Plot binomial GAM in ggplot-CodePudding

I'm trying to visualize a dataset that uses a binomial response variable (proportions). I'm using a gam to examine the trend, but having difficult getting it to plot with ggplot. How do I get the smooth added to the plot?

Example:

set.seed(42)
df <- data.frame(y1 = sample.int(100),
                 y2 = sample.int(100),
                 x  = runif(100, 0, 100))
ggplot(data = df,
      aes(y = y1/(y1 y2), x = x))  
  geom_point(shape = 1)  
  geom_smooth(method = "gam",
              method.args = list(family = binomial),
              formula = cbind(y1, y2) ~ s(x))

Warning message:
Computation failed in `stat_smooth()`
Caused by error in `cbind()`:
! object 'y1' not found

CodePudding user response：

The formula in geom_smooth has to be in terms of x and y, representing the variables on your x and y axes, so you can't pass in y1 and y2.

The way round this is that rather than attempting to use the cbind type left-hand side of your gam, you can expand the counts into 1s and 0s so that there is only a single y variable. Although this makes for a little extra pre-processing, it allows you to draw your points just as easily using stat = 'summary' inside geom_point and makes your geom_smooth very straightforward:

library(tidyverse)

set.seed(42)
df <- data.frame(y1 = sample.int(100),
                 y2 = sample.int(100),
                 x  = runif(100, 0, 100))

df %>% 
  rowwise() %>%
  summarize(y = rep(c(1, 0), times = c(y1, y2)), x = x) %>%
  ggplot(aes(x, y))  
  geom_point(stat = 'summary', fun = mean, shape = 1)  
  geom_smooth(method = "gam",
              method.args = list(family = binomial),
              formula = y ~ s(x))  
  theme_classic()

^{Created on 2023-01-20 with reprex v2.0.2}