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In ?lme4::ranef, it is stated:

condVar: a logical argument indicating if the conditional variance-covariance matrices of the random effects should be added as an attribute.

If condVar is TRUE, each data frame has an attribute called "postVar".

If there is a single random-effects term for a given grouping factor, this attribute is a three-dimensional array with symmetric faces; each face contains the variance-covariance matrix for a particular level of the grouping factor.

While in ?nlme::getVarCov

Extract the variance-covariance matrix from a fitted model, such as a mixed-effects model.

type: For models fit by lme() the type argument specifies the type of variance-covariance matrix, either "random.effects" for the random-effects variance-covariance (the default) or "conditional" for the conditional. variance-covariance of the responses or "marginal" for the marginal variance-covariance of the responses.

Then I try

library("nlme")
library("lme4")
fm1 <- lme(distance ~ age, data = Orthodont, random = ~ 1 | Subject)
lfm1 <- lmer(distance ~ age + (1 | Subject), data = Orthodont)

getVarCov(fm1, individuals = "F01", type = "conditional")
Subject F01 
Conditional variance covariance matrix
       1      2      3      4
1 2.0495 0.0000 0.0000 0.0000
2 0.0000 2.0495 0.0000 0.0000
3 0.0000 0.0000 2.0495 0.0000
4 0.0000 0.0000 0.0000 2.0495
  Standard Deviations: 1.4316 1.4316 1.4316 1.4316 

# Looking at ranef(lfm1) I see subject 'F01' is the 20th
attr(ranef(lfm1)[["Subject"]], "postVar")[, , 20]
[1] 0.4596965

Why is there this difference? Is it possible to get the lme4 var-cov matrix from a nlme model?

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1 Answer 1

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The difference is explained by the fact that these are two different variances. In particular, the model both lme() and lmer() fit in this case is

$$\left\{ \begin{array}{l} \texttt{distance}_{ij} = \beta_0 + \beta_1 \texttt{age}_{ij} + b_{i0} + \varepsilon_{ij}\\\\ b_{i0} \sim \mathcal N(0, \sigma_b^2), \quad \varepsilon_{ij} \sim \mathcal N(0, \sigma^2) \end{array} \right.$$

Individual F01 has four measurements, and conditional on the random intercept, these measurements are independent with variance $\sigma^2$. The conditional model is given in the first line of the equation above. This is what you get from the call getVarCov(fm1, individuals = "F01", type = "conditional").

The postVar component that you get from the call to lme4::ranef(..., ) is the posterior variance for the random effect, i.e., $\mbox{var}(b_{i0} \mid \texttt{distance}_{ij})$. I don't know if you can get this from an lme model.

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