or Codon Evolution

Simulates nucleotide data based on parameters under the SELAC model

SelacSimulator(phy, pars, aa.optim_array, codon.freq.by.aa = NULL,
  codon.freq.by.gene = NULL, numcode = 1, aa.properties = NULL,
  nuc.model, include.gamma = FALSE, gamma.type = "quadrature",
  ncats = 4, k.levels = 0, diploid = TRUE, site.cats.vector = NULL)

`phy`	The phylogenetic tree with branch lengths.
`pars`	A vector of parameters used for the simulation. They are ordered as follows: C.q.phi, alpha, beta, Ne, base.freqs for A C G, and the rates for the nucleotide model.
`aa.optim_array`	A vector of optimal amino acids for each site to be simulated.
`codon.freq.by.aa`	A matrix of codon frequencies for each possible optimal amino acid. Rows are aa (including stop codon), cols are codons.
`codon.freq.by.gene`	A matrix of codon frequencies for each gene.
`numcode`	The ncbi genetic code number for translation. By default the standard (numcode=1) genetic code is used.
`aa.properties`	User-supplied amino acid distance properties. By default we assume Grantham (1974) properties.
`nuc.model`	Indicates what type nucleotide model to use. There are three options: "JC", "GTR", or "UNREST".
`include.gamma`	A logical indicating whether or not to include a discrete gamma model.
`gamma.type`	Indicates what type of gamma distribution to use. Options are "quadrature" after the Laguerre quadrature approach of Felsenstein 2001 or median approach of Yang 1994.
`ncats`	The number of discrete categories.
`k.levels`	Provides how many levels in the polynomial. By default we assume a single level (i.e., linear).
`diploid`	A logical indicating whether or not the organism is diploid or not.
`site.cats.vector`	A vector designating the rate category for phi when include.gamma=TRUE.

Simulates a nucleotide matrix using parameters under the SELAC model. Note that the output can be written to a fasta file using the write.dna() function in the ape package.

bomeara/selac documentation built on Nov. 11, 2021, 12:37 a.m.