[R] panel ordering in nlme and augPred plots
Petr Pikal
petr.pikal at precheza.cz
Tue Apr 26 10:08:06 CEST 2005
Hi
So FYI attached is source file limity.txt which, with the code
limity.1 <- dget("limity.txt")
limity.gr <- groupedData(konverze~tepl|spol.f, limity.1,
order.groups=F)
plot(limity.gr) # panel order is OK
fit.nlsList1 <- nlsList(SSfpl,limity.gr)
fit.nlme1 <- nlme(fit.nlsList1, random=xmid+scal~1)
plot(augPred(fit.nlme1, level=0:1)) # panel order is mismatched
gives me different ordering of these two plots. After
ooo <- order(limity.gr$zdrzeni, limity.gr$mvykon.c)
limity.gr <- update(limity.gr[ooo,])
both plots are in the same (correct) order. The key is probably in
order of limity.gr file, which is different after updating.
Cheers
Petr
On 25 Apr 2005 at 18:25, Deepayan Sarkar <deepayan at sta wrote:
> Thank you.
>
> On 25 Apr 2005 at 10:29, Deepayan Sarkar wrote:
>
> > On Monday 25 April 2005 09:40, Petr Pikal wrote:
> > > Dear all
> > >
> > > I am trying nlme together with Pinheiro/Bates book. I constructed
> > > grouped data object with suitable plotting layout (according to
> > > some common factor, panels from bottom to top are in increasing
> > > order).
> > >
> > > When I do nlme(... some stuff...) I get fitted object which I can
> > > plot with
> > >
> > > plot(augPred(fit.nlme6, level=0:1))
> > >
> > > but it results in completely different ordering. Is there any way
> > > how I can plot panels in some defined order e.g.
> >
> > Could you give us a reproducible example? Following the example on
> > the help page
> >
>
> Not yet, I try.
>
> I made my grouped.data with ooo ordering
>
> limity.gr<-groupedData(konverze~tepl|spol.f, limity[ooo,],
> order.groups=F)
>
> which led to correct ordering in
>
> plot(limity.gr)
>
> but it probably left limity.gr in the same order as limity
>
> > head(limity[,1:2])
> pokus vzorek
> 1 1 6
> 2 1 7
> 3 1 8
> 4 1 9
> 5 1 10
> 6 2 8
> > head(limity.gr[,1:2])
> pokus vzorek
> 1 1 6
> 2 1 7
> 3 1 8
> 4 1 9
> 5 1 10
> 6 2 8
> > head(limity.gr[ooo,1:2])
> pokus vzorek
> 33 10 3
> 34 10 4
> 35 10 5
> 36 10 7
> 37 10 8
> 38 10 9
> > head(limity[ooo,1:2])
> pokus vzorek
> 26 7 5
> 27 7 6
> 28 7 7
> 78 15 9
> 79 15 10
> 80 15 11
>
> When I reordered the limity.gr file in desired order and I made the
> nlme analysis based on this newly ordered data, augPred plot was OK.
>
> <snip>
>
> >
> > Possibly. plot.augPred produces a Trellis plot, and usually
> > arguments to the underlying plotting function can be passed on
> > through the top-level call. e.g., with the Orthodont data
> >
> > plot(augPred(fm1, level = 0:1), skip = rep(c(F,T), c(16, 2)))
>
> That's it! Together with suitable layout I got what I wanted.
>
> Great.
> Thanks a lot
>
> Best regards
> Petr
>
> >
> > or
> >
> > p <- plot(augPred(fm1, level = 0:1))
> > update(p, skip = rep(c(F,T), c(16, 2)))
> >
> > You would of course have to know what valid arguments are; for that
> > see ?xyplot and ?update.trellis (in the lattice package).
> >
> > Deepayan
>
>
Petr Pikal
petr.pikal at precheza.cz
-------------- next part --------------
structure(list(pokus = c(1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 4,
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