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: bian...@uic.edu Phone: 312-355-3231 Fax: 312-413-2435 http://www2.uic.edu/~bianno2 [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology