I am applying a GAM model to my data: cell abundance over time.
The model works just fine (although I am aware of a pattern in my resiudals, but this is a different issue not relevant here).
It just fails to display the partial residuals in the final plot, although i set residuals = TRUE. Here is my output:
https://i.sstatic.net/C1MlY.png
also I used mgcv package.
Previously this code worked as I wanted, but on different data. Any ideas on why it is not working are welcome!
GAM_EA <- mgcv::gam(EUB_FISH ~ s(Day, by = Heatwave), data = HnH, method = "REML")
gam.check(GAM_EA) #Checking the model
mgcv::anova.gam(GAM_EA) #Retrieving the statistical results. See ?anova.gam
summary.gam(GAM_EA)
plot(GAM_EA, shift = coef(GAM_EA)[1], residuals = TRUE)
See argument by.resid in ?plot.gam. They way these are used in plot.gam would been meaningless for factor by terms unless you were to subset the partial residuals and plot only the residuals for observations in the specific level of the by factor.