binaryPGLMM function

Phylogenetic GLM for binary data

Fitting phylogenetic generalized linear models for binary data (0 and 1).

binaryPGLMM(
  formula,
  data = list(),
  phy,
  s2.init = 0.1,
  B.init = NULL,
  tol.pql = 10^-6,
  maxit.pql = 200,
  maxit.reml = 100
)

Arguments

• formula: Regression formula.
• data: Data frame to fit the model with.
• phy: Phylogenetic tree of type phylo with branch lengths.
• s2.init: Initial variance values for random terms, default is 0.1.
• B.init: Initial coefficient values for fixed terms, if not provided, will use those from lm.
• tol.pql: Tolerance value, default is 10^-6.
• maxit.pql: The number of iterations, default is 200.
• maxit.reml: The number of iterations for optim, default is 100.

Returns

A large list with class as binaryPGLMM.