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3 messages · Peter B. Mandeville, Douglas Bates, Brian Ripley

Peter B. Mandeville
# 
Happy New Year to all,

I am using RW0631 and WIN98.

	1. The command DATA only works for the base library. 

	2. The following code on page 312 of Venables and Ripley 1997

sitka.lme <-
lme(size~treat*ordered(Time),random=~1,cluster=~tree,data=Sitka,
serial.structure="ar1.continuous",serial.covariate=~Time)

produced the following error message

Error in lme(size ~ treat * ordered(Time), random = ~1, cluster = ~tree, :
unused argument to function

The example listed on the help for LME worked without problem.

I don't know if my last error reports got out of Mexico or not so here they
are again.

	3. The following code on page 236 of Venables and Ripley 1997 

birthwt.step2 <-
step(birthwt.glm,~.^2+I(scale(age)^2)+I(scale(lwt)^2),trace=F)

produced the following warning message 8 times

Warning: ignored non function "scale"

	4. The following code on page 358 of Venables and Venables 1997 

plot(survfit(leuk.coxs),lty=2:3,lwd=3,add=T,log=T)

produced the following warning message

Warning: parameter "add" couldn't be set in high-level plot() function

Finally, is if possible to automatically load libraries when R is started
and if so how?

Thank you

Peter B.


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Douglas Bates
# 
PBM> 	2. The following code on page 312 of Venables and Ripley 1997

  PBM> sitka.lme <-
  PBM> lme(size~treat*ordered(Time),random=~1,cluster=~tree,data=Sitka,
  PBM> serial.structure="ar1.continuous",serial.covariate=~Time)

  PBM> produced the following error message

  PBM> Error in lme(size ~ treat * ordered(Time), random = ~1, cluster
  PBM> = ~tree, : unused argument to function

  PBM> The example listed on the help for LME worked without problem.

  PBM> I don't know if my last error reports got out of Mexico or not
  PBM> so here they are again.

The version of the lme library in R is a beta version of nlme 3.0.
The version that is documented in Venables and Ripley (1997) is version
2.1, the only version that was available at the time they wrote the
book.

Jose' Pinheiro and I have made incompatible changes in the calling
sequence of lme between the two versions of the nlme library.  We did
this because we felt the current version is much easier to use and to
understand.  The corresponding call in the current version would be

sitka.lme <-
 lme(size ~ treat*ordered(Time), data = Sitka, random = ~ 1 | tree,
     correlation = corCAR1(form = ~ Time))

This is still going to produce a massive number of coefficients from
the ordered(Time) term.

By the way, it would help if you had your system administration
reconfigure your mailer so it provides a system name in the From: line
rather than an IP address.
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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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Brian Ripley
#
On Thu, 7 Jan 1999, Peter B. Mandeville wrote:

            

      
      
      
    

        
Not so. It works for the MASS library, for example, in that version of R.

            

      
      
      
    

        
I really think I am wasting my time trying to help R users. In the VR
bundle from which you got the Sitka data (even though you claim
data(Sitka) did not work) is a set of scripts modified to run under R,
and there are on-line complements for `R'. PLEASE USE THEM.

You cannot reasonably expect a book about S-PLUS to work unchanged on R,
especially one finished in 1996 to work on R as it has become in 1999.
There is a fair chance that the 1999 3rd edition will work with 
minimal changes on current R.

            

      
      
      
    

        
That example is for S-PLUS, not R. See the scripts for the changes. Doug
Bates has pointed out one way to do: this is one of those cases where
lme-2.9 has a different interface from any S version (2.1 or 3.0).

            

      
      
      
    

        
Yes, an R scoping problem.  The example works, though.  Current S-PLUS is
clever enough to know that a function is required, so one never gets that
warning.

            

      
      
      
    

        
Uh Oh. Try reading the cover once again.

            

      
      
      
    

        
Please read the instructions (on page 357, or in the R version of the
scripts): you need library(MASS) loaded after library(survival4),
to make sure MASS is found first.

            

      
      
      
    

        
Put them in .Rprofile: see our on-line complements for one source of info.
As it says

If there are commands that you want to have invoked for each session
(like \sfn{library(MASS)}, of course), you can put these in a file
called \sfn{.Rprofile}. This searched for first in the current
directory then in the user's home directory, but only the first file
found (if any) is read in.

That is true for rw0631 too: earlier Windows versions used Rprofile.


Peter, we have repeated ask you for a signature, as your reply address
is invalid. My patience at having to post replies to you is wearing 
rather thin. Please be a good net citizen and give us a valid reply
address.