Hello, >From capture data, I would like to assess the effect of longitudinal changes >in proportion of forests on abundance of skunks. To test this, I built this >GAM where the dependent variable is the number of unique skunks and the >independent variables are the X coordinates of the centroids of trapping sites >(called "X" in the GAM) and the proportion of forests within the trapping >sites (called "prop_forest" in the GAM):
mod <- gam(nb_unique ~ s(x,prop_forest), offset=log_trap_eff, family=nb(theta=NULL, link="log"), data=succ_capt_skunk, method = "REML", select = TRUE) summary(mod) Family: Negative Binomial(13.446) Link function: log Formula: nb_unique ~ s(x, prop_forest) Parametric coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.02095 0.03896 -51.87 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Approximate significance of smooth terms: edf Ref.df Chi.sq p-value s(x,prop_forest) 3.182 29 17.76 0.000102 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 R-sq.(adj) = 0.37 Deviance explained = 49% -REML = 268.61 Scale est. = 1 n = 58 I built a GAM for the negative binomial family. When I use the function `predict.gam`, the predictions of capture success from the GAM and the values of capture success from original data are very different. What is the reason for differences occur? **With GAM:** modPred <- predict.gam(mod, se.fit=TRUE,type="response") summary(modPred$fit) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.1026 0.1187 0.1333 0.1338 0.1419 0.1795 **With original data:** summary(succ_capt_skunk$nb_unique) Min. 1st Qu. Median Mean 3rd Qu. Max. 17.00 59.00 82.00 81.83 106.80 147.00 The question has already been posted on Cross validated (http://stats.stackexchange.com/questions/247347/gam-with-the-negative-binomial-distribution-why-do-predictions-no-match-with-or) without success. Thanks a lot for your time. Have a nice day Marine [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.