[R] extra panel arguments to plot.nmGroupedData {nlme}

From: Dylan Beaudette <dylan.beaudette_at_gmail.com>
Date: Sun 28 Jan 2007 - 20:59:58 GMT


Greetings,

I have a groupedData (nmGroupedData) object created with the following syntax:

Soil <- groupedData(
  ksat ~ conc | soil_id/sar/rep,
  data=soil.data,
  labels=list(x='Solution Concentration', y='Saturated Hydraulic Conductivity'),   units=list(x='(cmol_c)', y='(cm/s)')
)

the original data represents longitudinal observations in the form of: 'data.frame': 1197 obs. of 5 variables:
$ soil_id: Factor w/ 19 levels "Arbuckle","Campbell",..: 16 16 16 16
16 16 16 16 16 16 ...
$ sar : int 12 12 12 12 12 12 12 6 6 6 ...
$ conc : num 500 100 50 10 5 1 0.003 500 100 50 ...
$ rep : Factor w/ 3 levels "C1","C2","C3": 1 1 1 1 1 1 1 1 1 1 ...
$ ksat : num 0.000214 0.000207 0.000198 0.000160 0.000108 ...

the default plotting behaviour of this groupedData object works as expected: plot(
  Soil,
  collapse=1, inner=~sar, aspect='fill',   scales=list( x=list(log=TRUE), y=list(log=TRUE)) )

... however, there is no way for me to alter the panels...

for example, attempting to add a horizontal line with a call to panel.abline= ... :
plot(
  Soil,
  collapse=1, inner=~sar, aspect='fill',   scales=list( x=list(log=TRUE), y=list(log=TRUE)),
  FUN=mean,
  panel= function(x,y, subscripts, groups) {     panel.xyplot(x, y, type='o')
    panel.abline(h=0.005, col='black', lty=2)     }
)

... results in an identical plot. Trying to re-create the results of plot.nmGroupedData with a direct call to xyplot() has thus far been unsucsessful- as I cannot figure out how to specifiy the original formula in a meaningful way to xyplot: ksat ~ conc | soil_id/sar/rep .

Any tips on passing panel arguments to plot.nmGroupedData() would be greatly appreciated.

Cheers,

Dylan



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