Dear R users,

I am analyzing data using a gls model from the nlme package

The model is:

m2<-gls(C~LDH + SI3, method = "ML", weights = vpDist) ## I will later fit
this model using REML

C = total soil carbon, LDH = log of a distance that I am interested in, and
SI3 = is a index of invasion severity, but these details are not important.

I am trying to plot for the effects of LDH and SI3 individually on C while
controlling for the other factor. The "effects" package achieves this
through the code below:

plot(effect('LDH', m2)) ## effects of LDH on C, while controlling for the
effects of SI3

The graph that is produced shows predicted linear relationship and a 95%
CI, but does not actual show data values for C.

I tried to add the points using the code below, but the problem is that the
points that I add to the effects graph are not on the correct scale. That
is their values are not graphed correctly.

y1<-c(min(C), max(C))
x1<-c(min(LDH), max(LDH))
plot.new()
plot(effect('LDH', m2), xlim = x1, ylim = y1) ## called from the "effects"
package
points(LDH, C, ylim = y1, xlim = x1, pch = 16, col = "black")

NOTE: I use the "plot.new()" because sometimes if I do not the points do
not show up on the graph.

So my question is, how do I place points over an effects graph in a way
that the value (x,y coordinates) of the points are correct (i.e., on the
same scale as the axes of the effects graph)?

I hope this makes sense. I was not sure how to attach my data file to this
email so that people can try this code out for themselves, but the made up
example below generates the same issue. NOTE: I tried graphing two ways:
one where I specify the scale of the points and the later where I do not.
Neither way seems to work.

X<-rnorm(100)
Y<-rnorm(100)
Z<-rnorm(100)

m1<-gls(Y~X+Z)
summary(m1)

plot.new()
y1<-c(min(Y), max(Y))
x1<-c(min(X), max(X))
plot(effect('X', m1), xlim = x1, ylim = y1)
points(Y~X, ylim = y1, xlim = x1, pch = 16, col = "black")

plot.new()
y1<-c(min(Y), max(Y))
x1<-c(min(X), max(X))
plot(effect('X', m1), xlim = x1, ylim = y1)
points(Y~X, pch = 16, col = "black")

Thanks a bunch for any suggestions that anyone can offer.

-- 
Basil Iannone
University of Illinois at Chicago
Department of Biological Sciences (MC 066)
845 W. Taylor St.
Chicago, IL  60607-7060
Email: bianno2@uic.edu
Phone: 312-355-3231
Fax: 312-413-2435
http://www2.uic.edu/~bianno2

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