On Tuesday 15 February 2005 08:15, CG Pettersson wrote: > Hello all! > > R2.0.1, W2k > > I posted this question to the list last Sunday without getting any > replies on the list. I got two off the list though, suggesting me to > plot "manually" as a second step, from estimable() or intervals() > objects respectively. As this was not really what I wished for, I > take the risk to upset somebody with a trivial question, and re-post > it (just a little edited). > > So, here it is again: > > I use lme() from nlme to make mean estimates from series of field > experiments where not all treatments (like "variety") are present in > all experiments. (An old problem in variety evaluation). > > A typical call is: > > yield.lme <- lme(Yield ~ Variety, data = data, > na.action = na.omit, > random = ~ 1 | Experiment/Block) > > This works well, even when observations are lacking. I have checked > against the accepted method for doing this in Sweden, which is > PROC MIXED in SAS, and the fitted fixed effects are more or less > identical. I use estimable() from gmodels (gregmisc package) to > extract estimates, standard errors and such. I use matrices with the > variety names as row names, it works smooth. > > What I am unable to, as yet, is to make nice plots of the estimates > for a given set of varieties. To use only the fixed call directly on > the dataset works for many plooting functions, but produces the wrong > graphs, as the structure is not used. The structure (the random call) > has to be used, as there are NA:s in the dataset.
It's not clear to me what you are looking for. In particular, exactly what 'estimates' do you want to plot? Could you give us a reproducible example (preferably using a dataset from nlme) and describe the plot you are looking for in terms of that example? Deepayan > Pinheiro & Bates have a lot of graphics on lme objects, but they try > to illustrate more sophisticated relations than my need. Iīve looked > through gplots and the graphic parts of nlme without any hits. > Probably, my difficulties are just due to my own lack of skill. Some > standard plotting facility plotting directly from the lme object > ought to work, but I donīt understand how. > > How should I do this? > > Cheers > /CG ______________________________________________ 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