Extract or Get Generalize Components from a Fitted Mixed Effects Model

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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".

The function theta is short for getME(, "theta").

Usage

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## S3 method for class 'rlmerMod'
getME(object,
      name = c("X", "Z", "Zt", "Ztlist", "y", "mu",
               "u", "b.s", "b", "Gp", "Tp", "Lambda",
               "Lambdat","A", "U_b", "Lind", "sigma",
               "flist", "beta", "theta", "n_rtrms",
               "n_rfacs", "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", "is_REML"), ...)

  theta(object)

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

y

response vector

mu

conditional mean of the response

u

conditional mode of the “spherical” random effects variable

b.s

synonym for “u”

b

onditional 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

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

n_rtrms

number of random-effects terms

n_rfacs

number of distinct random-effects grouping factors

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

offset

model offset

lower

lower bounds on model parameters (random effects parameters only)

rho_e

rho function used for the residuals

rho_b

list of rho functions used for the random effects

rho_sigma_e

rho function used for the residuals when estimating sigma

rho_sigma_b

list of rho functions used for the random effects when estimating the covariance parameters

M

list of matrices, blocks of the Henderson's equations and the matrices used for computing the linear approximations of the estimates of beta and spherical random effects.

w_e

robustness weights associated with the observations

w_b

robustness weights associated with the spherical random effects, returned in the same format as ranef()

w_b_vector

robustness weights associated with the spherical random effects, returned as one long vector

w_sigma_e

robustness weights associated with the observations when estimating sigma

w_sigma_b

robustness weights associated with the spherical random effects when estimating the covariance parameters, returned in the same format as ranef()

w_sigma_b_vector

robustness weights associated with the spherical random effects when estimating the covariance parameters, returned as one long vector

is_REML

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

...

potentially further arguments passed to and from methods; none here at the moment.

Details

The goal is to provide “everything a user may want” from a fitted "rlmerMod" object as far as it is not available by methods, such as fixef, ranef, vcov, etc.

Value

Unspecified, as very much depending on the name.

See Also

getCall(); more standard methods for rlmerMod objects, such as ranef, fixef, vcov, etc.: see methods(class="rlmerMod")

Examples

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## shows many methods you should consider *before* using getME():
methods(class = "rlmerMod")

## doFit = FALSE to speed up example
(fm1 <- rlmer(Reaction ~ Days + (Days|Subject), sleepstudy,
              method="DASvar", doFit=FALSE))
Z <- getME(fm1, "Z")
stopifnot(is(Z, "CsparseMatrix"),
          c(180,36) == dim(Z),
	  all.equal(fixef(fm1), getME(fm1, "beta"),
		    check.attributes=FALSE, tolerance = 0))

## All that can be accessed [potentially ..]:
(nmME <- eval(formals(robustlmm:::getME.rlmerMod)$name))
% dont..
stopifnot(all.equal(theta(fm1), getME(fm1, "theta")))