[R] Fwd: User defined panel functions in lattice
Duncan Mackay
mackay at northnet.com.au
Sat Apr 21 00:36:33 CEST 2012
Hi ilai
Thank you for your advice I think I can now get what I need from what
you have said here.
I think I may have to get involved in packet.number but the original
packet.number with its arguments has stuck in my mind and I have not used it.
I find locfit better than loess etc for a lot of the data I work with.
I am trying to construct a function/s to cover as many of the normal
situations as possible.
Usually I have to amend colours lines etc to distinguish the data.
I want to cover a number of situations
1 Conditioned by panel no groups
2 Conditioned by panel and groups.
3 Multiple values for above - to show colleagues (EDA)
4 Conditioned by panel and groups + an overall fit for all the data
within a panel
5 Several y values in a panel eg Y1+Y2 and outer = FALSE with a fit
for each of Y1 and Y2
I am trying to cover as many of the above situations in 1 function
before resulting to trellis.focus or
overlaying. The graphs that I normally create are not simple,
generally involving useOuterStrips
which may have different y scales for panel rows
(combindeLimits/manual) and different panel row heights.
locfit is like loess but 2 arguments for smoothing; the degree of
smoothing produced by the defaults
is approximately that of loess but I normally need less smoothing
(the same would be apply for loess).
Most of the questions to Rhelp are for 1 with just a small number for
5 and they are not applicable here
and understanding the requirements for passing arguments in these
different situations I find difficult.
I would like to reduce the number of panel functions to the minimum
to cover the general situaltions because
my graphs are usually not normal and then add to them for a
particular situation.
Regards
Duncan
At 01:38 21/04/2012, you wrote:
>Duncan,
>First off, I admit it is not clear to me what you are trying to
>achieve and more importantly, why? by "why" I mean 1) I don't see the
>advantage of writing one general panel function for completely
>different situations (one/multiple smoothers, grouping levels etc.) 2)
>your intended result as I understand it seems rather cluttered, google
><chartjunk>. 3) I am unfamiliar with locfit package, but are we
>reinventing the wheel here ? i.e. will modifying settings in xyplot(y
>~x, xx, groups = Farm, type=c('p','smooth')) achieve the same ?
>
>With your initial reproducible example (thank you) it was easy to
>eliminate the errors, but clearly the resulting plots are not what you
>intended (continue inline):
>
>On Thu, Apr 19, 2012 at 4:23 PM, Duncan Mackay <mackay at northnet.com.au> wrote:
><snip>
> > 3. What I want to be able to add in the above is extra lines with different
> > values of nn.
> > I think I will have to modify panel.Locfit so that it goes through
> > different values of nn in each of the panels and groups if I want different
> > colours for extra lines with different nn values
>
>Yes you could. There are several options:
>add group.number to the arguments of panel.locfit and use it to make
>nn a vector, along the lines of
> panel.foo <- function(x,y,group.number,theta,...){
> smpar <- theta[group.number]
> panel.loess(x,y,smpar,...)
> panel.xyplot(x,y,...)
> }
>
>xyplot(y~x,xx,group=Farm,theta=c(4,1,.4),panel=panel.superpose,panel.groups=panel.foo)
>
> # or
>xyplot(y~x|Farm,xx,group=Padd,theta=c(.6,1),
> panel=panel.superpose,panel.groups=panel.foo)
>
>Here you will need to modify the Farm group to 6 levels - 3*two smoothers.
>
>You could make nn a list and loop over it inside the panel function.
>Looks like you tried something like that with specifying 2
>panel.Locfit, one suggestion to your code:
>
> panel.Locfit(x,y,...) # default 0.7
> panel.Locfit(x,y,nn=0.9) # i.e. remove the
>... to avoid clashes
>
>Finally, use ?trellis.focus to plot the second smoother "post-hoc".
>also the latticeExtra package has many useful tools to create layers
>of the same (or different) plot with different settings.
>
> > 4 Produce an extra line for a fit for all the groups in 1/2+ panels.
> > As for 3 but I do not know how to group all the x and y's for
> each of the
> > panes using panel.groups
>
>Why does it matter ? seems you have failed to learn the lesson from
>the first post - the same functionality applies to 1 as to multiple
>panels. Does each panel have a different grouping structure ? use
>packet.number() for panels similar to group.number idea.
>
> > I need to do this and then scale up for a panel function to include
> > confidence bands
>
>than expand the xlim,ylim or scales in ?xyplot
>
> >
> > For the record making Farm and Padd factors. With 1 panel and groups = Farm
> > works with the extra line the same colour for its group
> > a similar situation for the three panels when conditioned by Farm
> and groups
> > = Pad
>
>????
>
>Like I said I am a little lost on this problem but I hope this helps
>giving some direction.
