diff --git a/ChangeLog.md b/ChangeLog.md
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+
+# Changelog for ELynx
+
+
+## Version 0.2.1
+
+- Validation and repetition of previous analyses is finally possible with the
+ new `elynx` binary.
+- A library `elynx-markov` for running Markov processes along phylogenetic trees
+ has been split off `elynx-seq`. This library performs the computations when
+ executing `slynx simulate ...`.
+- Many other small improvements.
+
diff --git a/LICENSE b/LICENSE
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--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
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+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ Copyright (C)
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. 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
+.
+
+ 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
+.
diff --git a/README.md b/README.md
new file mode 100644
--- /dev/null
+++ b/README.md
@@ -0,0 +1,714 @@
+
+
+# The ELynx Suite
+
+Version: 0.2.1.
+Reproducible evolution made easy.
+
+A Haskell library and tool set for computational biology. The goal of ELynx is
+reproducible research. Evolutionary sequences and phylogenetic trees can be
+read, viewed, modified and simulated. The command line with all arguments is
+logged consistently, and automatically. Data integrity is verified using SHA256
+sums so that validation of past analyses is possible without the need to
+recompute the result.
+
+The Elynx Suite consists of four library packages and three executables providing
+a range of sub commands.
+
+The library packages are:
+
+- **elynx-markov:** Simulate multi sequence alignments along phylogenetic trees.
+- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments.
+- **elynx-tools:** Tools for the provided executables.
+- **elynx-tree:** Handle phylogenetic trees.
+
+The executables are:
+
+- **slynx:** Analyze, modify, and simulate evolutionary sequences.
+- **tlynx:** Analyze, modify, and simulate phylogenetic trees.
+- **elynx:** Validate and redo past analyses.
+
+**ELynx is actively developed. We happily receive comments, ideas, feature
+requests, and 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 to the
+ [PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.
+
+
+# SLynx
+
+Handle evolutionary sequences.
+
+ slynx --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
+ [-f|--force] 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
+ -f,--force Ignore previous analysis and overwrite existing
+ output files.
+
+ Available commands:
+ concatenate Concatenate sequences found in input files.
+ examine Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
+ filter-columns Filter columns of multi sequence alignments.
+ filter-rows Filter rows (or sequences) found in input files.
+ simulate Simulate multi sequence alignments.
+ sub-sample Sub-sample columns from multi sequence alignments.
+ translate Translate from DNA to Protein or DNAX to ProteinX.
+
+ Available sequence file formats:
+ - FASTA
+
+ Available alphabets:
+ - 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)
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Concatenate
+
+Concatenate multi sequence alignments.
+
+ slynx concatenate --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
+ Concatenate sequences found in input files.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -a,--alphabet NAME Specify alphabet type NAME
+ INPUT-FILE Read sequences from INPUT-FILE
+ -h,--help Show this help text
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Examine
+
+Examine sequence with `slynx examine`.
+
+ slynx examine --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
+ Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Filter
+
+Filter sequences with `filer-rows`.
+
+ slynx filter-rows --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]
+ [--shorter-than LENGTH] [--standard-characters]
+ Filter rows (or sequences) found in input files.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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
+ --standard-characters Only keep sequences containing at least one standard
+ (i.e., non-IUPAC) character
+ -h,--help Show this help text
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+Filter columns of multi sequence alignments with `filter-columns`.
+
+ slynx filter-columns --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE
+ [--standard-chars DOUBLE]
+ Filter columns of multi sequence alignments.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Simulate
+
+Simulate sequences with `slynx simulate`.
+
+ slynx simulate --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
+ [-m|--mixture-model MODEL] [-e|--edm-file NAME]
+ [-p|--siteprofile-files NAMES]
+ [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
+ [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]
+ (-l|--length NUMBER) [-S|--seed [INT]]
+ Simulate multi sequence alignments.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -t,--tree-file Name Read tree from Newick 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
+ -p,--siteprofile-files NAMES
+ File names of site profiles 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, F81, HKY, GTR4.
+ For example,
+ -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}
+ -s GTR4[e_AC,e_AG,e_AT,e_CG,e_CT,e_GT]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}
+ where the 'e_XY' are the exchangeabilities from nucleotide X to Y.
+ Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom, GTR20.
+ MODEL-Custom means that only the exchangeabilities of MODEL are used,
+ and a custom stationary distribution is provided.
+ For example,
+ -s LG
+ -s LG-Custom{...}
+ -s GTR20[e_AR,e_AN,...]{...}
+ the 'e_XY' are the exchangeabilities from amino acid X to Y (alphabetical order).
+ Notes: The F81 model for DNA is equivalent to the Poisson-Custom for proteins.
+ The GTR4 model for DNA is equivalent to the GTR20 for proteins.
+
+ Mixture models:
+ -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2[PARAMETERS]{STATIONARY_DISTRIBUTION},...)"
+ 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.
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Sub-sample
+
+Sub-sample columns from multi sequence alignments.
+
+ slynx sub-sample --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
+ (-n|--number-of-sites INT)
+ (-m|--number-of-alignments INT) [-S|--seed [INT]]
+ Sub-sample columns from multi sequence alignments.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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
+
+ Create a given number of multi sequence alignments, each of which contains a given number of random sites drawn from the original multi sequence alignment.
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Translate
+
+Translate sequences.
+
+ slynx translate --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
+ (-u|--universal-code CODE)
+ Translate from DNA to Protein or DNAX to ProteinX.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+# TLynx
+
+Handle phylogenetic trees in Newick format.
+
+ tlynx --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
+ [-f|--force] 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
+ -f,--force Ignore previous analysis and overwrite existing
+ output files.
+
+ Available commands:
+ coalesce Simulate phylogenetic trees using the coalescent processes (see also the 'simulate' command for simulations using the birth and death process).
+ compare Compare two phylogenetic trees (compute distances and branch-wise differences).
+ connect Connect two phylogenetic trees in all ways (possibly honoring constraints).
+ distance Compute distances between many phylogenetic trees.
+ examine Compute summary statistics of phylogenetic trees.
+ shuffle Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).
+ simulate Simulate phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).
+
+ Available tree file formats:
+ - Newick Standard: Branch support values are stored in square brackets after branch lengths.
+ - Newick IqTree: Branch support values are stored as node names after the closing bracket of forests.
+ - Newick RevBayes Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are IGNORED at the moment.
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Compare
+
+Compute distances between phylogenetic trees.
+
+ tlynx compare --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
+ [-f|--newick-format FORMAT] NAME
+ Compare two phylogenetic trees (compute distances and branch-wise differences).
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -n,--normalize Normalize trees before comparison
+ -b,--bipartitions Print and plot common and missing bipartitions
+ -t,--intersect Compare intersections; i.e., before comparison, drop
+ leaves that are not present in the other tree
+ -f,--newick-format FORMAT
+ Newick tree format; see 'tlynx
+ --help' (default: Standard)
+ NAME Tree file
+ -h,--help Show this help text
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Examine
+
+Compute summary statistics of phylogenetic trees.
+
+ tlynx examine --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
+ Compute summary statistics of phylogenetic trees.
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ INPUT-FILE Read trees from INPUT-FILE
+ -f,--newick-format FORMAT
+ Newick tree format; see 'tlynx
+ --help' (default: Standard)
+ -h,--help Show this help text
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+## Simulate
+
+Simulate phylogenetic trees using birth and death processes.
+
+ tlynx simulate --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ 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 phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+ -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.
+ 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
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+# ELynx
+
+Validate and (optionally) redo past ELynx analyses.
+
+ elynx --help
+
+ ELynx Suite version 0.2.1.
+ Developed by Dominik Schrempf.
+ Compiled on April 27, 2020, at 06:31 am, UTC.
+
+ Usage: elynx COMMAND
+ Validate and redo past ELynx analyses
+
+ Available options:
+ -h,--help Show this help text
+ -V,--version Show version
+
+ Available commands:
+ validate Validate an ELynx analysis
+ redo Redo an ELynx analysis
+
+
+ ELynx
+ -----
+ A Haskell library and tool set for computational biology. The goal of ELynx is
+ reproducible research. Evolutionary sequences and phylogenetic trees can be
+ read, viewed, modified and simulated. The command line with all arguments is
+ logged consistently, and automatically. Data integrity is verified using SHA256
+ sums so that validation of past analyses is possible without the need to
+ recompute the result.
+
+ slynx Analyze, modify, and simulate evolutionary sequences.
+ tlynx Analyze, modify, and simulate phylogenetic trees.
+ elynx Validate and redo past analyses.
+
+ Get help for sub commands:
+ slynx examine --help
+
+
+# Library documentation
+
+Documentation of the libraries can be found on [Hackage](https://hackage.haskell.org/):
+
+- [elynx-markov](https://hackage.haskell.org/package/elynx-markov)
+- [elynx-seq](https://hackage.haskell.org/package/elynx-seq)
+- [elynx-tools](https://hackage.haskell.org/package/elynx-tools)
+- [elynx-tree](https://hackage.haskell.org/package/elynx-tree)
+
+Documentation of the executables is also available:
+
+- [elynx](https://hackage.haskell.org/package/elynx)
+- [slynx](https://hackage.haskell.org/package/slynx)
+- [tlynx](https://hackage.haskell.org/package/tlynx)
+
diff --git a/elynx-markov.cabal b/elynx-markov.cabal
new file mode 100644
--- /dev/null
+++ b/elynx-markov.cabal
@@ -0,0 +1,92 @@
+cabal-version: 1.12
+name: elynx-markov
+version: 0.2.1
+license: GPL-3
+license-file: LICENSE
+copyright: Dominik Schrempf (2020)
+maintainer: dominik.schrempf@gmail.com
+author: Dominik Schrempf
+homepage: https://github.com/dschrempf/elynx#readme
+bug-reports: https://github.com/dschrempf/elynx/issues
+synopsis: Simulate molecular sequences along trees
+description:
+ Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at .
+category: Bioinformatics
+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.MarkovProcess.AminoAcid
+ ELynx.Data.MarkovProcess.CXXModels
+ ELynx.Data.MarkovProcess.CXXModelsData
+ ELynx.Data.MarkovProcess.GammaRateHeterogeneity
+ ELynx.Data.MarkovProcess.MixtureModel
+ ELynx.Data.MarkovProcess.Nucleotide
+ ELynx.Data.MarkovProcess.PhyloModel
+ ELynx.Data.MarkovProcess.RateMatrix
+ ELynx.Data.MarkovProcess.SubstitutionModel
+ ELynx.Import.MarkovProcess.EDMModelPhylobayes
+ ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
+ ELynx.Simulate.MarkovProcess
+ ELynx.Simulate.MarkovProcessAlongTree
+ hs-source-dirs: src
+ other-modules:
+ Paths_elynx_markov
+ default-language: Haskell2010
+ ghc-options: -Wall -fllvm
+ build-depends:
+ base >=4.13.0.0 && <4.14,
+ bytestring >=0.10.10.0 && <0.11,
+ containers >=0.6.2.1 && <0.7,
+ elynx-seq >=0.2.1 && <0.3,
+ elynx-tools >=0.2.1 && <0.3,
+ elynx-tree >=0.2.1 && <0.3,
+ hmatrix >=0.20.0.0 && <0.21,
+ integration >=0.2.1 && <0.3,
+ math-functions >=0.3.3.0 && <0.4,
+ megaparsec >=8.0.0 && <8.1,
+ mwc-random >=0.14.0.0 && <0.15,
+ parallel >=3.2.2.0 && <3.3,
+ primitive >=0.7.0.1 && <0.8,
+ statistics >=0.15.2.0 && <0.16,
+ vector >=0.12.1.2 && <0.13
+
+test-suite markov-test
+ type: exitcode-stdio-1.0
+ main-is: Spec.hs
+ hs-source-dirs: test
+ other-modules:
+ ELynx.Data.MarkovProcess.AminoAcidSpec
+ ELynx.Data.MarkovProcess.NucleotideSpec
+ ELynx.Data.MarkovProcess.RateMatrixSpec
+ ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
+ ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
+ ELynx.Simulate.MarkovProcessAlongTreeSpec
+ Paths_elynx_markov
+ default-language: Haskell2010
+ ghc-options: -Wall -fllvm -threaded -rtsopts -with-rtsopts=-N
+ build-depends:
+ base >=4.13.0.0 && <4.14,
+ bytestring >=0.10.10.0 && <0.11,
+ containers >=0.6.2.1 && <0.7,
+ elynx-markov -any,
+ elynx-tools >=0.2.1 && <0.3,
+ elynx-tree >=0.2.1 && <0.3,
+ hmatrix >=0.20.0.0 && <0.21,
+ hspec >=2.7.1 && <2.8,
+ hspec-megaparsec >=2.1.0 && <2.2,
+ integration >=0.2.1 && <0.3,
+ math-functions >=0.3.3.0 && <0.4,
+ megaparsec >=8.0.0 && <8.1,
+ mwc-random >=0.14.0.0 && <0.15,
+ parallel >=3.2.2.0 && <3.3,
+ primitive >=0.7.0.1 && <0.8,
+ statistics >=0.15.2.0 && <0.16,
+ vector >=0.12.1.2 && <0.13
diff --git a/src/ELynx/Data/MarkovProcess/AminoAcid.hs b/src/ELynx/Data/MarkovProcess/AminoAcid.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/AminoAcid.hs
@@ -0,0 +1,620 @@
+{- |
+Module : ELynx.Data.MarkovProcess.AminoAcid
+Description : Amino acid rate matrices such as LG
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 09:29:19 2019.
+
+The order of amino acids is alphabetic.
+
+-}
+
+module ELynx.Data.MarkovProcess.AminoAcid
+ ( lg
+ , lgCustom
+ , wag
+ , wagCustom
+ , poisson
+ , poissonCustom
+ , gtr20
+ )
+where
+
+import Data.List ( elemIndex )
+import Data.Maybe ( fromMaybe )
+import Data.Word ( Word8 )
+import Numeric.LinearAlgebra
+
+import ELynx.Data.Alphabet.Alphabet
+
+import ELynx.Tools
+
+import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.Data.MarkovProcess.SubstitutionModel
+
+n :: Int
+n = 20
+
+-- Some matrices have to be converted from PAML order to alphabetical order. See
+-- 'pamlToAlphaVec' and 'pamlToAlphaMat'.
+
+-- Amno acids in alphabetical order.
+aaAlphaOrder :: [Word8]
+aaAlphaOrder = map
+ c2w
+ [ 'A'
+ , 'C'
+ , 'D'
+ , 'E'
+ , 'F'
+ , 'G'
+ , 'H'
+ , 'I'
+ , 'K'
+ , 'L'
+ , 'M'
+ , 'N'
+ , 'P'
+ , 'Q'
+ , 'R'
+ , 'S'
+ , 'T'
+ , 'V'
+ , 'W'
+ , 'Y'
+ ]
+
+-- Amino acids in PAML oder.
+aaPamlOrder :: [Word8]
+aaPamlOrder = map
+ c2w
+ [ 'A'
+ , 'R'
+ , 'N'
+ , 'D'
+ , 'C'
+ , 'Q'
+ , 'E'
+ , 'G'
+ , 'H'
+ , 'I'
+ , 'L'
+ , 'K'
+ , 'M'
+ , 'F'
+ , 'P'
+ , 'S'
+ , 'T'
+ , 'W'
+ , 'Y'
+ , 'V'
+ ]
+
+-- -- This is a very slow implementation; since I only convert matrices once it
+-- -- should not be a problem. A map would be better if performance is an issue.
+-- pamlIndexToAlphaIndex :: Int -> Int
+-- pamlIndexToAlphaIndex i = fromMaybe
+-- (error $ "Could not convert index " ++ show i ++ ".")
+-- (elemIndex aa aaAlphaOrder)
+-- where aa = aaPamlOrder !! i
+
+-- This is a very slow implementation; since I only convert matrices once it
+-- should not be a problem. A map would be better if performance is an issue.
+alphaIndexToPamlIndex :: Int -> Int
+alphaIndexToPamlIndex i = fromMaybe
+ (error $ "Could not convert index " ++ show i ++ ".")
+ (elemIndex aa aaPamlOrder)
+ where aa = aaAlphaOrder !! i
+
+-- Convert an amino acid vector in PAML order to a vector in alphabetical order.
+pamlToAlphaVec :: Vector R -> Vector R
+pamlToAlphaVec v = build n (\i -> v ! alphaIndexToPamlIndex (round i))
+
+
+-- Convert an amino acid matrix in PAML order to a matrix in alphabetical order.
+pamlToAlphaMat :: Matrix R -> Matrix R
+pamlToAlphaMat m = build
+ (n, n)
+ (\i j -> m ! alphaIndexToPamlIndex (round i) ! alphaIndexToPamlIndex (round j)
+ )
+
+-- Lower triangular matrix of LG exchangeabilities in PAML order and in form of
+-- a list.
+lgExchRawPaml :: [Double]
+lgExchRawPaml =
+ [ 0.425093
+ , 0.276818
+ , 0.751878
+ , 0.395144
+ , 0.123954
+ , 5.076149
+ , 2.489084
+ , 0.534551
+ , 0.528768
+ , 0.062556
+ , 0.969894
+ , 2.807908
+ , 1.695752
+ , 0.523386
+ , 0.084808
+ , 1.038545
+ , 0.363970
+ , 0.541712
+ , 5.243870
+ , 0.003499
+ , 4.128591
+ , 2.066040
+ , 0.390192
+ , 1.437645
+ , 0.844926
+ , 0.569265
+ , 0.267959
+ , 0.348847
+ , 0.358858
+ , 2.426601
+ , 4.509238
+ , 0.927114
+ , 0.640543
+ , 4.813505
+ , 0.423881
+ , 0.311484
+ , 0.149830
+ , 0.126991
+ , 0.191503
+ , 0.010690
+ , 0.320627
+ , 0.072854
+ , 0.044265
+ , 0.008705
+ , 0.108882
+ , 0.395337
+ , 0.301848
+ , 0.068427
+ , 0.015076
+ , 0.594007
+ , 0.582457
+ , 0.069673
+ , 0.044261
+ , 0.366317
+ , 4.145067
+ , 0.536518
+ , 6.326067
+ , 2.145078
+ , 0.282959
+ , 0.013266
+ , 3.234294
+ , 1.807177
+ , 0.296636
+ , 0.697264
+ , 0.159069
+ , 0.137500
+ , 1.124035
+ , 0.484133
+ , 0.371004
+ , 0.025548
+ , 0.893680
+ , 1.672569
+ , 0.173735
+ , 0.139538
+ , 0.442472
+ , 4.273607
+ , 6.312358
+ , 0.656604
+ , 0.253701
+ , 0.052722
+ , 0.089525
+ , 0.017416
+ , 1.105251
+ , 0.035855
+ , 0.018811
+ , 0.089586
+ , 0.682139
+ , 1.112727
+ , 2.592692
+ , 0.023918
+ , 1.798853
+ , 1.177651
+ , 0.332533
+ , 0.161787
+ , 0.394456
+ , 0.075382
+ , 0.624294
+ , 0.419409
+ , 0.196961
+ , 0.508851
+ , 0.078281
+ , 0.249060
+ , 0.390322
+ , 0.099849
+ , 0.094464
+ , 4.727182
+ , 0.858151
+ , 4.008358
+ , 1.240275
+ , 2.784478
+ , 1.223828
+ , 0.611973
+ , 1.739990
+ , 0.990012
+ , 0.064105
+ , 0.182287
+ , 0.748683
+ , 0.346960
+ , 0.361819
+ , 1.338132
+ , 2.139501
+ , 0.578987
+ , 2.000679
+ , 0.425860
+ , 1.143480
+ , 1.080136
+ , 0.604545
+ , 0.129836
+ , 0.584262
+ , 1.033739
+ , 0.302936
+ , 1.136863
+ , 2.020366
+ , 0.165001
+ , 0.571468
+ , 6.472279
+ , 0.180717
+ , 0.593607
+ , 0.045376
+ , 0.029890
+ , 0.670128
+ , 0.236199
+ , 0.077852
+ , 0.268491
+ , 0.597054
+ , 0.111660
+ , 0.619632
+ , 0.049906
+ , 0.696175
+ , 2.457121
+ , 0.095131
+ , 0.248862
+ , 0.140825
+ , 0.218959
+ , 0.314440
+ , 0.612025
+ , 0.135107
+ , 1.165532
+ , 0.257336
+ , 0.120037
+ , 0.054679
+ , 5.306834
+ , 0.232523
+ , 0.299648
+ , 0.131932
+ , 0.481306
+ , 7.803902
+ , 0.089613
+ , 0.400547
+ , 0.245841
+ , 3.151815
+ , 2.547870
+ , 0.170887
+ , 0.083688
+ , 0.037967
+ , 1.959291
+ , 0.210332
+ , 0.245034
+ , 0.076701
+ , 0.119013
+ , 10.649107
+ , 1.702745
+ , 0.185202
+ , 1.898718
+ , 0.654683
+ , 0.296501
+ , 0.098369
+ , 2.188158
+ , 0.189510
+ , 0.249313
+ ]
+
+
+-- Exchangeabilities of LG model in alphabetical order.
+lgExch :: ExchangeabilityMatrix
+lgExch = pamlToAlphaMat $ exchFromListLower n lgExchRawPaml
+
+-- Stationary distribution in PAML order.
+lgStatDistPaml :: StationaryDistribution
+lgStatDistPaml = normalizeSumVec 1.0 $ fromList
+ [ 0.079066
+ , 0.055941
+ , 0.041977
+ , 0.053052
+ , 0.012937
+ , 0.040767
+ , 0.071586
+ , 0.057337
+ , 0.022355
+ , 0.062157
+ , 0.099081
+ , 0.064600
+ , 0.022951
+ , 0.042302
+ , 0.044040
+ , 0.061197
+ , 0.053287
+ , 0.012066
+ , 0.034155
+ , 0.069147
+ ]
+
+-- Stationary distribution of LG model in alphabetical order.
+lgStatDist :: StationaryDistribution
+lgStatDist = pamlToAlphaVec lgStatDistPaml
+
+-- | LG substitution model.
+lg :: SubstitutionModel
+lg = substitutionModel Protein "LG" [] lgStatDist lgExch
+
+-- | LG substitution model with maybe a name and a custom stationary distribution.
+lgCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+lgCustom mnm d = substitutionModel Protein nm [] d lgExch
+ where nm = fromMaybe "LG-Custom" mnm
+
+-- WAG exchangeability list in PAML order.
