Re: [R] Error Message from Variogram.lme Example
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, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] 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 BIClogLik 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. Time 0.35964 0.091140 157 3.946019 0.0001 Diet2 200.66549 22.679516 13 8.847873 0. Diet3 252.07168 22.679516 13 11.114509 0. Time:Diet20.60584 0.157859 157 3.837858 0.0002 Time:Diet30.29834 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. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 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, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Message from Variogram.lme Example
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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
