[R] Fwd: User defined panel functions in lattice
ilai
keren at math.montana.edu
Sat Apr 21 06:21:56 CEST 2012
On Fri, Apr 20, 2012 at 8:15 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> Another puzzle. In the original posting there was this segment:
> ---
>
> 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
> ---
>
> On my mailer that formal argument starts with a capital "I" but the code
> seemed to be attempting a lowercase "l".
>
> I could never see reason offered for defining a new panel.locfit, but I'm
> wondering if the sometimes similar representation of those two different
> letters could be causing an obscure conflict?
>
If that is indeed what's happening, it will be the first time for me.
My mailer shows upper case "L" too, I assume that this is correct and
the OP's intention is exactly that - not redefine panel.locfit but
create his own (if that is good use of his/our time is another matter
altogether). Seems to me the source of this error was, as the error
message suggested, simply the "default" formals:
panel.Locfit <-
function(x,y, nn, h, col, col.line, lwd = lwd, lty = lty, ...){
...
}
Which is why this solved it:
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,...)
}
)
With my new found understanding of the OP's real intentions, maybe a
call to trellis.par.get('superpose.line') inside panel.Locfit is the
answer?
Cheers
> --
> David.
>
>>
>> Cheers
>>
>>
>>>> ?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
>>>
>>>
>>> ______________________________________________
>>> 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.
>
>
> David Winsemius, MD
> West Hartford, CT
>
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