+wagExchRawPaml :: [Double]
+wagExchRawPaml =
+ [ 55.15710
+ , 50.98480
+ , 63.53460
+ , 73.89980
+ , 14.73040
+ , 542.94200
+ , 102.70400
+ , 52.81910
+ , 26.52560
+ , 3.02949
+ , 90.85980
+ , 303.55000
+ , 154.36400
+ , 61.67830
+ , 9.88179
+ , 158.28500
+ , 43.91570
+ , 94.71980
+ , 617.41600
+ , 2.13520
+ , 546.94700
+ , 141.67200
+ , 58.46650
+ , 112.55600
+ , 86.55840
+ , 30.66740
+ , 33.00520
+ , 56.77170
+ , 31.69540
+ , 213.71500
+ , 395.62900
+ , 93.06760
+ , 24.89720
+ , 429.41100
+ , 57.00250
+ , 24.94100
+ , 19.33350
+ , 18.69790
+ , 55.42360
+ , 3.94370
+ , 17.01350
+ , 11.39170
+ , 12.73950
+ , 3.04501
+ , 13.81900
+ , 39.79150
+ , 49.76710
+ , 13.15280
+ , 8.48047
+ , 38.42870
+ , 86.94890
+ , 15.42630
+ , 6.13037
+ , 49.94620
+ , 317.09700
+ , 90.62650
+ , 535.14200
+ , 301.20100
+ , 47.98550
+ , 7.40339
+ , 389.49000
+ , 258.44300
+ , 37.35580
+ , 89.04320
+ , 32.38320
+ , 25.75550
+ , 89.34960
+ , 68.31620
+ , 19.82210
+ , 10.37540
+ , 39.04820
+ , 154.52600
+ , 31.51240
+ , 17.41000
+ , 40.41410
+ , 425.74600
+ , 485.40200
+ , 93.42760
+ , 21.04940
+ , 10.27110
+ , 9.61621
+ , 4.67304
+ , 39.80200
+ , 9.99208
+ , 8.11339
+ , 4.99310
+ , 67.93710
+ , 105.94700
+ , 211.51700
+ , 8.88360
+ , 119.06300
+ , 143.85500
+ , 67.94890
+ , 19.50810
+ , 42.39840
+ , 10.94040
+ , 93.33720
+ , 68.23550
+ , 24.35700
+ , 69.61980
+ , 9.99288
+ , 41.58440
+ , 55.68960
+ , 17.13290
+ , 16.14440
+ , 337.07900
+ , 122.41900
+ , 397.42300
+ , 107.17600
+ , 140.76600
+ , 102.88700
+ , 70.49390
+ , 134.18200
+ , 74.01690
+ , 31.94400
+ , 34.47390
+ , 96.71300
+ , 49.39050
+ , 54.59310
+ , 161.32800
+ , 212.11100
+ , 55.44130
+ , 203.00600
+ , 37.48660
+ , 51.29840
+ , 85.79280
+ , 82.27650
+ , 22.58330
+ , 47.33070
+ , 145.81600
+ , 32.66220
+ , 138.69800
+ , 151.61200
+ , 17.19030
+ , 79.53840
+ , 437.80200
+ , 11.31330
+ , 116.39200
+ , 7.19167
+ , 12.97670
+ , 71.70700
+ , 21.57370
+ , 15.65570
+ , 33.69830
+ , 26.25690
+ , 21.24830
+ , 66.53090
+ , 13.75050
+ , 51.57060
+ , 152.96400
+ , 13.94050
+ , 52.37420
+ , 11.08640
+ , 24.07350
+ , 38.15330
+ , 108.60000
+ , 32.57110
+ , 54.38330
+ , 22.77100
+ , 19.63030
+ , 10.36040
+ , 387.34400
+ , 42.01700
+ , 39.86180
+ , 13.32640
+ , 42.84370
+ , 645.42800
+ , 21.60460
+ , 78.69930
+ , 29.11480
+ , 248.53900
+ , 200.60100
+ , 25.18490
+ , 19.62460
+ , 15.23350
+ , 100.21400
+ , 30.12810
+ , 58.87310
+ , 18.72470
+ , 11.83580
+ , 782.13000
+ , 180.03400
+ , 30.54340
+ , 205.84500
+ , 64.98920
+ , 31.48870
+ , 23.27390
+ , 138.82300
+ , 36.53690
+ , 31.47300
+ ]
+
+-- WAG exchangeability matrix n alphabetical order.
+wagExch :: ExchangeabilityMatrix
+wagExch = pamlToAlphaMat $ exchFromListLower n wagExchRawPaml
+
+-- WAG stationary distribution in PAML order.
+wagStatDistPaml :: StationaryDistribution
+wagStatDistPaml = normalizeSumVec 1.0 $ fromList
+ [ 0.0866279
+ , 0.043972
+ , 0.0390894
+ , 0.0570451
+ , 0.0193078
+ , 0.0367281
+ , 0.0580589
+ , 0.0832518
+ , 0.0244313
+ , 0.048466
+ , 0.086209
+ , 0.0620286
+ , 0.0195027
+ , 0.0384319
+ , 0.0457631
+ , 0.0695179
+ , 0.0610127
+ , 0.0143859
+ , 0.0352742
+ , 0.0708957
+ ]
+
+-- WAG stationary distribution in alphabetical order.
+wagStatDist :: StationaryDistribution
+wagStatDist = pamlToAlphaVec wagStatDistPaml
+
+-- | LG substitution model.
+wag :: SubstitutionModel
+wag = substitutionModel Protein "WAG" [] wagStatDist wagExch
+
+-- | LG substitution model with maybe a name and a custom stationary distribution.
+wagCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+wagCustom mnm d = substitutionModel Protein nm [] d wagExch
+ where nm = fromMaybe "WAG-Custom" mnm
+
+uniformExch :: ExchangeabilityMatrix
+uniformExch = matrixSetDiagToZero $ matrix n $ replicate (n * n) 1.0
+
+poissonExch :: ExchangeabilityMatrix
+poissonExch = uniformExch
+
+-- | Poisson substitution model.
+poisson :: SubstitutionModel
+poisson = substitutionModel Protein "Poisson" [] (uniformVec n) poissonExch
+
+-- | Poisson substitution model with maybe a name and a custom stationary distribution.
+poissonCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel
+poissonCustom mnm d = substitutionModel Protein nm [] d poissonExch
+ where nm = fromMaybe "Poisson-Custom" mnm
+
+-- | General time reversible (GTR) substitution model for amino acids.
+gtr20 :: [Double] -> StationaryDistribution -> SubstitutionModel
+gtr20 es d = substitutionModel Protein "GTR" es d e
+ where e = exchFromListUpper n es
diff --git a/src/ELynx/Data/MarkovProcess/CXXModels.hs b/src/ELynx/Data/MarkovProcess/CXXModels.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/CXXModels.hs
@@ -0,0 +1,146 @@
+{- |
+Module : ELynx.Data.MarkovProcess.CXXModels
+Description : C10 to C60 models
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Feb 26 16:44:33 2019.
+
+Quang, L. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
+phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
+
+XXX: For now, I only provide Poisson exchangeabilities.
+
+-}
+
+module ELynx.Data.MarkovProcess.CXXModels
+ ( cxx
+ )
+where
+
+import Data.List.NonEmpty ( fromList )
+
+import ELynx.Data.MarkovProcess.AminoAcid
+import ELynx.Data.MarkovProcess.CXXModelsData
+import qualified ELynx.Data.MarkovProcess.MixtureModel
+ as M
+import ELynx.Data.MarkovProcess.RateMatrix
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+
+-- | Create CXX model with given number of components and probably with custom
+-- weights.
+cxx :: Int -> Maybe [M.Weight] -> M.MixtureModel
+cxx 10 (Just ws) = c10CustomWeights ws
+cxx 20 (Just ws) = c20CustomWeights ws
+cxx 30 (Just ws) = c30CustomWeights ws
+cxx 40 (Just ws) = c40CustomWeights ws
+cxx 50 (Just ws) = c50CustomWeights ws
+cxx 60 (Just ws) = c60CustomWeights ws
+cxx 10 Nothing = c10
+cxx 20 Nothing = c20
+cxx 30 Nothing = c30
+cxx 40 Nothing = c40
+cxx 50 Nothing = c50
+cxx 60 Nothing = c60
+cxx n _ =
+ error $ "cxx: cannot create CXX model with " ++ show n ++ " components."
+
+-- | C10 model.
+c10 :: M.MixtureModel
+c10 = cxxFromStatDistsAndWeights c10Weights c10StatDists
+
+-- | C20 model.
+c20 :: M.MixtureModel
+c20 = cxxFromStatDistsAndWeights c20Weights c20StatDists
+
+-- | C30 model.
+c30 :: M.MixtureModel
+c30 = cxxFromStatDistsAndWeights c30Weights c30StatDists
+
+-- | C40 model.
+c40 :: M.MixtureModel
+c40 = cxxFromStatDistsAndWeights c40Weights c40StatDists
+
+-- | C50 model.
+c50 :: M.MixtureModel
+c50 = cxxFromStatDistsAndWeights c50Weights c50StatDists
+
+-- | C60 model.
+c60 :: M.MixtureModel
+c60 = cxxFromStatDistsAndWeights c60Weights c60StatDists
+
+-- | C10 model with custom weights.
+c10CustomWeights :: [M.Weight] -> M.MixtureModel
+c10CustomWeights ws
+ | length ws == 10 = cxxFromStatDistsAndWeights ws c10StatDists
+ | otherwise = error "Number of weights does not match C10 model."
+
+-- | C20 model with custom weights.
+c20CustomWeights :: [M.Weight] -> M.MixtureModel
+c20CustomWeights ws
+ | length ws == 20 = cxxFromStatDistsAndWeights ws c20StatDists
+ | otherwise = error "Number of weights does not match C20 model."
+
+-- | C30 model with custom weights.
+c30CustomWeights :: [M.Weight] -> M.MixtureModel
+c30CustomWeights ws
+ | length ws == 30 = cxxFromStatDistsAndWeights ws c30StatDists
+ | otherwise = error "Number of weights does not match C30 model."
+
+-- | C40 model with custom weights.
+c40CustomWeights :: [M.Weight] -> M.MixtureModel
+c40CustomWeights ws
+ | length ws == 40 = cxxFromStatDistsAndWeights ws c40StatDists
+ | otherwise = error "Number of weights does not match C40 model."
+
+-- | C50 model with custom weights.
+c50CustomWeights :: [M.Weight] -> M.MixtureModel
+c50CustomWeights ws
+ | length ws == 50 = cxxFromStatDistsAndWeights ws c50StatDists
+ | otherwise = error "Number of weights does not match C50 model."
+
+-- | C60 model with custom weights.
+c60CustomWeights :: [M.Weight] -> M.MixtureModel
+c60CustomWeights ws
+ | length ws == 60 = cxxFromStatDistsAndWeights ws c60StatDists
+ | otherwise = error "Number of weights does not match C60 model."
+
+cxxName :: Int -> String
+cxxName nComps = 'C' : show nComps
+
+componentName :: Int -> Int -> String
+componentName nComps comp = cxxName nComps ++ "; component " ++ show comp
+
+-- Keep in mind, that when using different exchangeabilities, I have to decide
+-- about global or local normalization.
+cxxSubstitutionModelFromStatDist
+ :: Int -> Int -> StationaryDistribution -> S.SubstitutionModel
+cxxSubstitutionModelFromStatDist nComps comp d = poissonCustom
+ (Just name)
+ (normalizeSD d)
+ where name = componentName nComps comp
+
+cxxSubstitutionModelsFromStatDists
+ :: [StationaryDistribution] -> [S.SubstitutionModel]
+cxxSubstitutionModelsFromStatDists ds = zipWith
+ (cxxSubstitutionModelFromStatDist nComp)
+ [1 ..]
+ ds
+ where nComp = length ds
+
+-- XXX: The use of `Data.List.NonEmpty.fromList` is daring, but since this
+-- function is not exported and only applied to predefined non-empty lists, it
+-- should be OK.
+cxxFromStatDistsAndWeights
+ :: [M.Weight] -> [StationaryDistribution] -> M.MixtureModel
+cxxFromStatDistsAndWeights ws ds = M.fromSubstitutionModels (cxxName n)
+ (fromList ws)
+ sms
+ where
+ n = length ds
+ sms = fromList $ cxxSubstitutionModelsFromStatDists ds
diff --git a/src/ELynx/Data/MarkovProcess/CXXModelsData.hs b/src/ELynx/Data/MarkovProcess/CXXModelsData.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/CXXModelsData.hs
@@ -0,0 +1,4722 @@
+{- |
+Module : ELynx.Data.MarkovProcess.CXXModelsData
+Description : Stationary distributions and weights
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Feb 26 17:17:35 2019.
+
+Quang, L. S., Gascuel, O. & Lartillot, N. Empirical profile mixture models for
+phylogenetic reconstruction. Bioinformatics 24, 2317–2323 (2008).
+
+-}
+
+module ELynx.Data.MarkovProcess.CXXModelsData
+ ( c10StatDists
+ , c10Weights
+ , c20StatDists
+ , c20Weights
+ , c30StatDists
+ , c30Weights
+ , c40StatDists
+ , c40Weights
+ , c50StatDists
+ , c50Weights
+ , c60StatDists
+ , c60Weights
+ )
+where
+
+import qualified Data.Vector.Storable as V
+
+import ELynx.Data.MarkovProcess.RateMatrix
+
+-- | Stationary distribution of C10 model.
+c10StatDists :: [StationaryDistribution]
+c10StatDists = map
+ V.fromList
+ [ [ 0.408257
+ , 0.0349388
+ , 0.00698709
+ , 0.00978467
+ , 0.00616043
+ , 0.122161
+ , 0.00391518
+ , 0.0125784
+ , 0.00596702
+ , 0.0158339
+ , 0.00813132
+ , 0.00962854
+ , 0.0394156
+ , 0.00752797
+ , 0.0081783
+ , 0.168245
+ , 0.0658133
+ , 0.0604427
+ , 0.00187516
+ , 0.00415797
+ ]
+ , [ 0.102776
+ , 0.0149663
+ , 0.0155944
+ , 0.0419667
+ , 0.0180729
+ , 0.0138806
+ , 0.0158865
+ , 0.106608
+ , 0.0436344
+ , 0.113194
+ , 0.04378
+ , 0.0213272
+ , 0.0223251
+ , 0.0440685
+ , 0.0418664
+ , 0.0529608
+ , 0.108174
+ , 0.160665
+ , 0.00451472
+ , 0.0137374
+ ]
+ , [ 0.0351766
+ , 0.00787065
+ , 0.000676874
+ , 0.00196868
+ , 0.0126221
+ , 0.00224206
+ , 0.00128783
+ , 0.351582
+ , 0.00188565
+ , 0.127818
+ , 0.0242632
+ , 0.00165915
+ , 0.00297716
+ , 0.00165596
+ , 0.00196786
+ , 0.00499981
+ , 0.0255378
+ , 0.388864
+ , 0.00119078
+ , 0.00375393
+ ]
+ , [ 0.0408514
+ , 0.00376029
+ , 0.233381
+ , 0.0901239
+ , 0.00251082
+ , 0.115833
+ , 0.0373197
+ , 0.00255236
+ , 0.0485017
+ , 0.00521646
+ , 0.00225718
+ , 0.218565
+ , 0.0108334
+ , 0.0380451
+ , 0.0269887
+ , 0.0804527
+ , 0.030288
+ , 0.00444811
+ , 0.00108153
+ , 0.00698909
+ ]
+ , [ 0.0185493
+ , 0.00704165
+ , 0.000977506
+ , 0.00248916
+ , 0.073333
+ , 0.00289529
+ , 0.0040104
+ , 0.163242
+ , 0.00435709
+ , 0.444308
+ , 0.120282
+ , 0.00248957
+ , 0.00488276
+ , 0.00835394
+ , 0.00623624
+ , 0.00516424
+ , 0.0131807
+ , 0.0968581
+ , 0.00687598
+ , 0.0144734
+ ]
+ , [ 0.110675
+ , 0.00148349
+ , 0.163644
+ , 0.263846
+ , 0.00232568
+ , 0.0325228
+ , 0.0163804
+ , 0.00683349
+ , 0.0677158
+ , 0.014068
+ , 0.00489881
+ , 0.0405186
+ , 0.0298982
+ , 0.0877962
+ , 0.035219
+ , 0.0562888
+ , 0.0426922
+ , 0.0181079
+ , 0.0010339
+ , 0.00405223
+ ]
+ , [ 0.0522658
+ , 0.0143325
+ , 0.0297745
+ , 0.0388387
+ , 0.0624033
+ , 0.0228101
+ , 0.155164
+ , 0.0187406
+ , 0.0439469
+ , 0.065378
+ , 0.0207189
+ , 0.0714837
+ , 0.0145475
+ , 0.073654
+ , 0.0668295
+ , 0.0549018
+ , 0.037014
+ , 0.0267512
+ , 0.0193757
+ , 0.111069
+ ]
+ , [ 0.0116587
+ , 0.0105341
+ , 0.00217425
+ , 0.00242511
+ , 0.365099
+ , 0.00347091
+ , 0.0366787
+ , 0.0187185
+ , 0.00266947
+ , 0.067649
+ , 0.0143535
+ , 0.00640111
+ , 0.00311599
+ , 0.00402037
+ , 0.00509901
+ , 0.00948485
+ , 0.00737139
+ , 0.0206341
+ , 0.0509565
+ , 0.357486
+ ]
+ , [ 0.0627196
+ , 0.00526629
+ , 0.0236193
+ , 0.0686285
+ , 0.00391818
+ , 0.0256175
+ , 0.0332612
+ , 0.0128968
+ , 0.227084
+ , 0.0305628
+ , 0.0124037
+ , 0.0428629
+ , 0.0140441
+ , 0.109811
+ , 0.203878
+ , 0.0483152
+ , 0.0463378
+ , 0.0197063
+ , 0.00251435
+ , 0.00655211
+ ]
+ , [ 0.114552
+ , 0.00985495
+ , 0.0416192
+ , 0.0364908
+ , 0.0046606
+ , 0.0503818
+ , 0.0165233
+ , 0.00929495
+ , 0.0423027
+ , 0.0139154
+ , 0.00822408
+ , 0.0750615
+ , 0.0379222
+ , 0.0339625
+ , 0.0324009
+ , 0.261065
+ , 0.184583
+ , 0.0195769
+ , 0.0017549
+ , 0.00585383
+ ]
+ ]
+
+-- | Weights of C10 model.
+c10Weights :: [Double]
+c10Weights =
+ [ 0.119134
+ , 0.0874372
+ , 0.103711
+ , 0.0922585
+ , 0.107049
+ , 0.132995
+ , 0.0538028
+ , 0.0691986
+ , 0.131994
+ , 0.10242
+ ]
+
+-- | Stationary distribution of C20 model.
+c20StatDists :: [StationaryDistribution]
+c20StatDists = map
+ V.fromList
+ [ [ 0.0862413
+ , 0.0130505
+ , 0.0329909
+ , 0.0184527
+ , 0.00441553
+ , 0.0366905
+ , 0.0108013
+ , 0.00979071
+ , 0.0220195
+ , 0.0112826
+ , 0.00878215
+ , 0.0791293
+ , 0.0189273
+ , 0.0169047
+ , 0.0171944
+ , 0.317815
+ , 0.27117
+ , 0.0179753
+ , 0.00153173
+ , 0.00483429
+ ]
+ , [ 0.203558
+ , 0.0348667
+ , 0.00316561
+ , 0.00708594
+ , 0.0112429
+ , 0.0195236
+ , 0.0024392
+ , 0.115257
+ , 0.00423808
+ , 0.0789777
+ , 0.0309187
+ , 0.00770524
+ , 0.0164189
+ , 0.00640441
+ , 0.00509808
+ , 0.0496777
+ , 0.111895
+ , 0.284906
+ , 0.00177626
+ , 0.00484482
+ ]
+ , [ 0.0211547
+ , 0.00481886
+ , 0.000549287
+ , 0.00145396
+ , 0.0128252
+ , 0.00114309
+ , 0.00113464
+ , 0.392846
+ , 0.00135799
+ , 0.125064
+ , 0.0209789
+ , 0.0012755
+ , 0.00202472
+ , 0.00123288
+ , 0.00149462
+ , 0.00262407
+ , 0.0171914
+ , 0.386068
+ , 0.00115911
+ , 0.0036028
+ ]
+ , [ 0.0376904
+ , 0.00640738
+ , 0.0109469
+ , 0.0358365
+ , 0.00363498
+ , 0.0191107
+ , 0.0329514
+ , 0.0101712
+ , 0.289763
+ , 0.0237496
+ , 0.00965289
+ , 0.0365411
+ , 0.0105337
+ , 0.0893564
+ , 0.28852
+ , 0.0356314
+ , 0.0355927
+ , 0.0144622
+ , 0.00279252
+ , 0.00665572
+ ]
+ , [ 0.00845978
+ , 0.0084909
+ , 0.00244879
+ , 0.00250555
+ , 0.342046
+ , 0.00242771
+ , 0.0433214
+ , 0.0097713
+ , 0.0026741
+ , 0.0380507
+ , 0.00807248
+ , 0.00725259
+ , 0.00214187
+ , 0.00427815
+ , 0.00535899
+ , 0.00804189
+ , 0.00553221
+ , 0.012141
+ , 0.049484
+ , 0.4375
+ ]
+ , [ 0.17599
+ , 0.00175587
+ , 0.130126
+ , 0.218217
+ , 0.0025277
+ , 0.0409535
+ , 0.0130708
+ , 0.00856221
+ , 0.0542946
+ , 0.0159531
+ , 0.00540458
+ , 0.0332846
+ , 0.037102
+ , 0.0707184
+ , 0.0290429
+ , 0.0793481
+ , 0.0540083
+ , 0.0249553
+ , 0.00105921
+ , 0.00362591
+ ]
+ , [ 0.16344
+ , 0.00886599
+ , 0.0374273
+ , 0.0220612
+ , 0.00306413
+ , 0.529672
+ , 0.00900061
+ , 0.00175694
+ , 0.0167118
+ , 0.00611563
+ , 0.00293908
+ , 0.0438702
+ , 0.0126458
+ , 0.0137555
+ , 0.0195541
+ , 0.0829343
+ , 0.0142836
+ , 0.00579857
+ , 0.00286407
+ , 0.00323983
+ ]
+ , [ 0.0917469
+ , 0.0284015
+ , 0.0133819
+ , 0.0196876
+ , 0.0998479
+ , 0.0249899
+ , 0.0449766
+ , 0.0583556
+ , 0.0164916
+ , 0.115501
+ , 0.0395995
+ , 0.0290699
+ , 0.0209916
+ , 0.0255085
+ , 0.0265853
+ , 0.0736483
+ , 0.0661518
+ , 0.0831856
+ , 0.0246464
+ , 0.0972327
+ ]
+ , [ 0.0646701
+ , 0.00771176
+ , 0.0168734
+ , 0.0544978
+ , 0.0219148
+ , 0.0148894
+ , 0.0313852
+ , 0.0505983
+ , 0.0907931
+ , 0.184428
+ , 0.077484
+ , 0.0228907
+ , 0.0105004
+ , 0.0996415
+ , 0.0988016
+ , 0.0321196
+ , 0.0411766
+ , 0.0505824
+ , 0.0084303
+ , 0.0206106
+ ]
+ , [ 0.0135994
+ , 0.010009
+ , 0.00079517
+ , 0.00180118
+ , 0.264097
+ , 0.00267946
+ , 0.00724019
+ , 0.0814027
+ , 0.00251581
+ , 0.366142
+ , 0.0734965
+ , 0.00184694
+ , 0.00389941
+ , 0.00464208
+ , 0.00434084
+ , 0.00436688
+ , 0.00752485
+ , 0.0573473
+ , 0.0261565
+ , 0.0660971
+ ]
+ , [ 0.147804
+ , 0.00488258
+ , 0.0534743
+ , 0.0727246
+ , 0.00299039
+ , 0.0907726
+ , 0.0262289
+ , 0.00357811
+ , 0.105166
+ , 0.0126777
+ , 0.00596218
+ , 0.072663
+ , 0.0156558
+ , 0.0757166
+ , 0.0842845
+ , 0.14599
+ , 0.0634877
+ , 0.00927198
+ , 0.00159285
+ , 0.00507607
+ ]
+ , [ 0.0186377
+ , 0.00549689
+ , 0.00083297
+ , 0.00202485
+ , 0.0385383
+ , 0.00217135
+ , 0.0023666
+ , 0.202081
+ , 0.00291207
+ , 0.437038
+ , 0.124186
+ , 0.00198652
+ , 0.00406723
+ , 0.00658901
+ , 0.00420552
+ , 0.00461774
+ , 0.0149904
+ , 0.118938
+ , 0.00268717
+ , 0.00563241
+ ]
+ , [ 0.0477624
+ , 0.00757917
+ , 0.0141349
+ , 0.0462688
+ , 0.0130691
+ , 0.00523279
+ , 0.0165352
+ , 0.17415
+ , 0.0577575
+ , 0.112125
+ , 0.0330288
+ , 0.0209574
+ , 0.0124375
+ , 0.0429297
+ , 0.0505743
+ , 0.0264989
+ , 0.0951755
+ , 0.20937
+ , 0.00316605
+ , 0.0112466
+ ]
+ , [ 0.416419
+ , 0.0406938
+ , 0.00451317
+ , 0.00632298
+ , 0.00484384
+ , 0.0946185
+ , 0.00310574
+ , 0.00764432
+ , 0.00389418
+ , 0.00998854
+ , 0.00693232
+ , 0.00917014
+ , 0.0187841
+ , 0.00613205
+ , 0.00561008
+ , 0.236077
+ , 0.0746275
+ , 0.0459225
+ , 0.00121726
+ , 0.00348258
+ ]
+ , [ 0.0402296
+ , 0.0124783
+ , 0.0365524
+ , 0.0372197
+ , 0.0459095
+ , 0.0233618
+ , 0.210831
+ , 0.00934787
+ , 0.0482411
+ , 0.0360561
+ , 0.010029
+ , 0.103665
+ , 0.0098504
+ , 0.0826558
+ , 0.0735203
+ , 0.0533383
+ , 0.0310209
+ , 0.015248
+ , 0.0140077
+ , 0.106438
+ ]
+ , [ 0.0323453
+ , 0.00359763
+ , 0.24315
+ , 0.0710274
+ , 0.00244293
+ , 0.101607
+ , 0.0366225
+ , 0.00314108
+ , 0.0470129
+ , 0.00519805
+ , 0.00240287
+ , 0.252045
+ , 0.00948378
+ , 0.0330831
+ , 0.0236283
+ , 0.0848355
+ , 0.0359083
+ , 0.00487046
+ , 0.000873093
+ , 0.00672477
+ ]
+ , [ 0.147626
+ , 0.00323272
+ , 0.0403052
+ , 0.0576893
+ , 0.00471772
+ , 0.0330851
+ , 0.0146393
+ , 0.0108267
+ , 0.0451351
+ , 0.0256201
+ , 0.00586514
+ , 0.0211973
+ , 0.347371
+ , 0.0371554
+ , 0.0334507
+ , 0.0892065
+ , 0.0485899
+ , 0.0282336
+ , 0.00163587
+ , 0.00441772
+ ]
+ , [ 0.103145
+ , 0.00617625
+ , 0.0386402
+ , 0.0923369
+ , 0.00676664
+ , 0.0202338
+ , 0.0246762
+ , 0.0376904
+ , 0.0921699
+ , 0.0376284
+ , 0.0161883
+ , 0.0435172
+ , 0.0128302
+ , 0.0786603
+ , 0.0717748
+ , 0.095145
+ , 0.137857
+ , 0.0740454
+ , 0.00221447
+ , 0.00830416
+ ]
+ , [ 0.0837543
+ , 0.00207351
+ , 0.0804871
+ , 0.194776
+ , 0.00230634
+ , 0.022903
+ , 0.0268459
+ , 0.00740798
+ , 0.145929
+ , 0.019025
+ , 0.00673952
+ , 0.0518811
+ , 0.0085616
+ , 0.14565
+ , 0.0899383
+ , 0.045574
+ , 0.0451081
+ , 0.0150303
+ , 0.00107713
+ , 0.00493253
+ ]
+ , [ 0.0578736
+ , 0.00111308
+ , 0.294674
+ , 0.34021
+ , 0.00170349
+ , 0.0293911
+ , 0.0139817
+ , 0.00305257
+ , 0.0363365
+ , 0.00626119
+ , 0.0027296
+ , 0.0491422
+ , 0.0156106
+ , 0.059825
+ , 0.0138314
+ , 0.0358045
+ , 0.0249942
+ , 0.00876742
+ , 0.000866434
+ , 0.0038313
+ ]
+ ]
+
+-- | Weights of C20 model.
