# Error Message from Variogram.lme Example

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## Error Message from Variogram.lme Example

 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. ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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## Re: Error Message from Variogram.lme Example

 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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## Re: Error Message from Variogram.lme Example

 In reply to this post by Rick Bilonick-3 Rick Bilonick 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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## Re: Error Message from Variogram.lme Example

 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html