[R] NLME 3 (R version) again!

[Prof Brian Ripley]

> Date: Mon, 31 Jul 2000 12:42:45 +0100
> From: Anthony Lacey <a.lacey at man.ac.uk>
> To: jcp at research.bell-labs.com, r-help at stat.math.ethz.ch

(Jose' Pinheiro is not the primary maintainer of nlme for R: should
the DESCRIPTION file be clarified to send comment to Doug Bates?)

> Well after trying to fix the assign commands in version 3.1.7 of your nlme 
package
> I still cannot get the plot functions to work.  Basically I have no other 
packages installed (apart from those provided with R) so nlme is the first.
> 
> my R version info is;
> 
> platform sparc-sun-solaris2.7
> arch     sparc               
> os       solaris2.7          
> system   sparc, solaris2.7   
> status                       
> major    1                   
> minor    1.0                 
> year     2000                
> month    June                
> day      15                  
> language R   
> 
> I have downloaded nlme version 3_1.7 from the CRAN site.
> 
> I have been trying the example code from the plot.gls command. However, the 
plotcommand fails because the assigns use where instead of envir.  So I changed 
these and still recieved and error telling me that envir was being misused. From 
what I could see the envir were being used in default mode so I simply removed 
them.  Now when I run the code I get the following;
> 
> library(nlme)
> Loading required package: nls 
> > data(Ovary)
> > fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
> +            correlation = corAR1(form = ~ 1 | Mare))
> > plot(fm1, resid(., type = "p") ~ fitted(.) | Mare, abline = 0)
> [[1]]
> coplot
> 
> $show.given
> [1] FALSE
> 
> 
> (and a very blank graph screen).

example(plot.gls) does no plotting, which is a fair indication that this
is not supposed to work.

> Also if I run the following (plot.variogram example) I get the following;

Did you mean plot.Variogram?

> > data(Ovary)
> > 
> > fm1 <- lme(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary)
> > plot(Variogram(fm1, form = ~ Time | Mare, maxDist = 0.7))
> Error in FUN(X[[1]], ...) : couldn't find function "dist"

dist is in library(mva), and again the code is omitted in 
example(plot.Variogram),

> Has anybody got this code to work.  I suspect looking at the code and the 
calls to bwplot and xyplot (all of which are S-plus) that not all this code has 
been converted.  I am new to R and thus am I being niave to expect all the code 
(particularly the plotting routines) to work with R?

Yes. I thought it said so in the package, but can't see it at a quick glance.
Should nlme have a STATUS or PORTING file as some other R packages do?

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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