Staffan, Take a look at ?predict.gam. You need to use type="terms" with se=TRUE to get the quantities that you need.
Simon ps. with binary data, method="REML" or method="ML" for the gam fit are often somewhat more reliable than the default. On Monday 14 September 2009 19:30, Staffan Roos wrote: > Dear package mgcv users, > > > > I am using package mgcv to describe presence of a migratory bird species as > a function of several variables, including year, day number (i.e. > day-of-the-year), duration of survey, latitude and longitude. Thus, the > "global model" is: > > > > global_model<-gam(present ~ as.factor(year) + s(dayno, k=5) + s(duration, > k=5) + s(x, k=5) + s(y, k=5), family = binomial(link = logit), data = > presence, gamma =1.4) > > > > The model works fine, suggesting that all the variables have strong, > non-linear, influences on the probability of detecting the species. My main > interest is in the effect "dayno" has on presence, given the inclusion of > the other explanatory variables. Thus, I would like to extract the values > of the partial prediction of "dayno" and its associated 2 standard errors > above and below the main effect, as shown by the code "plot(global_model)". > > > > I have tried to extract the values by using > "fitted.values(global_model,dayno)", but when plotted, the figure doesn't > look like the partial prediction for "dayno". Instead, it gives me a very > scattered figure ("shotgun effect"). > > > > Has anyone tried to extract the partial predictions? If so, please could > you advise me how to do this? > > > > Thanks, > > > > Staffan > > > > P.S.. For comparison, please have a look at Simon Woods paper in R News, > 1(2):20-25, June 2001, especially the figures showing the partial > predictions of Mackerel egg densities. Using those graphs as an example, I > would like to extract the partial predictions for e.g. "s(b.depth)", given > the inclusion of the other variables. > > -- > Staffan Roos, PhD > Research Ecologist > BTO Scotland > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html and provide commented, minimal, > self-contained, reproducible code. -- > Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK > +44 1225 386603 www.maths.bath.ac.uk/~sw283 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.