GAM model error

Question

My data frame looks like:

head(bush_status)
distance  status count
       0 endemic   844
       1 exotic     8
       5 native     3
      10 endemic    5
      15 endemic    4
      20 endemic    3

The count data is non-normally distributed. I'm trying to fit a generalized additive model to my data in two ways so i can use anova to see if the p-value supports m2.

m1 <- gam(count ~ s(distance) + status, data=bush_status, family="nb")
m2 <- gam(count ~ s(distance, by=status) + status, data=bush_status, family="nb")

m1 works fine, but m2 sends the error message:

"Error in smoothCon(split$smooth.spec[[i]], data, knots, absorb.cons, 
scale.penalty = scale.penalty,  : 
  Can't find by variable"

This is pretty beyond me so if anyone could offer any advice that would be much appreciated!

Answer 1

From your comments it became clear that you passed a character variable to by in the smoother. You must pass a factor variable there. This has been a frequent gotcha for me too and I consider it a design flaw (because base R regression functions deal with character variables just fine).