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gamm4 model fit error

3 messages · Nicholas Lange, Ben Bolker

Original
Nicholas Lange
# 
Hello,

I'm running R.3.1.1 on Mac OS X 10.6.8 with gamm4 version 0.2-2 and lme4 version 1.1-7. I get the following error when trying to fit the simplest gamm4 model I can think of:
Warning message:
In deviance.merMod(ret$mer) :
 deviance() is deprecated for REML fits; use REMLcrit for the REML criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit.
$mer
Linear mixed model fit by REML ['lmerMod']
REML criterion at convergence: 3891.265
Random effects:
 Groups   Name        Std.Dev.
 LabID    (Intercept) 112.16  
 Xr       s(AgeYears) 452.89  
 Residual              35.24  
Number of obs: 343, groups:  LabID, 156; Xr, 8
Fixed Effects:
   X(Intercept)  Xs(AgeYears)Fx1  
        1310.73            23.13  

$gam

Family: gaussian 
Link function: identity 

Formula:
TotalBrain ~ s(AgeYears)

Estimated degrees of freedom:
5.28  total = 6.28 

lmer.REML score: 3891.265     

Not the usual regression summary table, no p-values.

Does anyone see what's wrong? Any help would be greatly appreciated.

Nick
Ben Bolker
#
On 14-07-13 08:13 AM, Nicholas Lange wrote:
Note that in R terminology this is a warning, not an error (sorry to
be fussy about terminology, but it helps to be precise).  This is
due to a change in 1.1-7 -- we apologize to the gamm4 maintainers,
presumably they can fix this up in a future release.  It should
be harmless, though.
It's been a while since I've looked at gamm4.  Just to be precise,
is this the first time you've used gamm4 -- i.e. this is not a change
from previous versions?  I *think* the answer is that you need to
operate on the $mer component of the result, e.g.

coef(summary(fit$mer))

... but perhaps someone with more experience of gamm4 can comment.


  Ben Bolker
Nicholas Lange
# 
Hello,

I figured it out: fit$gam for the full table.
(this was a Warning, not an Error.)

Nick