[R] trellis/ panel.superpose/ passing in superscripts/ groups

From: McClatchie, Sam (PIRSA-SARDI) <mcclatchie.sam_at_saugov.sa.gov.au>
Date: Tue 15 Mar 2005 - 15:14:45 EST


Background:
OS: Linux Mandrake 10.1
release: R 2.0.0
editor: GNU Emacs 21.3.2
front-end: ESS 5.2.3


Colleagues

I'm plotting fish egg densities in temperature-salinity space (i.e. mean temperature ~ mean salinity | fish egg densities) for two survey years. The bivariate plot is overlaid on a temperature ~ salinity plot (not means) showing the distribution of water masses, so I can see the association of the eggs with water masses.

It is all working, but I have had to replace a call to panel.superpose with panel.xyplot to plot the two years with different symbols. The problem may be related to one raised by Volker Franz <http://maths.newcastle.edu.au/~rking/R/devel/02b/0993.html> that was reported to be fixed. On the other hand, I may just be using panel.superpose incorrectly. You can see that I've messed around with the groups variable to try and get it working.

My code is as follows.

"sardine.egg.T.S.space.2001.and.2002.exp" <-   function()
  {
    library(lattice)

# trellis.device(postscript,
#
file="../figures/sardine.egg.T.S.space.2001.and.2002.ps",

# horizontal=FALSE,
color=TRUE)     

    year <- as.factor(rep(2001, dim(mn.ts.e.2001)[1]))     year.2001 <- cbind(mn.ts.e.2001,year)     year <- as.factor(rep(2002, dim(mn.ts.e.2002)[1]))     year.2002 <- cbind(mn.ts.e.2002,year)     mn.ts.e.both <- rbind(year.2001, year.2002)

#browser()
###trellis plot

    ##int <- matrix(c(0,5,6,10,11,20,21,40,41,80,81,160), ncol=2, byrow=TRUE)

    int <- matrix(c(0,2,3,4,5,8,9,16,17,32,33,64), ncol=2, byrow=TRUE)     egg.counts <- shingle(mn.ts.e.both$eggs2.Pilch.Eggs, intervals = int)     larvae.counts <- shingle(mn.ts.e.both$eggs2.Pilch.Larv, intervals = int)     

    out1 <- xyplot(mn.t ~ mn.s | egg.counts,

                   data = mn.ts.e.both,

#groups = year,
xlim = c(35,38), ylim = c(12,24), xlab = "mean salinity", ylab = "mean temperature (deg. C)", main = "2001 and 2002 egg densities in Temperature-Salinity space", aspect = "xy", jitter = T, layout = c(1,6), auto.key=TRUE, panel = function(x, y, subscripts = c(2,3)){ panel.xyplot(data.2001$Salinity, data.2001$Temperature.oC, pch=".", col="yellow") panel.xyplot(data.2002$Salinity, data.2002$Temperature.oC, pch=".", col="orange") panel.text(37.8, 15, "Upwelling") panel.text(37.8, 17.5, "Warm pool") panel.text(37.8, 19.75, "Shelf break") panel.text(37.8, 21.5, "Spencer Gulf") panel.abline(h = c(16,19,20.5), v = 36.5, col="red", lty=2) ## panel.superpose(x,y, ## subscripts=c(2,3), ## groups = mn.ts.e.both$year, ## cex=0.5) ##auto.key = T panel.xyplot(year.2001$mn.s, year.2001$mn.t, col="cyan") panel.xyplot(year.2002$mn.s, year.2002$mn.t, col="purple") } ) print(out1)
# graphics.off()

  }

Any suggestions regarding how to get panel.superpose working would be gratefully received. Sorry I cannot provide the data so the code is easily used. Data are a bit large to paste into an email.

Sam



Sam McClatchie,
Biological oceanography
South Australian Aquatic Sciences Centre PO Box 120, Henley Beach 5022
Adelaide, South Australia
email <mcclatchie.sam@saugov.sa.gov.au>
Telephone: (61-8) 8207 5448
FAX: (61-8) 8200 2481
Research home page <http://www.members.iinet.net.au/~s.mcclatchie/>   
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