, we can use the formula from Tanja Stadler.+ | otherwise = do+ t <- D.genContVar (TOD n l m) g+ simulate n (Just (t, False)) l m g+-- Time of origin is given.+simulate n (Just (t, c)) l m g+ | n < 1 = error "Number of samples needs to be one or larger."+ | t < 0.0 = error "Time of origin needs to be positive."+ | l < 0.0 = error "Birth rate needs to be positive."+ -- See Stadler, T., & Steel, M. (2019). Swapping birth and death: symmetries+ -- and transformations in phylodynamic models. , (), .+ -- http://dx.doi.org/10.1101/494583. Should be possible now.+ -- -- | m < 0.0 = error "Death rate needs to be positive."+ -- Now, we have three different cases.+ -- 1. The critical branching process.+ -- 2. The near critical branching process.+ -- 3. Normal values :).+ | (m =~= l) && not c = do+ !vs <- replicateM (n-1) (D.genContVar (BDCD t l) g)+ return $ PointProcess [0..(n-1)] vs t+ | (abs (m - l) <= epsNearCriticalPointProcess) && not c = do+ !vs <- replicateM (n-1) (D.genContVar (BDNCD t l m) g)+ return $ PointProcess [0..(n-1)] vs t+ | not c = do+ !vs <- replicateM (n-1) (D.genContVar (BDD t l m) g)+ return $ PointProcess [0..(n-1)] vs t+ | (m =~= l) && c = do+ !vs <- replicateM (n-2) (D.genContVar (BDCD t l) g)+ vs' <- randomInsert t vs g+ return $ PointProcess [0..(n-1)] vs' t+ | (abs (m - l) <= epsNearCriticalPointProcess) && c = do+ !vs <- replicateM (n-2) (D.genContVar (BDNCD t l m) g)+ vs' <- randomInsert t vs g+ return $ PointProcess [0..(n-1)] vs' t+ | c = do+ !vs <- replicateM (n-2) (D.genContVar (BDD t l m) g)+ vs' <- randomInsert t vs g+ return $ PointProcess [0..(n-1)] vs' t+ | otherwise = error "simulate: Fell through guard, this should never happen."++-- | Sort the values of a point process and their indices to be (the indices+-- that they will have while creating the tree).+sort :: (Ord b) => PointProcess a b -> ([b], [Int])+sort (PointProcess _ vs _) = (vsSorted, isSorted)+ where vsIsSorted = sortWithIndices vs+ vsSorted = map fst vsIsSorted+ isSorted = flattenIndices $ map snd vsIsSorted++-- Decrement indices that are above the one that is merged.+flattenIndices :: [Int] -> [Int]+flattenIndices is = snd $ mapAccumL fAcc [] is++-- The accumulating function. Count the number of indices which are before the+-- current index and lower than the current index.+fAcc :: [Int] -> Int -> ([Int], Int)+fAcc is i = (i:is, i')+ where i' = i - length (filter (<i) is)++-- | See 'simulateReconstructedTree', but n times.+simulateNReconstructedTrees+ :: (PrimMonad m)+ => Int -- ^ Number of trees+ -> Int -- ^ Number of points (samples)+ -> TimeSpec -- ^ Time of origin or MRCA+ -> Rate -- ^ Birth rate+ -> Rate -- ^ Death rate+ -> Gen (PrimState m) -- ^ Generator (see 'System.Random.MWC')+ -> m [Tree PhyloIntLabel]+simulateNReconstructedTrees nT nP t l m g+ | nT <= 0 = return []+ | otherwise = replicateM nT $ simulateReconstructedTree nP t l m g++-- | Use the point process to simulate a reconstructed tree (see+-- 'toReconstructedTree') possibly with specific height and a fixed number of+-- leaves according to the birth and death process.