+c20Weights :: [Double]
+c20Weights =
+ [ 0.0559911
+ , 0.0514825
+ , 0.0812922
+ , 0.0721977
+ , 0.0556719
+ , 0.0331003
+ , 0.0589502
+ , 0.0263757
+ , 0.0307584
+ , 0.0376701
+ , 0.0303058
+ , 0.0808776
+ , 0.0263349
+ , 0.0579101
+ , 0.0371248
+ , 0.0586868
+ , 0.0561479
+ , 0.0349811
+ , 0.0544937
+ , 0.0596472
+ ]
+
+-- | Stationary distribution of C30 model.
+c30StatDists :: [StationaryDistribution]
+c30StatDists = map
+ V.fromList
+ [ [ 0.110045
+ , 0.00190472
+ , 0.159541
+ , 0.109896
+ , 0.00166295
+ , 0.0684302
+ , 0.0137951
+ , 0.00262831
+ , 0.0358554
+ , 0.00733965
+ , 0.00247064
+ , 0.0640338
+ , 0.166936
+ , 0.0310187
+ , 0.0171295
+ , 0.138179
+ , 0.0568343
+ , 0.00823656
+ , 0.000466112
+ , 0.00359702
+ ]
+ , [ 0.0874125
+ , 0.00498264
+ , 0.032612
+ , 0.0951701
+ , 0.00489966
+ , 0.0144043
+ , 0.0210627
+ , 0.0399884
+ , 0.11472
+ , 0.0301585
+ , 0.0126489
+ , 0.0382152
+ , 0.0137397
+ , 0.0798169
+ , 0.080632
+ , 0.087377
+ , 0.155862
+ , 0.0793881
+ , 0.00151228
+ , 0.00539745
+ ]
+ , [ 0.0225477
+ , 0.00500182
+ , 0.000595928
+ , 0.00150305
+ , 0.0089216
+ , 0.0011571
+ , 0.000937432
+ , 0.394469
+ , 0.00136009
+ , 0.0889573
+ , 0.0189103
+ , 0.00130346
+ , 0.0018312
+ , 0.00114366
+ , 0.00149005
+ , 0.00283364
+ , 0.0189813
+ , 0.425056
+ , 0.000669375
+ , 0.00233037
+ ]
+ , [ 0.0602158
+ , 0.000952546
+ , 0.290008
+ , 0.361087
+ , 0.00146256
+ , 0.0281926
+ , 0.0130501
+ , 0.00305162
+ , 0.0352705
+ , 0.00604019
+ , 0.00274606
+ , 0.0414988
+ , 0.0127175
+ , 0.0621611
+ , 0.0136833
+ , 0.0318109
+ , 0.022528
+ , 0.00932584
+ , 0.000794803
+ , 0.00340246
+ ]
+ , [ 0.0101224
+ , 0.00859894
+ , 0.000637919
+ , 0.00112496
+ , 0.278538
+ , 0.00240852
+ , 0.00477534
+ , 0.0701153
+ , 0.00167485
+ , 0.413591
+ , 0.0744863
+ , 0.00129289
+ , 0.00404666
+ , 0.00350286
+ , 0.00283449
+ , 0.00370872
+ , 0.00523793
+ , 0.040886
+ , 0.0200223
+ , 0.0523939
+ ]
+ , [ 0.133583
+ , 0.00105145
+ , 0.112578
+ , 0.209957
+ , 0.00167936
+ , 0.0207552
+ , 0.012133
+ , 0.00735265
+ , 0.0771772
+ , 0.0133278
+ , 0.00305717
+ , 0.0213892
+ , 0.18902
+ , 0.0565844
+ , 0.028479
+ , 0.0484054
+ , 0.0373318
+ , 0.0225174
+ , 0.000926699
+ , 0.00269464
+ ]
+ , [ 0.0408277
+ , 0.0153918
+ , 0.00306349
+ , 0.00660109
+ , 0.157505
+ , 0.00581131
+ , 0.0245212
+ , 0.148751
+ , 0.00759232
+ , 0.16378
+ , 0.0385527
+ , 0.00804649
+ , 0.00583522
+ , 0.0102922
+ , 0.0124492
+ , 0.0151579
+ , 0.033222
+ , 0.154771
+ , 0.0264937
+ , 0.121334
+ ]
+ , [ 0.246906
+ , 0.103941
+ , 0.00274183
+ , 0.00549448
+ , 0.0251776
+ , 0.0373263
+ , 0.00857523
+ , 0.0292404
+ , 0.00561231
+ , 0.0535091
+ , 0.0302246
+ , 0.016893
+ , 0.00780989
+ , 0.0103988
+ , 0.0106279
+ , 0.164235
+ , 0.123989
+ , 0.0955868
+ , 0.00531559
+ , 0.0163954
+ ]
+ , [ 0.0549429
+ , 0.0099281
+ , 0.00929153
+ , 0.0417085
+ , 0.024386
+ , 0.0105564
+ , 0.0363512
+ , 0.0569585
+ , 0.115252
+ , 0.168183
+ , 0.0592328
+ , 0.0202958
+ , 0.00830554
+ , 0.0906036
+ , 0.130543
+ , 0.0283779
+ , 0.0412594
+ , 0.0592101
+ , 0.00963554
+ , 0.024978
+ ]
+ , [ 0.0462773
+ , 0.0172727
+ , 0.0182504
+ , 0.0224266
+ , 0.133632
+ , 0.0160971
+ , 0.135785
+ , 0.0164967
+ , 0.0239396
+ , 0.0598936
+ , 0.0164507
+ , 0.0412365
+ , 0.0117413
+ , 0.0348991
+ , 0.0362984
+ , 0.0454156
+ , 0.0304388
+ , 0.0253979
+ , 0.0330338
+ , 0.235016
+ ]
+ , [ 0.047438
+ , 0.00823324
+ , 0.0112117
+ , 0.0388101
+ , 0.0116644
+ , 0.00559986
+ , 0.0149157
+ , 0.183217
+ , 0.0467851
+ , 0.110069
+ , 0.0356444
+ , 0.0222454
+ , 0.0100245
+ , 0.0374051
+ , 0.041018
+ , 0.0317171
+ , 0.111435
+ , 0.219931
+ , 0.00266856
+ , 0.00996601
+ ]
+ , [ 0.0213608
+ , 0.00610249
+ , 0.00129412
+ , 0.00362973
+ , 0.0371808
+ , 0.0030017
+ , 0.00384259
+ , 0.130947
+ , 0.00545678
+ , 0.456699
+ , 0.194784
+ , 0.0039879
+ , 0.00407473
+ , 0.0139566
+ , 0.00699762
+ , 0.00769915
+ , 0.0198019
+ , 0.0693208
+ , 0.00340864
+ , 0.00645457
+ ]
+ , [ 0.0919632
+ , 0.0117031
+ , 0.0306717
+ , 0.0171908
+ , 0.00415894
+ , 0.0370685
+ , 0.0100793
+ , 0.00931237
+ , 0.0205386
+ , 0.0097241
+ , 0.00757673
+ , 0.0764682
+ , 0.0179686
+ , 0.016006
+ , 0.0160005
+ , 0.325447
+ , 0.274438
+ , 0.0178218
+ , 0.00138874
+ , 0.00447397
+ ]
+ , [ 0.464925
+ , 0.0233329
+ , 0.00507317
+ , 0.00579942
+ , 0.00255882
+ , 0.149524
+ , 0.00232984
+ , 0.00433612
+ , 0.00285254
+ , 0.00559955
+ , 0.00393132
+ , 0.00753048
+ , 0.0186467
+ , 0.00435713
+ , 0.00430132
+ , 0.215019
+ , 0.047703
+ , 0.0292668
+ , 0.00090381
+ , 0.00200872
+ ]
+ , [ 0.205133
+ , 0.00209159
+ , 0.107098
+ , 0.198973
+ , 0.00182351
+ , 0.0487574
+ , 0.0127143
+ , 0.00581247
+ , 0.0667787
+ , 0.0133472
+ , 0.00437834
+ , 0.0339418
+ , 0.0110998
+ , 0.0822742
+ , 0.0439661
+ , 0.0873962
+ , 0.0519782
+ , 0.0193174
+ , 0.00073616
+ , 0.00238214
+ ]
+ , [ 0.026369
+ , 0.00394624
+ , 0.311772
+ , 0.0694354
+ , 0.00233519
+ , 0.0799842
+ , 0.0309615
+ , 0.00275212
+ , 0.0288631
+ , 0.00385797
+ , 0.00183637
+ , 0.272716
+ , 0.00624576
+ , 0.0218979
+ , 0.0133614
+ , 0.0798729
+ , 0.0324143
+ , 0.00427053
+ , 0.000722966
+ , 0.00638577
+ ]
+ , [ 0.15265
+ , 0.00402153
+ , 0.0237392
+ , 0.0377949
+ , 0.00585844
+ , 0.0306214
+ , 0.014193
+ , 0.0123318
+ , 0.0375543
+ , 0.0290062
+ , 0.00644732
+ , 0.016823
+ , 0.38645
+ , 0.0341734
+ , 0.0332784
+ , 0.0880336
+ , 0.0489543
+ , 0.0313553
+ , 0.00182526
+ , 0.00488778
+ ]
+ , [ 0.00802476
+ , 0.00234121
+ , 0.000338596
+ , 0.000781895
+ , 0.0311968
+ , 0.000540383
+ , 0.00100264
+ , 0.317706
+ , 0.00125983
+ , 0.373789
+ , 0.0488212
+ , 0.00063274
+ , 0.00206875
+ , 0.00155079
+ , 0.00174086
+ , 0.00120951
+ , 0.00656968
+ , 0.19446
+ , 0.00163092
+ , 0.00433436
+ ]
+ , [ 0.059995
+ , 0.0016885
+ , 0.0889731
+ , 0.0962701
+ , 0.00118007
+ , 0.0588796
+ , 0.0327277
+ , 0.00214673
+ , 0.182586
+ , 0.00708764
+ , 0.00339794
+ , 0.133492
+ , 0.0141408
+ , 0.0864856
+ , 0.100054
+ , 0.0779002
+ , 0.0448817
+ , 0.00422414
+ , 0.000624903
+ , 0.00326411
+ ]
+ , [ 0.0393521
+ , 0.00990719
+ , 0.0431198
+ , 0.039464
+ , 0.0188681
+ , 0.0282866
+ , 0.209572
+ , 0.00761014
+ , 0.0596434
+ , 0.025834
+ , 0.00845867
+ , 0.142548
+ , 0.00968405
+ , 0.101979
+ , 0.0838171
+ , 0.0624999
+ , 0.0347088
+ , 0.0127686
+ , 0.00546458
+ , 0.0564145
+ ]
+ , [ 0.00727155
+ , 0.00678525
+ , 0.00276038
+ , 0.00250694
+ , 0.127148
+ , 0.00808347
+ , 0.0113218
+ , 0.00566096
+ , 0.00177351
+ , 0.03942
+ , 0.00798661
+ , 0.00197568
+ , 0.00410981
+ , 0.00433393
+ , 0.0140999
+ , 0.00522444
+ , 0.00430223
+ , 0.00942264
+ , 0.627357
+ , 0.108456
+ ]
+ , [ 0.090707
+ , 0.00636999
+ , 0.0745873
+ , 0.0386802
+ , 0.00288592
+ , 0.475005
+ , 0.016809
+ , 0.00147211
+ , 0.0343856
+ , 0.00551498
+ , 0.00246921
+ , 0.0860678
+ , 0.0112151
+ , 0.0259377
+ , 0.0290062
+ , 0.073111
+ , 0.0153706
+ , 0.00392819
+ , 0.00229148
+ , 0.00418607
+ ]
+ , [ 0.00552919
+ , 0.00721059
+ , 0.00114134
+ , 0.000968304
+ , 0.374409
+ , 0.0016071
+ , 0.0325831
+ , 0.00829184
+ , 0.00138494
+ , 0.0353678
+ , 0.00744868
+ , 0.00460866
+ , 0.00133746
+ , 0.00226922
+ , 0.00246263
+ , 0.00574027
+ , 0.00372796
+ , 0.00988026
+ , 0.0330334
+ , 0.460998
+ ]
+ , [ 0.244326
+ , 0.027388
+ , 0.00315909
+ , 0.00767156
+ , 0.00606194
+ , 0.019609
+ , 0.00201894
+ , 0.101744
+ , 0.00454923
+ , 0.0468424
+ , 0.0201286
+ , 0.00624227
+ , 0.0185219
+ , 0.0053594
+ , 0.00453866
+ , 0.0497754
+ , 0.11708
+ , 0.310493
+ , 0.000957725
+ , 0.00353337
+ ]
+ , [ 0.0863111
+ , 0.00244198
+ , 0.0600903
+ , 0.20361
+ , 0.00293931
+ , 0.0175221
+ , 0.0245245
+ , 0.0105994
+ , 0.148579
+ , 0.027121
+ , 0.00958244
+ , 0.0313963
+ , 0.00682768
+ , 0.167235
+ , 0.0984812
+ , 0.03478
+ , 0.0408211
+ , 0.0202271
+ , 0.00140013
+ , 0.00551054
+ ]
+ , [ 0.0643926
+ , 0.00231659
+ , 0.162821
+ , 0.17627
+ , 0.00430667
+ , 0.0297139
+ , 0.0303504
+ , 0.0088163
+ , 0.072714
+ , 0.0148017
+ , 0.00567484
+ , 0.103121
+ , 0.00992703
+ , 0.0752535
+ , 0.0369049
+ , 0.0926434
+ , 0.083313
+ , 0.0161551
+ , 0.00112371
+ , 0.00938015
+ ]
+ , [ 0.173668
+ , 0.00835966
+ , 0.0285985
+ , 0.0483894
+ , 0.0058274
+ , 0.0781901
+ , 0.0266135
+ , 0.00686419
+ , 0.0964012
+ , 0.0219499
+ , 0.0112303
+ , 0.0520405
+ , 0.0169661
+ , 0.0722447
+ , 0.0943629
+ , 0.15478
+ , 0.0751702
+ , 0.0172524
+ , 0.00287745
+ , 0.00821304
+ ]
+ , [ 0.0347857
+ , 0.00627549
+ , 0.00923552
+ , 0.0323568
+ , 0.00343035
+ , 0.0170288
+ , 0.0306439
+ , 0.00919323
+ , 0.302085
+ , 0.0224429
+ , 0.00937208
+ , 0.0314157
+ , 0.0104447
+ , 0.0861073
+ , 0.307598
+ , 0.0326883
+ , 0.0328713
+ , 0.0130832
+ , 0.00252449
+ , 0.00641713
+ ]
+ , [ 0.108774
+ , 0.0247877
+ , 0.00158232
+ , 0.00417699
+ , 0.0316523
+ , 0.0134703
+ , 0.00247658
+ , 0.164346
+ , 0.00270004
+ , 0.233715
+ , 0.0539213
+ , 0.00326798
+ , 0.0154887
+ , 0.0057932
+ , 0.0051781
+ , 0.0188188
+ , 0.0474912
+ , 0.251283
+ , 0.00376565
+ , 0.00731064
+ ]
+ , [ 0.110101
+ , 0.00726998
+ , 0.0579269
+ , 0.0828181
+ , 0.0269154
+ , 0.0314463
+ , 0.0308557
+ , 0.0530866
+ , 0.029386
+ , 0.109679
+ , 0.0458729
+ , 0.0435099
+ , 0.0296431
+ , 0.0615197
+ , 0.0324325
+ , 0.0715888
+ , 0.0685882
+ , 0.0754042
+ , 0.00623241
+ , 0.0257238
+ ]
+ ]
+
+-- | Weights of C30 model.
+c30Weights :: [Double]
+c30Weights =
+ [ 0.00957833
+ , 0.0248476
+ , 0.0636309
+ , 0.0537939
+ , 0.0295886
+ , 0.0117588
+ , 0.0132013
+ , 0.0236869
+ , 0.0261688
+ , 0.0239822
+ , 0.0257101
+ , 0.0465072
+ , 0.0546795
+ , 0.0536085
+ , 0.0270623
+ , 0.0403914
+ , 0.0474213
+ , 0.0458816
+ , 0.0214037
+ , 0.0290386
+ , 0.0123392
+ , 0.056935
+ , 0.0419688
+ , 0.0339027
+ , 0.0388777
+ , 0.0196344
+ , 0.0233086
+ , 0.0622723
+ , 0.0184803
+ , 0.0203395
+ ]
+
+-- | Stationary distribution of C40 model.
