update lphy doc for 1.3.0

LinguaPhylo · Jun 20, 2022 · 674d5df · 674d5df
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diff --git a/lphy/doc/distributions/BirthDeath.md b/lphy/doc/distributions/BirthDeath.md
@@ -3,7 +3,7 @@ BirthDeath distribution
 BirthDeath(Number **lambda**, Number **mu**, Integer **n**, Object **taxa**, Number **rootAge**)
 ------------------------------------------------------------------------------------------------
 
-A tree of only extant species, which is conceptually embedded in a full species tree produced by a speciation-extinction (birth-death) branching process.<br>Conditioned on root age and on number of taxa.
+A tree of only extant species, which is conceptually embedded<br>in a full species tree produced by a speciation-extinction (birth-death) branching process.<br>Conditioned on root age and on number of taxa.
 
 ### Parameters
 
@@ -17,7 +17,9 @@ A tree of only extant species, which is conceptually embedded in a full species
 
 - TimeTree
 
+### Reference
 
+Joseph Heled, Alexei J. Drummond, Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference, Systematic Biology, Volume 64, Issue 3, May 2015.[https://doi.org/10.1093/sysbio/syu089](https://doi.org/10.1093/sysbio/syu089)
 
 BirthDeath(Number **diversification**, Number **turnover**, Number **rootAge**)
 -------------------------------------------------------------------------------

diff --git a/lphy/doc/distributions/BirthDeathSampling.md b/lphy/doc/distributions/BirthDeathSampling.md
@@ -16,7 +16,9 @@ The Birth-death-sampling tree distribution over tip-labelled time trees.<br>Cond
 
 - TimeTree
 
+### Reference
 
+Tanja Stadler, Roger Kouyos, ..., Sebastian Bonhoeffer, Estimating the Basic Reproductive Number from Viral Sequence Data, Molecular Biology and Evolution, Volume 29, Issue 1, January 2012.[https://doi.org/10.1093/molbev/msr217](https://doi.org/10.1093/molbev/msr217)
 
 BirthDeathSampling(Number **diversification**, Number **turnover**, Number **rho**, Number **rootAge**)
 -------------------------------------------------------------------------------------------------------
@@ -34,5 +36,7 @@ The Birth-death-sampling tree distribution over tip-labelled time trees.<br>Cond
 
 - TimeTree
 
+### Reference
 
+Tanja Stadler, Mammalian phylogeny reveals recent diversification rate shifts, Proceedings of the National Academy of Sciences, 108 (15), 2011.[https://doi.org/10.1073/pnas.1016876108](https://doi.org/10.1073/pnas.1016876108)
 
diff --git a/lphy/doc/distributions/Coalescent.md b/lphy/doc/distributions/Coalescent.md
@@ -18,5 +18,5 @@ The Kingman coalescent with serially sampled data. (Rodrigo and Felsenstein, 199
 
 ### Reference
 
-Kingman JFC. The Coalescent. Stochastic Processes and their Applications 13, 235–248 (1982)[https://doi.org/10.1016/0304-4149(82)90011-4](https://doi.org/10.1016/0304-4149(82)90011-4)
+Rodrigo AG, Felsenstein J. (1999). Coalescent Approaches to HIV Population Genetics, The Evolution of HIV, Chapter 8, edited by Crandall K., Johns Hopkins Univ. Press, Baltimore.
 
diff --git a/lphy/doc/distributions/Exp.md b/lphy/doc/distributions/Exp.md
@@ -1,13 +1,13 @@
 Exp distribution
 ================
-Exp(Double **mean**)
+Exp(Number **mean**)
 --------------------
 
 The exponential probability distribution.
 
 ### Parameters
 
-- Double **mean** - the mean of an exponential distribution.
+- Number **mean** - the mean of an exponential distribution.
 
 ### Return type
 

diff --git a/lphy/doc/distributions/FossilBirthDeathTree.md b/lphy/doc/distributions/FossilBirthDeathTree.md
@@ -18,5 +18,7 @@ A tree of extant species and those sampled through time, which is conceptually e
 
 - TimeTree
 
+### Reference
 
+Tracy A. Heath, John P. Huelsenbeck, and Tanja Stadler, The fossilized birth–death process for coherent calibration of divergence-time estimates, Proceedings of the National Academy of Sciences, 111 (29), 2014.[https://doi.org/10.1073/pnas.1319091111](https://doi.org/10.1073/pnas.1319091111)
 
diff --git a/lphy/doc/distributions/FullBirthDeath.md b/lphy/doc/distributions/FullBirthDeath.md
@@ -16,5 +16,7 @@ A birth-death tree with both extant and extinct species.<br>Conditioned on age o
 
 - TimeTree
 
+### Reference
 
+David G. Kendall. On the Generalized "Birth-and-Death" Process, The Annals of Mathematical Statistics, Ann. Math. Statist. 19(1), 1-15, March, 1948.[https://doi.org/10.1214/aoms/1177730285](https://doi.org/10.1214/aoms/1177730285)
 
diff --git a/lphy/doc/distributions/Gamma.md b/lphy/doc/distributions/Gamma.md
@@ -1,14 +1,14 @@
 Gamma distribution
 ==================
-Gamma(Double **shape**, Double **scale**)
+Gamma(Number **shape**, Number **scale**)
 -----------------------------------------
 
 The gamma probability distribution.
 