+simulateReconstructedTree+ :: (PrimMonad m)+ => Int -- ^ Number of points (samples)+ -> TimeSpec -- ^ Time of origin or MRCA+ -> Rate -- ^ Birth rate+ -> Rate -- ^ Death rate+ -> Gen (PrimState m) -- ^ Generator (see 'System.Random.MWC')+ -> m (Tree PhyloIntLabel)+simulateReconstructedTree n t l m g = toReconstructedTree <$> simulate n t l m g++-- | Convert a point process to a reconstructed tree. See Lemma 2.2.++-- Of course, I decided to only use one tree structure with extinct and extant+-- leaves (actually a complete tree). So a tree created here just does not+-- contain extinct leaves. A function 'isReconstructed' is provided to test if a+-- tree is reconstructed (and not complete) in this sense. However, a complete+-- tree might show up as "reconstructed", just because, by chance, it does not+-- contain extinct leaves. I wanted to use a Monoid constraint to get the unit+-- element, but this fails for classical 'Int's. So, I rather have another+-- (useless) argument.+toReconstructedTree :: PointProcess Int Double+ -> Tree PhyloIntLabel+toReconstructedTree pp@(PointProcess ps vs o)+ | length ps /= length vs + 1 = error "Too few or too many points."+ | length vs <= 1 = error "Too few values."+ -- -- XXX: Test is deactivated.+ -- -- | otherwise = if isReconstructed treeOrigin then treeOrigin else error "Error in algorithm."+ | otherwise = treeOrigin+ where (vsSorted, isSorted) = sort pp+ !lvs = [ singleton (PhyloLabel p Nothing 0) | p <- ps ]+ !heights = replicate (length ps) 0+ !treeRoot = toReconstructedTree' isSorted vsSorted lvs heights+ !h = last vsSorted+ !treeOrigin = lengthenRoot (o-h) treeRoot++-- Move up the tree, connect nodes when they join according to the point process.+toReconstructedTree' :: [Int] -- Sorted indices, see 'sort'.+ -> [Double] -- Sorted merge values.+ -> [Tree PhyloIntLabel] -- Leaves with accumulated root branch lengths.+ -> [Double] -- Accumulated heights of the leaves.+ -> Tree PhyloIntLabel+toReconstructedTree' [] [] trs _ = head trs+toReconstructedTree' is vs trs hs = toReconstructedTree' is' vs' trs'' hs'+ -- For the algorithm, see 'ELynx.Coalescent.simulate', but index starts+ -- at zero.+ where !i = head is+ !is' = tail is+ !v = head vs+ !vs' = tail vs+ -- Left: l, right: r.+ !hl = hs !! i+ !hr = hs !! (i+1)+ !dvl = v - hl+ !dvr = v - hr+ !tl = lengthenRoot dvl $ trs !! i+ !tr = lengthenRoot dvr $ trs !! (i+1)+ !h' = hl + dvl -- Should be the same as 'hr + dvr'.+ !tm = Node (PhyloLabel 0 Nothing 0) [tl, tr]+ !trs'' = take i trs ++ [tm] ++ drop (i+2) trs+ !hs' = take i hs ++ [h'] ++ drop (i+2) hs
+ test/ELynx/Data/Tree/BipartitionSpec.hs view
