ggplot alpha = 0 not working

If you're trying to reproduce the first chart, the x-axis should be time and the y-axis is the residuals of the fit. So you need to combine the original data macs, containing time, with the residuals in fit. I would use broom::augment for that.

For the alpha issue, you need to convert the values to factors then work with scale_alpha_discrete.

library(tidyverse)
library(broom)

fit %>% 
  augment() %>% 
  bind_cols(macs) %>% 
  mutate(alpha = factor(alpha)) %>%
  ggplot(aes(time, .resid)) + 
    geom_line(aes(group = id, alpha = alpha)) + 
    scale_alpha_discrete(range = c(0, 1)) + 
    geom_point(size = 0.5) + 
    guides(alpha = FALSE) + 
    theme_bw()

The problem has got to do with the color behavior in ggplot. A simple fix is to explicitly specify its color to be NA when the corresponding alpha is 0. Here's the code I would add before the ggplot call:

color_rule <- ifelse(macs$alpha == 0, NA, "black")

And slight modifications to ggplot:

ggplot(data = macs, aes(x = fitted(fit), y = resid(fit))) +
  geom_point(aes(alpha=1), size = 0.5) +  
  geom_line(aes(alpha=alpha, group=id), color=color_rule) + 
  guides(alpha=FALSE)

This would get you the following plot:

A clean, fully transparent geom_line by having color=NA. Just for comparison, ff you remove the color=NA argument from geom_line, even with alpha=0 you'll get what is effectively the "default color" of the line: