Predicted probabilities for logistic regression models using R and ggplot2

predicted-probabilities-for-logistic-regression.R

# convenience function for logit models
invlogit <- function(x){ 1 / (1 + exp(-x)) }

# some data cribbed from the R help pages
dd <- data.frame(ldose = rep(0:5, 2),
                 dead = c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16),
                 sex = rep(c("M", "F"), each = 6))
# 30 trials in each row of which 'dead' beasties died

# fit a model
mod <- glm(cbind(dead, 20 - dead) ~ sex * ldose, family = binomial, data = dd)

# cases / range that we want predicted probabilities for
ndata <- expand.grid(ldose = seq(0, 5, 0.1), sex = c("M", "F"))

# get predicted probabilities
preds <- predict(mod, newdata = ndata, se.fit = TRUE)

# construct intervals by transforming predictions and 2*SEs
# and bundle with ndata for ease of plotting together
plottable <- with(preds, 
                  data.frame(ndata, 
                             fit = invlogit(fit),
                             lwr = invlogit(fit + 2*se.fit),
                             upr = invlogit(fit - 2*se.fit)) )

# plot the lot
library(ggplot2)
theme_set(theme_minimal()) # replace default 'mouldy waffle' background

ggplot(plottable, aes(x = ldose, y = fit, col = sex, fill = sex)) + 
  geom_ribbon(aes(ymin = lwr, ymax = upr), alpha = 0.4, colour = NA) +
  geom_line(size = 1, alpha = 0.4) +
  scale_color_brewer(palette="Set1") +  # replace default colors and fill
  scale_fill_brewer(palette="Set1") +
  labs(x = "Dose", y = "Probability of death", title = "Dead Beetles")

Many thanks for sharing the code. There are some issues for me about the code. I just copy-pasted the code to RStudio and run it.
Here are my issues:

1. ggplot shows Male in Pink and Female in Blue. Blue is the traditional color to represent Male, and Pink is the traditional color to represent Female in world. So, is there an error in the code while labelling the gender in legend of the plot? Or labelling was done without caring their traditional coloring?

2. You say, " 30 trials in each row of which 'dead' beasties died"

N	dose	dead male	dead female
1	0	1	0
2	1	4	2
3	2	9	6
4	3	13	10
5	4	18	12
6	5	20	16

Is it 30 or 12? Could you please explain the experiment design and problem you deal with this code a bit further?
I couldn't grasp the problem that this code solved.
Best and warmest regards.