@@ -0,0 +1,79 @@+{-# LANGUAGE OverloadedStrings #-}++{- |+Module : ELynx.Data.Tree.BipartitionSpec+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Aug 30 09:38:50 2019.++-}++module ELynx.Data.Tree.BipartitionSpec+ (spec+ ) where++import qualified Data.ByteString.Lazy as L+import qualified Data.Map as M+import Data.Monoid+import qualified Data.Set as S+import Data.Tree+import Test.Hspec++import ELynx.Data.Tree.Bipartition+import ELynx.Data.Tree.PhyloTree+import ELynx.Import.Tree.Newick+import ELynx.Tools.InputOutput++treeFileSimple :: FilePath+treeFileSimple = "data/TreeDist.trees"++getSimpleTrees :: IO [Tree PhyloByteStringLabel]+getSimpleTrees = parseFileWith manyNewick treeFileSimple++bipartitionToBranchAnswer :: M.Map (Bipartition L.ByteString) (Sum Double)+bipartitionToBranchAnswer =+ M.fromList [ (bp (S.fromList ["B"]) (S.fromList ["A","C","D","E"]), Sum {getSum = 0.3})+ , (bp (S.fromList ["B","C","D","E"]) (S.fromList ["A"]), Sum {getSum = 0.1})+ , (bp (S.fromList ["B","C","E"]) (S.fromList ["A","D"]), Sum {getSum = 5.0e-2})+ , (bp (S.fromList ["B","E"]) (S.fromList ["A","C","D"]), Sum {getSum = 0.4})+ , (bp (S.fromList ["C"]) (S.fromList ["A","B","D","E"]), Sum {getSum = 1.0e-2})+ , (bp (S.fromList ["D"]) (S.fromList ["A","B","C","E"]), Sum {getSum = 0.25})+ , (bp (S.fromList ["E"]) (S.fromList ["A","B","C","D"]), Sum {getSum = 0.8}) ]++bipartitionsFirstTree :: S.Set (Bipartition L.ByteString)+bipartitionsFirstTree = S.fromList [ bp (S.fromList ["B"]) (S.fromList ["A","C","D","E"])+ , bp (S.fromList ["B","C","D","E"]) (S.fromList ["A"])+ , bp (S.fromList ["B","D","E"]) (S.fromList ["A","C"])+ , bp (S.fromList ["B","E"]) (S.fromList ["A","C","D"])+ , bp (S.fromList ["C"]) (S.fromList ["A","B","D","E"])+ , bp (S.fromList ["D"]) (S.fromList ["A","B","C","E"])+ , bp (S.fromList ["E"]) (S.fromList ["A","B","C","D"]) ]++bipartitionsSecondTree :: S.Set (Bipartition L.ByteString)+bipartitionsSecondTree = S.fromList [ bp (S.fromList ["B"]) (S.fromList ["A","C","D","E"])+ , bp (S.fromList ["B","C","D","E"]) (S.fromList ["A"])+ , bp (S.fromList ["B","C","E"]) (S.fromList ["A","D"])+ , bp (S.fromList ["B","E"]) (S.fromList ["A","C","D"])+ , bp (S.fromList ["C"]) (S.fromList ["A","B","D","E"])+ , bp (S.fromList ["D"]) (S.fromList ["A","B","C","E"])+ , bp (S.fromList ["E"]) (S.fromList ["A","B","C","D"])]++spec :: Spec+spec = do+ describe "bipartitions" $+ it "calculates correct bipartitions for sample trees" $ do+ simpleTrees <- map removeBrLen <$> getSimpleTrees+ let t1 = head simpleTrees+ t2 = simpleTrees !! 1+ bipartitions t1 `shouldBe` bipartitionsFirstTree+ bipartitions t2 `shouldBe` bipartitionsSecondTree+ describe "bipartitionToBranch" $+ it "creates a map from bipartitions to branch lengths" $ do+ simpleTrees <- getSimpleTrees+ bipartitionToBranch pLabel (Sum . pBrLen) (simpleTrees !! 2)+ `shouldBe` bipartitionToBranchAnswer
+ test/ELynx/Data/Tree/DistanceSpec.hs view
@@ -0,0 +1,99 @@+{-# LANGUAGE FlexibleInstances #-}+{- |+Module : ELynx.Data.Tree.DistanceSpec+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Aug 30 09:38:50 2019.