 ### Parameters
 
-- Double **shape** - the shape of the distribution.
-- Double **scale** - the scale of the distribution.
+- Number **shape** - the shape of the distribution.
+- Number **scale** - the scale of the distribution.
 
 ### Return type
 

diff --git a/lphy/doc/distributions/MultispeciesCoalescent.md b/lphy/doc/distributions/MultispeciesCoalescent.md
@@ -14,7 +14,7 @@ The Kingman coalescent distribution within each branch of species tree gives ris
 
 ### Return type
 
-- Object
+- TimeTree
 
 
 
diff --git a/lphy/doc/distributions/Normal.md b/lphy/doc/distributions/Normal.md
@@ -1,14 +1,14 @@
 Normal distribution
 ===================
-Normal(Double **mean**, Double **sd**)
+Normal(Number **mean**, Number **sd**)
 --------------------------------------
 
 The normal probability distribution.
 
 ### Parameters
 
-- Double **mean** - the mean of the distribution.
-- Double **sd** - the standard deviation of the distribution.
+- Number **mean** - the mean of the distribution.
+- Number **sd** - the standard deviation of the distribution.
 
 ### Return type
 

diff --git a/lphy/doc/distributions/PhyloMultivariateBrownian.md b/lphy/doc/distributions/PhyloMultivariateBrownian.md
@@ -3,6 +3,8 @@ PhyloMultivariateBrownian distribution
 PhyloMultivariateBrownian(TimeTree **tree**, Double[][] **diffusionMatrix**, Double[] **y0**)
 ---------------------------------------------------------------------------------------------
 
+The phylogenetic multivariate Brownian motion distribution.
+
 ### Parameters
 
 - TimeTree **tree** - the time tree.

diff --git a/lphy/doc/distributions/StructuredCoalescent.md b/lphy/doc/distributions/StructuredCoalescent.md
@@ -17,5 +17,7 @@ The structured coalescent distribution over tip-labelled time trees.
 
 - TimeTree
 
+### Reference
 
+Müller, N. F., Rasmussen, D. A., & Stadler, T. (2017). The structured coalescent and its approximations. Molecular biology and evolution, 34(11), 2970-2981.[https://doi.org/10.1093/molbev/msx186](https://doi.org/10.1093/molbev/msx186)
 
diff --git a/lphy/doc/functions/f81.md b/lphy/doc/functions/f81.md
@@ -14,5 +14,7 @@ The F81 instantaneous rate matrix. Takes base frequencies and produces an F81 ra
 
 - Double[][]
 
+### Reference
 
+Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution, 17(6), 368-376.[https://doi.org/10.1007/BF01734359](https://doi.org/10.1007/BF01734359)
 
diff --git a/lphy/doc/functions/gtr.md b/lphy/doc/functions/gtr.md
@@ -17,5 +17,5 @@ The GTR instantaneous rate matrix. Takes relative rates and base frequencies and
 
 ### Reference
 
-Rodriguez, F. J. L. O. J., Oliver, J. L., Marín, A., & Medina, J. R. (1990). The general stochastic model of nucleotide substitution. Journal of theoretical biology, 142(4), 485-501.[https://doi.org/10.1016/S0022-5193(05)80104-3](https://doi.org/10.1016/S0022-5193(05)80104-3)
+Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences, 17(2), 57-86.
 
diff --git a/lphy/doc/functions/hky.md b/lphy/doc/functions/hky.md
@@ -17,5 +17,5 @@ The HKY instantaneous rate matrix. Takes a kappa and base frequencies (and optio
 
 ### Reference
 
-Hasegawa, M., Kishino, H. & Yano, T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160–174 (1985)[https://doi.org/10.1007/BF02101694](https://doi.org/10.1007/BF02101694)
+Hasegawa, M., Kishino, H. & Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160–174[https://doi.org/10.1007/BF02101694](https://doi.org/10.1007/BF02101694)
 
diff --git a/lphy/doc/functions/k80.md b/lphy/doc/functions/k80.md
@@ -14,5 +14,8 @@ The K80 instantaneous rate matrix. Takes a kappa and produces a K80 rate matrix.
 
