Hi David
if you go
library(locfit)
? panel.locfit
The function will do contour/wireframe like plots using par.settings
of region as well as normal 2D plots
I could not get panel.locfit to work using par.settings and created
my own panel function as panel.Locfit
at the time I did not think that I would be putting it on the web.
(I knew it would be confusing to some but forgot to change the name.
[its been a long week]).
In the first instance I wanted a panel function to produce confidence
bands which I cobbled up, but then wanted lines in another situation.
Duncan
At 09:29 21/04/2012, you wrote:
>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