getME: Extract or Get Generalize Components from a Fitted Mixed Effects Model

Description

Extract (or “get”) “components” -- in a generalized sense -- from a fitted mixed-effects model, i.e. from an object of class rlmerMod or merMod.

Usage

# S3 method for rlmerMod
getME(
  object,
  name = c("X", "Z", "Zt", "Ztlist", "mmList", "y", "mu", "u", "b.s", "b", "Gp", "Tp",
    "Lambda", "Lambdat", "Tlist", "A", "U_b", "Lind", "sigma", "flist", "fixef", "beta",
    "theta", "ST", "is_REML", "n_rtrms", "n_rfacs", "N", "n", "p", "q", "p_i", "l_i",
    "q_i", "k", "m_i", "m", "cnms", "devcomp", "offset", "lower", "rho_e", "rho_b",
    "rho_sigma_e", "rho_sigma_b", "M", "w_e", "w_b", "w_b_vector", "w_sigma_e",
    "w_sigma_b", "w_sigma_b_vector"),
  ...
)
theta(object)

Value

Unspecified, as very much depending on the name.

Arguments

object

a fitted mixed-effects model of class rlmerMod, i.e. typically the result of rlmer().

name

a character string specifying the name of the “component”. Possible values are:

"X":: fixed-effects model matrix

"Z":

random-effects model matrix

"Zt":

transpose of random-effects model matrix

"Ztlist":

list of components of the transpose of the random-effects model matrix, separated by individual variance component

"mmList":

list of raw model matrices associated with random effects terms

"y":

response vector

"mu":

conditional mean of the response

"u":

conditional mode of the “spherical” random effects variable

"b.s":

synonym for “u”

"b":

conditional mode of the random effects variable

"Gp":

groups pointer vector. A pointer to the beginning of each group of random effects corresponding to the random-effects terms.

"Tp":

theta pointer vector. A pointer to the beginning of the theta sub-vectors corresponding to the random-effects terms, beginning with 0 and including a final element giving the total number of random effects

"Lambda":

relative covariance factor of the random effects.

"U_b":

synonym for “Lambda”

"Lambdat":

transpose of the relative covariance factor of the random effects.

"Lind":

index vector for inserting elements of \(\theta\) into the nonzeros of \(\Lambda\)

"A":

Scaled sparse model matrix (class dgCMatrix) for the unit, orthogonal random effects, \(U\), equal to getME(.,"Zt") %*% getME(.,"Lambdat")

"sigma":

residual standard error

"flist":

a list of the grouping variables (factors) involved in the random effect terms

"fixef":

fixed-effects parameter estimates

"beta":

fixed-effects parameter estimates (identical to the result of fixef, but without names)

"theta":

random-effects parameter estimates: these are parameterized as the relative Cholesky factors of each random effect term

"ST":

A list of S and T factors in the TSST' Cholesky factorization of the relative variance matrices of the random effects associated with each random-effects term. The unit lower triangular matrix, \(T\), and the diagonal matrix, \(S\), for each term are stored as a single matrix with diagonal elements from \(S\) and off-diagonal elements from \(T\).

"is_REML":

returns TRUE for rlmerMod-objects (for compatibility with lme4)

"n_rtrms":

number of random-effects terms

"n_rfacs":

number of distinct random-effects grouping factors

"N":

number of rows of X

"n":

length of the response vector, y

"p":

number of columns of the fixed effects model matrix, X

"q":

number of columns of the random effects model matrix, Z

"p_i":

numbers of columns of the raw model matrices, mmList

"l_i":

numbers of levels of the grouping factors

"q_i":

numbers of columns of the term-wise model matrices, ZtList

"k":

number of random effects terms

"m_i":

numbers of covariance parameters in each term

"m":

total number of covariance parameters, i.e., the same as dim@nth below.

"cnms":

the “component names”, a ‘list’.

"devcomp":

a list consisting of a named numeric vector, cmp, and a named integer vector, dims, describing the fitted model. The elements of cmp are:

ldL2: always NA, for consistency with lme4 output

ldRX2