Why do I get an error when I try to simulate autocorrelation, even if it was after this example in Pinheiro and Bates (2009)?

Question

Here is an excerpt from the Mixed Effect Model in the S and S-Plus page 238 :

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this is the code i used to recreate this example:

library(nlme)
spatDat <- data.frame(x = c(0,0.25,0.5,0.75,1), y = c(0,0.25,0.5,0.50,0.75))
cs1Exp <- corExp(1, form = ~x+y)
cs1Exp <- initialize(cs1Exp, spatDat)

but when i do this i get this error:

Error in getClass(Class) : 
  c("\"corExp\" is not a defined class", "\"corSpatial\" is not a defined class", "\"corStruct\" is not a defined class")
In addition: Warning message:
In if (!is.na(match(Class, .BasicClasses))) return(newBasic(Class,  :
  the condition has length > 1 and only the first element will be used

Why am I getting this error?

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application

R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] nlme_3.1-101

loaded via a namespace (and not attached):
[1] grid_2.13.0     lattice_0.19-26

Answer 1

The reason is that it Initializetakes capital Iin nlme, so it should not be confused with Initializec base. And then there is Vivi's comment onspatdat$y

It works:

> library(nlme)
> spatDat <- data.frame(x = c(0,0.25,0.5,0.75,1), y = c(0,0.25,0.50,0.75,1.0))
> cs1Exp <- corExp( 1, form = ~x+y )
> cs1Exp <- Initialize( cs1Exp, spatDat )
> corMatrix( cs1Exp )
          [,1]      [,2]      [,3]      [,4]      [,5]
[1,] 1.0000000 0.7021885 0.4930687 0.3462272 0.2431167
[2,] 0.7021885 1.0000000 0.7021885 0.4930687 0.3462272
[3,] 0.4930687 0.7021885 1.0000000 0.7021885 0.4930687
[4,] 0.3462272 0.4930687 0.7021885 1.0000000 0.7021885
[5,] 0.2431167 0.3462272 0.4930687 0.7021885 1.0000000

Answer 2

There are a couple of problems with your code. Here's the adjusted version:

library(nlme)    
spatDat <- data.frame(x = c(0, 0.25, 0.5, 0.75, 1), y = c(0, 0.25, 0.5, 0.75, 1.0))    
cs1Exp <- corExp(1, form = ~x+y)    
cs1Exp <- Initialize(cs1Exp, spatDat)  
corMatrix(cs1Exp)  

          [,1]      [,2]      [,3]      [,4]      [,5]
[1,] 1.0000000 0.7021885 0.4930687 0.3462272 0.2431167
[2,] 0.7021885 1.0000000 0.7021885 0.4930687 0.3462272
[3,] 0.4930687 0.7021885 1.0000000 0.7021885 0.4930687
[4,] 0.3462272 0.4930687 0.7021885 1.0000000 0.7021885
[5,] 0.2431167 0.3462272 0.4930687 0.7021885 1.0000000

Answer 3

To emphasize the quality of the documentation (and, I hope, to save some time while working with such a well-documented textbook package), I will indicate that this code is contained in the help file in the section ?corExp

Examples:

     # Pinheiro and Bates, p. 238
     spatDat <- data.frame(x = (0:4)/4, y = (0:4)/4)

     cs1Exp <- corExp(1, form = ~ x + y)
     cs1Exp <- Initialize(cs1Exp, spatDat)
     corMatrix(cs1Exp)
     ...