Visualizing Logistic GAMs

Nonlinear Modeling with Generalized Additive Models (GAMs) in R

Noam Ross

Senior Research Scientist, EcoHealth Alliance

Transforming scales

Log-odds plots

plot(binom_mod)

Converting partial effects

plot(binom_mod, pages = 1, trans = plogis)

Converting partial effects (2)

plot(binom_mod, pages = 1, trans = plogis)

Adding an intercept

plot(binom_mod, pages = 1, trans = plogis,
     shift = coef(binom_mod)[1])

Adding an intercept (2)

plot(binom_mod, pages = 1, trans = plogis,
     shift = coef(binom_mod)[1])

Incorporating intercept uncertainty

plot(binom_mod, pages = 1, trans = plogis,
     shift = coef(binom_mod)[1],
     seWithMean = TRUE)

Improving the plot

plot(binom_mod, pages = 1, trans = plogis, shift = coef(binom_mod)[1],
     seWithMean = TRUE, rug = FALSE, shade = TRUE, 
     shade.col = "lightgreen", col = "purple")

Let's practice!

Nonlinear Modeling with Generalized Additive Models (GAMs) in R