+c40StatDists :: [StationaryDistribution]
+c40StatDists = map
+ V.fromList
+ [ [ 0.066026
+ , 0.00565867
+ , 0.105447
+ , 0.0440361
+ , 0.00131048
+ , 0.0711239
+ , 0.0168195
+ , 0.00390887
+ , 0.036669
+ , 0.0055316
+ , 0.00374124
+ , 0.159982
+ , 0.0176359
+ , 0.0273928
+ , 0.0231862
+ , 0.249769
+ , 0.150708
+ , 0.0065529
+ , 0.000672321
+ , 0.00382902
+ ]
+ , [ 0.0232377
+ , 0.00379875
+ , 0.353209
+ , 0.0739378
+ , 0.00240321
+ , 0.0576668
+ , 0.0315867
+ , 0.00310928
+ , 0.0259363
+ , 0.00387116
+ , 0.00173556
+ , 0.275965
+ , 0.00631169
+ , 0.0197339
+ , 0.0122683
+ , 0.0657068
+ , 0.0270484
+ , 0.00475317
+ , 0.000760289
+ , 0.00696025
+ ]
+ , [ 0.0166487
+ , 0.00366657
+ , 0.000565145
+ , 0.00133563
+ , 0.00827757
+ , 0.000889475
+ , 0.000823185
+ , 0.412937
+ , 0.00119041
+ , 0.0884689
+ , 0.0186055
+ , 0.00126222
+ , 0.001403
+ , 0.00106698
+ , 0.00125948
+ , 0.00213394
+ , 0.0162167
+ , 0.420686
+ , 0.000608205
+ , 0.00195532
+ ]
+ , [ 0.239474
+ , 0.0283812
+ , 0.00447417
+ , 0.010553
+ , 0.00559911
+ , 0.013511
+ , 0.00389298
+ , 0.0765957
+ , 0.0071093
+ , 0.0358495
+ , 0.0199496
+ , 0.0120537
+ , 0.0114266
+ , 0.00865589
+ , 0.00729013
+ , 0.0847799
+ , 0.179728
+ , 0.245468
+ , 0.0009838
+ , 0.00422407
+ ]
+ , [ 0.119461
+ , 0.0150527
+ , 0.0134273
+ , 0.0192173
+ , 0.0550467
+ , 0.0337676
+ , 0.0214746
+ , 0.0579002
+ , 0.0147261
+ , 0.144631
+ , 0.0561243
+ , 0.0294552
+ , 0.0631355
+ , 0.0301538
+ , 0.0233256
+ , 0.0925267
+ , 0.083123
+ , 0.0811758
+ , 0.0131636
+ , 0.0331118
+ ]
+ , [ 0.0567044
+ , 0.00089248
+ , 0.29555
+ , 0.379515
+ , 0.00129723
+ , 0.023047
+ , 0.0118361
+ , 0.0031182
+ , 0.0314206
+ , 0.00601375
+ , 0.00285841
+ , 0.0364734
+ , 0.0124746
+ , 0.0609517
+ , 0.0117359
+ , 0.0300335
+ , 0.0227051
+ , 0.00946396
+ , 0.000773876
+ , 0.00313438
+ ]
+ , [ 0.0179027
+ , 0.016076
+ , 0.000887041
+ , 0.00231821
+ , 0.334486
+ , 0.00398298
+ , 0.0127293
+ , 0.0404651
+ , 0.00279947
+ , 0.167614
+ , 0.0424172
+ , 0.00356977
+ , 0.00201151
+ , 0.00453955
+ , 0.00409671
+ , 0.00758416
+ , 0.00682273
+ , 0.0326045
+ , 0.0518381
+ , 0.245254
+ ]
+ , [ 0.271217
+ , 0.200383
+ , 0.0021017
+ , 0.002323
+ , 0.020299
+ , 0.0502501
+ , 0.0053728
+ , 0.0150685
+ , 0.00206463
+ , 0.0330003
+ , 0.0154811
+ , 0.0141045
+ , 0.0045351
+ , 0.00482641
+ , 0.00564808
+ , 0.17642
+ , 0.0839578
+ , 0.0741934
+ , 0.00462652
+ , 0.0141271
+ ]
+ , [ 0.0894737
+ , 0.00455383
+ , 0.0272183
+ , 0.127508
+ , 0.00565902
+ , 0.0115686
+ , 0.0215746
+ , 0.0469424
+ , 0.138205
+ , 0.0512035
+ , 0.0147657
+ , 0.0190192
+ , 0.00955465
+ , 0.116809
+ , 0.104003
+ , 0.0383954
+ , 0.0836653
+ , 0.0819556
+ , 0.00170794
+ , 0.00621813
+ ]
+ , [ 0.0495441
+ , 0.0182506
+ , 0.0143641
+ , 0.0215379
+ , 0.141805
+ , 0.01402
+ , 0.110854
+ , 0.0247066
+ , 0.0258142
+ , 0.0700288
+ , 0.0188272
+ , 0.0315864
+ , 0.0112101
+ , 0.0316504
+ , 0.0375346
+ , 0.0456094
+ , 0.0361428
+ , 0.0369178
+ , 0.0371985
+ , 0.222397
+ ]
+ , [ 0.170431
+ , 0.000974733
+ , 0.109856
+ , 0.253646
+ , 0.00133213
+ , 0.0249846
+ , 0.010139
+ , 0.00587494
+ , 0.0903324
+ , 0.0116526
+ , 0.00365127
+ , 0.0271109
+ , 0.0293614
+ , 0.09173
+ , 0.0415784
+ , 0.0561766
+ , 0.0479046
+ , 0.02033
+ , 0.000669682
+ , 0.00226373
+ ]
+ , [ 0.0162725
+ , 0.00506141
+ , 0.00101821
+ , 0.00251413
+ , 0.0376246
+ , 0.00219354
+ , 0.00299143
+ , 0.132817
+ , 0.00401204
+ , 0.490444
+ , 0.192993
+ , 0.00218762
+ , 0.00343332
+ , 0.0104414
+ , 0.00548261
+ , 0.00401221
+ , 0.0127074
+ , 0.064772
+ , 0.00321076
+ , 0.00581006
+ ]
+ , [ 0.0823766
+ , 0.00656943
+ , 0.0311745
+ , 0.0675531
+ , 0.00647179
+ , 0.0178962
+ , 0.0251144
+ , 0.0291162
+ , 0.0982302
+ , 0.0287904
+ , 0.0168023
+ , 0.059839
+ , 0.0114045
+ , 0.0686451
+ , 0.0734226
+ , 0.1303
+ , 0.182037
+ , 0.0540271
+ , 0.00227246
+ , 0.00795733
+ ]
+ , [ 0.359497
+ , 0.0251417
+ , 0.00314844
+ , 0.00649627
+ , 0.00920205
+ , 0.119468
+ , 0.00229704
+ , 0.0458767
+ , 0.00501688
+ , 0.0468054
+ , 0.0215569
+ , 0.00334215
+ , 0.0443916
+ , 0.00490143
+ , 0.00724072
+ , 0.0465271
+ , 0.0477755
+ , 0.194216
+ , 0.00245402
+ , 0.00464504
+ ]
+ , [ 0.201558
+ , 0.00323653
+ , 0.095415
+ , 0.153491
+ , 0.00256433
+ , 0.0667292
+ , 0.0155219
+ , 0.00677408
+ , 0.0547323
+ , 0.0165114
+ , 0.0060163
+ , 0.0425386
+ , 0.00919706
+ , 0.0772011
+ , 0.0430162
+ , 0.118598
+ , 0.0625473
+ , 0.0202798
+ , 0.000956551
+ , 0.003115
+ ]
+ , [ 0.104273
+ , 0.00224501
+ , 0.242407
+ , 0.177482
+ , 0.00125703
+ , 0.169782
+ , 0.0132649
+ , 0.00189295
+ , 0.0220652
+ , 0.00425426
+ , 0.00164412
+ , 0.0621646
+ , 0.0317042
+ , 0.0356499
+ , 0.0147062
+ , 0.0778636
+ , 0.0288516
+ , 0.00602502
+ , 0.00069309
+ , 0.00177419
+ ]
+ , [ 0.0781183
+ , 0.0194449
+ , 0.00415417
+ , 0.0116634
+ , 0.0262794
+ , 0.0111524
+ , 0.00635894
+ , 0.135453
+ , 0.00937298
+ , 0.245757
+ , 0.108778
+ , 0.015927
+ , 0.0055294
+ , 0.0240152
+ , 0.0111498
+ , 0.0408519
+ , 0.0860514
+ , 0.148276
+ , 0.00315476
+ , 0.00851085
+ ]
+ , [ 0.0856592
+ , 0.0136073
+ , 0.0135062
+ , 0.00786026
+ , 0.0047153
+ , 0.0245401
+ , 0.00553791
+ , 0.0100592
+ , 0.0127319
+ , 0.0103344
+ , 0.00806758
+ , 0.0441923
+ , 0.0175274
+ , 0.00925906
+ , 0.0101233
+ , 0.340648
+ , 0.357329
+ , 0.019367
+ , 0.00142431
+ , 0.00350998
+ ]
+ , [ 0.0674595
+ , 0.00216342
+ , 0.0662588
+ , 0.0865501
+ , 0.00182127
+ , 0.0368557
+ , 0.0381149
+ , 0.00332388
+ , 0.189974
+ , 0.009384
+ , 0.00394874
+ , 0.116311
+ , 0.0151208
+ , 0.093936
+ , 0.116173
+ , 0.0842204
+ , 0.0565954
+ , 0.00645142
+ , 0.00071873
+ , 0.00461894
+ ]
+ , [ 0.0572262
+ , 0.00153015
+ , 0.179393
+ , 0.199226
+ , 0.00137018
+ , 0.0316472
+ , 0.0291392
+ , 0.00458046
+ , 0.101562
+ , 0.010074
+ , 0.00402046
+ , 0.108388
+ , 0.00636741
+ , 0.0903669
+ , 0.0494724
+ , 0.0621143
+ , 0.0496102
+ , 0.00859413
+ , 0.000666929
+ , 0.00464976
+ ]
+ , [ 0.00360202
+ , 0.00454848
+ , 0.00208716
+ , 0.00178577
+ , 0.0855715
+ , 0.00563916
+ , 0.00649688
+ , 0.00292929
+ , 0.00104198
+ , 0.0232635
+ , 0.00445923
+ , 0.00134555
+ , 0.0024992
+ , 0.00327181
+ , 0.0102713
+ , 0.00306718
+ , 0.00259003
+ , 0.00586684
+ , 0.761782
+ , 0.067881
+ ]
+ , [ 0.203202
+ , 0.00981316
+ , 0.0135012
+ , 0.00838182
+ , 0.00196196
+ , 0.618489
+ , 0.00277479
+ , 0.00118285
+ , 0.00445989
+ , 0.00398268
+ , 0.00206318
+ , 0.0143744
+ , 0.00858704
+ , 0.00445146
+ , 0.00838957
+ , 0.073992
+ , 0.0108922
+ , 0.00607691
+ , 0.00186061
+ , 0.00156387
+ ]
+ , [ 0.00508988
+ , 0.00617765
+ , 0.00161262
+ , 0.00120404
+ , 0.356313
+ , 0.00163342
+ , 0.0393461
+ , 0.00590888
+ , 0.00137137
+ , 0.0249344
+ , 0.00497952
+ , 0.0057093
+ , 0.00141364
+ , 0.00246931
+ , 0.00287408
+ , 0.00595277
+ , 0.00365368
+ , 0.00819341
+ , 0.0357987
+ , 0.485365
+ ]
+ , [ 0.0403336
+ , 0.00815495
+ , 0.00982186
+ , 0.0375407
+ , 0.0119141
+ , 0.00479344
+ , 0.0176736
+ , 0.189342
+ , 0.0607377
+ , 0.105186
+ , 0.03056
+ , 0.0216052
+ , 0.00775506
+ , 0.0383639
+ , 0.0540186
+ , 0.025711
+ , 0.100991
+ , 0.221091
+ , 0.002878
+ , 0.0115277
+ ]
+ , [ 0.0790086
+ , 0.00249479
+ , 0.0546012
+ , 0.199788
+ , 0.00237734
+ , 0.0192656
+ , 0.02707
+ , 0.00756675
+ , 0.155311
+ , 0.0254542
+ , 0.00980244
+ , 0.0309384
+ , 0.00566407
+ , 0.184338
+ , 0.106544
+ , 0.0332371
+ , 0.0359575
+ , 0.0145306
+ , 0.00116828
+ , 0.00488208
+ ]
+ , [ 0.0722241
+ , 0.00647553
+ , 0.119488
+ , 0.134589
+ , 0.0348233
+ , 0.0287815
+ , 0.0699011
+ , 0.0173589
+ , 0.0490342
+ , 0.051987
+ , 0.0154411
+ , 0.067893
+ , 0.0145597
+ , 0.070897
+ , 0.0489728
+ , 0.058958
+ , 0.0425973
+ , 0.0317884
+ , 0.00879138
+ , 0.0554387
+ ]
+ , [ 0.108584
+ , 0.00125026
+ , 0.152967
+ , 0.166485
+ , 0.00145535
+ , 0.0336098
+ , 0.0134902
+ , 0.00388218
+ , 0.0576227
+ , 0.00898614
+ , 0.0024339
+ , 0.0441956
+ , 0.19901
+ , 0.0405398
+ , 0.020645
+ , 0.084675
+ , 0.0454715
+ , 0.0113416
+ , 0.000590283
+ , 0.00276502
+ ]
+ , [ 0.0309526
+ , 0.0065594
+ , 0.00823521
+ , 0.0291974
+ , 0.00368916
+ , 0.0154206
+ , 0.0310385
+ , 0.00982516
+ , 0.306263
+ , 0.02379
+ , 0.00970717
+ , 0.0301337
+ , 0.00950291
+ , 0.0832608
+ , 0.319589
+ , 0.0295285
+ , 0.0303052
+ , 0.0133037
+ , 0.00281253
+ , 0.00688506
+ ]
+ , [ 0.00989537
+ , 0.00282767
+ , 0.000374823
+ , 0.00091821
+ , 0.0298607
+ , 0.000699707
+ , 0.00104195
+ , 0.311504
+ , 0.00139605
+ , 0.375039
+ , 0.0474451
+ , 0.000730793
+ , 0.00252963
+ , 0.0017337
+ , 0.00196045
+ , 0.0014628
+ , 0.0075739
+ , 0.1973
+ , 0.00167998
+ , 0.00402599
+ ]
+ , [ 0.116321
+ , 0.00347923
+ , 0.0731918
+ , 0.138088
+ , 0.00941177
+ , 0.0193193
+ , 0.0160241
+ , 0.0712243
+ , 0.035512
+ , 0.0771474
+ , 0.0242841
+ , 0.0250164
+ , 0.0508927
+ , 0.0586677
+ , 0.0273321
+ , 0.047556
+ , 0.0726552
+ , 0.123571
+ , 0.00268927
+ , 0.0076166
+ ]
+ , [ 0.128522
+ , 0.0172929
+ , 0.040275
+ , 0.0250692
+ , 0.0199118
+ , 0.112703
+ , 0.0606981
+ , 0.010935
+ , 0.028875
+ , 0.0258416
+ , 0.0167593
+ , 0.117984
+ , 0.0180675
+ , 0.0439706
+ , 0.0373073
+ , 0.174149
+ , 0.0648968
+ , 0.0182067
+ , 0.0063575
+ , 0.0321772
+ ]
+ , [ 0.0372287
+ , 0.014494
+ , 0.00237032
+ , 0.00485851
+ , 0.146377
+ , 0.00464339
+ , 0.0186795
+ , 0.182046
+ , 0.00581985
+ , 0.17801
+ , 0.0371334
+ , 0.00533773
+ , 0.00485386
+ , 0.00790971
+ , 0.0094528
+ , 0.0103571
+ , 0.0284162
+ , 0.184992
+ , 0.0211294
+ , 0.0958905
+ ]
+ , [ 0.0535644
+ , 0.00962562
+ , 0.0113537
+ , 0.0391699
+ , 0.0264214
+ , 0.0120279
+ , 0.0384888
+ , 0.0522748
+ , 0.0996038
+ , 0.189239
+ , 0.0712219
+ , 0.0239173
+ , 0.00837206
+ , 0.0928585
+ , 0.11598
+ , 0.0299114
+ , 0.0389485
+ , 0.0500948
+ , 0.0104232
+ , 0.026503
+ ]
+ , [ 0.133242
+ , 0.0246514
+ , 0.00127392
+ , 0.00404615
+ , 0.0156995
+ , 0.00891392
+ , 0.00158647
+ , 0.197128
+ , 0.00237132
+ , 0.125129
+ , 0.0286947
+ , 0.0022705
+ , 0.0118846
+ , 0.00308435
+ , 0.00331477
+ , 0.0171462
+ , 0.0563298
+ , 0.356621
+ , 0.00173418
+ , 0.00487784
+ ]
+ , [ 0.149866
+ , 0.00354374
+ , 0.0280355
+ , 0.0435381
+ , 0.00475339
+ , 0.0311113
+ , 0.0140626
+ , 0.0101953
+ , 0.0393125
+ , 0.0251434
+ , 0.00515483
+ , 0.0176453
+ , 0.39238
+ , 0.0348151
+ , 0.0326607
+ , 0.0874497
+ , 0.0473307
+ , 0.0271597
+ , 0.00152152
+ , 0.00432083
+ ]
+ , [ 0.421437
+ , 0.018761
+ , 0.00733051
+ , 0.00868378
+ , 0.00271561
+ , 0.0902333
+ , 0.0030262
+ , 0.00393628
+ , 0.00515087
+ , 0.00471933
+ , 0.00383066
+ , 0.012159
+ , 0.020894
+ , 0.00727486
+ , 0.0061426
+ , 0.290119
+ , 0.0651922
+ , 0.0252211
+ , 0.000810824
+ , 0.00236228
+ ]
+ , [ 0.177071
+ , 0.00783489
+ , 0.02265
+ , 0.0509767
+ , 0.00405142
+ , 0.089739
+ , 0.0220667
+ , 0.00595198
+ , 0.125769
+ , 0.020537
+ , 0.00929825
+ , 0.0311657
+ , 0.0264088
+ , 0.0752471
+ , 0.133278
+ , 0.116959
+ , 0.0565567
+ , 0.0165087
+ , 0.00299471
+ , 0.00493467
+ ]
+ , [ 0.0293984
+ , 0.00317291
+ , 0.109971
+ , 0.046427
+ , 0.00150396
+ , 0.422242
+ , 0.0272495
+ , 0.000799733
+ , 0.0622314
+ , 0.00376343
+ , 0.00166571
+ , 0.148362
+ , 0.00564818
+ , 0.0388688
+ , 0.0370902
+ , 0.0472252
+ , 0.0086569
+ , 0.00203639
+ , 0.000917602
+ , 0.00276931
+ ]
+ , [ 0.0265779
+ , 0.0101369
+ , 0.0280314
+ , 0.0269057
+ , 0.0276961
+ , 0.0173377
+ , 0.281513
+ , 0.0064647
+ , 0.0474749
+ , 0.026821
+ , 0.00723753
+ , 0.13186
+ , 0.0083015
+ , 0.0989711
+ , 0.0791105
+ , 0.0426277
+ , 0.0259043
+ , 0.0100147
+ , 0.00785289
+ , 0.0891598
+ ]
+ , [ 0.00960965
+ , 0.00773017
+ , 0.000633186
+ , 0.00104719
+ , 0.263017
+ , 0.00202274
+ , 0.00390014
+ , 0.0733098
+ , 0.00149315
+ , 0.445169
+ , 0.0732575
+ , 0.00131044
+ , 0.00427681
+ , 0.00338994
+ , 0.00271362
+ , 0.00361174
+ , 0.00579284
+ , 0.0425173
+ , 0.0181276
+ , 0.0370698
+ ]
+ ]
+
+-- | Weights of C40 model.
+c40Weights :: [Double]
+c40Weights =
+ [ 0.0223854
+ , 0.0338892
+ , 0.0577169
+ , 0.0252416
+ , 0.0108608
+ , 0.0462374
+ , 0.0102293
+ , 0.0147524
+ , 0.0143161
+ , 0.0182303
+ , 0.0204025
+ , 0.0425505
+ , 0.0248627
+ , 0.0105893
+ , 0.0188239
+ , 0.00866634
+ , 0.0148496
+ , 0.0343037
+ , 0.0225335
+ , 0.0174069
+ , 0.0112208
+ , 0.0443532
+ , 0.0392573
+ , 0.0196757
+ , 0.028769
+ , 0.0114441
+ , 0.0112339
+ , 0.0582694
+ , 0.0444272
+ , 0.0112011
+ , 0.0145176
+ , 0.0114629
+ , 0.0239628
+ , 0.0266266
+ , 0.0481201
+ , 0.0371147
+ , 0.0160477
+ , 0.0237249
+ , 0.0235226
+ , 0.0261998
+ ]
+
+-- | Stationary distribution of C50 model.
+c50StatDists :: [StationaryDistribution]
+c50StatDists = map
+ V.fromList
+ [ [ 0.115682
+ , 0.00212412
+ , 0.125699
+ , 0.0919063
+ , 0.0016175
+ , 0.0391977
+ , 0.0108596
+ , 0.00344834
+ , 0.0344439
+ , 0.0125587
+ , 0.00467132
+ , 0.0530851
+ , 0.206661
+ , 0.0264814
+ , 0.0147638
+ , 0.154493
+ , 0.0841319
+ , 0.0134754
+ , 0.000392551
+ , 0.00430762
+ ]
+ , [ 0.0983768
+ , 0.00160659
+ , 0.0456633
+ , 0.0935028
+ , 0.00112009
+ , 0.0251388
+ , 0.0191777
+ , 0.00367483
+ , 0.151407
+ , 0.0115555
+ , 0.00258422
+ , 0.0266318
+ , 0.229718
+ , 0.0694385
+ , 0.0855866
+ , 0.0696565
+ , 0.0498854
+ , 0.0123983
+ , 0.00069296
+ , 0.00218381
+ ]
+ , [ 0.0214598
+ , 0.00446298
+ , 0.000555089
+ , 0.00135258
+ , 0.00855351
+ , 0.00112246
+ , 0.000813505
+ , 0.399631
+ , 0.00128242
+ , 0.0868331
+ , 0.0170323
+ , 0.00117488
+ , 0.00183519
+ , 0.00101872
+ , 0.00142423
+ , 0.00233511
+ , 0.0161891
+ , 0.430205
+ , 0.00061736
+ , 0.00210206
+ ]
+ , [ 0.117155
+ , 0.032654
+ , 0.00620066
+ , 0.00998032
+ , 0.0657132
+ , 0.0333659
+ , 0.0134621
+ , 0.0557335
+ , 0.00794829
+ , 0.199356
+ , 0.0938018
+ , 0.0221831
+ , 0.0115415
+ , 0.0204903
+ , 0.0146873
+ , 0.0842555
+ , 0.0920314
+ , 0.0798031
+ , 0.0127314
+ , 0.0269048
+ ]
+ , [ 0.0371284
+ , 0.0131607
+ , 0.00255462
+ , 0.00465054
+ , 0.156922
+ , 0.00416133
+ , 0.019977
+ , 0.178808
+ , 0.00498614
+ , 0.165159
+ , 0.0352649
+ , 0.0057612
+ , 0.00512406
+ , 0.00679862
+ , 0.00826841
+ , 0.0102949
+ , 0.0275498
+ , 0.181807
+ , 0.0221255
+ , 0.109498
+ ]
+ , [ 0.0540087
+ , 0.000836323
+ , 0.306245
+ , 0.38187
+ , 0.00111469
+ , 0.0245756
+ , 0.0116353
+ , 0.00254509
+ , 0.030937
+ , 0.00536416
+ , 0.00256903
+ , 0.0359123
+ , 0.0122515
+ , 0.0586791
+ , 0.0115134
+ , 0.0277199
+ , 0.020314
+ , 0.00828799
+ , 0.000720693
+ , 0.00290032
+ ]
+ , [ 0.0404572
+ , 0.028652
+ , 0.00495693
+ , 0.0068813
+ , 0.242849
+ , 0.0103569
+ , 0.0318377
+ , 0.0329142
+ , 0.0105561
+ , 0.143431
+ , 0.0485779
+ , 0.0105988
+ , 0.00489299
+ , 0.0118557
+ , 0.0126873
+ , 0.0229136
+ , 0.0212457
+ , 0.0349069
+ , 0.0593874
+ , 0.220042
+ ]
+ , [ 0.319667
+ , 0.138968
+ , 0.00144847
+ , 0.00200138
+ , 0.00997903
+ , 0.0503464
+ , 0.00296588
+ , 0.0182219
+ , 0.00202126
+ , 0.0260477
+ , 0.0136422
+ , 0.00936868
+ , 0.00591365
+ , 0.00358722
+ , 0.00435407
+ , 0.1656
+ , 0.118413
+ , 0.0996664
+ , 0.00164228
+ , 0.00614589
+ ]
+ , [ 0.0977328
+ , 0.00251083
+ , 0.0724816
+ , 0.197027
+ , 0.00556062
+ , 0.0117997
+ , 0.0154288
+ , 0.0563751
+ , 0.0613631
+ , 0.047368
+ , 0.0159721
+ , 0.0241106
+ , 0.0149
+ , 0.0909736
+ , 0.034432
+ , 0.0408092
+ , 0.0929289
+ , 0.111482
+ , 0.00122744
+ , 0.00551621
+ ]
+ , [ 0.0195453
+ , 0.0107627
+ , 0.0127492
+ , 0.011794
+ , 0.14032
+ , 0.0061666
+ , 0.215761
+ , 0.00826718
+ , 0.0118897
+ , 0.0328258
+ , 0.00664433
+ , 0.0423533
+ , 0.00528472
+ , 0.0258824
+ , 0.024497
+ , 0.0203711
+ , 0.0124449
+ , 0.0133889
+ , 0.0330587
+ , 0.345993
+ ]
+ , [ 0.185338
+ , 0.00185224
+ , 0.161345
+ , 0.234878
+ , 0.00192286
+ , 0.054278
+ , 0.0109591
+ , 0.00550122
+ , 0.0382027
+ , 0.00925008
+ , 0.00343293
+ , 0.033406
+ , 0.0233824
+ , 0.0551124
+ , 0.0201268
+ , 0.0884267
+ , 0.051789
+ , 0.0177494
+ , 0.000835994
+ , 0.00221142
+ ]
+ , [ 0.0143603
+ , 0.0036047
+ , 0.000411253
+ , 0.00108887
+ , 0.0196479
+ , 0.00187385
+ , 0.000991664
+ , 0.285685
+ , 0.00213672
+ , 0.317288
+ , 0.150556
+ , 0.00155703
+ , 0.00122034
+ , 0.0028111
+ , 0.00194519
+ , 0.00344669
+ , 0.0196686
+ , 0.167294
+ , 0.000843478
+ , 0.00356936
+ ]
+ , [ 0.150577
+ , 0.00957632
+ , 0.0227565
+ , 0.0358641
+ , 0.0104881
+ , 0.0285062
+ , 0.0171219
+ , 0.0577109
+ , 0.0276149
+ , 0.0531781
+ , 0.0298859
+ , 0.0514957
+ , 0.0243637
+ , 0.0354202
+ , 0.0272841
+ , 0.132633
+ , 0.169554
+ , 0.104387
+ , 0.00219421
+ , 0.00938724
+ ]
+ , [ 0.277615
+ , 0.0280749
