simulateSites: Simulate data

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

Description

Simulates data without an error model

Usage

simulateSites(tr, covariateTable, rateFormula, rateParams = NULL,
  piFormula = NULL, piParams = NULL, lineageTable = NULL,
  rateBounds = c(10^-4, 5))

Arguments

tr	tree
covariateTable	a data.frame where each column is a covariate and each row is a site (columns have covariate names)
rateFormula	a formula object specifying how covariates are combined to compute the rate
rateParams	a matrix of parameters where the columns correspond to the covariate label and the rows are the edgeGroup from the lineage table
piFormula	a formula object specifying how covariates are combined to compute the stationary distribution
piParams	a matrix of parameters where the columns correspond to the covariate label and the rows are each seperate alleles (note nAlleles = nrow(piParams)+1)
lineageTable	a data.frame with three columns, parent, child, and edgeGroup. Can be used to specify different rate parameters for different edges
rateBounds	two element numeric vector which gives upper and lower bounds for rate

Value

list with the simulated data and the number of alleles

ndukler/phyloGLM documentation built on Sept. 25, 2019, 9:17 p.m.