6
$\begingroup$

So i was just having a nice evening trying to simulate some hierarchical models by myself and estimate their parameters. First model I tried to simulate and estimate was $$y_{ij}=\beta_0+\varepsilon_{ij},$$ where $b_0=\gamma_{00}+u_{0j}$. So actually what I was estimating was $y_{ij}=\gamma_{00}+u_{0j}+\varepsilon_{ij}$. I have generated some data and estimated parameters $\gamma_{00}$ and variances of error terms and everything was fine:

set.seed(1)
N <- 100
nj <- 100
g00 <- 10
e <- rnorm(N*nj)
j <- c(sapply(1:N, function(x) rep(x, nj)))
uj <- c(sapply(1:N, function(x)rep(rnorm(1), nj)))
d <- data.frame(j, y=g00+uj+e)
library(nlme)
lme(y~1, data=d, random=~1|j)

Linear mixed-effects model fit by REML
  Data: d 
  Log-restricted-likelihood: -14520.94
  Fixed: y ~ 1 
(Intercept) 
   10.00215 

Random effects:
 Formula: ~1 | j
        (Intercept) Residual
StdDev:   0.7752422 1.012683

Number of Observations: 10000
Number of Groups: 100 

Then I tried different model: $$y_{ij}=\beta_0+\beta_1 x_{ij}+\varepsilon_{ij},$$ where $\beta_0=\gamma_{00}+u_{0j}$ and $\beta_1=\gamma_{10}+u_{1j}$. So I had to estimate the equation $$y_{ij}=\gamma_{00}+u_{0j}+(\gamma_{10}+u_{1j}) \cdot x_{ij}+\varepsilon_{ij}=\gamma_{00}+\gamma_{10}x_ij+u_{0j}+u_{1j}x_{ij}+\varepsilon_{ij}.$$ I did the same thing that I had before, but this time lme did not converge. I tried this, but it didn't seem to work.

g10 <- 10
u0j <- uj
u1j <- c(sapply(1:N, function(x)rep(rnorm(1), nj)))
x1 <- rnorm(N*nj)
d1 <- data.frame(j, y=g00+u0j+(g10+u1j)*x1, x1)
lme(y~1+x1, data=d1, random=~1+x1|j)

Here is what last call to lme spit out:

Error in lme.formula(y ~ 1 + x1, data = d1, random = ~1 + x1 | j) : 
  nlminb problem, convergence error code = 1
  message = false convergence (8)

What can you suggest me to do? Maybe the problem is with my model specification, redundant parameters, singular matrix or something else?

$\endgroup$

4 Answers 4

12
+25
$\begingroup$

As ?lmeControl says, the default optimizer function is nlminb rather than optim. ?nlminb, however, says that optim is preferred and, indeed, the following works.

lme(y~1+x1, data=d1, random=~1+x1|j, control = lmeControl(opt = "optim"))
Linear mixed-effects model fit by REML
  Data: d1 
  Log-restricted-likelihood: 320824.3
  Fixed: y ~ 1 + x1 
(Intercept)          x1 
   8.302459    8.183053 

Random effects:
 Formula: ~1 + x1 | j
 Structure: General positive-definite, Log-Cholesky parametrization
            StdDev       Corr  
(Intercept) 1.699207e+00 (Intr)
x1          1.952189e+00 0.752 
Residual    1.347943e-15       

Number of Observations: 10000
Number of Groups: 100 

It's hard to say why exactly that's the case. In general, one can see that false convergence (8) means

the gradient $\nabla f(x)$ may be computed incorrectly, the other stopping tolerances may be too tight, or either $f$ or $\nabla f$ may be discontinuous near the current iterate $x$

$\endgroup$
2
$\begingroup$

d1 <- data.frame(j, y=g00+u0j+(g10+u1j)*x1+e, x1) # You need to add error terms

My intuition is that when we simulatated a mixed model data set without error terms, sometimes it may be difficult to converge. This is likely to be a zero residual problem.

enter image description here

$\endgroup$
2
  • 2
    $\begingroup$ Can you provide some explanation/intuition with the code? Having the code only does not fully address the OP's concerns. $\endgroup$
    – Andy
    Dec 2, 2013 at 21:33
  • $\begingroup$ @Hua: thanks for the solution. Obviously jem forgot the error term. Andi: I think the answer of Julius needs some explanation and not the answer of Hua. $\endgroup$
    – giordano
    May 3, 2014 at 16:26
0
$\begingroup$

I might be missing a simpler answer (i.e., mis-specification in your model), but /if/ I was sure that the mixed model should converge, I would move on to using openbugs, which will let you drag out a much longer mcmc sample.

$\endgroup$
0
$\begingroup$

This works for me. Instead of using nlme or lmer, I use mgcv::gamm and specify a gaussian link as follows:

GAMM(y~1+x1, data=d1, random=~1+x1|j,family = gaussian)

The estimation results are close to nlme/lmer mixed models and is applicable for most of the cases. In fact, the HLM/mixed model is a specific case of GAMM.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.