+ , 0.00194439
+ , 0.00537302
+ , 0.0070772
+ , 0.0234861
+ , 0.0012257
+ , 0.0949678
+ , 0.00308357
+ , 0.0474515
+ , 0.0189616
+ , 0.0034483
+ , 0.0134815
+ , 0.00374076
+ , 0.00354151
+ , 0.0423818
+ , 0.0932708
+ , 0.326207
+ , 0.000963513
+ , 0.00370386
+ ]
+ , [ 0.205879
+ , 0.00249091
+ , 0.075426
+ , 0.161651
+ , 0.00210732
+ , 0.0463391
+ , 0.0159993
+ , 0.00515537
+ , 0.0913036
+ , 0.0166911
+ , 0.00536596
+ , 0.0366042
+ , 0.00849072
+ , 0.0973331
+ , 0.0696431
+ , 0.088244
+ , 0.0501877
+ , 0.0172747
+ , 0.000776174
+ , 0.0030381
+ ]
+ , [ 0.0704473
+ , 0.00149732
+ , 0.187469
+ , 0.208434
+ , 0.0013217
+ , 0.0409359
+ , 0.0247326
+ , 0.00339884
+ , 0.0739754
+ , 0.00761491
+ , 0.00270559
+ , 0.0965448
+ , 0.00673196
+ , 0.0820493
+ , 0.0355811
+ , 0.0832004
+ , 0.0610002
+ , 0.00788473
+ , 0.000646918
+ , 0.00382803
+ ]
+ , [ 0.108767
+ , 0.00735776
+ , 0.0100122
+ , 0.0249269
+ , 0.015562
+ , 0.0114116
+ , 0.00730171
+ , 0.0923916
+ , 0.0138538
+ , 0.112308
+ , 0.0251594
+ , 0.00831075
+ , 0.259979
+ , 0.0187962
+ , 0.0142911
+ , 0.0329858
+ , 0.0608007
+ , 0.162244
+ , 0.0049709
+ , 0.00857003
+ ]
+ , [ 0.109878
+ , 0.0295589
+ , 0.000867374
+ , 0.00267084
+ , 0.028604
+ , 0.0101436
+ , 0.00159952
+ , 0.171472
+ , 0.0015037
+ , 0.241889
+ , 0.0488425
+ , 0.00201796
+ , 0.00631863
+ , 0.00393786
+ , 0.00336164
+ , 0.0148413
+ , 0.0393773
+ , 0.273667
+ , 0.00359303
+ , 0.00585493
+ ]
+ , [ 0.058736
+ , 0.00692528
+ , 0.0144651
+ , 0.0412403
+ , 0.0154694
+ , 0.015436
+ , 0.0243546
+ , 0.0388984
+ , 0.0996366
+ , 0.207192
+ , 0.103832
+ , 0.0289715
+ , 0.00833815
+ , 0.108218
+ , 0.0976056
+ , 0.0350037
+ , 0.0432645
+ , 0.0338957
+ , 0.00652556
+ , 0.0119916
+ ]
+ , [ 0.0642736
+ , 0.00525071
+ , 0.144305
+ , 0.153274
+ , 0.0286093
+ , 0.0265312
+ , 0.0545105
+ , 0.0231701
+ , 0.0452879
+ , 0.058794
+ , 0.0192273
+ , 0.071063
+ , 0.0146855
+ , 0.066931
+ , 0.0405954
+ , 0.054046
+ , 0.043602
+ , 0.0350962
+ , 0.00655203
+ , 0.0441953
+ ]
+ , [ 0.00487716
+ , 0.00503139
+ , 0.00209095
+ , 0.00192293
+ , 0.0983777
+ , 0.00615619
+ , 0.00725617
+ , 0.00400789
+ , 0.000993075
+ , 0.0277171
+ , 0.00537714
+ , 0.00145717
+ , 0.0029039
+ , 0.00350461
+ , 0.0112195
+ , 0.00329284
+ , 0.00295187
+ , 0.00708726
+ , 0.724652
+ , 0.0791231
+ ]
+ , [ 0.0552756
+ , 0.0115894
+ , 0.00846155
+ , 0.0432312
+ , 0.00961795
+ , 0.0074182
+ , 0.0218432
+ , 0.0843826
+ , 0.163327
+ , 0.0631707
+ , 0.0228359
+ , 0.0221225
+ , 0.00652522
+ , 0.0639538
+ , 0.146077
+ , 0.0387464
+ , 0.100713
+ , 0.118118
+ , 0.00298298
+ , 0.00960875
+ ]
+ , [ 0.00449551
+ , 0.00619902
+ , 0.000890609
+ , 0.000674178
+ , 0.400884
+ , 0.0013356
+ , 0.0223834
+ , 0.00805107
+ , 0.00105813
+ , 0.0341606
+ , 0.00701178
+ , 0.00318917
+ , 0.00130624
+ , 0.00157564
+ , 0.00181707
+ , 0.00502515
+ , 0.00337803
+ , 0.00946203
+ , 0.0345278
+ , 0.452575
+ ]
+ , [ 0.0505469
+ , 0.00768183
+ , 0.0101983
+ , 0.0470721
+ , 0.0160596
+ , 0.00517598
+ , 0.0176387
+ , 0.169463
+ , 0.0497501
+ , 0.209444
+ , 0.0474166
+ , 0.0132404
+ , 0.00844474
+ , 0.053753
+ , 0.051076
+ , 0.0149657
+ , 0.03846
+ , 0.172926
+ , 0.00437246
+ , 0.0123139
+ ]
+ , [ 0.0749936
+ , 0.0124353
+ , 0.0203869
+ , 0.0100161
+ , 0.0038092
+ , 0.0270453
+ , 0.00581932
+ , 0.00743392
+ , 0.014732
+ , 0.00838354
+ , 0.00640172
+ , 0.0530316
+ , 0.0176075
+ , 0.0096947
+ , 0.0117746
+ , 0.3482
+ , 0.348235
+ , 0.0157071
+ , 0.00137596
+ , 0.00291601
+ ]
+ , [ 0.0569785
+ , 0.00176591
+ , 0.102737
+ , 0.106157
+ , 0.00132179
+ , 0.0360979
+ , 0.034465
+ , 0.00311879
+ , 0.185459
+ , 0.00858711
+ , 0.00431374
+ , 0.139374
+ , 0.00855798
+ , 0.0898676
+ , 0.101042
+ , 0.0669467
+ , 0.0422839
+ , 0.00552428
+ , 0.000686497
+ , 0.00471478
+ ]
+ , [ 0.0746973
+ , 0.00394557
+ , 0.0423454
+ , 0.0906599
+ , 0.00363883
+ , 0.0183504
+ , 0.0229406
+ , 0.0156166
+ , 0.12297
+ , 0.0167059
+ , 0.00901115
+ , 0.0672502
+ , 0.0127747
+ , 0.0811334
+ , 0.0755385
+ , 0.132886
+ , 0.170553
+ , 0.0324157
+ , 0.00152093
+ , 0.00504616
+ ]
+ , [ 0.17313
+ , 0.00938612
+ , 0.0203504
+ , 0.0387504
+ , 0.00448721
+ , 0.0867075
+ , 0.0227177
+ , 0.00492238
+ , 0.125544
+ , 0.0156727
+ , 0.00787132
+ , 0.0400476
+ , 0.0180405
+ , 0.0680443
+ , 0.133335
+ , 0.142136
+ , 0.0670614
+ , 0.0136107
+ , 0.00287027
+ , 0.00531475
+ ]
+ , [ 0.00751784
+ , 0.00212117
+ , 0.000341917
+ , 0.000667876
+ , 0.0310677
+ , 0.000466913
+ , 0.000898937
+ , 0.320302
+ , 0.00103903
+ , 0.384419
+ , 0.0335748
+ , 0.000602706
+ , 0.00243131
+ , 0.00137426
+ , 0.00152778
+ , 0.00115498
+ , 0.00552329
+ , 0.199295
+ , 0.00172716
+ , 0.00394622
+ ]
+ , [ 0.113459
+ , 0.0281671
+ , 0.0268294
+ , 0.0283293
+ , 0.0928796
+ , 0.0494616
+ , 0.0733971
+ , 0.0152335
+ , 0.0176739
+ , 0.037425
+ , 0.0140126
+ , 0.0539481
+ , 0.0259048
+ , 0.0303861
+ , 0.0259068
+ , 0.121621
+ , 0.0621544
+ , 0.0350518
+ , 0.0240853
+ , 0.124074
+ ]
+ , [ 0.0810974
+ , 0.00899714
+ , 0.0930492
+ , 0.0372909
+ , 0.002713
+ , 0.0907986
+ , 0.0275326
+ , 0.00533957
+ , 0.0362449
+ , 0.00831441
+ , 0.00615441
+ , 0.177093
+ , 0.0120848
+ , 0.0316411
+ , 0.025247
+ , 0.233557
+ , 0.106302
+ , 0.00814021
+ , 0.000950692
+ , 0.00745168
+ ]
+ , [ 0.00757098
+ , 0.00716117
+ , 0.00049456
+ , 0.000891326
+ , 0.297029
+ , 0.00155605
+ , 0.00342729
+ , 0.0711141
+ , 0.00107067
+ , 0.416918
+ , 0.0635143
+ , 0.000864035
+ , 0.00349893
+ , 0.00251506
+ , 0.00186372
+ , 0.00271598
+ , 0.00424124
+ , 0.041488
+ , 0.0202374
+ , 0.0518279
+ ]
+ , [ 0.086899
+ , 0.00542266
+ , 0.0274343
+ , 0.117345
+ , 0.00568342
+ , 0.0162895
+ , 0.0386176
+ , 0.0182492
+ , 0.149526
+ , 0.048245
+ , 0.0150062
+ , 0.0265186
+ , 0.00577334
+ , 0.159013
+ , 0.149227
+ , 0.0416278
+ , 0.0492401
+ , 0.0283951
+ , 0.00272523
+ , 0.00876225
+ ]
+ , [ 0.0501736
+ , 0.0113806
+ , 0.00768113
+ , 0.0191841
+ , 0.0119036
+ , 0.00521331
+ , 0.00988204
+ , 0.203482
+ , 0.0206446
+ , 0.0870652
+ , 0.036001
+ , 0.0197961
+ , 0.0061624
+ , 0.0180415
+ , 0.0178215
+ , 0.0399964
+ , 0.162255
+ , 0.262373
+ , 0.00172457
+ , 0.00921833
+ ]
+ , [ 0.177098
+ , 0.00357587
+ , 0.0740854
+ , 0.0713923
+ , 0.00385864
+ , 0.211235
+ , 0.0161904
+ , 0.0040472
+ , 0.0370753
+ , 0.00826202
+ , 0.00369757
+ , 0.0494737
+ , 0.0543871
+ , 0.0396583
+ , 0.0340392
+ , 0.140615
+ , 0.0532238
+ , 0.0108131
+ , 0.00212448
+ , 0.00514764
+ ]
+ , [ 0.242384
+ , 0.0115188
+ , 0.00720908
+ , 0.00544261
+ , 0.00229719
+ , 0.593273
+ , 0.00205723
+ , 0.00208173
+ , 0.00287156
+ , 0.00491
+ , 0.00271204
+ , 0.00899551
+ , 0.00763059
+ , 0.00285962
+ , 0.00600369
+ , 0.0738385
+ , 0.0108329
+ , 0.00968775
+ , 0.00178961
+ , 0.00160391
+ ]
+ , [ 0.032912
+ , 0.00319267
+ , 0.143899
+ , 0.0532755
+ , 0.00166462
+ , 0.463509
+ , 0.0175283
+ , 0.000876108
+ , 0.0317056
+ , 0.00297349
+ , 0.0012156
+ , 0.131603
+ , 0.00688601
+ , 0.0251373
+ , 0.0184844
+ , 0.0491059
+ , 0.00984294
+ , 0.00239178
+ , 0.0008917
+ , 0.00290456
+ ]
+ , [ 0.0388306
+ , 0.00489943
+ , 0.0491655
+ , 0.0413874
+ , 0.00170354
+ , 0.345044
+ , 0.0421499
+ , 0.00103798
+ , 0.123725
+ , 0.00726049
+ , 0.00335164
+ , 0.119727
+ , 0.00562115
+ , 0.0664068
+ , 0.0881106
+ , 0.0460192
+ , 0.00791813
+ , 0.0020819
+ , 0.00195492
+ , 0.00360516
+ ]
+ , [ 0.0373301
+ , 0.00916334
+ , 0.0396965
+ , 0.0362168
+ , 0.0144959
+ , 0.0269081
+ , 0.220512
+ , 0.00638711
+ , 0.0634517
+ , 0.0225147
+ , 0.00718608
+ , 0.152708
+ , 0.00995802
+ , 0.108449
+ , 0.0882553
+ , 0.0609295
+ , 0.0332848
+ , 0.0105312
+ , 0.00429315
+ , 0.047729
+ ]
+ , [ 0.0171508
+ , 0.00565843
+ , 0.00111564
+ , 0.00268175
+ , 0.0490847
+ , 0.00219974
+ , 0.00370226
+ , 0.116938
+ , 0.00407925
+ , 0.500942
+ , 0.1832
+ , 0.00280387
+ , 0.00400697
+ , 0.0115255
+ , 0.00613355
+ , 0.00539456
+ , 0.0140434
+ , 0.0579479
+ , 0.00419195
+ , 0.00719895
+ ]
+ , [ 0.0238117
+ , 0.00329378
+ , 0.370777
+ , 0.0831676
+ , 0.0022275
+ , 0.053433
+ , 0.0290274
+ , 0.00288609
+ , 0.0258098
+ , 0.00370314
+ , 0.00159506
+ , 0.259554
+ , 0.00668902
+ , 0.0201877
+ , 0.0117854
+ , 0.0626213
+ , 0.0278627
+ , 0.00464381
+ , 0.000688992
+ , 0.0062349
+ ]
+ , [ 0.209736
+ , 0.0105937
+ , 0.0311812
+ , 0.0613839
+ , 0.00991105
+ , 0.0855144
+ , 0.0226071
+ , 0.0296058
+ , 0.0455281
+ , 0.0792591
+ , 0.0306389
+ , 0.019447
+ , 0.0213982
+ , 0.0610672
+ , 0.0588191
+ , 0.0820738
+ , 0.0527883
+ , 0.0722389
+ , 0.00513
+ , 0.0110785
+ ]
+ , [ 0.0295833
+ , 0.00588894
+ , 0.00852018
+ , 0.0296344
+ , 0.00323424
+ , 0.0154495
+ , 0.02992
+ , 0.00752729
+ , 0.317117
+ , 0.0212988
+ , 0.00874154
+ , 0.0312424
+ , 0.00843308
+ , 0.0831654
+ , 0.323587
+ , 0.0294177
+ , 0.0283085
+ , 0.0100345
+ , 0.00257807
+ , 0.00631797
+ ]
+ , [ 0.0937098
+ , 0.00289961
+ , 0.0255803
+ , 0.0577481
+ , 0.0140839
+ , 0.0182984
+ , 0.0300827
+ , 0.0312422
+ , 0.0867966
+ , 0.067914
+ , 0.01767
+ , 0.0206426
+ , 0.213942
+ , 0.0611154
+ , 0.0902988
+ , 0.0526724
+ , 0.0464314
+ , 0.0509513
+ , 0.00365078
+ , 0.01427
+ ]
+ , [ 0.419507
+ , 0.0176715
+ , 0.00719436
+ , 0.00880545
+ , 0.00285112
+ , 0.0865515
+ , 0.00330323
+ , 0.00419601
+ , 0.00503365
+ , 0.0048203
+ , 0.00393323
+ , 0.012443
+ , 0.0192167
+ , 0.00750218
+ , 0.00609116
+ , 0.295973
+ , 0.0660748
+ , 0.0253174
+ , 0.000942289
+ , 0.00257126
+ ]
+ , [ 0.0368106
+ , 0.0124259
+ , 0.0102859
+ , 0.0343205
+ , 0.0759532
+ , 0.00772969
+ , 0.0938663
+ , 0.0458547
+ , 0.0701169
+ , 0.133403
+ , 0.031916
+ , 0.0265402
+ , 0.00749485
+ , 0.0673302
+ , 0.10388
+ , 0.0271625
+ , 0.0353789
+ , 0.0485031
+ , 0.0254607
+ , 0.105568
+ ]
+ , [ 0.0665479
+ , 0.00185956
+ , 0.183575
+ , 0.149215
+ , 0.00127224
+ , 0.0634659
+ , 0.019684
+ , 0.00262142
+ , 0.0655694
+ , 0.00750609
+ , 0.00151282
+ , 0.0699101
+ , 0.182105
+ , 0.0446839
+ , 0.0292035
+ , 0.075452
+ , 0.0278833
+ , 0.00484561
+ , 0.000723776
+ , 0.00236318
+ ]
+ , [ 0.16002
+ , 0.00397537
+ , 0.019682
+ , 0.0286161
+ , 0.00458768
+ , 0.0326662
+ , 0.0114325
+ , 0.00722291
+ , 0.0232558
+ , 0.0202542
+ , 0.00379358
+ , 0.0142832
+ , 0.460797
+ , 0.0260458
+ , 0.0217875
+ , 0.0913633
+ , 0.0427326
+ , 0.0227118
+ , 0.0012566
+ , 0.0035159
+ ]
+ , [ 0.0843584
+ , 0.00129715
+ , 0.0847585
+ , 0.260552
+ , 0.00143564
+ , 0.0191268
+ , 0.0174708
+ , 0.00556223
+ , 0.144172
+ , 0.014456
+ , 0.00550323
+ , 0.0336163
+ , 0.00724868
+ , 0.160704
+ , 0.0742581
+ , 0.0323411
+ , 0.0355032
+ , 0.0136662
+ , 0.000760206
+ , 0.00320994
+ ]
+ , [ 0.152149
+ , 0.000925399
+ , 0.116471
+ , 0.220438
+ , 0.00150071
+ , 0.0172039
+ , 0.0095692
+ , 0.00747151
+ , 0.0529323
+ , 0.0148756
+ , 0.00356173
+ , 0.0157411
+ , 0.217335
+ , 0.0489135
+ , 0.0171707
+ , 0.044102
+ , 0.0323715
+ , 0.023915
+ , 0.000908902
+ , 0.00244332
+ ]
+ ]
+
+-- | Weights of C50 model.
+c50Weights :: [Double]
+c50Weights =
+ [ 0.00509464
+ , 0.00753314
+ , 0.0595801
+ , 0.0100458
+ , 0.0109109
+ , 0.0427412
+ , 0.00632106
+ , 0.0192362
+ , 0.0119168
+ , 0.0154209
+ , 0.0148037
+ , 0.014293
+ , 0.0164064
+ , 0.0272538
+ , 0.0178737
+ , 0.0125183
+ , 0.00698661
+ , 0.0140027
+ , 0.0140399
+ , 0.0109043
+ , 0.011579
+ , 0.0138661
+ , 0.0377329
+ , 0.0118586
+ , 0.0356688
+ , 0.0161327
+ , 0.0200601
+ , 0.0133087
+ , 0.0357641
+ , 0.0119353
+ , 0.0241183
+ , 0.0243098
+ , 0.0178039
+ , 0.0200988
+ , 0.00579569
+ , 0.0397441
+ , 0.0240799
+ , 0.00868054
+ , 0.0239822
+ , 0.042803
+ , 0.0335193
+ , 0.00636191
+ , 0.0547546
+ , 0.00544598
+ , 0.0354219
+ , 0.0120158
+ , 0.0047506
+ , 0.036392
+ , 0.0270346
+ , 0.00709747
+ ]
+
+-- | Stationary distribution of C60 model.
+c60StatDists :: [StationaryDistribution]
+c60StatDists = map
+ V.fromList
+ [ [ 0.153436
+ , 0.00473066
+ , 0.0546757
+ , 0.0529324
+ , 0.00355543
+ , 0.110378
+ , 0.017448
+ , 0.00503439
+ , 0.0603929
+ , 0.0130294
+ , 0.00755506
+ , 0.0796727
+ , 0.0249524
+ , 0.0514333
+ , 0.0444389
+ , 0.202963
+ , 0.0957668
+ , 0.0101809
+ , 0.00144445
+ , 0.00598003
+ ]
+ , [ 0.0281985
+ , 0.00195035
+ , 0.00915493
+ , 0.038853
+ , 0.00159193
+ , 0.00840283
+ , 0.0155385
+ , 0.0107873
+ , 0.347604
+ , 0.0217787
+ , 0.0109905
+ , 0.0312955
+ , 0.00715399
+ , 0.0939884
+ , 0.303106
+ , 0.0197479
+ , 0.0328352
+ , 0.0135303
+ , 0.000920999
+ , 0.0025714
+ ]
+ , [ 0.00836807
+ , 0.00204339
+ , 0.000222837
+ , 0.000473154
+ , 0.0123984
+ , 0.000482575
+ , 0.000518999
+ , 0.376845
+ , 0.000629617
+ , 0.260833
+ , 0.0315701
+ , 0.000612345
+ , 0.000959592
+ , 0.000949869
+ , 0.000731977
+ , 0.000974638
+ , 0.00499908
+ , 0.293808
+ , 0.000865776
+ , 0.00171323
+ ]
+ , [ 0.222723
+ , 0.164029
+ , 0.000799759
+ , 0.00272808
+ , 0.0228667
+ , 0.0202703
+ , 0.00371839
+ , 0.0455406
+ , 0.00228329
+ , 0.088335
+ , 0.0348095
+ , 0.00612065
+ , 0.00354716
+ , 0.00510519
+ , 0.00648461
+ , 0.085004
+ , 0.101285
+ , 0.169858
+ , 0.00484248
+ , 0.00965
+ ]
+ , [ 0.041214
+ , 0.0204716
+ , 0.00174344
+ , 0.00372634
+ , 0.2239
+ , 0.00691075
+ , 0.0180294
+ , 0.115428
+ , 0.00429003
+ , 0.169356
+ , 0.0414067
+ , 0.00510677
+ , 0.00584164
+ , 0.00575385
+ , 0.00676271
+ , 0.0149106
+ , 0.0239548
+ , 0.120034
+ , 0.0332237
+ , 0.137935
+ ]
+ , [ 0.048055
+ , 0.00378018
+ , 0.208461
+ , 0.185518
+ , 0.0196001
+ , 0.0191402
+ , 0.0872162
+ , 0.00946854
+ , 0.0375741
+ , 0.0277341
+ , 0.00883084
+ , 0.0940629
+ , 0.00812678
+ , 0.0747677
+ , 0.0308438
+ , 0.0439681
+ , 0.0324589
+ , 0.0181769
+ , 0.00346657
+ , 0.03875
+ ]
+ , [ 0.00628487
+ , 0.00730276
+ , 0.000532415
+ , 0.000974149
+ , 0.397455
+ , 0.00195782
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+ , 0.00236089
+ , 0.00607663
+ , 0.0333347
+ , 0.510789
+ ]
+ , [ 0.199501
+ , 0.058459
+ , 0.00949551
+ , 0.0125535
+ , 0.0634434
+ , 0.0939787
+ , 0.0341857
+ , 0.014021
+ , 0.0118723
+ , 0.0449388
+ , 0.0246991
+ , 0.0392255
+ , 0.0145385
+ , 0.0254265
+ , 0.0236079
+ , 0.166392
+ , 0.0533159
+ , 0.0367303
+ , 0.0129803
+ , 0.0606346
+ ]
+ , [ 0.0319449
+ , 0.00660403
+ , 0.0378075
+ , 0.0279488
+ , 0.0108916
+ , 0.0365541
+ , 0.208864
+ , 0.00475423
+ , 0.0868665
+ , 0.0156546
+ , 0.00432533
+ , 0.208471
+ , 0.00608996
+ , 0.0766373
+ , 0.101167
+ , 0.0577657
+ , 0.0302051
+ , 0.00605852
+ , 0.00260019
+ , 0.0387897
+ ]
+ , [ 0.07768
+ , 0.0140093
+ , 0.00806517
+ , 0.0112622
+ , 0.0173585
+ , 0.0136868
+ , 0.013373
+ , 0.123964
+ , 0.0129145
+ , 0.0724671
+ , 0.0420745
+ , 0.0403217
+ , 0.0117084
+ , 0.0179996
+ , 0.0142519
+ , 0.0922724
+ , 0.23169
+ , 0.167914
+ , 0.00281536
+ , 0.0141727
+ ]
+ , [ 0.118366
+ , 0.00356248
+ , 0.0495595
+ , 0.153759
+ , 0.00686657
+ , 0.0194993
+ , 0.0229373
+ , 0.0302661
+ , 0.0982304
+ , 0.0571251
+ , 0.0171727
+ , 0.0259525
+ , 0.0175153
+ , 0.120492
+ , 0.0805193
+ , 0.0486588
+ , 0.0635796
+ , 0.0553336
+ , 0.00230083
+ , 0.00830274
+ ]
+ , [ 0.052856
+ , 0.000862588
+ , 0.209276
+ , 0.402419
+ , 0.00126507
+ , 0.0155838
+ , 0.0124149
+ , 0.00548648
+ , 0.0497017
+ , 0.00902565
+ , 0.00423571
+ , 0.0264744
+ , 0.00631856
+ , 0.121241
+ , 0.0193569
+ , 0.0197263
+ , 0.0235464
+ , 0.0159764
+ , 0.000838161
+ , 0.00339487
+ ]
+ , [ 0.0344366
+ , 0.0020986
+ , 0.113901
+ , 0.054178
+ , 0.00315576
+ , 0.336164
+ , 0.0461777
+ , 0.000346342
+ , 0.0667553
+ , 0.00483557
+ , 0.00197045
+ , 0.163672
+ , 0.00403698
+ , 0.0605414
+ , 0.0426222
+ , 0.0481173
+ , 0.00891481
+ , 0.00201106
+ , 0.00065101
+ , 0.00541456
+ ]
+ , [ 0.115309
+ , 0.00149624
+ , 0.175552
+ , 0.174941
+ , 0.00157002
+ , 0.0394181
+ , 0.0132402
+ , 0.0056913
+ , 0.0433118
+ , 0.010141
+ , 0.00303321
+ , 0.0458477
+ , 0.16658
+ , 0.0366731
+ , 0.0151279
+ , 0.0871536
+ , 0.0468261
+ , 0.0141932
+ , 0.00075157
+ , 0.00314327
+ ]
+ , [ 0.386515
+ , 0.0218928
+ , 0.00223668
+ , 0.00313878
+ , 0.00392814
+ , 0.369435
+ , 0.00146729
+ , 0.00853761
+ , 0.00188405
+ , 0.0127257
+ , 0.00805817
+ , 0.00304205
+ , 0.0158688
+ , 0.00214647
+ , 0.00375793
+ , 0.0808877
+ , 0.0305196
+ , 0.0410635
+ , 0.000992288
+ , 0.00190203
+ ]
+ , [ 0.0146571
+ , 0.00243179
+ , 0.000521057
+ , 0.00148744
+ , 0.00916375
+ , 0.00209533
+ , 0.00101819
+ , 0.19139
+ , 0.00228984
+ , 0.44328
+ , 0.221743
+ , 0.00129983
+ , 0.000768515
+ , 0.00493628
+ , 0.00288413
+ , 0.00272515
+ , 0.0170997
+ , 0.0778557
+ , 0.000877938
+ , 0.0014756
+ ]
+ ]
+
+-- | Weights of C60 model.
