[R] Fwd: User defined panel functions in lattice
David Winsemius
dwinsemius at comcast.net
Sat Apr 21 01:29:51 CEST 2012
On Apr 20, 2012, at 6:36 PM, Duncan Mackay wrote:
> 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'm a bit puzzled by this exchange. I know there is a 'panel.locfit',
but you two are spelling it differently. Can you explain why you are
doing so?
> ?panel.Locfit
No documentation for ‘panel.Locfit’ in specified packages and libraries:
you could try ‘??panel.Locfit’
> ?panel.locfit
{locfit} R Documentation
Locfit panel function
Description
This panel function can be used to add locfit fits to plots generated
by trellis.
> 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
>> >> >
>> >> >
>> >> >
>
David Winsemius, MD
West Hartford, CT
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