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. I´ve 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 don´t understand how.
How should I do this?
Cheers
/CG
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