+c60Weights :: [Double]
+c60Weights =
+ [ 0.0169699
+ , 0.0211683
+ , 0.0276589
+ , 0.0065676
+ , 0.0141221
+ , 0.00687748
+ , 0.014691
+ , 0.00672258
+ , 0.00183967
+ , 0.0102547
+ , 0.0230896
+ , 0.0057941
+ , 0.0125395
+ , 0.0204526
+ , 0.00706296
+ , 0.0117983
+ , 0.00683347
+ , 0.0433776
+ , 0.0318279
+ , 0.0222546
+ , 0.0102265
+ , 0.0150546
+ , 0.013416
+ , 0.0148552
+ , 0.0239112
+ , 0.0128776
+ , 0.0222319
+ , 0.0247445
+ , 0.0214275
+ , 0.0115002
+ , 0.00760174
+ , 0.0130259
+ , 0.0093702
+ , 0.0467194
+ , 0.044194
+ , 0.0322263
+ , 0.0403
+ , 0.0150234
+ , 0.010459
+ , 0.0214742
+ , 0.0154958
+ , 0.010179
+ , 0.022798
+ , 0.0123205
+ , 0.00667776
+ , 0.000415008
+ , 0.0344385
+ , 0.0113663
+ , 0.0127143
+ , 0.0124324
+ , 0.0262124
+ , 0.0064995
+ , 0.0103203
+ , 0.0142464
+ , 0.02156
+ , 0.0199151
+ , 0.00389642
+ , 0.0113449
+ , 0.0128596
+ , 0.0117657
+ ]
diff --git a/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs b/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/GammaRateHeterogeneity.hs
@@ -0,0 +1,131 @@
+{- |
+Module : ELynx.Data.MarkovProcess.GammaRateHeterogeneity
+Description : Discrete gamma rate heterogeneity
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Thu Feb 28 14:09:11 2019.
+
+At the moment, a mixture model is used to emulate gamma rate heterogeneity. This
+does not come with huge run time increases when simulating data. For inference
+however, it would make a lot of sense to reuse the Eigendecomposition for all
+rate heterogeneity components though.
+
+-}
+
+module ELynx.Data.MarkovProcess.GammaRateHeterogeneity
+ ( summarizeGammaRateHeterogeneity
+ , expand
+ )
+where
+
+import Prelude hiding ( repeat )
+
+import qualified Data.ByteString.Lazy.Char8 as L
+import qualified Data.List.NonEmpty as N
+import Data.List.NonEmpty ( NonEmpty )
+import Numeric.Integration.TanhSinh
+import Statistics.Distribution
+import Statistics.Distribution.Gamma
+
+import qualified ELynx.Data.MarkovProcess.MixtureModel
+ as M
+import qualified ELynx.Data.MarkovProcess.PhyloModel
+ as P
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+
+-- | Short summary of gamma rate heterogeneity parameters.
+summarizeGammaRateHeterogeneity :: Int -> Double -> [L.ByteString]
+summarizeGammaRateHeterogeneity n alpha = map
+ L.pack
+ [ "Discrete gamma rate heterogeneity."
+ , "Number of categories: " ++ show n
+ , "Shape parameter of gamma distribution: " ++ show alpha
+ , "Rates: " ++ show (getMeans n alpha)
+ ]
+
+-- | For a given number of rate categories, a gamma shape parameter alpha and a
+-- substitution model, compute the scaled substitution models corresponding to
+-- the gamma rates.
+expand :: Int -> Double -> P.PhyloModel -> P.PhyloModel
+expand n alpha (P.SubstitutionModel sm) =
+ P.MixtureModel $ expandSubstitutionModel n alpha sm
+expand n alpha (P.MixtureModel mm) =
+ P.MixtureModel $ expandMixtureModel n alpha mm
+
+getName :: Int -> Double -> String
+getName n alpha =
+ " with discrete gamma rate heterogeneity; "
+ ++ show n
+ ++ " categories; "
+ ++ "shape parameter "
+ ++ show alpha
+
+splitSubstitutionModel
+ :: Int -> Double -> S.SubstitutionModel -> NonEmpty S.SubstitutionModel
+splitSubstitutionModel n alpha sm = renamedSMs
+ where
+ means = getMeans n alpha
+ scaledSMs = N.map (`S.scale` sm) means
+ names = N.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
+ renamedSMs = N.zipWith S.appendName names scaledSMs
+
+expandSubstitutionModel
+ :: Int -> Double -> S.SubstitutionModel -> M.MixtureModel
+expandSubstitutionModel n alpha sm = M.fromSubstitutionModels name ws sms
+ where
+ name = S.name sm <> getName n alpha
+ ws = N.repeat 1.0
+ sms = splitSubstitutionModel n alpha sm
+
+expandMixtureModel :: Int -> Double -> M.MixtureModel -> M.MixtureModel
+expandMixtureModel n alpha mm = M.concatenate name renamedMMs
+ where
+ name = M.name mm <> getName n alpha
+ means = getMeans n alpha
+ scaledMMs = N.map (`M.scale` mm) means
+ names = N.fromList $ map (("; gamma rate category " ++) . show) [1 :: Int ..]
+ renamedMMs = N.zipWith M.appendNameComponents names scaledMMs
+
+-- For a given number of rate categories 'n' and a shape parameter 'alpha' (the
+-- rate or scale is set such that the mean is 1.0), return a list of rates that
+-- represent the respective categories. Use the mean rate for each category.
+getMeans :: Int -> Double -> NonEmpty Double
+getMeans n alpha = N.fromList $ means <> pure lastMean
+ where
+ gamma = gammaDistr alpha (1.0 / alpha)
+ quantiles =
+ [ quantile gamma (fromIntegral i / fromIntegral n) | i <- [0 .. n] ]
+ -- Calculate the mean rate. Multiplication with the number of rate
+ -- categories 'n' is necessary because in each n-quantile the
+ -- probability mass is 1/n.
+ meanFunc x = fromIntegral n * x * density gamma x
+ -- Only calculate the first (n-1) categories with normal integration.
+ means =
+ [ integralAToB meanFunc (quantiles !! i) (quantiles !! (i + 1))
+ | i <- [0 .. n - 2]
+ ]
+ -- The last category has to be calculated with an improper integration.
+ lastMean = integralAToInf meanFunc (quantiles !! (n - 1))
+
+-- The error of integration.
+eps :: Double
+eps = 1e-6
+
+-- The integration method to use
+method :: (Double -> Double) -> Double -> Double -> [Result]
+method = parSimpson
+
+-- Helper function for a normal integral from 'a' to 'b'.
+integralAToB :: (Double -> Double) -> Double -> Double -> Double
+integralAToB f a b = result . absolute eps $ method f a b
+
+-- Helper function for an improper integral from 'a' to infinity.
+integralAToInf :: (Double -> Double) -> Double -> Double
+integralAToInf f a =
+ (result . absolute eps $ nonNegative method f) - integralAToB f 0 a
diff --git a/src/ELynx/Data/MarkovProcess/MixtureModel.hs b/src/ELynx/Data/MarkovProcess/MixtureModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/MixtureModel.hs
@@ -0,0 +1,158 @@
+{- |
+Module : ELynx.Data.MarkovProcess.MixtureModel
+Description : Mixture models are a set of substitution models with weights
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 19:17:40 2019.
+
+To be imported qualified.
+
+-}
+
+module ELynx.Data.MarkovProcess.MixtureModel
+ ( -- * Types
+ Weight
+ , Component
+ , MixtureModel(name)
+ , -- * Getters
+ getAlphabet
+ , getWeights
+ , getSubstitutionModels
+ -- * Building mixture models
+ , fromSubstitutionModels
+ -- * Transformations
+ , concatenate
+ , scale
+ , normalize
+ , appendNameComponents
+ -- * Output
+ , summarizeComponent
+ , summarize
+ )
+where
+
+import Prelude hiding ( map
+ , head
+ , zipWith
+ , length
+ )
+
+import qualified Data.ByteString.Builder as L
+import qualified Data.ByteString.Lazy.Char8 as L
+import Data.List.NonEmpty hiding ( zip )
+import Data.Semigroup
+
+import ELynx.Data.Alphabet.Alphabet
+
+import ELynx.Tools
+
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+
+-- | Mixture model component weight.
+type Weight = Double
+
+-- | A mixture model component has a weight and a substitution model.
+data Component = Component
+ { weight :: Weight
+ , substModel :: S.SubstitutionModel
+ }
+ deriving (Show, Read)
+
+-- | A mixture model with its components.
+data MixtureModel = MixtureModel
+ { name :: S.Name -- ^ Name
+ , alphabet :: Alphabet
+ , components :: NonEmpty Component
+ }
+ deriving (Show, Read)
+
+-- | Get alphabet used with mixture model. Throws error if components use
+-- different 'Alphabet's.
+getAlphabet :: MixtureModel -> Alphabet
+getAlphabet = alphabet
+
+-- | Get weights.
+getWeights :: MixtureModel -> NonEmpty Weight
+getWeights = map weight . components
+
+-- | Get substitution models.
+getSubstitutionModels :: MixtureModel -> NonEmpty S.SubstitutionModel
+getSubstitutionModels = map substModel . components
+
+-- | Create a mixture model from a list of substitution models.
+fromSubstitutionModels
+ :: S.Name -> NonEmpty Weight -> NonEmpty S.SubstitutionModel -> MixtureModel
+fromSubstitutionModels n ws sms = if allEqual $ toList alphs
+ then MixtureModel n (head alphs) comps
+ else error
+ "fromSubstitutionModels: alphabets of substitution models are not equal."
+ where
+ comps = zipWith Component ws sms
+ alphs = map S.alphabet sms
+
+-- | Concatenate mixture models.
+concatenate :: S.Name -> NonEmpty MixtureModel -> MixtureModel
+concatenate n mms = fromSubstitutionModels n ws sms
+ where
+ comps = sconcat $ map components mms
+ ws = map weight comps
+ sms = map substModel comps
+
+scaleComponent :: Double -> Component -> Component
+scaleComponent s c = c { substModel = s' } where s' = S.scale s $ substModel c
+
+-- | Scale all substitution models of the mixture model.
+scale :: Double -> MixtureModel -> MixtureModel
+scale s m = m { components = cs' }
+ where
+ cs = components m
+ cs' = map (scaleComponent s) cs
+
+-- | Globally normalize a mixture model so that on average one event happens per
+-- unit time.
+normalize :: MixtureModel -> MixtureModel
+normalize mm = scale (1 / c) mm
+ where
+ c = sum $ zipWith (*) weights scales
+ weights = getWeights mm
+ scales = map S.totalRate $ getSubstitutionModels mm
+
+appendNameComponent :: S.Name -> Component -> Component
+appendNameComponent n c = c { substModel = s' }
+ where s' = S.appendName n $ substModel c
+
+-- | Append byte string to all substitution models of mixture model.
+appendNameComponents :: S.Name -> MixtureModel -> MixtureModel
+appendNameComponents n m = m { components = cs' }
+ where
+ cs = components m
+ cs' = map (appendNameComponent n) cs
+
+-- | Summarize a mixture model component; lines to be printed to screen or log.
+summarizeComponent :: Component -> [L.ByteString]
+summarizeComponent c =
+ L.pack "Weight: "
+ <> (L.toLazyByteString . L.doubleDec $ weight c)
+ : S.summarize (substModel c)
+
+-- | Summarize a mixture model; lines to be printed to screen or log.
+summarize :: MixtureModel -> [L.ByteString]
+summarize m =
+ [ L.pack $ "Mixture model: " ++ name m ++ "."
+ , L.pack $ "Number of components: " ++ show n ++ "."
+ ]
+ ++ detail
+ where
+ n = length $ components m
+ detail = if n <= 100
+ then concat
+ [ L.pack ("Component " ++ show i ++ ":") : summarizeComponent c
+ | (i, c) <- zip [1 :: Int ..] (toList $ components m)
+ ]
+ else []
diff --git a/src/ELynx/Data/MarkovProcess/Nucleotide.hs b/src/ELynx/Data/MarkovProcess/Nucleotide.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/Nucleotide.hs
@@ -0,0 +1,104 @@
+{- |
+Module : ELynx.Data.MarkovProcess.Nucleotide
+Description : Substitution models using nucleotides
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Thu Jan 24 08:33:26 2019.
+
+XXX: Maybe rename to something like /DNA substitution models/. Nucleotide ~
+Alphabet; DNA ~ Character.
+
+The order of nucleotides is A, C, G, T; see 'ELynx.Data.Character.Nucleotide'.
+
+For the different DNA substitution models, please see
+https://en.wikipedia.org/wiki/Models_of_DNA_evolution
+
+-}
+
+module ELynx.Data.MarkovProcess.Nucleotide
+ ( jc
+ , f81
+ , hky
+ , gtr4
+ )
+where
+
+import Numeric.LinearAlgebra hiding ( normalize )
+
+import ELynx.Data.Alphabet.Alphabet
+
+import ELynx.Tools
+
+import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.Data.MarkovProcess.SubstitutionModel
+
+-- XXX: Another idea of structuring the code. This would probably be cleaner in
+-- the long run.
+
+-- data PhyloModel = MixtureModel | SubstitutionModel
+
+--
+-- I think it could simply be:
+-- data PhyloModel = [(Weight, SubstitutionModel)]
+--
+
+-- data MixtureModel = [(Weight, SubstitutionModel)]
+
+-- data SubstitutionModel = SMDNA DNASubstitutionModel | SMAA AASubstitutionModel
+
+-- data DNASubstitutionModel = JC | HKY Double StationaryDistribution
+
+-- data AASubstitutionModel = LG | ...
+
+n :: Int
+-- n = length (alphabet :: [Nucleotide])
+-- Hard code this here. Reduces model dependencies, and number of nucleotides
+-- will not change.
+n = 4
+
+-- | JC model matrix.
+jcExch :: ExchangeabilityMatrix
+jcExch = (n >< n)
+ [ 0.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 0.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 0.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 1.0
+ , 0.0
+ ]
+
+-- | JC substitution model.
+jc :: SubstitutionModel
+jc = substitutionModel DNA "JC" [] d jcExch where d = uniformVec n
+
+-- | F81 substitution model.
+f81 :: StationaryDistribution -> SubstitutionModel
+f81 d = substitutionModel DNA "F81" [] d jcExch
+
+hkyExch :: Double -> ExchangeabilityMatrix
+hkyExch k = (n >< n)
+ [0.0, 1.0, k, 1.0, 1.0, 0.0, 1.0, k, k, 1.0, 0.0, 1.0, 1.0, k, 1.0, 0.0]
+
+-- | HKY substitution model.
+hky :: Double -> StationaryDistribution -> SubstitutionModel
+hky k d = substitutionModel DNA "HKY" [k] d e where e = hkyExch k
+
+-- | HKY substitution model.
+gtr4 :: [Double] -> StationaryDistribution -> SubstitutionModel
+gtr4 es d = substitutionModel DNA "GTR" es d e
+ where e = exchFromListUpper n es
diff --git a/src/ELynx/Data/MarkovProcess/PhyloModel.hs b/src/ELynx/Data/MarkovProcess/PhyloModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/PhyloModel.hs
@@ -0,0 +1,50 @@
+{- |
+Module : ELynx.Data.MarkovProcess.PhyloModel
+Description : Phylogenetic model
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Fri Feb 1 12:43:06 2019.
+
+A phylogenetic model is a complete description of the evolutionary process. At
+the moment, it is either a mixture model or a plain substitution model, but more
+complicated models may be added in the future.
+
+To be imported qualified.
+
+-}
+
+module ELynx.Data.MarkovProcess.PhyloModel
+ ( PhyloModel(..)
+ , getAlphabet
+ , summarize
+ )
+where
+
+import qualified Data.ByteString.Lazy.Char8 as L
+
+import ELynx.Data.Alphabet.Alphabet
+
+import qualified ELynx.Data.MarkovProcess.MixtureModel
+ as M
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+
+-- | A phylogenetic model is a mixture model or a substitution model. More
+-- complicated models may be added.
+data PhyloModel = MixtureModel M.MixtureModel | SubstitutionModel S.SubstitutionModel
+ deriving (Show, Read)
+
+-- | Extract code from phylogenetic model.
+getAlphabet :: PhyloModel -> Alphabet
+getAlphabet (MixtureModel mm) = M.getAlphabet mm
+getAlphabet (SubstitutionModel sm) = S.alphabet sm
+
+-- | Summarize a phylogenetic model; lines to be printed to screen or log.
+summarize :: PhyloModel -> [L.ByteString]
+summarize (MixtureModel mm) = M.summarize mm
+summarize (SubstitutionModel sm) = S.summarize sm
diff --git a/src/ELynx/Data/MarkovProcess/RateMatrix.hs b/src/ELynx/Data/MarkovProcess/RateMatrix.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/RateMatrix.hs
@@ -0,0 +1,210 @@
+{-# LANGUAGE FlexibleContexts #-}
+
+{- |
+Description : Rate matrix helper functions
+Copyright : (c) Dominik Schrempf 2017
+License : GPLv3
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : non-portable (not tested)
+
+Some helper functions that come handy when working with rate matrices of
+continuous-time discrete-state Markov processes.
+
+* Changelog
+
+To be imported qualified.
+
+-}
+
+module ELynx.Data.MarkovProcess.RateMatrix
+ ( RateMatrix
+ , ExchangeabilityMatrix
+ , StationaryDistribution
+ , isValid
+ , normalizeSD
+ , totalRate
+ , totalRateWith
+ , normalize
+ , normalizeWith
+ , setDiagonal
+ , toExchangeabilityMatrix
+ , fromExchangeabilityMatrix
+ , getStationaryDistribution
+ , exchFromListLower
+ , exchFromListUpper
+ )
+where
+
+import Prelude hiding ( (<>) )
+
+import Numeric.LinearAlgebra hiding ( normalize )
+import Numeric.SpecFunctions
+
+import ELynx.Tools
+
+-- | A rate matrix is just a real matrix.
+type RateMatrix = Matrix R
+
+-- | A matrix of exchangeabilities, we have q = e * pi, where q is a rate
+-- matrix, e is the exchangeability matrix and pi is the diagonal matrix
+-- containing the stationary frequency distribution.
+type ExchangeabilityMatrix = Matrix R
+
+-- | Stationary distribution of a rate matrix.
+type StationaryDistribution = Vector R
+
+-- | True if distribution sums to 1.0.
+isValid :: StationaryDistribution -> Bool
+isValid d = nearlyEqWith eps' (norm_1 d) 1.0
+
+-- | Normalize a stationary distribution so that the elements sum to 1.0.
+normalizeSD :: StationaryDistribution -> StationaryDistribution
+normalizeSD d = d / scalar (norm_1 d)
+
+-- | Get average number of substitutions per unit time.
+totalRateWith :: StationaryDistribution -> RateMatrix -> Double
+totalRateWith d m = norm_1 $ d <# matrixSetDiagToZero m
+
+-- | Get average number of substitutions per unit time.
+totalRate :: RateMatrix -> Double
+totalRate m = totalRateWith (getStationaryDistribution m) m
+
+-- | Normalizes a Markov process generator such that one event happens per unit
+-- time. Calculates stationary distribution from rate matrix.
+normalize :: RateMatrix -> RateMatrix
+normalize m = normalizeWith (getStationaryDistribution m) m
+
+-- | Normalizes a Markov process generator such that one event happens per unit
+-- time. Faster, but stationary distribution has to be given.
+normalizeWith :: StationaryDistribution -> RateMatrix -> RateMatrix
+normalizeWith d m = scale (1.0 / totalRateWith d m) m
+
+-- | Set the diagonal entries of a matrix such that the rows sum to 0.
+setDiagonal :: RateMatrix -> RateMatrix
+setDiagonal m = diagZeroes - diag (fromList rowSums)
+ where
+ diagZeroes = matrixSetDiagToZero m
+ rowSums = map norm_1 $ toRows diagZeroes
+
+-- | Extract the exchangeability matrix from a rate matrix.
+toExchangeabilityMatrix
+ :: RateMatrix -> StationaryDistribution -> ExchangeabilityMatrix
+toExchangeabilityMatrix m f = m <> diag oneOverF
+ where oneOverF = cmap (1.0 /) f
+
+-- | Convert exchangeability matrix to rate matrix.
+fromExchangeabilityMatrix
+ :: ExchangeabilityMatrix -> StationaryDistribution -> RateMatrix
+fromExchangeabilityMatrix em d = setDiagonal $ em <> diag d
+
+-- | Get stationary distribution from 'RateMatrix'. Involves eigendecomposition.
+-- If the given matrix does not satisfy the required properties of transition
+-- rate matrices and no eigenvector with an eigenvalue nearly equal to 0 is
+-- found, an error is thrown. Is there an easier way to calculate the stationary
+-- distribution or a better way to handle errors (of course I could use the
+-- Maybe monad, but then the error report is just delayed to the calling
+-- function)?
+getStationaryDistribution :: RateMatrix -> StationaryDistribution
+getStationaryDistribution m = if magnitude (eVals ! i) `nearlyEq` 0
+ then normalizeSumVec 1.0 distReal
+ else error
+ "getStationaryDistribution: Could not retrieve stationary distribution."
+ where
+ (eVals, eVecs) = eig (tr m)
+ i = minIndex eVals
+ distComplex = toColumns eVecs !! i
+ distReal = cmap realPart distComplex
+
+-- The next functions tackle the somewhat trivial, but not easily solvable
+-- problem of converting a triangular matrix (excluding the diagonal) given as a
+-- list into a symmetric matrix. The diagonal entries are set to zero.
+
+-- Lower triangular matrix. This is how the exchangeabilities are specified in
+-- PAML. Conversion from matrix indices (i,j) to list index k.
+--
+-- (i,j) k
+--
+-- (0,0) -
+-- (1,0) 0 (1,1) -
+-- (2,0) 1 (2,1) 2 (2,2) -
+-- (3,0) 3 (3,1) 4 (3,2) 5 (3,3) -
+-- (4,0) 6 (4,1) 7 (4,2) 8 (4,3) 9 (4,4) -
+-- .
+-- .
+-- .
+--
+-- k = (i choose 2) + j.
+ijToKLower :: Int -> Int -> Int
+ijToKLower i j
+ | i > j = round (i `choose` 2) + j
+ | otherwise = error "ijToKLower: not defined for upper triangular matrix."
+
+
+-- Upper triangular matrix. Conversion from matrix indices (i,j) to list index
+-- k. Matrix is square of size n.
+--
+-- (i,j) k
+--
+-- (0,0) - (0,1) 0 (0,2) 1 (0,3) 2 (0,4) 3 ...
+-- (1,1) - (1,2) n-1 (1,3) n (1,4) n+1
+-- (2,2) - (2,3) 2n-3 (2,4) 2n-2
+-- (3,3) - (3,4) 3n-6
+-- (4,4) -
+-- ...
+--
+-- k = i*(n-2) - (i choose 2) + (j - 1)
+ijToKUpper :: Int -> Int -> Int -> Int
+ijToKUpper n i j
+ | i < j = i * (n - 2) - round (i `choose` 2) + j - 1
+ | otherwise = error "ijToKUpper: not defined for lower triangular matrix."
+
+-- The function is a little weird because HMatrix uses Double indices for Matrix
+-- Double builders.
+fromListBuilderLower :: RealFrac a => [a] -> a -> a -> a
+fromListBuilderLower es i j
+ | i > j = es !! ijToKLower iI jI
+ | i == j = 0.0
+ | i < j = es !! ijToKLower jI iI
+ | otherwise = error
+ "Float indices could not be compared during matrix creation."
+ where
+ iI = round i :: Int
+ jI = round j :: Int
+
+-- The function is a little weird because HMatrix uses Double indices for Matrix
+-- Double builders.
+fromListBuilderUpper :: RealFrac a => Int -> [a] -> a -> a -> a
+fromListBuilderUpper n es i j
+ | i < j = es !! ijToKUpper n iI jI
+ | i == j = 0.0
+ | i > j = es !! ijToKUpper n jI iI
+ | otherwise = error
+ "Float indices could not be compared during matrix creation."
