Error Message from Variogram.lme Example

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Error Message from Variogram.lme Example

Rick Bilonick-3
When I try to run the example from Variogram with an lme object, I get
an error (although summary works):

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.1  (2005-12-20 r36812)
ISBN 3-900051-07-0
...

>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
Error: couldn't find function "lme"
>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
Error: couldn't find function "Variogram"
> library(nlme)
>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
Error in "$<-.data.frame"(`*tmp*`, "n.pairs", value = c(160, 0, 160,
16,  :
        replacement has 10 rows, data has 9


> summary(fm1)
Linear mixed-effects model fit by REML
 Data: BodyWeight
       AIC      BIC    logLik
  1171.720 1203.078 -575.8599

Random effects:
 Formula: ~Time | Rat
 Structure: General positive-definite, Log-Cholesky parametrization
            StdDev     Corr
(Intercept) 36.9390723 (Intr)
Time         0.2484113 -0.149
Residual     4.4436052

Fixed effects: weight ~ Time * Diet
                Value Std.Error  DF   t-value p-value
(Intercept) 251.65165 13.094025 157 19.218816  0.0000
Time          0.35964  0.091140 157  3.946019  0.0001
Diet2       200.66549 22.679516  13  8.847873  0.0000
Diet3       252.07168 22.679516  13 11.114509  0.0000
Time:Diet2    0.60584  0.157859 157  3.837858  0.0002
Time:Diet3    0.29834  0.157859 157  1.889903  0.0606
 Correlation:
           (Intr) Time   Diet2  Diet3  Tm:Dt2
Time       -0.160
Diet2      -0.577  0.092
Diet3      -0.577  0.092  0.333
Time:Diet2  0.092 -0.577 -0.160 -0.053
Time:Diet3  0.092 -0.577 -0.053 -0.160  0.333

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max
-3.25558796 -0.42196874  0.08229384  0.59933559  2.78994477

Number of Observations: 176
Number of Groups: 16


                Information on package 'nlme'

Description:

Package:       nlme
Version:       3.1-68.1
Date:          2006-01-05


Rick B.

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Re: Error Message from Variogram.lme Example

Prof Brian Ripley
So this is most likely a bug in package nlme.  However, we need a
reproducible example to be able to do anything about it, and without even
the traceback() we cannot be sure that it is in nlme.

Please follow the bug-reporting procedure.


On Mon, 13 Mar 2006, Rick Bilonick wrote:

> When I try to run the example from Variogram with an lme object, I get
> an error (although summary works):
>
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.2.1  (2005-12-20 r36812)
> ISBN 3-900051-07-0
> ...
>
>>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
> Error: couldn't find function "lme"
>>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
> Error: couldn't find function "Variogram"
>> library(nlme)
>>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
>>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
> Error in "$<-.data.frame"(`*tmp*`, "n.pairs", value = c(160, 0, 160,
> 16,  :
>        replacement has 10 rows, data has 9

[...]

>                Information on package 'nlme'
>
> Description:
>
> Package:       nlme
> Version:       3.1-68.1
> Date:          2006-01-05


--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Error Message from Variogram.lme Example

Dieter Menne
In reply to this post by Rick Bilonick-3
Rick Bilonick <rab45+ <at> pitt.edu> writes:

>
> When I try to run the example from Variogram with an lme object, I get
> an error (although summary works):
>
> > library(nlme)
> >  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
> >      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
> Error in "$<-.data.frame"(`*tmp*`, "n.pairs", value = c(160, 0, 160,
> 16,  :
>         replacement has 10 rows, data has 9
>

The example is does not run, but if you leave out nint=10 (giving default
nint=20), or use any number nint >=12, it works.

The example has a "don't run" in the docs, but it could easily be cleaned up.
If it should serve as documentation of the error message, it's a bit confusing.

Dieter

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Re: Error Message from Variogram.lme Example

Prof Brian Ripley
In reply to this post by Prof Brian Ripley
On Tue, 14 Mar 2006, Prof Brian Ripley wrote:

> So this is most likely a bug in package nlme.  However, we need a
> reproducible example to be able to do anything about it, and without even
> the traceback() we cannot be sure that it is in nlme.
>
> Please follow the bug-reporting procedure.

It does seem to be a bug in Variogram.lme (assuming this is the BodyWeight
dataset from package nlme).  The lines

         val <- na.omit(val)
         val$n.pairs <- as.vector(table(na.omit(cutDist)))

need to be interchanged since one bin has a zero count and gets omitted.

>
>
> On Mon, 13 Mar 2006, Rick Bilonick wrote:
>
>> When I try to run the example from Variogram with an lme object, I get
>> an error (although summary works):
>>
>> R : Copyright 2005, The R Foundation for Statistical Computing
>> Version 2.2.1  (2005-12-20 r36812)
>> ISBN 3-900051-07-0
>> ...
>>
>>>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
>> Error: couldn't find function "lme"
>>>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
>> Error: couldn't find function "Variogram"
>>> library(nlme)
>>>  fm1 <- lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
>>>      Variogram(fm1, form = ~ Time | Rat, nint = 10, robust = TRUE)
>> Error in "$<-.data.frame"(`*tmp*`, "n.pairs", value = c(160, 0, 160,
>> 16,  :
>>        replacement has 10 rows, data has 9
>
> [...]
>
>>                Information on package 'nlme'
>>
>> Description:
>>
>> Package:       nlme
>> Version:       3.1-68.1
>> Date:          2006-01-05
>
>
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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