Description Usage Arguments Details
Simulates nucleotide data based on parameters under the SELAC model but assumes either Phi or Ne evolves along the tree.
1 2 3 4 |
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, and Ne. |
aa.optim_array |
A vector of optimal amino acids for each site to be simulated. |
root.codon.frequencies |
A vector of codon frequencies for each possible optimal amino acid. Thus, the vector is of length 64x64. |
numcode |
The 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". |
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. |
pars.to.evolve |
Indicates which parameters to assume evolve along the tree. Only two options: "phi" or "Ne". |
evolve.type |
The process by which the focal parameter evovles. There are two options: Brownian motion ("BM") or Ornstein-Uhlenbeck ("OU"). |
evolve.pars |
The process parameters used to simulate focal parameter evolution. Under "BM", the order is root.state, rate; under "OU", the order is alpha, sigma.sq, and the mean. |
Ne.vals.evolved |
Under selac we assume a global Ne for all genes. Thus, when the focal parameter to evolve is "Ne", then a user specified vector of simulated Ne values are provided here. |
Simulates a nucleotide matrix using parameters under the SELAC model, but allows either Phi or Ne to evolve along the tree. Note that the output can be written to a fasta file using the write.dna() function in the ape
package.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.