+ where
+ iI = round i :: Int
+ jI = round j :: Int
+
+checkEs :: RealFrac a => Int -> [a] -> [a]
+checkEs n es | length es == nExp = es
+ | otherwise = error eStr
+ where
+ nExp = round (n `choose` 2)
+ eStr = unlines
+ [ "exchFromListlower: the number of exchangeabilities does not match the matrix size"
+ , "matrix size: " ++ show n
+ , "expected number of exchangeabilities: " ++ show nExp
+ , "received number of exchangeabilities: " ++ show (length es)
+ ]
+
+-- | Build exchangeability matrix from list denoting lower triangular matrix,
+-- and excluding diagonal. This is how the exchangeabilities are specified in
+-- PAML.
+exchFromListLower :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
+exchFromListLower n es = build (n, n) (fromListBuilderLower (checkEs n es))
+
+-- | Build exchangeability matrix from list denoting upper triangular matrix,
+-- and excluding diagonal.
+exchFromListUpper :: (RealFrac a, Container Vector a) => Int -> [a] -> Matrix a
+exchFromListUpper n es = build (n, n) (fromListBuilderUpper n (checkEs n es))
diff --git a/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs b/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Data/MarkovProcess/SubstitutionModel.hs
@@ -0,0 +1,143 @@
+{- |
+Module : ELynx.Data.MarkovProcess.SubstitutionModel
+Description : Data type describing substitution model
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 19:10:46 2019.
+
+To be imported qualified.
+
+-}
+
+module ELynx.Data.MarkovProcess.SubstitutionModel
+ ( -- * Types
+ Name
+ , Params
+ , SubstitutionModel
+ -- * Lenses and other accessors
+ , alphabet
+ , name
+ , stationaryDistribution
+ , exchangeabilityMatrix
+ , rateMatrix
+ , totalRate
+ -- * Building substitution models
+ , substitutionModel
+ -- * Transformations
+ , scale
+ , normalize
+ , appendName
+ -- * Output
+ , summarize
+ )
+where
+
+import qualified Data.ByteString.Lazy.Char8 as L
+import qualified Numeric.LinearAlgebra as LinAlg
+
+import ELynx.Data.Alphabet.Alphabet
+
+import ELynx.Tools
+
+import qualified ELynx.Data.MarkovProcess.RateMatrix
+ as R
+
+-- | Name of substitution model; abstracted and subject to change.
+type Name = String
+
+-- | Parameters of substitution model. May be the empty list.
+type Params = [Double]
+
+-- XXX: Use a proper data type. For example:
+-- data SubstitutionModelAA = LG | WAG | LG-Custom dist | ...
+-- data SubstitutionModelNuc = JC | HKY p1 p2 ... | GTR p1 p2 ...
+--
+-- I thought about this a lot, and it seems easier like it is at the moment.
+-- Since the data types are abstracted anyways, not much harm can be done. Of
+-- course, conflicting substitution models can be declared, or duplicate ones
+-- with different names, but well...
+
+-- | Complete definition of a substitution model. Create instances with
+-- 'substitutionModel'. A substitution model has an alphabet, a name, and a list
+-- of parameters (e.g., the kappa value for the HKY model). Further, the
+-- transition rate matrix is defined by a stationary distribution and a set of
+-- exchangeabilities.
+data SubstitutionModel = SubstitutionModel
+ { alphabet :: Alphabet -- ^ Alphabet
+ , name :: Name -- ^ Name
+ , params :: Params -- ^ List of parameters
+ , stationaryDistribution :: R.StationaryDistribution -- ^ Stationary distribution
+ , exchangeabilityMatrix :: R.ExchangeabilityMatrix -- ^ Exchangeability matrix
+ }
+ deriving (Show, Read)
+
+-- | Calculate rate matrix from substitution model.
+rateMatrix :: SubstitutionModel -> R.RateMatrix
+rateMatrix sm = R.fromExchangeabilityMatrix (exchangeabilityMatrix sm)
+ (stationaryDistribution sm)
+
+-- | Get scale of substitution model.
+totalRate :: SubstitutionModel -> Double
+totalRate sm = R.totalRate (rateMatrix sm)
+
+-- | Create normalized 'SubstitutionModel'. See 'normalize'.
+substitutionModel
+ :: Alphabet
+ -> Name
+ -> Params
+ -> R.StationaryDistribution
+ -> R.ExchangeabilityMatrix
+ -> SubstitutionModel
+substitutionModel c n ps d e = if R.isValid d
+ then normalize $ SubstitutionModel c n ps d' e
+ else
+ error
+ $ "substitionModel: Stationary distribution does not sum to 1.0: "
+ ++ show d
+ where d' = normalizeSumVec 1.0 d
+
+-- | Scale the rate of a substitution model by given factor.
+scale :: Double -> SubstitutionModel -> SubstitutionModel
+scale r sm = sm { exchangeabilityMatrix = em' }
+ where em' = LinAlg.scale r $ exchangeabilityMatrix sm
+
+-- | Normalize a substitution model, so that, on average, one substitution
+-- happens per unit time.
+normalize :: SubstitutionModel -> SubstitutionModel
+normalize sm = scale (1.0 / r) sm where r = totalRate sm
+
+-- | Abbend to name.
+appendName :: Name -> SubstitutionModel -> SubstitutionModel
+appendName n sm = sm { name = n' } where n' = name sm <> n
+
+-- | Summarize a substitution model; lines to be printed to screen or log.
+summarize :: SubstitutionModel -> [L.ByteString]
+summarize sm =
+ map L.pack
+ $ (show (alphabet sm) ++ " substitution model: " ++ name sm ++ ".")
+ : [ "Parameters: " ++ show (params sm) ++ "." | not (null (params sm)) ]
+ ++ case alphabet sm of
+ DNA ->
+ [ "Stationary distribution: "
+ ++ dispv precision (stationaryDistribution sm)
+ ++ "."
+ , "Exchangeability matrix:\n"
+ ++ dispmi 2 precision (exchangeabilityMatrix sm)
+ ++ "."
+ , "Scale: " ++ show (roundN precision $ totalRate sm) ++ "."
+ ]
+ Protein ->
+ [ "Stationary distribution: "
+ ++ dispv precision (stationaryDistribution sm)
+ ++ "."
+ , "Scale: " ++ show (roundN precision $ totalRate sm) ++ "."
+ ]
+ _ ->
+ error
+ "Extended character sets are not supported with substitution models."
+
diff --git a/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs b/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Import/MarkovProcess/EDMModelPhylobayes.hs
@@ -0,0 +1,75 @@
+{- |
+Module : ELynx.Import.MarkovProcess.EDMModelPhylobayes
+Description : Import stationary distributions from Phylobayes format
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 12:12:55 2019.
+
+-}
+
+module ELynx.Import.MarkovProcess.EDMModelPhylobayes
+ ( Parser
+ , EDMComponent
+ , phylobayes
+ )
+where
+
+import Control.Monad
+import qualified Data.ByteString.Lazy.Char8 as L
+import qualified Data.Vector.Storable as V
+import Data.Void
+import Text.Megaparsec
+import Text.Megaparsec.Byte
+import Text.Megaparsec.Byte.Lexer
+
+import ELynx.Data.MarkovProcess.MixtureModel
+ ( Weight )
+
+import ELynx.Tools
+
+-- | Shortcut.
+type Parser = Parsec Void L.ByteString
+
+-- | An empirical mixture model component has a weight and a stationary
+-- distribution.
+type EDMComponent = (Weight, V.Vector Double)
+
+-- | Parse stationary distributions from Phylobayes format.
+phylobayes :: Parser [EDMComponent]
+phylobayes = do
+ n <- headerLine
+ k <- kComponentsLine
+ cs <- count k $ dataLine n
+ _ <- many newline *> eof "phylobayes"
+ return cs
+
+horizontalSpace :: Parser ()
+horizontalSpace = skipMany $ char (c2w ' ') <|> tab
+
+headerLine :: Parser Int
+headerLine = do
+ n <- decimal
+ _ <- horizontalSpace
+ -- FIXME: This should be more general, but then we also want to ensure that
+ -- the order of states is correct.
+ _ <- chunk (L.pack "A C D E F G H I K L M N P Q R S T V W Y")
+ <|> chunk (L.pack "A C G T")
+ _ <- many newline "headerLine"
+ return n
+
+kComponentsLine :: Parser Int
+kComponentsLine = decimal <* newline "kComponentsLine"
+
+dataLine :: Int -> Parser EDMComponent
+dataLine n = do
+ weight <- float
+ _ <- horizontalSpace
+ vals <- float `sepBy` horizontalSpace
+ when (length vals /= n) (error "Did not find correct number of entries.")
+ _ <- many newline "dataLine"
+ return (weight, V.fromList vals)
diff --git a/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs b/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Import/MarkovProcess/SiteprofilesPhylobayes.hs
@@ -0,0 +1,77 @@
+{- |
+Module : ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
+Description : Import site profiles in Phylobayes format
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 12:12:55 2019.
+
+For now I just try to go with a huge empirical distribution mixture model. Let's
+see if performance is good enough.
+
+There are subtle differences between
+`ELynx.Import.MarkovProcess.EDMModelPhylobayes` and this module, which collects
+one stationary distribution for each site.
+
+-}
+
+module ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
+ ( siteprofiles
+ )
+where
+
+import Control.Monad
+import Data.List ( nub )
+import qualified Data.Vector.Storable as V
+import Text.Megaparsec
+import Text.Megaparsec.Byte
+import Text.Megaparsec.Byte.Lexer
+
+import ELynx.Tools
+
+import ELynx.Import.MarkovProcess.EDMModelPhylobayes
+ ( Parser
+ , EDMComponent
+ )
+
+-- | Parse stationary distributions from Phylobayes format.
+siteprofiles :: Parser [EDMComponent]
+siteprofiles = do
+ _ <- headerLines
+ cs <- many dataLine
+ _ <- many newline *> eof "phylobayes siteprofiles"
+ let ls = map length cs
+ nLs = length $ nub ls
+ when (nLs /= 1)
+ (error "The site profiles have a different number of entries.")
+ return cs
+
+horizontalSpace :: Parser ()
+horizontalSpace = skipMany $ char (c2w ' ') <|> tab
+
+line :: Parser ()
+line = do
+ _ <- many $ noneOf [c2w '\n']
+ pure ()
+
+-- For now, just ignore the header.
+headerLines :: Parser ()
+headerLines = do
+ _ <- line
+ _ <- many newline "headerLine"
+ pure ()
+
+dataLine :: Parser EDMComponent
+dataLine = do
+ -- Ignore site number.
+ _ <- decimal :: Parser Integer
+ _ <- horizontalSpace
+ -- Also ignore additional white space on line.
+ vals <- float `sepEndBy1` horizontalSpace
+ _ <- many newline "dataLine"
+ -- Set the weight to 1.0 for all sites.
+ return (1.0, V.fromList vals)
diff --git a/src/ELynx/Simulate/MarkovProcess.hs b/src/ELynx/Simulate/MarkovProcess.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Simulate/MarkovProcess.hs
@@ -0,0 +1,78 @@
+{- |
+Module : ELynx.Simulate.MarkovProcess
+Description : Markov process helpers
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Thu Jan 24 09:02:25 2019.
+
+-}
+
+module ELynx.Simulate.MarkovProcess
+ ( ProbMatrix
+ , State
+ , probMatrix
+ , jump
+ )
+where
+
+import Control.Monad.Primitive
+import Numeric.LinearAlgebra
+import System.Random.MWC
+import System.Random.MWC.Distributions
+
+import ELynx.Data.MarkovProcess.RateMatrix
+
+-- | A probability matrix, P_ij(t) = Pr (X_t = j | X_0 = i).
+type ProbMatrix = Matrix R
+
+-- | Make type signatures a little clearer.
+type State = Int
+
+-- | The important matrix that gives the probabilities to move from one state to
+-- another in a specific time (branch length).
+probMatrix :: RateMatrix -> Double -> ProbMatrix
+probMatrix q t
+ | t == 0 = if rows q == cols q
+ then ident (rows q)
+ else error "probMatrix: Matrix is not square."
+ | t < 0 = error "probMatrix: Time is negative."
+ | otherwise = expm $ scale t q
+
+-- | Move from a given state to a new one according to a transition probability
+-- matrix (for performance reasons this probability matrix needs to be given as
+-- a list of generators, see
+-- https://hackage.haskell.org/package/distribution-1.1.0.0/docs/Data-Distribution-Sample.html).
+-- This function is the bottleneck of the simulator and takes up most of the
+-- computation time. However, I was not able to find a faster implementation
+-- than the one from Data.Distribution.
+jump :: (PrimMonad m) => State -> ProbMatrix -> Gen (PrimState m) -> m State
+jump i p = categorical (p ! i)
+
+-- XXX: Maybe for later, use condensed tables.
+--
+-- Write storable instance, compilation is really slow otherwise. instance
+-- Storable (Int, R) where sizeOf (x, y) = sizeOf x + sizeOf y
+--
+-- Do not generate table for each jump.
+--
+-- jump :: (PrimMonad m) => State -> ProbMatrix -> Gen (PrimState m) -> m State
+-- jump i p = genFromTable table
+-- where
+-- ws = toList $ p ! i
+-- vsAndWs = fromList [ (v, w) | (v, w) <- zip [(0 :: Int) ..] ws
+-- , w > 0 ]
+-- table = tableFromProbabilities vsAndWs
+
+-- -- | Perform N jumps from a given state and according to a transition
+-- -- probability matrix transformed to a list of generators. This implementation
+-- -- uses 'foldM' and I am not sure how to access or store the actual chain. This
+-- -- could be done by an equivalent of 'scanl' for general monads, which I was
+-- -- unable to find. This function is neat, but will most likely not be needed.
+-- -- However, it is instructive and is left in place.
+-- jumpN :: (MonadRandom m) => State -> [Generator State] -> Int -> m State
+-- jumpN s p n = foldM jump s (replicate n p)
diff --git a/src/ELynx/Simulate/MarkovProcessAlongTree.hs b/src/ELynx/Simulate/MarkovProcessAlongTree.hs
new file mode 100644
--- /dev/null
+++ b/src/ELynx/Simulate/MarkovProcessAlongTree.hs
@@ -0,0 +1,222 @@
+{- |
+ Description : Work with transition probability matrices on rooted trees
+ Copyright : (c) Dominik Schrempf 2017
+ License : GPLv3
+
+ Maintainer : dominik.schrempf@gmail.com
+ Stability : unstable
+ Portability : non-portable (not tested)
+
+Calculate transition probability matrices, map rate matrices on trees, populate
+a tree with states according to a stationary distribution, etc.
+
+The implementation of the Markov process is more than basic and can be improved
+in a lot of ways.
+
+-}
+
+module ELynx.Simulate.MarkovProcessAlongTree
+ ( -- * Single rate matrix.
+ simulate
+ , simulateAndFlatten
+ -- * Mixture models.
+ , simulateMixtureModel
+ , simulateAndFlattenMixtureModel
+ , simulateAndFlattenMixtureModelPar
+ )
+where
+
+import Control.Monad
+import Control.Monad.Primitive
+import Control.Parallel.Strategies
+import Data.Tree
+import Numeric.LinearAlgebra
+import System.Random.MWC ( Gen
+ , GenIO
+ )
+import System.Random.MWC.Distributions
+ ( categorical )
+
+import ELynx.Data.Tree
+
+import ELynx.Tools
+
+import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.Simulate.MarkovProcess
+
+toProbTree :: (Measurable a) => RateMatrix -> Tree a -> Tree ProbMatrix
+toProbTree q = fmap (probMatrix q . getLen)
+
+getRootStates
+ :: PrimMonad m
+ => Int
+ -> StationaryDistribution
+ -> Gen (PrimState m)
+ -> m [State]
+getRootStates n d g = replicateM n $ categorical d g
+
+-- | Simulate a number of sites for a given substitution model. Only the states
+-- at the leafs are retained. The states at internal nodes are removed. This has
+-- a lower memory footprint.
+--
+-- XXX: Improve performance. Use vectors, not lists.
+simulateAndFlatten
+ :: (PrimMonad m, Measurable a)
+ => Int
+ -> StationaryDistribution
+ -> ExchangeabilityMatrix
+ -> Tree a
+ -> Gen (PrimState m)
+ -> m [[State]]
+simulateAndFlatten n d e t g = do
+ let q = fromExchangeabilityMatrix e d
+ pt = toProbTree q t
+ is <- getRootStates n d g
+ simulateAndFlatten' is pt g
+
+-- This is the heart of the simulation. Take a tree and a list of root states.
+-- Recursively jump down the branches to the leafs. Forget states at internal.
+simulateAndFlatten'
+ :: (PrimMonad m)
+ => [State]
+ -> Tree ProbMatrix
+ -> Gen (PrimState m)
+ -> m [[State]]
+simulateAndFlatten' is (Node p f) g = do
+ is' <- mapM (\i -> jump i p g) is
+ if null f
+ then return [is']
+ else concat <$> sequence [ simulateAndFlatten' is' t g | t <- f ]
+
+-- | Simulate a number of sites for a given substitution model. Keep states at
+-- internal nodes. The result is a tree with the list of simulated states as
+-- node labels.
+simulate
+ :: (PrimMonad m, Measurable a)
+ => Int
+ -> StationaryDistribution
+ -> ExchangeabilityMatrix
+ -> Tree a
+ -> Gen (PrimState m)
+ -> m (Tree [State])
+simulate n d e t g = do
+ let q = fromExchangeabilityMatrix e d
+ pt = toProbTree q t
+ is <- getRootStates n d g
+ simulate' is pt g
+
+-- This is the heart of the simulation. Take a tree and a list of root states.
+-- Recursively jump down the branches to the leafs.
+simulate'
+ :: (PrimMonad m)
+ => [State]
+ -> Tree ProbMatrix
+ -> Gen (PrimState m)
+ -> m (Tree [State])
+simulate' is (Node p f) g = do
+ is' <- mapM (\i -> jump i p g) is
+ f' <- sequence [ simulate' is' t g | t <- f ]
+ return $ Node is' f'
+
+toProbTreeMixtureModel
+ :: (Measurable a) => [RateMatrix] -> Tree a -> Tree [ProbMatrix]
+toProbTreeMixtureModel qs =
+ fmap (\a -> [ probMatrix q . getLen $ a | q <- qs ] `using` parList rpar)
+
+getComponentsAndRootStates
+ :: PrimMonad m
+ => Int
+ -> Vector R
+ -> [StationaryDistribution]
+ -> Gen (PrimState m)
+ -> m ([Int], [State])
+getComponentsAndRootStates n ws ds g = do
+ cs <- replicateM n $ categorical ws g
+ is <- sequence [ categorical (ds !! c) g | c <- cs ]
+ return (cs, is)
+
+-- | Simulate a number of sites for a given set of substitution models with
+-- corresponding weights. Forget states at internal nodes. See also
+-- 'simulateAndFlatten'.
+simulateAndFlattenMixtureModel
+ :: (PrimMonad m, Measurable a)
+ => Int
+ -> Vector R
+ -> [StationaryDistribution]
+ -> [ExchangeabilityMatrix]
+ -> Tree a
+ -> Gen (PrimState m)
+ -> m [[State]]
+simulateAndFlattenMixtureModel n ws ds es t g = do
+ let qs = zipWith fromExchangeabilityMatrix es ds
+ pt = toProbTreeMixtureModel qs t
+ (cs, is) <- getComponentsAndRootStates n ws ds g
+ simulateAndFlattenMixtureModel' is cs pt g
+
+simulateAndFlattenMixtureModel'
+ :: (PrimMonad m)
+ => [State]
+ -> [Int]
+ -> Tree [ProbMatrix]
+ -> Gen (PrimState m)
+ -> m [[State]]
+simulateAndFlattenMixtureModel' is cs (Node ps f) g = do
+ is' <- sequence [ jump i (ps !! c) g | (i, c) <- zip is cs ]
+ if null f
+ then return [is']
+ else concat
+ <$> sequence [ simulateAndFlattenMixtureModel' is' cs t g | t <- f ]
+
+-- | See 'simulateAndFlattenMixtureModel', parallel version;
+-- needs to be run in IO monad.
+simulateAndFlattenMixtureModelPar
+ :: Measurable a
+ => Int
+ -> Vector R
+ -> [StationaryDistribution]
+ -> [ExchangeabilityMatrix]
+ -> Tree a
+ -> GenIO
+ -> IO [[[State]]]
+simulateAndFlattenMixtureModelPar n ws ds es t g = do
+ let qs = zipWith fromExchangeabilityMatrix es ds
+ pt = toProbTreeMixtureModel qs t
+ parComp
+ n
+ (\n' g' -> do
+ (cs, is) <- getComponentsAndRootStates n' ws ds g'
+ simulateAndFlattenMixtureModel' is cs pt g'
+ )
+ g
+
+-- | Simulate a number of sites for a given set of substitution models with
+-- corresponding weights. Keep states at internal nodes. See also
+-- 'simulate'.
+simulateMixtureModel
+ :: (PrimMonad m, Measurable a)
+ => Int
+ -> Vector R
+ -> [StationaryDistribution]
+ -> [ExchangeabilityMatrix]
+ -> Tree a
+ -> Gen (PrimState m)
+ -> m (Tree [State])
+simulateMixtureModel n ws ds es t g = do
+ let qs = zipWith fromExchangeabilityMatrix es ds
+ pt = toProbTreeMixtureModel qs t
+ (cs, is) <- getComponentsAndRootStates n ws ds g
+ simulateMixtureModel' is cs pt g
+
+-- See 'simulateAlongProbTree', only we have a number of mixture components. The
+-- starting states and the components for each site have to be provided.
+simulateMixtureModel'
+ :: (PrimMonad m)
+ => [State]
+ -> [Int]
+ -> Tree [ProbMatrix]
+ -> Gen (PrimState m)
+ -> m (Tree [State])
+simulateMixtureModel' is cs (Node ps f) g = do
+ is' <- sequence [ jump i (ps !! c) g | (i, c) <- zip is cs ]
+ f' <- sequence [ simulateMixtureModel' is' cs t g | t <- f ]
+ return $ Node is' f'
diff --git a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
@@ -0,0 +1,525 @@
+{- |
+Module : ELynx.Data.MarkovProcess.AminoAcidSpec
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 10:47:40 2019.
