LPhy Language Reference (version 1.6.0)
This an automatically generated language reference of the LinguaPhylo (LPhy) statistical phylogenetic modeling language.
Parametric distribution
- Bernoulli
- Beta
- Categorical
- Cauchy
- Dirichlet
- DiscretizeGamma
- Exp
- ExpMarkovChain
- Gamma
- Geometric
- InverseGamma
- LogNormal
- NegativeBinomial
- Normal
- NormalGamma
- Poisson
- RandomBooleanArray
- RandomComposition
- Uniform
- UniformDiscrete
- Weibull
- WeightedDirichlet
Tree models
- BirthDeathSampling
- BirthDeathSerialSampling
- BirthDeath
- CalibratedYule
- FossilBirthDeathTree
- FullBirthDeath
- MultispeciesCoalescent
- CoalescentPopFunc
- RhoSampleTree
- Coalescent
- SimBDReverse
- SimFBDAge
- SimFossilsPoisson
- SkylineCoalescent
- StructuredCoalescent
- Yule
Other generative distributions
- ErrorModel
- MissingSites
- Multinomial
- PhyloBrownian
- PhyloCTMC
- PhyloMultivariateBrownian
- PhyloOU
- sample
- SampleBranch
- Sequence
- SubsampledTree
- bSiteRates
Sequence type
Taxa & alignment
- copySites
- taxa
- extantTaxa
- extractTrait
- invariableSites
- readDelim
- readFasta
- readNexus
- rmTaxa
- selectSites
- species
- variableSites
- fasta
Substitution and site models
- bModelSet
- binaryCovarion
- binaryRateMatrix
- f81
- gtr
- generalTimeReversible
- hky
- jukesCantor
- k80
- lewisMK
- migrationMatrix
- nucleotideModel
- strToDouble
- wag
- bSiteModel
Tree functions
Other functions
- arange
- argi
- concat2Str
- concatArray
- constantPopFunc
- setDifference
- elementsAt
- expansionPopFunc
- exponentialPopFunc
- get
- gompertzPopFunc_f0
- gompertzPopFunc_t50
- ifelse
- intersect
- labelClade
- length
- localClock
- logisticPopFunc
- mrca
- map
- nchar
- ntaxa
- parseInt
- rangeInt
- rep
- repArray
- stochasticVariableSelection
- select
- simulate
- slice
- sort
- split
- substituteClade
- sum
- hammingWeight
- sumCols
- sumRows
- setUnion
- unique
Types
- Boolean[]
- Double[]
- Integer[]
- Number[]
- Object[]
- String[]
- PopulationFunction[]
- TimeTree[]
- Double[][]
- Number[][]
- String[][]
- Boolean
- Double
- Integer
- Number
- Object
- String
- SequenceType
- BModelSet
- NChar
- Taxa
- Alignment
- ContinuousCharacterData
- FastaAlignment
- MetaDataAlignment
- SimpleAlignment
- PopulationFunction
- SVSPopulation
- SiteModel
- TimeTree
- TimeTreeNode
- Table