On Wed, Oct 14, 2015 at 7:19 PM, David Duffy
<David.Duffy at qimrberghofer.edu.au> wrote:
Is it because Mind is not declared a factor?
dat$Mind <- factor(dat$Mind)
lmer( y3s ~ x1s + x2s + x3s + (x1s | Mind), data = dat)
Linear mixed model fit by REML ['lmerMod']
Formula: y3s ~ x1s + x2s + x3s + (x1s | Mind)
Data: dat
REML criterion at convergence: 33271.78
Random effects:
Groups Name Std.Dev. Corr
Mind (Intercept) 0.6837
x1s 0.1373 1.00
Residual 0.6997
Number of obs: 15419, groups: Mind, 100
Fixed Effects:
(Intercept) x1s x2s x3s
-0.003039 0.117080 -0.163680 0.055911
| David Duffy (MBBS PhD)
| email: David.Duffy at qimrberghofer.edu.au ph: INT+61+7+3362-0217 fax:
| Genetic Epidemiology, QIMR Berghofer Institute of Medical Research
| 300 Herston Rd, Brisbane, Queensland 4006, Australia GPG 4D0B994A
Interesting. I think there's a ghost in the machine.
I see no benefit.
The unscaled one still fails:
dat$Mind <- as.factor(dat$Mind)
mm3 <- lmer( y3 ~ x1 + x2 + x3 + (1|Mind) + (0 + x1 | Mind), data=dat,
verbose=3)
...
350: 143253.09: 9.88456e-06 0.00975148
351: 143253.09: 9.88260e-06 0.00975168
352: 143253.09: 9.69049e-06 0.00975152
353: 143253.09: 9.44279e-06 0.00975152
354: 143253.09: 9.61561e-06 0.00975152
At return
eval: 354 fn: 143253.09 par: 9.44279e-06 0.00975152
Warning message:
In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model is nearly unidentifiable: very large eigenvalue
- Rescale variables?
And the scaled one is still a failure on my system
dat[ , c("x1s", "x2s", "x3s")] <- lapply(dat[, c("x1", "x2", "x3")], scale)
dat$y3s <- scale(dat$y3)
mm3 <- lmer( y3s ~ x1s + x2s + x3s + (1 | Mind) + (0 + x1 | Mind),
data=dat, verbose = 3)
rho: 2.0e-07 eval: 186 fn: 33271.8 par: 0.00000 0.00975124
187: 33271.783: 0.00000 0.00975151
188: 33271.783: 5.40934e-07 0.00975153
189: 33271.783: 1.08231e-06 0.00975153
190: 33271.783: 6.32312e-07 0.00975153
At return
eval: 190 fn: 33271.783 par: 5.40934e-07 0.00975153
Warning message:
In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model is nearly unidentifiable: very large eigenvalue
- Rescale variables?
Since you don't get errors, I wonder if it means you are using
different version of R, or lmer? Can we see your sessionInfo for
comparison:
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lme4_1.1-10 Matrix_1.2-2 MASS_7.3-44
loaded via a namespace (and not attached):
[1] minqa_1.2.4 compiler_3.2.2 tools_3.2.2 Rcpp_0.12.1
[5] splines_3.2.2 nlme_3.1-122 grid_3.2.2 nloptr_1.0.4
[9] lattice_0.20-33
--
Paul E. Johnson
Professor, Political Science Director
1541 Lilac Lane, Room 504 Center for Research Methods
University of Kansas University of Kansas
http://pj.freefaculty.org http://crmda.ku.edu