[R-sig-ME] trouble using the lmer function

[Julie Bertrand]

Dear All,

I meet trouble using the lmer function on a data set simulated with a 
gamma Emax Model.

I use the following code, where initial conditions are set to the true 
values :
GammaEmaxmodel<-function(D,lE0,lE50,lEmax,lHill)exp(lE0)+exp(lEmax)*D^exp(lHill)/(exp(lE50)^exp(lHill)+D^exp(lHill))
grMod <- deriv(body(GammaEmaxmodel), namevec = 
c("lE0","lE50","lEmax","lHill"), func = GammaEmaxmodel)

fit.lme4<-nlmer(DV~grMod(DOSE,lE0,lE50,lEmax,lHill)~(lE0+lEmax+lE50)|ID,#
        donnees,
        start = c(lE0=log(5),lE50=log(500),lEmax=log(30),lHill=log(2))
        )
and obtain the error message : "Erreur dans asMethod(object) : matrix is 
not symmetric [1,2]"

I am on Windows XP, with R version 2.9.1 (2009-06-26) and lme4_0.999375-31.
 
When I do not try to estimate the Hill parameter I obtain no error message :
 > 
GammaEmaxmodel<-function(D,lE0,lE50,lEmax)exp(lE0)+exp(lEmax)*D/(exp(lE50)+D)
 > grMod <- deriv(body(GammaEmaxmodel), namevec = 
c("lE0","lE50","lEmax"), func = GammaEmaxmodel)
 >
 >
 > fit.lme4<-nlmer(DV~grMod(DOSE,lE0,lE50,lEmax)~(lE0+lEmax+lE50)|ID,#
+ donnees,
+ start = c(lE0=log(5),lE50=log(500),lEmax=log(30))
+ )
 > fit.lme4
Nonlinear mixed model fit by the Laplace approximation
Formula: DV ~ grMod(DOSE, lE0, lE50, lEmax) ~ (lE0 + lEmax + lE50) | ID
   Data: donnees
  AIC  BIC logLik deviance
 2235 2273  -1107     2215
Random effects:
 Groups   Name  Variance Std.Dev. Corr         
 ID       lE0    1.7172  1.3104                
          lEmax 18.8214  4.3384   -0.171       
          lE50  27.4499  5.2393   -0.128  0.954
 Residual        4.2807  2.0690                
Number of obs: 324, groups: ID, 81

Fixed effects:
      Estimate Std. Error t value
lE0     1.2769     0.1591   8.024
lE50    7.9102     0.6817  11.603
lEmax   4.6933     0.5867   7.999

Correlation of Fixed Effects:
      lE0    lE50 
lE50  -0.058      
lEmax -0.098  0.962

Further, I succeed in estimating the Hill parameter using the nlme 
function (nlme_3.1-93) :

 > fit.nlme2<-nlme(DV~GammaEmaxmodel(DOSE,lE0,lE50,lEmax,lHill),
+ data=dat,
+ fixed=lE0+lEmax+lE50+lHill~1,
+ random=lE0+lEmax+lE50~1,
+             start = 
c(lE0=log(5),lE50=log(500),lEmax=log(30),lHill=log(2)),
+ weights=NULL
+      )
 > fit.nlme2
Nonlinear mixed-effects model fit by maximum likelihood
  Model: DV ~ GammaEmaxmodel(DOSE, lE0, lE50, lEmax, lHill)
  Data: dat
  Log-likelihood: -1007.409
  Fixed: lE0 + lEmax + lE50 + lHill ~ 1
      lE0     lEmax      lE50     lHill
1.4964002 3.2601144 6.0436652 0.4885341

Random effects:
 Formula: list(lE0 ~ 1, lEmax ~ 1, lE50 ~ 1)
 Level: ID
 Structure: General positive-definite, Log-Cholesky parametrization
         StdDev       Corr     
lE0      7.642895e-02 lE0  lEmax
lEmax    5.686393e-01 1.00     
lE50     3.690756e-05 0.01 0.01
Residual 3.906402e+00          

Number of Observations: 324
Number of Groups: 81

The data are simulated with Hill=2, please find enclose the data set 
that leads to these outputs (simdat.txt).
I also simulated a correlation between the lEmax and lE50 parameters 
however I coul not figure out how to code such a random effects matrix 
in lmer.

The first error message is due to lmer trouble in estimating the Hill 
parameter on this data set, or must I change something in my code or 
data set ?

Thank you in advance.

Julie Bertrand

-- 
UMR 738, INSERM, Université Paris Diderot



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