R help - Mar 2011 - lattice custom axis function -- right side margins

Dear R help list,

I have a plot with two different vertical scales that I want to display
on either side of the plot.  It's quite similar to the
Fahrenheit-Centigrade example in the examples section of the
documentation for axis.default.  

The right-side axis is clipped off, though, and I haven't been able to
figure out anything with viewport() and clipping or trellis.par.set to
fix that...  Any help greatly appreciated!  Minimal example below.

I would also like to add a label to the right-side vertical axis similar
to the "sill..." label on the left.  Bonus points if anyone can throw
that in...

Many thanks,
Tim

--

Timothy W. Hilton
PhD Candidate, Department of Meteorology
The Pennsylvania State University
503 Walker Building, University Park, PA   16802
hilton at meteo.psu.edu

--------------------------------------------------
code to produce the plot with right-side labels clipped off



example_data <-
structure(list(year = structure(c(4L, 2L, 2L, 7L, 2L, 2L, 4L, 
2L, 2L, 2L, 2L, 2L, 2L, 1L, 4L, 4L, 2L, 7L, 3L, 2L, 5L), .Label =
c("2000",
"2001", "2002", "2003", "2004",
"2005", "2006"), class = "factor"),
    var = structure(c(2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 2L, 
    2L, 2L, 2L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L), .Label =
c("NEE.model",
    "NEE.model.res", "NEE.obs"), class =
"factor"), par_set = structure(c(6L,
    1L, 3L, 6L, 7L, 2L, 7L, 5L, 1L, 6L, 3L, 4L, 1L, 1L, 4L, 1L, 
    7L, 5L, 9L, 9L, 9L), .Label = c("all.all", "all.ann",
"all.mon",
    "pft.all", "pft.ann", "pft.mon",
"site.all", "site.ann",
    "site.mon"), class = "factor"), sigmasq =
c(11430.2595455547,
    12118.5387166954, 12982.4722525337, 16366.3059675243, 16650.2206047512, 
    19730.2121989498, 19958.3416187217, 20491.4117984889, 20647.8829877428, 
    21389.0300281264, 21413.7674128747, 21445.7255788782, 22002.8026436862, 
    22042.9802472953, 22201.0461487030, 22340.9959465200, 24782.8974616218, 
    27207.1283451608, 59450.6758048182, 94725.119215293, 694716.769010273
    )), .Names = c("year", "var", "par_set",
"sigmasq"), row.names = c(94L,
8L, 20L, 43L, 44L, 68L, 100L, 86L, 2L, 92L, 74L, 80L, 62L, 1L, 
82L, 64L, 98L, 37L, 57L, 56L, 59L), class = "data.frame")

sigsq2sig <- function(sigmasq) sqrt(2 * sigmasq)
sig2sigsq <- function(sig) 0.5 * (sig)^2

# axis method to add a std deviation axis to the right side of a sill plot 
axis.sigmasq <- function(side, ...) {
  switch(side,
         left = {
           ylim <- current.panel.limits()$ylim
           pretty_sigmasq <- pretty(ylim)
           panel.axis(side = side, outside = TRUE,
                      at = pretty_sigmasq, labels = pretty_sigmasq)
         },
         right = {
           ylim <- current.panel.limits()$ylim
           pretty_sigmasq <- pretty(ylim)
           pos_sigmasq <- pretty_sigmasq[pretty_sigmasq >= 0]
           pretty_sigma <- pretty(sigsq2sig(pos_sigmasq))
           panel.axis(side = side, outside = TRUE,
                      at = sig2sigsq(pretty_sigma),
                      labels = pretty_sigma)
         },
         axis.default(side = side, ...))
}

my_plot <- function(best.fits, ...) {

  y.main.label <- expression(sill~group("[", group("(",
mu*mol~s^-1~m^-2 ,")")^2, "]"))
  #plot the parameter values, one per year
  plt <- xyplot(sigmasq~interaction(var, par_set),
                data=best.fits,
                groups=year,
                axis = axis.sigmasq,
                scales=list(x=list(rot=45)),
                xlab=list(label="NEE measure"),
                ylab=list(label=y.main.label),
                ...)
  return(plt)
}

print(my_plot(example_data))

print(my_plot(example_data, ylab.right=expression(e==mc^2)),
position=c(0,0,.95,1))

You will need a recent R version for the ylab.right argument.

On Thu, Mar 3, 2011 at 12:52 PM, Timothy W. Hilton
<hilton@meteo.psu.edu>wrote:
> Dear R help list,
>
	[[alternative HTML version deleted]]

To clarify the trouble I'm having with ylab.right, I am not getting an
error message; the right-side label just does not appear on the plot.

-Tim
> On Thu, Mar 3, 2011 at 1:50 PM, Timothy W. Hilton <hilton at
meteo.psu.edu>wrote:
> 
> > Many thanks, Richard -- the position argument does exactly what I
> > needed.  I'm not having any luck with the ylab.right argument.  My
R and
> > lattice are up to date (below); is there something else I should
check?
> >
> > Thanks for the help,
> > Tim
> >
> > > sessionInfo()
> > R version 2.12.2 (2011-02-25)
> > Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] lattice_0.19-17
> >
> > loaded via a namespace (and not attached):
> > [1] grid_2.12.2  tools_2.12.2
> >
> > On Thu, Mar 2011, 03 at 01:05:49PM -0500, Richard M. Heiberger wrote:
> > > print(my_plot(example_data, ylab.right=expression(e==mc^2)),
> > > position=c(0,0,.95,1))
> > >
> > > You will need a recent R version for the ylab.right argument.
> > >
> > > On Thu, Mar 3, 2011 at 12:52 PM, Timothy W. Hilton <hilton at
meteo.psu.edu
> > >wrote:
> > >
> > > > Dear R help list,
> > > >
> >