Hi, 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). Also if I run the following (plot.variogram example) I get the following;> 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" 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? Many thanks for any help. -- Dr. Tony Lacey (PhD) - Imaging Science & Bio-medical Engineering, University of Manchester, Stopford Building, Oxford Rd., Manchester. UK. M13 9PT [+44 (0)161 275 7669] a.lacey at man.ac.uk http://www.niac.man.ac.uk/~ajl/ `Linux. The choice of a GNU generation.' -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
> 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 nlmepackage> I still cannot get the plot functions to work. Basically I have no otherpackages 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, theplotcommand 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 thecalls 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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Anthony Lacey <a.lacey at man.ac.uk> writes:> 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.Many of the plot functions in nlme require the Trellis displays which are only in SPlus. There are some plans to develop a similar package ("lattice") for R, but they are not advancing very quickly. Re. the dist function, the one in the mva library seems usable in some circumstances, but even with that the variograms (just calculating them) didn't seem to work for me. If you have ideas for how to make useful plotting commands for nlme in R, I'm sure the nlme developers would like to know about them. It's likely to be a rather large undertaking, though, and the nlme developers are for the same reason well excused for skipping these issues in the R version. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._