+
+-}
+
+module ELynx.Data.MarkovProcess.AminoAcidSpec
+ ( spec
+ )
+where
+
+import Numeric.LinearAlgebra
+import Test.Hspec
+
+import ELynx.Tools
+
+import ELynx.Data.MarkovProcess.AminoAcid
+import qualified ELynx.Data.MarkovProcess.RateMatrix
+ as R
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+
+statDistLGPython :: R.StationaryDistribution
+statDistLGPython = normalizeSumVec 1.0 $ fromList
+ [ 0.079066
+ , 0.012937
+ , 0.053052
+ , 0.071586
+ , 0.042302
+ , 0.057337
+ , 0.022355
+ , 0.062157
+ , 0.064600
+ , 0.099081
+ , 0.022951
+ , 0.041977
+ , 0.044040
+ , 0.040767
+ , 0.055941
+ , 0.061197
+ , 0.053287
+ , 0.069147
+ , 0.012066
+ , 0.034155
+ ]
+
+exchLGPython :: R.ExchangeabilityMatrix
+exchLGPython = fromLists
+ [ [ 0.0000000e+00
+ , 2.4890840e+00
+ , 3.9514400e-01
+ , 1.0385450e+00
+ , 2.5370100e-01
+ , 2.0660400e+00
+ , 3.5885800e-01
+ , 1.4983000e-01
+ , 5.3651800e-01
+ , 3.9533700e-01
+ , 1.1240350e+00
+ , 2.7681800e-01
+ , 1.1776510e+00
+ , 9.6989400e-01
+ , 4.2509300e-01
+ , 4.7271820e+00
+ , 2.1395010e+00
+ , 2.5478700e+00
+ , 1.8071700e-01
+ , 2.1895900e-01
+ ]
+ , [ 2.4890840e+00
+ , 0.0000000e+00
+ , 6.2556000e-02
+ , 3.4990000e-03
+ , 1.1052510e+00
+ , 5.6926500e-01
+ , 6.4054300e-01
+ , 3.2062700e-01
+ , 1.3266000e-02
+ , 5.9400700e-01
+ , 8.9368000e-01
+ , 5.2876800e-01
+ , 7.5382000e-02
+ , 8.4808000e-02
+ , 5.3455100e-01
+ , 2.7844780e+00
+ , 1.1434800e+00
+ , 1.9592910e+00
+ , 6.7012800e-01
+ , 1.1655320e+00
+ ]
+ , [ 3.9514400e-01
+ , 6.2556000e-02
+ , 0.0000000e+00
+ , 5.2438700e+00
+ , 1.7416000e-02
+ , 8.4492600e-01
+ , 9.2711400e-01
+ , 1.0690000e-02
+ , 2.8295900e-01
+ , 1.5076000e-02
+ , 2.5548000e-02
+ , 5.0761490e+00
+ , 3.9445600e-01
+ , 5.2338600e-01
+ , 1.2395400e-01
+ , 1.2402750e+00
+ , 4.2586000e-01
+ , 3.7967000e-02
+ , 2.9890000e-02
+ , 1.3510700e-01
+ ]
+ , [ 1.0385450e+00
+ , 3.4990000e-03
+ , 5.2438700e+00
+ , 0.0000000e+00
+ , 1.8811000e-02
+ , 3.4884700e-01
+ , 4.2388100e-01
+ , 4.4265000e-02
+ , 1.8071770e+00
+ , 6.9673000e-02
+ , 1.7373500e-01
+ , 5.4171200e-01
+ , 4.1940900e-01
+ , 4.1285910e+00
+ , 3.6397000e-01
+ , 6.1197300e-01
+ , 6.0454500e-01
+ , 2.4503400e-01
+ , 7.7852000e-02
+ , 1.2003700e-01
+ ]
+ , [ 2.5370100e-01
+ , 1.1052510e+00
+ , 1.7416000e-02
+ , 1.8811000e-02
+ , 0.0000000e+00
+ , 8.9586000e-02
+ , 6.8213900e-01
+ , 1.1127270e+00
+ , 2.3918000e-02
+ , 2.5926920e+00
+ , 1.7988530e+00
+ , 8.9525000e-02
+ , 9.4464000e-02
+ , 3.5855000e-02
+ , 5.2722000e-02
+ , 3.6181900e-01
+ , 1.6500100e-01
+ , 6.5468300e-01
+ , 2.4571210e+00
+ , 7.8039020e+00
+ ]
+ , [ 2.0660400e+00
+ , 5.6926500e-01
+ , 8.4492600e-01
+ , 3.4884700e-01
+ , 8.9586000e-02
+ , 0.0000000e+00
+ , 3.1148400e-01
+ , 8.7050000e-03
+ , 2.9663600e-01
+ , 4.4261000e-02
+ , 1.3953800e-01
+ , 1.4376450e+00
+ , 1.9696100e-01
+ , 2.6795900e-01
+ , 3.9019200e-01
+ , 1.7399900e+00
+ , 1.2983600e-01
+ , 7.6701000e-02
+ , 2.6849100e-01
+ , 5.4679000e-02
+ ]
+ , [ 3.5885800e-01
+ , 6.4054300e-01
+ , 9.2711400e-01
+ , 4.2388100e-01
+ , 6.8213900e-01
+ , 3.1148400e-01
+ , 0.0000000e+00
+ , 1.0888200e-01
+ , 6.9726400e-01
+ , 3.6631700e-01
+ , 4.4247200e-01
+ , 4.5092380e+00
+ , 5.0885100e-01
+ , 4.8135050e+00
+ , 2.4266010e+00
+ , 9.9001200e-01
+ , 5.8426200e-01
+ , 1.1901300e-01
+ , 5.9705400e-01
+ , 5.3068340e+00
+ ]
+ , [ 1.4983000e-01
+ , 3.2062700e-01
+ , 1.0690000e-02
+ , 4.4265000e-02
+ , 1.1127270e+00
+ , 8.7050000e-03
+ , 1.0888200e-01
+ , 0.0000000e+00
+ , 1.5906900e-01
+ , 4.1450670e+00
+ , 4.2736070e+00
+ , 1.9150300e-01
+ , 7.8281000e-02
+ , 7.2854000e-02
+ , 1.2699100e-01
+ , 6.4105000e-02
+ , 1.0337390e+00
+ , 1.0649107e+01
+ , 1.1166000e-01
+ , 2.3252300e-01
+ ]
+ , [ 5.3651800e-01
+ , 1.3266000e-02
+ , 2.8295900e-01
+ , 1.8071770e+00
+ , 2.3918000e-02
+ , 2.9663600e-01
+ , 6.9726400e-01
+ , 1.5906900e-01
+ , 0.0000000e+00
+ , 1.3750000e-01
+ , 6.5660400e-01
+ , 2.1450780e+00
+ , 3.9032200e-01
+ , 3.2342940e+00
+ , 6.3260670e+00
+ , 7.4868300e-01
+ , 1.1368630e+00
+ , 1.8520200e-01
+ , 4.9906000e-02
+ , 1.3193200e-01
+ ]
+ , [ 3.9533700e-01
+ , 5.9400700e-01
+ , 1.5076000e-02
+ , 6.9673000e-02
+ , 2.5926920e+00
+ , 4.4261000e-02
+ , 3.6631700e-01
+ , 4.1450670e+00
+ , 1.3750000e-01
+ , 0.0000000e+00
+ , 6.3123580e+00
+ , 6.8427000e-02
+ , 2.4906000e-01
+ , 5.8245700e-01
+ , 3.0184800e-01
+ , 1.8228700e-01
+ , 3.0293600e-01
+ , 1.7027450e+00
+ , 6.1963200e-01
+ , 2.9964800e-01
+ ]
+ , [ 1.1240350e+00
+ , 8.9368000e-01
+ , 2.5548000e-02
+ , 1.7373500e-01
+ , 1.7988530e+00
+ , 1.3953800e-01
+ , 4.4247200e-01
+ , 4.2736070e+00
+ , 6.5660400e-01
+ , 6.3123580e+00
+ , 0.0000000e+00
+ , 3.7100400e-01
+ , 9.9849000e-02
+ , 1.6725690e+00
+ , 4.8413300e-01
+ , 3.4696000e-01
+ , 2.0203660e+00
+ , 1.8987180e+00
+ , 6.9617500e-01
+ , 4.8130600e-01
+ ]
+ , [ 2.7681800e-01
+ , 5.2876800e-01
+ , 5.0761490e+00
+ , 5.4171200e-01
+ , 8.9525000e-02
+ , 1.4376450e+00
+ , 4.5092380e+00
+ , 1.9150300e-01
+ , 2.1450780e+00
+ , 6.8427000e-02
+ , 3.7100400e-01
+ , 0.0000000e+00
+ , 1.6178700e-01
+ , 1.6957520e+00
+ , 7.5187800e-01
+ , 4.0083580e+00
+ , 2.0006790e+00
+ , 8.3688000e-02
+ , 4.5376000e-02
+ , 6.1202500e-01
+ ]
+ , [ 1.1776510e+00
+ , 7.5382000e-02
+ , 3.9445600e-01
+ , 4.1940900e-01
+ , 9.4464000e-02
+ , 1.9696100e-01
+ , 5.0885100e-01
+ , 7.8281000e-02
+ , 3.9032200e-01
+ , 2.4906000e-01
+ , 9.9849000e-02
+ , 1.6178700e-01
+ , 0.0000000e+00
+ , 6.2429400e-01
+ , 3.3253300e-01
+ , 1.3381320e+00
+ , 5.7146800e-01
+ , 2.9650100e-01
+ , 9.5131000e-02
+ , 8.9613000e-02
+ ]
+ , [ 9.6989400e-01
+ , 8.4808000e-02
+ , 5.2338600e-01
+ , 4.1285910e+00
+ , 3.5855000e-02
+ , 2.6795900e-01
+ , 4.8135050e+00
+ , 7.2854000e-02
+ , 3.2342940e+00
+ , 5.8245700e-01
+ , 1.6725690e+00
+ , 1.6957520e+00
+ , 6.2429400e-01
+ , 0.0000000e+00
+ , 2.8079080e+00
+ , 1.2238280e+00
+ , 1.0801360e+00
+ , 2.1033200e-01
+ , 2.3619900e-01
+ , 2.5733600e-01
+ ]
+ , [ 4.2509300e-01
+ , 5.3455100e-01
+ , 1.2395400e-01
+ , 3.6397000e-01
+ , 5.2722000e-02
+ , 3.9019200e-01
+ , 2.4266010e+00
+ , 1.2699100e-01
+ , 6.3260670e+00
+ , 3.0184800e-01
+ , 4.8413300e-01
+ , 7.5187800e-01
+ , 3.3253300e-01
+ , 2.8079080e+00
+ , 0.0000000e+00
+ , 8.5815100e-01
+ , 5.7898700e-01
+ , 1.7088700e-01
+ , 5.9360700e-01
+ , 3.1444000e-01
+ ]
+ , [ 4.7271820e+00
+ , 2.7844780e+00
+ , 1.2402750e+00
+ , 6.1197300e-01
+ , 3.6181900e-01
+ , 1.7399900e+00
+ , 9.9001200e-01
+ , 6.4105000e-02
+ , 7.4868300e-01
+ , 1.8228700e-01
+ , 3.4696000e-01
+ , 4.0083580e+00
+ , 1.3381320e+00
+ , 1.2238280e+00
+ , 8.5815100e-01
+ , 0.0000000e+00
+ , 6.4722790e+00
+ , 9.8369000e-02
+ , 2.4886200e-01
+ , 4.0054700e-01
+ ]
+ , [ 2.1395010e+00
+ , 1.1434800e+00
+ , 4.2586000e-01
+ , 6.0454500e-01
+ , 1.6500100e-01
+ , 1.2983600e-01
+ , 5.8426200e-01
+ , 1.0337390e+00
+ , 1.1368630e+00
+ , 3.0293600e-01
+ , 2.0203660e+00
+ , 2.0006790e+00
+ , 5.7146800e-01
+ , 1.0801360e+00
+ , 5.7898700e-01
+ , 6.4722790e+00
+ , 0.0000000e+00
+ , 2.1881580e+00
+ , 1.4082500e-01
+ , 2.4584100e-01
+ ]
+ , [ 2.5478700e+00
+ , 1.9592910e+00
+ , 3.7967000e-02
+ , 2.4503400e-01
+ , 6.5468300e-01
+ , 7.6701000e-02
+ , 1.1901300e-01
+ , 1.0649107e+01
+ , 1.8520200e-01
+ , 1.7027450e+00
+ , 1.8987180e+00
+ , 8.3688000e-02
+ , 2.9650100e-01
+ , 2.1033200e-01
+ , 1.7088700e-01
+ , 9.8369000e-02
+ , 2.1881580e+00
+ , 0.0000000e+00
+ , 1.8951000e-01
+ , 2.4931300e-01
+ ]
+ , [ 1.8071700e-01
+ , 6.7012800e-01
+ , 2.9890000e-02
+ , 7.7852000e-02
+ , 2.4571210e+00
+ , 2.6849100e-01
+ , 5.9705400e-01
+ , 1.1166000e-01
+ , 4.9906000e-02
+ , 6.1963200e-01
+ , 6.9617500e-01
+ , 4.5376000e-02
+ , 9.5131000e-02
+ , 2.3619900e-01
+ , 5.9360700e-01
+ , 2.4886200e-01
+ , 1.4082500e-01
+ , 1.8951000e-01
+ , 0.0000000e+00
+ , 3.1518150e+00
+ ]
+ , [ 2.1895900e-01
+ , 1.1655320e+00
+ , 1.3510700e-01
+ , 1.2003700e-01
+ , 7.8039020e+00
+ , 5.4679000e-02
+ , 5.3068340e+00
+ , 2.3252300e-01
+ , 1.3193200e-01
+ , 2.9964800e-01
+ , 4.8130600e-01
+ , 6.1202500e-01
+ , 8.9613000e-02
+ , 2.5733600e-01
+ , 3.1444000e-01
+ , 4.0054700e-01
+ , 2.4584100e-01
+ , 2.4931300e-01
+ , 3.1518150e+00
+ , 0.0000000e+00
+ ]
+ ]
+
+statDistUniform :: R.StationaryDistribution
+statDistUniform = vector $ replicate 20 0.05
+
+statDistLG :: R.StationaryDistribution
+statDistLG = S.stationaryDistribution lg
+
+exchLG :: R.ExchangeabilityMatrix
+exchLG = S.exchangeabilityMatrix lg
+
+rmLG :: R.RateMatrix
+rmLG = S.rateMatrix lg
+
+spec :: Spec
+spec = do
+ describe "statDistLG"
+ $ it "matches distribution from python library"
+ $ statDistLG
+ `nearlyEqVec` statDistLGPython
+ `shouldBe` True
+
+ describe "exchLG"
+ $ it "matches exchangeability matrix from python library"
+ $ do
+ exchLG `shouldSatisfy` nearlyEqMatWith 1e-4 exchLGPython
+ exchLG `nearlyEqMat` rmLG `shouldBe` False
+
+ describe "lg"
+ $ it "stationary distribution can be extracted"
+ $ nearlyEqVecWith 1e-4 (R.getStationaryDistribution rmLG) statDistLG
+ `shouldBe` True
+
+ describe "lgCustom" $ it "stationary distribution can be recovered" $ do
+ let f = R.getStationaryDistribution $ S.rateMatrix $ lgCustom
+ Nothing
+ statDistUniform
+ f `nearlyEqVec` statDistUniform `shouldBe` True
+
+ describe "poisson"
+ $ it "stationary distribution is uniform 1/20"
+ $ R.getStationaryDistribution (S.rateMatrix poisson)
+ `nearlyEqVec` statDistUniform
+ `shouldBe` True
+
+ describe "poissonCustom" $ it "stationary distribution can be recovered" $ do
+ let f = R.getStationaryDistribution $ S.rateMatrix $ poissonCustom
+ Nothing
+ statDistLGPython
+ f `nearlyEqVec` statDistLGPython `shouldBe` True
diff --git a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
@@ -0,0 +1,40 @@
+{- |
+Module : ELynx.Data.MarkovProcess.NucleotideSpec
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Fri Jan 25 16:47:28 2019.
+
+-}
+
+module ELynx.Data.MarkovProcess.NucleotideSpec
+ ( spec
+ )
+where
+
+import Data.Vector.Generic
+import Test.Hspec
+
+import ELynx.Tools
+
+import ELynx.Data.MarkovProcess.Nucleotide
+import ELynx.Data.MarkovProcess.RateMatrix
+import ELynx.Data.MarkovProcess.SubstitutionModel
+
+stationaryDist :: StationaryDistribution
+stationaryDist = fromList [0.2, 0.3, 0.3, 0.2]
+
+hkyModel :: SubstitutionModel
+hkyModel = hky 6.0 stationaryDist
+
+spec :: Spec
+spec =
+ describe "getStationaryDistribution"
+ $ it "extracts the stationary distribution from a rate matrix"
+ $ do
+ let sd = getStationaryDistribution (rateMatrix hkyModel)
+ sd `nearlyEqVec` stationaryDist `shouldBe` True
diff --git a/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs b/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Data/MarkovProcess/RateMatrixSpec.hs
@@ -0,0 +1,49 @@
+{- |
+Module : ELynx.Data.MarkovProcess.RateMatrixSpec
+Description : Unit tests for rate matrices
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Fri Apr 17 15:18:02 2020.
+
+-}
+
+module ELynx.Data.MarkovProcess.RateMatrixSpec
+ ( spec
+ )
+where
+
+import Numeric.LinearAlgebra
+import Test.Hspec
+
+import ELynx.Data.MarkovProcess.RateMatrix
+ ( exchFromListLower
+ , exchFromListUpper
+ )
+
+es :: [Double]
+es = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+
+exMLower :: Matrix R
+exMLower = (5 >< 5)
+ [0, 1, 2, 4, 7, 1, 0, 3, 5, 8, 2, 3, 0, 6, 9, 4, 5, 6, 0, 10, 7, 8, 9, 10, 0]
+
+exMUpper :: Matrix R
+exMUpper = (5 >< 5)
+ [0, 1, 2, 3, 4, 1, 0, 5, 6, 7, 2, 5, 0, 8, 9, 3, 6, 8, 0, 10, 4, 7, 9, 10, 0]
+
+spec :: Spec
+spec = do
+ describe "exchFromListLower"
+ $ it "correctly converts to matrix from list"
+ $ exMLower
+ `shouldBe` exchFromListLower 5 es
+ describe "exchFromListUpper"
+ $ it "correctly converts to matrix from list"
+ $ exMUpper
+ `shouldBe` exchFromListUpper 5 es
+
diff --git a/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs
@@ -0,0 +1,135 @@
+{- |
+Module : ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Tue Jan 29 12:26:49 2019.
+
+-}
+
+module ELynx.Import.MarkovProcess.EDMModelPhylobayesSpec
+ ( spec
+ )
+where
+
+import Numeric.LinearAlgebra ( fromList )
+import Test.Hspec
+
+import ELynx.Tools
+
+import ELynx.Import.MarkovProcess.EDMModelPhylobayes
+
+componentsFilePhylobayes :: FilePath
+componentsFilePhylobayes = "data/EDMDistsPhylobayes.txt"
+
+testComponents :: [EDMComponent]
+testComponents =
+ [ ( 0.3690726059430788
+ , fromList
+ [ 0.0746116859730418
+ , 0.0069967050701822
+ , 0.0792378063875672
+ , 0.1103113280153337
+ , 0.0084753541579630
+ , 0.0420976864270153
+ , 0.0359995156499732
+ , 0.0176053658394712
+ , 0.1140305648643406
+ , 0.0306656386818212
+ , 0.0143923751236750
+ , 0.0805907035564168
+ , 0.0136556223619922
+ , 0.0854829959418090
+ , 0.0907856579607629
+ , 0.0955855590305961
+ , 0.0585231905811694
+ , 0.0276404860443685
+ , 0.0024024774767569
+ , 0.0109092808557433
+ ]
+ )
+ , ( 0.28019163862430846
+ , fromList
+ [ 0.0379912838025543
+ , 0.0085917039746034
+ , 0.0016977963056655
+ , 0.0029780993213938
+ , 0.0369086689176780
+ , 0.0051768704164023
+ , 0.0027496797757250
+ , 0.2650202435999584
+ , 0.0035114356263963
+ , 0.2705514660371282
+ , 0.0634852940497682
+ , 0.0036512748214048
+ , 0.0030666766077233
+ , 0.0046946399741140
+ , 0.0039700770877914
+ , 0.0137110414055372
+ , 0.0286159990065166
+ , 0.2351259204392804
+ , 0.0018121721806795
+ , 0.0066896566496796
+ ]
+ )
+ , ( 0.23699880225859807
+ , fromList
+ [ 0.2699288544670601
+ , 0.0262695884363299
+ , 0.0119030286238640
+ , 0.0143694121662917
+ , 0.0113341089668980
+ , 0.1028437949687162
+ , 0.0097376980401260
+ , 0.0250662077996463
+ , 0.0137176088824149
+ , 0.0302792626622677
+ , 0.0151697996735645
+ , 0.0255041240872322
+ , 0.0194279535358810
+ , 0.0155053062932145
+ , 0.0146597721555602
+ , 0.2261838872893110
+ , 0.1040919090386891
+ , 0.0534187313840882
+ , 0.0024899475832214
+ , 0.0080990039456234
+ ]
+ )
+ , ( 0.11373695317401472
+ , fromList
+ [ 0.0325183213724537
+ , 0.0153142424565790
+ , 0.0072297704620506
+ , 0.0101526783552517
+ , 0.2682049848838039
+ , 0.0107298905683658
+ , 0.0420960604309369
+ , 0.0414751553493385
+ , 0.0131985876449809
+ , 0.1152120909184748
+ , 0.0300072241461393
+ , 0.0173787316286536
+ , 0.0062421326435569
+ , 0.0173124967325860
+ , 0.0181776303531701
+ , 0.0328778350287987
+ , 0.0250382111285986
+ , 0.0437257936268565
+ , 0.0258103804738129
+ , 0.2272977817955918
+ ]
+ )
+ ]
+
+spec :: Spec
+spec =
+ describe "phylobayes"
+ $ it "parses a text file with stationary distributions in phylobayes format"
+ $ do
+ cs <- parseFileWith phylobayes componentsFilePhylobayes
+ cs `shouldBe` testComponents
diff --git a/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs
@@ -0,0 +1,68 @@
+{- |
+Module : ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Wed Sep 18 09:51:35 2019.
+
+-}
+
+module ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
+ ( spec
+ )
+where
+
+import qualified Data.Vector.Storable as V
+import Test.Hspec
+
+import ELynx.Tools
+
+import ELynx.Import.MarkovProcess.EDMModelPhylobayes
+ ( EDMComponent )
+import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
+
+fn :: FilePath
+fn = "data/HSSPMany.siteprofiles"
+
+getProfiles :: IO [EDMComponent]
+getProfiles = parseFileWith siteprofiles fn
+
+firstProfile :: V.Vector Double
+firstProfile = V.fromList
+ [ 0.0267009
+ , 0.013874
+ , 0.022432
+ , 0.0440502
+ , 0.0485174
+ , 0.0407515
+ , 0.0170806
+ , 0.348043
+ , 0.0371379
+ , 0.0715536
+ , 0.0454168
+ , 0.0342213
+ , 0.0146872
+ , 0.0239681
+ , 0.0768379
+ , 0.0210387
+ , 0.0123336
+ , 0.0512678
+ , 0.0149093
+ , 0.0351776
+ ]
+
+spec :: Spec
+spec =
+ describe "import phylobayes siteprofiles"
+ $ it "parses a text file with siteprofiles in phylobayes format"
+ $ do
+ profiles <- getProfiles
+ length profiles `shouldBe` 701
+ map fst profiles `shouldBe` replicate 701 1.0
+ map (V.sum . snd) profiles
+ `shouldSatisfy` nearlyEqListWith 1e-5 (replicate 701 1.0)
+ snd (head profiles) `shouldBe` firstProfile
diff --git a/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs b/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs
new file mode 100644
--- /dev/null
+++ b/test/ELynx/Simulate/MarkovProcessAlongTreeSpec.hs
@@ -0,0 +1,66 @@
+{- |
+Module : ELynx.Simulate.MarkovProcessAlongTreeSpec
+Copyright : (c) Dominik Schrempf 2020
+License : GPL-3.0-or-later
+
+Maintainer : dominik.schrempf@gmail.com
+Stability : unstable
+Portability : portable
+
+Creation date: Thu Jan 24 15:25:49 2019.
+
+-}
+
+module ELynx.Simulate.MarkovProcessAlongTreeSpec
+ ( spec
+ )
+where
+
+import Data.Tree
+import System.Random.MWC
+import Test.Hspec
+
+import ELynx.Data.MarkovProcess.Nucleotide
+import qualified ELynx.Data.MarkovProcess.SubstitutionModel
+ as S
+import ELynx.Data.Tree
+import ELynx.Simulate.MarkovProcess
+import ELynx.Simulate.MarkovProcessAlongTree
+
+-- sampleNewickText :: T.Text
+-- sampleNewickText = T.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);"
+
+testTree :: Tree (PhyloLabel Int)
+testTree = Node
+ (PhyloLabel 0 Nothing (Just 0.0))
+ [ Node (PhyloLabel 1 Nothing (Just 1.0)) []
+ , Node (PhyloLabel 2 Nothing (Just 1.0)) []
+ ]
+
+-- testStateTree :: Tree State
+-- testStateTree = Node 0 [Node 3 [], Node 2 []]
+
+nullTree :: Tree (PhyloLabel Int)
+nullTree = Node (PhyloLabel 0 Nothing (Just 0.0)) []
+
+nullStateTree :: Tree State
+nullStateTree = fmap (const 0) nullTree
+
+-- uniformStationaryDistribution :: Int -> Vector R
+-- uniformStationaryDistribution n = fromList $ replicate n (1.0 / fromIntegral n)
+
+spec :: Spec
+spec = describe "simulateNSitesAlongTree" $ do
+ it "simulates one site along an easy tree" $ do
+ gen <- create
+ tr <- simulate 1 d e nullTree gen
+ fmap head tr `shouldBe` nullStateTree
+
+ it "simulates some sites along a harder tree" $ do
+ gen <- create
+ tr <- simulate 10 d e testTree gen
+ (length . rootLabel $ tr) `shouldBe` 10
+ where
+ d = S.stationaryDistribution jc
+ e = S.exchangeabilityMatrix jc
+
diff --git a/test/Spec.hs b/test/Spec.hs
new file mode 100644
--- /dev/null
+++ b/test/Spec.hs
@@ -0,0 +1,1 @@
+{-# OPTIONS_GHC -F -pgmF hspec-discover #-}