++-}++module ELynx.Data.Tree.DistanceSpec+ (spec+ ) where++import Data.Tree+import Test.Hspec+import Test.QuickCheck+import Test.QuickCheck.Instances.Containers ()++import ELynx.Data.Tree.Distance+import ELynx.Data.Tree.NamedTree+import ELynx.Data.Tree.PhyloTree+import ELynx.Import.Tree.Newick+import ELynx.Tools.Equality+import ELynx.Tools.InputOutput++treeFileSimple :: FilePath+treeFileSimple = "data/TreeDist.trees"++getSimpleTrees :: IO [Tree PhyloByteStringLabel]+getSimpleTrees = parseFileWith manyNewick treeFileSimple++treeFileMany :: FilePath+treeFileMany = "data/Many.trees"++getManyTrees :: IO [Tree PhyloByteStringLabel]+getManyTrees = parseFileWith manyNewick treeFileMany++-- I used treedist from Phylip to get the correct results.+-- See http://evolution.genetics.washington.edu/phylip/doc/treedist.html.+symmetricDistanceAnswers :: [Int]+symmetricDistanceAnswers =+ [ 6, 8, 0, 0, 12, 20, 18, 20, 10, 2, 10, 4, 4, 4, 4, 4, 10, 16, 8, 2, 4, 0, 0,+ 0, 10, 4, 0, 0, 2, 2, 0, 0, 4, 0, 2, 0, 8, 6, 2, 6, 4, 4, 8, 0, 0, 4, 2, 0,+ 10, 0, 0, 10 ]++branchScoreDistanceAnswers :: [Double]+branchScoreDistanceAnswers =+ [ 8.567916e-02, 9.570577e-02, 1.704571e-02, 7.603990e-03, 6.149761e-01,+ 3.557070e-01, 2.329811e-01, 3.820208e-01, 1.895421e-02, 6.302364e-03,+ 2.083286e-02, 1.023777e-03, 2.138244e-02, 1.444380e-02, 1.958628e-02,+ 6.089461e-03, 2.551873e-02, 8.041220e-02, 4.123102e-02, 8.241811e-03,+ 2.623805e-02, 2.109278e-02, 1.953769e-02, 4.459926e-03, 6.594537e-02,+ 7.040703e-02, 8.603133e-03, 3.878009e-03, 2.969969e-02, 2.505262e-02,+ 2.095988e-02, 8.461041e-03, 5.228005e-02, 6.001320e-02, 8.276652e-03,+ 6.966115e-03, 7.701581e-02, 4.946339e-02, 2.548024e-02, 5.800598e-03,+ 3.875927e-02, 2.836737e-02, 9.059706e-02, 1.333325e-02, 5.071356e-02,+ 7.433056e-02, 3.854717e-02, 3.255993e-02, 1.581909e-01, 6.813096e-02,+ 8.210513e-02, 7.664642e-02 ]++prop_dist_same_tree :: (Num b, Eq b) => (Tree a -> Tree a -> b) -> Tree a -> Bool+prop_dist_same_tree distanceMeasure t = distanceMeasure t t == 0++-- TODO: Microsporidia trees with branch support values.+-- getMicrospoPoissonTree :: IO (Tree PhyloByteStringLabel)+-- getMicrospoPoissonTree = parseFileWith newick "data/MicrospoPoisson.tree"+-- getMicrospoUDM32Tree = parseFileWith newick "data/MicrospoEDM32.tree"+-- getMicrospoUDM64Tree = parseFileWith newick "data/MicrospoEDM64.tree"++each :: Int -> [a] -> [a]+each n = map head . takeWhile (not . null) . iterate (drop n)++spec :: Spec+spec = do+ describe "symmetricDistance" $+ it "calculates correct distances for sample trees" $ do+ simpleTrees <- getSimpleTrees+ symmetricDistance (head simpleTrees) (simpleTrees !! 1) `shouldBe` 2+ manyTrees <- getManyTrees+ -- Since treedist computes the distance between adjacent pairs, in the+ -- following manner: [tr0, tr1, tr2, tr3] -> [dist tr0 tr1, dist tr2 tr3],+ -- we have to skip some distances.+ each 2 (computeAdjacentDistances (symmetricDistanceWith getName) manyTrees)+ `shouldBe` symmetricDistanceAnswers++ describe "incompatibleSplitDistance" $+ it "calculates correct distances for completely collapsed trees" $+ property $ prop_dist_same_tree (incompatibleSplitsDistance :: Tree PhyloIntLabel -> Tree PhyloIntLabel -> Int)++ describe "branchScoreDistance" $+ it "calculates correct distances for sample trees" $ do+ manyTrees <- getManyTrees+ print branchScoreDistanceAnswers+ each 2 (computeAdjacentDistances branchScoreDistance manyTrees)+ `shouldSatisfy` nearlyEqListWith 1e-5 branchScoreDistanceAnswers
