Extract variance components — var

This function provides the variance matrix quantities needed to evaluate heritability with respect to a target random-effect term in a fitted linear mixed model.

Usage

var_comp(
  model,
  target,
  calc_C22 = TRUE,
  calc_V = TRUE,
  calc_C11 = TRUE,
  marginal = TRUE,
  stratification = NULL,
  solver = c("direct", "LMM"),
  ...
)

Arguments

model: Model object of class lmerMod/merMod or asreml
target: The name of the random effect for which heritability is to be calculated.
calc_C22: Logical; whether to compute the prediction error variance (PEV) matrix for the transformed target effect.
calc_V: Logical; whether to retain the marginal variance matrix of the response and supporting quantities (V, G, Z, X, idx, and m) in the output.
calc_C11: Logical; whether to compute the variance matrix of the fixed-effect counterpart estimator for the transformed target effect.
marginal: Logical; if TRUE, construct marginal (strata-averaged) mappings so that each genotype receives a single averaged effect per term. If FALSE, mappings will only consider the main genotype effect and ignore the iteracting terms.
stratification: A one-row data frame defining the stratum in which genotype effects should be evaluated. The columns must correspond to model terms that interact with target.
solver: A string specifying the solver for the PEV matrix. Can be either "direct" (directly invert V) or "LMM" (Solve the LMM equation).
...: Additional arguments passed to downstream helper functions.

Value

A named list with the following elements:

n_g: Number of transformed genetic coefficients after applying the mapping matrix m.
gnames: Names of the transformed genetic coefficients.
G_g: Variance matrix of the transformed target genetic effect.
C22_g: Prediction error variance matrix of the transformed target effect, if calc_C22 = TRUE; otherwise NULL.
G_g_tilde: Variance matrix of the fixed-effect counterpart estimator for the transformed target effect, if calc_C11 = TRUE; otherwise NULL.
G_g_tilde_no_cov: Variance matrix of the fixed-effect counterpart estimator for the transformed target effect, without considering target covariance, if calc_C11 = TRUE; otherwise NULL.
C11_g: Estimation error variance matrix of the fixed-effect counterpart estimator for the transformed target effect, if calc_C11 = TRUE; otherwise NULL.
V: Marginal covariance matrix of the response, if calc_V = TRUE; otherwise NULL.
G: Variance matrix of all random effects, if calc_V = TRUE; otherwise NULL.
Z: Random-effect design matrix, if calc_V = TRUE; otherwise NULL.
X: Fixed-effect design matrix, if calc_V = TRUE; otherwise NULL.
idx: Indices of the random-effect coefficients associated with the target term, if calc_V = TRUE; otherwise NULL.
W: Linear mapping from the original target coefficients to the transformed target effect, if calc_V = TRUE; otherwise NULL.
marginal: Logical scalar indicating whether the returned quantities correspond to a marginal definition of the target effect.
stratification: The user-supplied stratification object, if any.