On Thu, 2008-10-23 at 14:44 -0500, Christopher Chizinski wrote: > Is there a way to output the X,Y,Z values for the contour lines from > ordisurf? > > For example, I am using this statement: > tmp<-with(enviro,ordisurf(fish.nmds,enviro$Temp,choices=c(1,2),add=TRUE)) > > names(tmp) > [1] "coefficients" "residuals" "fitted.values" > [4] "family" "linear.predictors" "deviance" > [7] "null.deviance" "iter" "weights" > [10] "prior.weights" "df.null" "y" > [13] "converged" "sig2" "edf" > [16] "hat" "boundary" "sp" > [19] "nsdf" "Ve" "Vp" > [22] "mgcv.conv" "gcv.ubre" "aic" > [25] "rank" "gcv.ubre.dev" "method" > [28] "smooth" "formula" "cmX" > [31] "model" "control" "terms" > [34] "pterms" "assign" "offset" > [37] "data" "df.residual" "min.edf" > [40] "call" > > I would like to get these XYZ values or find a way to calculate them > from the output for inclusion into SigmaPlot. It is probably an easy > solution but I could not find what I needed. > Dear Christopher Chizinski,
I assume you mean the ordisurf() function in the vegan package. If you mean something else, this message is not appropriate and you may stop reading. Function ordisurf (of vegan) returns visibly an object of function gam of the mgcv package (like documented). You can use all mgcv:::gam tools to handle this object, including predict.gam (of mgcv) which can be used to predict new values of surface (z) for any values of the coordinates (x, y). These results can be exported to SigmaPlot or anywhere. If you look inside the function ordisurf, you can see how predict.gam is used to find the predicted value of the surface for a grid of axis values. I changed the ordisurf function in http://r-forge.r-project.org/projects/vegan so that it now adds the data used by the contour() function in a new item called "grid" in the result. The returned data in "grid" contain vectors "x" and "y" for the grid values on the axis, and matrix "z" for the fitted surface values for each combination of "x" and "y" vectors. The values of "z" outside the convex hull of observed site are marked as NA. You can directly export these items or reuse them to draw the surface with the contour() command. The grid item is available from vegan working version 1.16-3 (revision 532) in R-Forge, and Windows binary is available (probably) from tomorrow morning (Central European Standard Time). Best wishes, Jari Oksanen -- Jari Oksanen <[EMAIL PROTECTED]> _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology