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I am reading a bit about mixed models but I am unsure over the terms used and quite how they go together. Pinheiro, on pg 62 of his book 'Mixed-effects models in S and S-Plus', describes the likelihood function.

enter image description here

The first term of the second equation is described as the conditional density of $\mathbf{y_i}$, and the second the marginal density of $\mathbf{b_i}$.

I have been trying to generate these log-likelihoods (ll) for simple random effect models, as I thought it would help my understanding, but I must be misinterpreting the derivations.


An example of where I have tried to calculate the ll's.

example model

library(lme4)
model <- lmer(angle  ~ temp + (1|replicate), data=cake, REML=FALSE)

conditional log-likelihood

I try to calculate the conditional log-likelihood for this model: it seems from $p(y_i \mid b_i, \beta, \sigma^2)$ that I should be able to calculate this by finding the density of the data at the predictions at the unit/replicate level.

sum(dnorm(cake$angle,
          predict(model), # predictions at replicate unit (XB + Zb) level
          sd=sigma(model),
          log=TRUE))
#[1] -801.6044

# Which seems to agree with
cAIC4::cAIC(model)$loglikelihood
# [1] -801.6044

# or should we really be using a multivariate normal density
# but doesn't make a difference as variance is \sigma^2 I_n
dmvnorm(cake$angle, predict(model), diag(sigma(model)^2,270, 270), log=TRUE)
#[1] -801.6044

marginal log-likelihood

I try to calculate the marginal log-likelihood, which lme4 gives as

logLik(model)
#'log Lik.' -834.1132 (df=4)

Taking a similar approach as before it seems from $p(y_i \mid \beta, \theta, \sigma^2)$ that I should be able to calculate this by finding the density of the data at the predictions at the population level, but it is not close.

sum(dnorm(cake$angle,
          predict(model, re.form=NA), # predictions at population (XB) level
          sd=sigma(model),
          log=TRUE))
# [1] -1019.202

So perhaps I need to use the second equation and need to use the conditional model for y and the marginal for b, but still not close.

sum(
  dnorm(cake$angle, predict(model), sd=sigma(model), log=TRUE) , # conditional
  dnorm(0,  ranef(model)$replicate[[1]], # RE predictions
            sd=sqrt(VarCorr(model)$replicate), log=TRUE) 
  ) 
# [1] -849.6086

Edit: Next go...

For the linear mixed model $Y = X\beta + Zb + \epsilon$, $b_i \sim N(0, \psi)$ and $e_i \sim N(0, \Sigma)$ I thought perhaps the variance for the likelihood calculation should be estimated as var(Y) = $Z\psi Z^T + \Sigma$, but wrong again!

So in code

z = getME(model, "Z")
zt =  getME(model, "Zt")
psi = bdiag(replicate(15, VarCorr(model)$replicate, simplify=FALSE))

betw = z%*%psi%*%zt
err = Diagonal(270, sigma(model)^2)
v = betw + err

sum(dnorm(cake$angle,
      predict(model, re.form=NA), 
      sd=sqrt(diag(v)),
      log=TRUE))
# [1] -935.652

My question:

  • Can you tell me where I went wrong in calculating the marginal likelihood. I am not really needing code to reproduce the ll but more a description of why the approach I tried does not work.

Many thanks.

PS. I did look at the function that generates these values, lme4:::logLik.merMod and lme4:::devCrit and see the authors use some difficult / technical approach, which again leads to me needing help why my approach is wrong.

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I can reproduce the marginal log-likelihood returned by lme4:::logLik.merMod by realising that the marginal distribution of Y is multivariate normal (MVN) (as the marginal distribution of b and the conditional of Y are MVN).

So this code will reproduce

library(mvtnorm)
dmvnorm(cake$angle, predict(model, re.form=NA), as.matrix(v), log=TRUE)
#[1] -834.1132

where cake$angle are the observations, predict(model, re.form=NA) are the population predictions (calculated using the fixed effect coefficients), and v is the variance of the marginal model (as shown in question).


A couple of comments on the failing efforts in my question.

When calculating the conditional log-likelihood I used the univariate normal density function, whereas I could/should of used the multivariate. In this case it doesn't make a difference as within unit variance is $\sigma^2 I_n$

mvtnorm::dmvnorm(cake$angle, predict(model), diag(sigma(model)^2,270, 270), log=TRUE)
#[1] -801.6044

Trying to calculate the marginal distribution

  • First try used the predictions at population (XB) level but the incorrect variance (it ignored the between unit error)

    sum(dnorm(cake$angle, predict(model, re.form=NA), sd=sigma(model), log=TRUE))
    
  • Second try was just nonsense I think

  • Third try uses the univariate rather than multivariate normal distribution.

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