+ test/ELynx/Data/Tree/TreeSpec.hs view
@@ -0,0 +1,66 @@+{- |+Module : ELynx.Data.Tree.TreeSpec+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Mon May 6 14:04:05 2019.++-}++module ELynx.Data.Tree.TreeSpec+ (spec+ ) where++import qualified Data.ByteString.Lazy.Char8 as L+import Data.Maybe+import Data.Tree+import Test.Hspec++import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.PhyloTree+import ELynx.Data.Tree.Tree+import ELynx.Import.Tree.Newick hiding (node)+import ELynx.Tools.InputOutput (parseByteStringWith)++node :: Int -> Tree Int+node n = Node n []++smallTree :: Tree Int+smallTree = Node 0 [node 1, node 2]++smallSubTree :: Tree Int+smallSubTree = Node 0 [node 1]++smallSubTreePruned :: Tree Int+smallSubTreePruned = node 1++sampleTreeBS :: L.ByteString+sampleTreeBS = L.pack "(Aeropyrum0:0.5478645225,(((((((((Arabidopsi:0.0701001024,Oryza_sati:0.0765988261):0.0309636193,Gymnosperm:0.0520325624):0.0338982245,Physcomitr:0.0768008916):0.0895714685,(Chlamydomo:0.1136227755,Dunaliella:0.1406347323):0.1117340620):0.0818876186,Rhodophyta:0.3405656487):0.0363527066,((((((Babesia_bo:0.1646969208,Theileria0:0.1519889486):0.1908081096,Plasmodium:0.3250696762):0.0637865908,(Toxoplasma:0.1153570425,Eimeria000:0.1671916078):0.0980136930):0.0518956330,Cryptospor:0.3175062809):0.1607708388,Ciliophora:0.5687502950):0.0624078848,(Phytophtho:0.2016424948,((Thalassios:0.1202730781,Phaeodacty:0.1290341329):0.1772775509,Phaeophyce:0.1989260715):0.0312359673):0.1154768302):0.0311952864):0.0149160316,(((((((((Candida_al:0.1027755272,Saccharomy:0.1190206560):0.1333487870,Neurospora:0.1977309079):0.0522926266,Schizosacc:0.2019603227):0.0567441011,(Cryptococc:0.1948614959,Ustilago_m:0.1564451295):0.0775729694):0.0323959951,Glomus_int:0.1573670796):0.0194701292,Chytridiom:0.2228415254):0.0384370601,Encephalit:1.4622174644):0.0416231688,(((Drosophila:0.2160627753,(Mammalians:0.1080484094,Tunicates0:0.1739253014):0.0289624371):0.0346633757,Hydrozoa00:0.2058137032):0.0480963050,Monosiga_b:0.3020637584):0.0654894239):0.0380915725,(Dictyostel:0.3453588998,Mastigamoe:0.3844779231):0.0478795653):0.0129578395):1.7592083381,((Archaeoglo:0.5402784445,Methanococ:0.4088567459):0.0993669265,Pyrococcus:0.4058713829):0.1734405968):0.2193511807,Pyrobaculu:0.7507718047):0.1646616482,Sulfolobus:0.5404967897);"+++largeTree :: Tree PhyloByteStringLabel+largeTree = parseByteStringWith "Sample newick byte string" newick sampleTreeBS++subSampleLargeTree :: Tree PhyloByteStringLabel+subSampleLargeTree = fromJust $ subTree ((== 'P') . L.head . pLabel) largeTree++spec :: Spec+spec = do+ describe "subTree" $ do+ it "returns nothing if no leaf satisfies prediacte" $+ subTree (==3) smallTree `shouldBe` Nothing+ it "returns the correct subtree for a small example" $+ subTree (==1) smallTree `shouldBe` Just smallSubTree++ describe "pruneWith" $ do+ it "leaves a normal tree untouched" $+ pruneWith const largeTree `shouldBe` largeTree+ it "correctly prunes a small example" $+ pruneWith const smallSubTree `shouldBe` smallSubTreePruned+ it "leaves height constant for Measurable trees" $+ height (prune subSampleLargeTree) `shouldBe` height subSampleLargeTree+
