[R] How to extract partial predictions, package mgcv

[Simon Wood]

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
>
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-- 
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603  www.maths.bath.ac.uk/~sw283