Oh ... one more thing.
You might explore the latticeExtra package. It permits use of a
layering paradigm -- like ggplot -- that largely obviates the need for
panel functions. There are also options in it to gracefully handle
(ignore) replicated arguments.
-- Bert
On Sat, Apr 21, 2012 at 2:28 AM, Duncan Mackay <mac...@northnet.com.au> wrote:
> Bert
> I have read Deepayan's book and done all the examples but there is no
> mention of panel.number and panel.groups in the books example.
>
> I just cannot get the fully meaning of what has been written regarding
> passing arguments to panel functions.
>
> Regards
>
> Duncan
>
>
>
> At 14:31 21/04/2012, you wrote:
>>
>> A comment...
>>
>> On Fri, Apr 20, 2012 at 8:32 PM, Duncan Mackay <mac...@northnet.com.au>
>> wrote:
>> > Hi David, ilai
>> >
>> > The root cause of the problem is the passing of arguments to panel
>> > functions
>> > to me and my colleagues.
>> > Just going through the archives there seems to be different ways for
>> > very
>> > similar/same outcomes and
>> > trying to get a pattern is hard to discern.
>>
>> Bad strategy! Trying to infer the rules from examples in complex
>> cases -- and as you said, different equivalent ways -- is nuts. You
>> need to read the docs carefully (including Deepayan's book, possibly)
>> and use the examples for understanding what is explained there.
>>
>> Finally, I don't know if this is relevant or helpful but:
>>
>> ## this code works fine
>> xyplot(rnorm(5) ~ 1:5, type="l",
>> panel = function(...)panel.xyplot(...,lwd=2))
>>
>> ## This code throws an error about repeat lwd arguments. Is it obvious
>> why?
>> xyplot(rnorm(5) ~ 1:5, lwd=1,type="l",
>> panel = function(...) panel.xyplot(...,lwd=2))
>>
>> -- Bert
>>
>> > I frequently have to use the subscripts or group.number to access other
>> > data.
>> > I thought I had things sorted out in my head with the panel.groups and
>> > group.number but this has shattered it.
>> >
>> > Thanks
>> >
>> > Duncan
>> >
>> > At 12:15 21/04/2012, you wrote:
>> >
>> >> On Apr 20, 2012, at 9:14 PM, ilai wrote:
>> >>
>> >>> Oops - that is "reply all"
>> >>> On Fri, Apr 20, 2012 at 5:29 PM, David Winsemius
>> >>> <dwinsem...@comcast.net
>> >>> > wrote:
>> >>>>
>> >>>>
>> >>>> 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?
>> >>>
>> >>>
>> >>> Hi David,
>> >>> Thanks for stepping in. panel.Locfit is the OP's local function (or
>> >>> just a wrapper ?) which I believe is here
>> >>> http://www.mail-archive.com/r-help@r-project.org/msg167164.html
>> >>>
>> >>> Note the two errors OP encountered (solved down the thread) were
>> >>> caused by the way he called the function in xyplot, not by
>> >>> panel.Locfit itself, which I did not modify. I guess now the issue is
>> >>> how to generalize panel.Locfit somehow, but I am not sure how. I
>> >>> suspect the problem is not my understanding but that there really
>> >>> isn't any one specific problem here for the list to solve, though,
>> >>> again, I am known for misinterpreting OP requests... :)
>> >>>
>> >>>>> ?panel.locfit
>> >>>
>> >>>
>> >>> As I said, I am unfamiliar with the package - but this doesn't
>> >>> surprise me. Thank you for pointing it out, wish you've noticed the
>> >>> exchange sooner...
>> >>
>> >>
>> >> 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?
>> >>
>> >> --
>> >> 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
>> >>>>>> <mac...@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
>> >>>>>>>> <mac...@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@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
>> >>
>> >
>> > ______________________________________________
>> > R-help@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.
>>
>>
>>
>> --
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>>
>> Internal Contact Info:
>> Phone: 467-7374
>> Website:
>>
>>
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>
> ______________________________________________
> R-help@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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