+ test/ELynx/Export/Tree/NewickSpec.hs view
@@ -0,0 +1,39 @@+{- |+Module : ELynx.Export.Tree.NewickSpec+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Wed Feb 13 11:01:53 2019.++-}++module ELynx.Export.Tree.NewickSpec+ (spec+ ) where++import qualified Data.ByteString.Lazy.Char8 as L+import Data.Tree+import Test.Hspec++import ELynx.Data.Tree.PhyloTree+import ELynx.Export.Tree.Newick+import ELynx.Import.Tree.Newick+import ELynx.Tools.InputOutput++samplePhyloByteStringTree :: Tree PhyloByteStringLabel+samplePhyloByteStringTree =+ parseByteStringWith "Sample newick byte string" newick sampleNewickByteString1++sampleNewickByteString1 :: L.ByteString+sampleNewickByteString1 = L.pack "(Aeropyrum0:0.5478645225,(((((((((Arabidopsi:0.0701001024,Oryza_sati:0.0765988261):0.0309636193,Gymnosperm:0.0520325624):0.0338982245,Physcomitr:0.0768008916):0.0895714685,(Chlamydomo:0.1136227755,Dunaliella:0.1406347323):0.1117340620):0.0818876186,Rhodophyta:0.3405656487):0.0363527066,((((((Babesia_bo:0.1646969208,Theileria0:0.1519889486):0.1908081096,Plasmodium:0.3250696762):0.0637865908,(Toxoplasma:0.1153570425,Eimeria000:0.1671916078):0.0980136930):0.0518956330,Cryptospor:0.3175062809):0.1607708388,Ciliophora:0.5687502950):0.0624078848,(Phytophtho:0.2016424948,((Thalassios:0.1202730781,Phaeodacty:0.1290341329):0.1772775509,Phaeophyce:0.1989260715):0.0312359673):0.1154768302):0.0311952864):0.0149160316,(((((((((Candida_al:0.1027755272,Saccharomy:0.1190206560):0.1333487870,Neurospora:0.1977309079):0.0522926266,Schizosacc:0.2019603227):0.0567441011,(Cryptococc:0.1948614959,Ustilago_m:0.1564451295):0.0775729694):0.0323959951,Glomus_int:0.1573670796):0.0194701292,Chytridiom:0.2228415254):0.0384370601,Encephalit:1.4622174644):0.0416231688,(((Drosophila:0.2160627753,(Mammalians:0.1080484094,Tunicates0:0.1739253014):0.0289624371):0.0346633757,Hydrozoa00:0.2058137032):0.0480963050,Monosiga_b:0.3020637584):0.0654894239):0.0380915725,(Dictyostel:0.3453588998,Mastigamoe:0.3844779231):0.0478795653):0.0129578395):1.7592083381,((Archaeoglo:0.5402784445,Methanococ:0.4088567459):0.0993669265,Pyrococcus:0.4058713829):0.1734405968):0.2193511807,Pyrobaculu:0.7507718047):0.1646616482,Sulfolobus:0.5404967897);"++spec :: Spec+spec = describe "parseByteStringWith newick $ toNewickPhyloByteString" $+ it "should be an invariant" $ do+ let bs = toNewick samplePhyloByteStringTree+ parseByteStringWith "Newick string converted from tree object"+ newick bs `shouldBe` samplePhyloByteStringTree
+ test/ELynx/Import/Tree/NewickSpec.hs view