>Cheers
>
>
> >
> > xyplot(y ~x, xx,
> > groups = Farm,
> >
> > par.settings = list(strip.background = list(col = "transparent"),
> > superpose.line = list(col =
> c("black","grey"),
> > lwd = c(1,2,3),
> > lty =
> c(2,1,3)),
> > superpose.symbol = list(cex = c(0.8, 0.7,0.7),
> > col =
> > c("red","black","blue"),
> > pch = c(20,4,16))
> > ),
> > auto.key=list(lines=T,points = T,rectangles=F),
> >
> > panel = panel.superpose,
> > panel.groups=function(x,y, ...){
> >
> > panel.xyplot(x,y,...)
> > panel.Locfit(x,y,...) # default 0.7
> > panel.Locfit(x,y,nn=0.9,...)
> >
> > }
> > ) ## xyplot
> >
> >
> > Regards
> >
> > Duncan
> >
> >
> > At 02:12 20/04/2012, you wrote:
> >>
> >> On Thu, Apr 19, 2012 at 2:30 AM, Duncan Mackay <mackay at northnet.com.au>
> >> wrote:
> >> > Hi
> >> >
> >> > xyplot(y ~x|Farm,xx,
> >> > groups = Padd,
> >> > panel = panel.superpose,
> >> > panel.groups=function(x,y, ...){
> >> > panel.Locfit(x,y,...)
> >> > panel.xyplot(x,y,...)
> >> > }
> >> > ) ## xyplot
> >> >
> >> > The above works nicely and also without par.setting giving lattice
> >> > defaults.
> >> > The par.setting is handy for a lot of graphs that I do.
> >> >
> >> > But when I tried a 1 panel plot I get the error message.
> >> >
> >> > xyplot(y ~x,xx,
> >> > groups = Farm,
> >> > auto.key=TRUE,
> >> > panel = function(x,y, ...){
> >> >
> >> > panel.Locfit(x,y,...)
> >> > panel.xyplot(x,y,...)
> >> > }
> >> > )
> >> >
> >>
> >> These two plots are NOT THE SAME. Did you want the same as the first
> >> but with groups being Farm and Padd ignored ? in that case you (again)
> >> need a panel.groups:
> >>
> >> xyplot(y ~x,xx,
> >> groups = Farm,
> >> auto.key=TRUE,
> >> panel = panel.superpose,panel.groups=function(x,y,...){
> >> panel.Locfit(x,y,...)
> >> panel.xyplot(x,y,...)
> >> }
> >> )
> >>
> >>
> >> > If I want to plot another curve with different smoothing
> >> > but gives an error message without par.settings if i want to add
> >> > panel.Locfit(x,y,nn= 0.9,lwd = c(1,2,3), ...)
> >> >
> >> > Error using packet 1
> >> > formal argument "Iwd" matched by multiple actual arguments
> >>
> >> It is all in the way you initially specified how to pass the arguments
> >> for panel.Locfit. This works without error:
> >>
> >> xyplot(y ~x,xx,
> >> groups = Farm,
> >> auto.key=TRUE,lwd=1:3,
> >> panel = panel.superpose,panel.groups=function(x,y,nn,...){
> >> panel.Locfit(x,y,nn=.9,...)
> >> panel.xyplot(x,y,...)
> >> }
> >> )
> >>
> >>
> >> HTH
> >>
> >>
> >>
> >> > I also need to plot a smoothed line for all groups trying groups,
> >> > subscripts
> >> > and panel.groups as arguments without success
> >> >
> >> > Any solutions to solve the above will be gratefully received and
> >> > faithfully
> >> > applied.
> >> >
> >> > Duncan
> >> >
> >> > sessionInfo()
> >> > R version 2.15.0 (2012-03-30)
> >> > Platform: i386-pc-mingw32/i386 (32-bit)
> >> >
> >> > locale:
> >> > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
> >> > LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> >> > LC_TIME=English_Australia.1252
> >> >
> >> > attached base packages:
> >> > [1] datasets utils stats graphics grDevices grid methods
> >> > base
> >> >
> >> > other attached packages:
> >> > [1] locfit_1.5-7 R.oo_1.9.3 R.methodsS3_1.2.2
> >> > foreign_0.8-49
> >> > chron_2.3-42 MASS_7.3-17 latticeExtra_0.6-19
> >> > RColorBrewer_1.0-5
> >> > [9] lattice_0.20-6
> >> >
> >> > loaded via a namespace (and not attached):
> >> > [1] tools_2.15.0
> >> >
> >> >
> >> >
> >> > Duncan Mackay
> >> > Department of Agronomy and Soil Science
> >> > University of New England
> >> > ARMIDALE NSW 2351
> >> > Email home: mackay at northnet.com.au
> >> >
> >> > ______________________________________________
> >> > R-help at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-help
> >> > PLEASE do read the posting guide
> >> > http://www.R-project.org/posting-guide.html
> >> > and provide commented, minimal, self-contained, reproducible code.
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
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