 - Double[][]
 
+### Reference
 
+Kimura, M. A simple method for estimating evolutionary rates of base substitutions
+through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120 (1980). [https://doi.org/10.1007/BF01731581](https://doi.org/10.1007/BF01731581)
 
diff --git a/lphy/doc/functions/lewisMK.md b/lphy/doc/functions/lewisMK.md
@@ -14,5 +14,7 @@ The LewisMK Q matrix construction function. Takes a mean rate and a number of st
 
 - Double[][]
 
+### Reference
 
+Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic biology, 50(6), 913-925.[https://doi.org/10.1080/106351501753462876](https://doi.org/10.1080/106351501753462876)
 
diff --git a/lphy/doc/functions/readFasta.md b/lphy/doc/functions/readFasta.md
@@ -3,7 +3,7 @@ readFasta function
 readFasta(String **file**, Object **options**)
 ----------------------------------------------
 
-A function that parses an alignment from a Nexus file.
+A function that parses an alignment from a fasta file.
 
 ### Parameters
 

diff --git a/lphy/doc/functions/readNexus.md b/lphy/doc/functions/readNexus.md
@@ -12,7 +12,7 @@ A function that parses an alignment from a Nexus file.
 
 ### Return type
 
-- Alignment
+- MetaDataAlignment
 
 
 
diff --git a/lphy/doc/functions/wag.md b/lphy/doc/functions/wag.md
@@ -14,5 +14,7 @@ The WAG instantaneous rate matrix for amino acid.
 
 - Double[][]
 
+### Reference
 
+Whelan, S., & Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular biology and evolution, 18(5), 691-699.[https://doi.org/10.1093/oxfordjournals.molbev.a003851](https://doi.org/10.1093/oxfordjournals.molbev.a003851)
 
diff --git a/lphy/doc/index.md b/lphy/doc/index.md
@@ -1,4 +1,4 @@
-LPhy Language Reference (version 1.2.0)
+LPhy Language Reference (version 1.3.0)
 =======================================
 This an automatically generated language reference of the LinguaPhylo (LPhy) statistical phylogenetic modeling language.
 
@@ -9,6 +9,7 @@ Generative distributions
 - [BirthDeathSampling](distributions/BirthDeathSampling.md)
 - [BirthDeathSerialSampling](distributions/BirthDeathSerialSampling.md)
 - [BirthDeath](distributions/BirthDeath.md)
+- [Cauchy](distributions/Cauchy.md)
 - [Dirichlet](distributions/Dirichlet.md)
 - [DiscreteUniform](distributions/DiscreteUniform.md)
 - [DiscretizeGamma](distributions/DiscretizeGamma.md)
@@ -18,6 +19,7 @@ Generative distributions
 - [FossilBirthDeathTree](distributions/FossilBirthDeathTree.md)
 - [FullBirthDeath](distributions/FullBirthDeath.md)
 - [Gamma](distributions/Gamma.md)
+- [Geometric](distributions/Geometric.md)
 - [InverseGamma](distributions/InverseGamma.md)
 - [LogNormal](distributions/LogNormal.md)
 - [MultispeciesCoalescent](distributions/MultispeciesCoalescent.md)
@@ -38,13 +40,15 @@ Generative distributions
 - [SkylineCoalescent](distributions/SkylineCoalescent.md)
 - [StructuredCoalescent](distributions/StructuredCoalescent.md)
 - [Uniform](distributions/Uniform.md)
+- [Weibull](distributions/Weibull.md)
 - [WeightedDirichlet](distributions/WeightedDirichlet.md)
 - [Yule](distributions/Yule.md)
 - [bSiteRates](distributions/bSiteRates.md)
 
 Functions
 ---------
 - [arange](functions/arange.md)
+- [aminoAcids](functions/aminoAcids.md)
 - [argi](functions/argi.md)
 - [bModelSet](functions/bModelSet.md)
 - [binaryDataType](functions/binaryDataType.md)
@@ -74,7 +78,7 @@ Functions
 - [nucleotides](functions/nucleotides.md)
 - [parseInt](functions/parseInt.md)
 - [pruneTree](functions/pruneTree.md)
-- [Range](functions/Range.md)
+- [rangeInt](functions/rangeInt.md)
 - [readFasta](functions/readFasta.md)
 - [readNexus](functions/readNexus.md)
 - [rep](functions/rep.md)
@@ -110,6 +114,7 @@ Types
 - [Taxa](types/Taxa.md)
 - [Alignment](types/Alignment.md)
 - [ContinuousCharacterData](types/ContinuousCharacterData.md)
+- [MetaDataAlignment](types/MetaDataAlignment.md)
 - [SiteModel](types/SiteModel.md)
 - [TimeTree](types/TimeTree.md)