@@ -0,0 +1,115 @@+{- |+Module : ELynx.Import.Tree.NewickSpec+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Jan 18 10:14:04 2019.++-}++module ELynx.Import.Tree.NewickSpec+ (spec) where++import qualified Data.ByteString.Lazy.Char8 as L+import Data.Tree+import ELynx.Data.Tree.PhyloTree+import ELynx.Import.Tree.Newick+import Test.Hspec+import Test.Hspec.Megaparsec+import Text.Megaparsec++sampleLabelByteString :: L.ByteString+sampleLabelByteString = L.pack "name:0.3"++sampleLabel :: PhyloByteStringLabel+sampleLabel = PhyloLabel (L.pack "name") Nothing 0.3++sampleForestByteString :: L.ByteString+sampleForestByteString = L.pack "(l,l,(a,b))"++sampleForest :: [Tree PhyloByteStringLabel]+sampleForest =+ [ Node { rootLabel = PhyloLabel (L.pack "l") Nothing 0+ , subForest = []+ }+ , Node { rootLabel = PhyloLabel (L.pack "l") Nothing 0+ , subForest = []+ }+ , Node { rootLabel = PhyloLabel (L.pack "") Nothing 0+ , subForest =+ [ Node {rootLabel = PhyloLabel (L.pack "a") Nothing 0, subForest = []}+ , Node {rootLabel = PhyloLabel (L.pack "b") Nothing 0, subForest = []}+ ]+ }+ ]++sampleNewickByteString1 :: L.ByteString+sampleNewickByteString1 = L.pack "(Aeropyrum0:0.5478645225,(((((((((Arabidopsi:0.0701001024,Oryza_sati:0.0765988261):0.0309636193,Gymnosperm:0.0520325624):0.0338982245,Physcomitr:0.0768008916):0.0895714685,(Chlamydomo:0.1136227755,Dunaliella:0.1406347323):0.1117340620):0.0818876186,Rhodophyta:0.3405656487):0.0363527066,((((((Babesia_bo:0.1646969208,Theileria0:0.1519889486):0.1908081096,Plasmodium:0.3250696762):0.0637865908,(Toxoplasma:0.1153570425,Eimeria000:0.1671916078):0.0980136930):0.0518956330,Cryptospor:0.3175062809):0.1607708388,Ciliophora:0.5687502950):0.0624078848,(Phytophtho:0.2016424948,((Thalassios:0.1202730781,Phaeodacty:0.1290341329):0.1772775509,Phaeophyce:0.1989260715):0.0312359673):0.1154768302):0.0311952864):0.0149160316,(((((((((Candida_al:0.1027755272,Saccharomy:0.1190206560):0.1333487870,Neurospora:0.1977309079):0.0522926266,Schizosacc:0.2019603227):0.0567441011,(Cryptococc:0.1948614959,Ustilago_m:0.1564451295):0.0775729694):0.0323959951,Glomus_int:0.1573670796):0.0194701292,Chytridiom:0.2228415254):0.0384370601,Encephalit:1.4622174644):0.0416231688,(((Drosophila:0.2160627753,(Mammalians:0.1080484094,Tunicates0:0.1739253014):0.0289624371):0.0346633757,Hydrozoa00:0.2058137032):0.0480963050,Monosiga_b:0.3020637584):0.0654894239):0.0380915725,(Dictyostel:0.3453588998,Mastigamoe:0.3844779231):0.0478795653):0.0129578395):1.7592083381,((Archaeoglo:0.5402784445,Methanococ:0.4088567459):0.0993669265,Pyrococcus:0.4058713829):0.1734405968):0.2193511807,Pyrobaculu:0.7507718047):0.1646616482,Sulfolobus:0.5404967897);"++sampleNewickByteString2 :: L.ByteString+sampleNewickByteString2 = L.pack "(Caenorhabd:0.0176707431,C0briggsae:0.0142817073,(Ancylostom:0.0711440844,(Pristionch:0.1301309005,((Brugia_mal:0.0757534325,Ascaris0su:0.0482660407)1:0.0563924634,(((Meloidogyn:0.1239621893,Heteroderi:0.0987968800)1:0.1136879428,Strongyloi:0.2483437292)1:0.0252467381,(Trichoceph:0.2985037612,((((((Coleoptera:0.0907850846,(Apis0melli:0.0754058285,Hemiptera0:0.1675359618)0.93:0.0085703192)1:0.0146980945,(Siphonapte:0.0556805916,Bombyx0mor:0.0968983509)1:0.0127867903)1:0.0167360185,((Drosophila:0.0492149086,Glossina0m:0.0534390467)1:0.0583462602,Anopheles0:0.0968919941)1:0.0431343553)1:0.0535616453,Crustacea0:0.2247268999)1:0.0252755187,Chelicerat:0.1537491558)1:0.0212497286,((Echinoderm:0.1803896615,(Cephalocho:0.1492264574,(Urochordat:0.2194747834,(Mammalia00:0.0393008407,Actinopter:0.0491700096):0.0858550024)1:0.0157515969)1:0.0132516777)1:0.0203423736,((((((((Neurospora:0.0721607581,Magnaporth:0.0814182810)1:0.0198940548,Gibberella:0.0858192964)1:0.0533872590,Eurotiomyc:0.1058840539)1:0.1266302603,(Candida0al:0.1349957509,Saccharomy:0.1553464572)1:0.1791344287)1:0.0529664967,Schizosacc:0.2550087905)1:0.0723650615,(Ustilago0m:0.2031812772,(Homobasidi:0.1473391802,Cryptococc:0.2070743149)1:0.0347868586)1:0.0790327507)1:0.0727415175,Glomales00:0.1779430068)1:0.0169066667,Chytridiom:0.3028920870)1:0.3311420273)1:0.0278566156)1:0.1049569161)1:0.1366217350)1:0.0171168289)1:0.0345725378)1:0.0542036935)1:0.0879337167)1;"+++sampleNewickEmptyByteString :: L.ByteString+sampleNewickEmptyByteString = L.pack "(,(,,),);"++sampleNewickEmpty :: Tree PhyloByteStringLabel+sampleNewickEmpty =+ Node { rootLabel = PhyloLabel (L.pack "") Nothing 0+ , subForest =+ [ Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest = []}+ , Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest =+ [ Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest = []}+ , Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest = []}+ , Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest = []}+ ]+ }+ , Node {rootLabel = PhyloLabel (L.pack "") Nothing 0, subForest = []}+ ]+ }++spec :: Spec+spec = do+ describe "branchLength" $ do+ it "parses a colon and a branch length" $+ parse branchLength "" (L.pack ":13.2") `shouldParse` 13.2++ it "returns 0 if no branch length is given" $+ parse branchLength "" (L.pack "") `shouldParse` 0++ describe "name" $ do+ it "parses a string of printable characters" $+ parse name "" (L.pack "aName") `shouldParse` L.pack "aName"++ it "parses blanks, colons, semicolons, parentheses, and sequare brackets" $+ parse name "" (L.pack "aName bla") `shouldParse` L.pack "aName"++ it "allows empty names" $+ parse name "" (L.pack "") `shouldParse` L.pack ""++ describe "node" $ do+ it "parses a tree node" $+ parse node "" sampleLabelByteString `shouldParse` sampleLabel++ it "parses tree nodes with empty names and branch lengths" $+ parse node "" (L.pack "") `shouldParse` PhyloLabel (L.pack "") Nothing 0++ describe "leaf" $+ it "parses a leaf of a tree" $+ parse leaf "" sampleLabelByteString `shouldParse` Node sampleLabel []++ describe "forest" $+ it "parses a set of trees within brackets" $+ parse forest "" sampleForestByteString `shouldParse` sampleForest++ describe "newick" $ do+ it "parses a newick trees" $ do+ parse newick "" `shouldSucceedOn` sampleNewickByteString1+ parse newick "" `shouldSucceedOn` sampleNewickByteString2++ it "parses a weird newick tree without node labels nor branch lengths" $+ parse newick "" sampleNewickEmptyByteString `shouldParse` sampleNewickEmpty
+ test/Spec.hs view
@@ -0,0 +1,1 @@+{-# OPTIONS_GHC -F -pgmF hspec-discover #-}