Get MAP estimates and Hessian

Get MAP estimates and Hessian

get_map(
  data,
  fn.gp,
  phi,
  phi0 = sqrt(1000),
  kappa = 0.002,
  nu = 0.002,
  kappa.u = 0.002,
  nu.u = 0.002,
  tu.lambda = NULL
)

Arguments

data

A list containing phenotype, genotype, treatment, and subject. The elements must be named "y", "g", "t", and "subject".

fn.gp

A character string specifying the function to model the relationship between the genotype and phenotype. This must be one of "nonlinear" and "linear", corresponding to nonlinear and linear models, respectively.

phi

A vector of hyperparameters of the effect prior.

phi0

A scalar specifying the hyperparameter on the intercept.

kappa

A scalar specifying the hyperparameter of the gamma prior on the residual error precision.

nu

A scalar specifying the hyperparameter of the gamma prior on the residual error precision.

kappa.u

A scalar specifying the hyperparameter of the gamma prior on the random intercept.

nu.u

A scalar specifying the hyperparameter of the gamma prior on the random intercept.

tu.lambda

A list containing the transposed eigenvector matrix and the eigenvalues of the covariance matrix. The element names must be "tU" and "lambda".

Value

A list object containing outputs from optim in the stats package for the eight models.