[R-sig-ME] Error: "Cannot get confidence intervals...", with lme, what does it means?

[Dimitris Rizopoulos]

check whether the following solves the problem:

Total$DietC <- relevel(Total$Diet, "C")

lmefit1 <- lme(Weight ~ Diet * Time, Total, random = ~ 1 | Place)
intervals(lmefit1)

lmefit2 <- lme(Weight ~ DietC * Time, Total, random = ~ 1 | Place)
intervals(lmefit2)


I hope it helps.

Best,
Dimtris


R.S. Cotter wrote:
> Hello,
> 
> In some occasions I get this error message: "Cannot get confidence
> intervals on var-cov components: Non-positive definite approximate
> variance-covariance".
> 
> I have tried to figure out this by using help function, but didn't
> find answer to the question. I address this question with describing
> the model and the primary task that I want to solve. Sorry if the
> question is clumsy formulated, I 'm not that experienced with R and
> statistics.
> 
> My model is:
> Response= Weight(continous)
> Explanatory variables= Time (continous) and Diet (kategorical, two groups; B&C)
> 
> The primary question of interest is wheter the growth rates
> (Weight/Time) differ among the two diets.
> 
> lmefit1<-lme(Weight ~ Diet*Time,random=~1|Place,data=Total)
> 
> Summary output is ok, so far so good. But I also wanted to get the
> slope and confidence intervals for the growth rates for both diets
> (B&C), so I ran intervals(). And I got the intercept, slope and
> confidence intervals for diet B, see below.
> 
> But I also wanted the same for the diet C, to do this I renamed diet C
> to A in the data sheet to force C to be the dummy variable. Is this
> the right way to do it?
> 
> When running the intervals () once again, I got this message: "Cannot
> get confidence intervals on var-cov components: Non-positive definite
> approximate variance-covariance". What could be wrong..? Is there
> other ways to get the slope and confidence intervals from a lme model?
> 
>> intervals(lmefit1)
> Approximate 95% confidence intervals
> 
>  Fixed effects:
>                           lower               est.                 upper
> (Intercept)           66.040673     108.122242     150.203810
> DietC                -175.080336   -109.638518     -44.196700
> Time                     4.177387         5.434087       6.690788
> DietC:Time          7.938101         11.180806     14.423511
> attr(,"label")
> [1] "Fixed effects:"
> 
>  Random Effects:
>   Level: Place
>                     lower     est.    upper
> sd((Intercept)) 0.1478599 13.50651 1233.775
> 
>  Within-group standard error:
>    lower     est.    upper
> 159.9128 174.8928 191.2761
> 
> Best regards Cotter
> 
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 
> 

-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center

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