Prediction and Confidence intervals for Logistic Regression - r

Question

Below is a set of fictitious probability data, which I converted into binomial with a threshold of 0.5. I ran a glm() model on the discrete data to test if the intervals returned from glm() were 'mean prediction intervals' ("Confidence Interval") or 'point prediction intervals'("Prediction Interval"). It appears from the plot below that the returned intervals are the latter--'Point Prediction Intervals'; note, with 95% confidence, 2/20 points fall outside of the line in this sample.
If this is indeed the case, how do I generate the the 'mean prediction interval' (i.e, "Confidence Intervals") in R for a binomial data set bound by 0 and 1 using glm()? Please show your code and plot similar to mine with the fit line, given probabilities, 'confidence intervals' and 'prediction intervals'.
# Fictitious data
xVal <- c(15,15,17,18,32,33,41,42,47,50,
53,55,62,63,64,65,66,68,70,79,
94,94,94,95,98)
randRatio <- c(.01,.03,.05,.04,.01,.2,.1,.08,.88,.2,
.2,.99,.49,.88,.2,.88,.66,.87,.66,.90,
.98,.88,.95,.95,.95)
# Converted to binomial
randBinom <- ifelse(randRatio < .5, 0, 1)
# Data frame for model
binomData <- data.frame(
randBinom = randBinom,
xVal = xVal
)
# Model
mode1 <- glm(randBinom~ xVal, data = binomData, family = binomial(link = "logit"))
# Predict all points in xVal range
frame <- data.frame(xVal=(0:100))
predAll <- predict(mode1, newdata = frame,type = "link", se.fit=TRUE)
# Params for intervals and plot
confidence <- .95
score <- qnorm((confidence / 2) + .5)
frame <- data.frame(xVal=(0:100))
#Plot
with(binomData, plot(xVal, randBinom, type="n", ylim=c(0, 1),
ylab = "Probability", xlab="xVal"))
lines(frame$xVal, plogis(predAll$fit), col = "red", lty = 1)
lines(frame$xVal, plogis(predAll$fit + score * predAll$se.fit), col = "red", lty = 3)
lines(frame$xVal, plogis(predAll$fit - score * predAll$se.fit), col = "red", lty = 3)
points(xVal, randRatio, col = "red") # Original probabilities
points(xVal, randBinom, col = "black", lwd = 3) # Binomial Points used in glm
Here's the plot, presumably with 'point prediction intervals' (i.e., "Prediction Intervals") in dashed red, and the mean fit in solid red. Black dots represent the discrete binomial data from original probabilities in randRatio:

Answer 1

I am not sure if you are asking for the straight up prediction interval, but if you are you can calculate it simply.
You can extract a traditional confidence interval for the model as such:
confint(model)
And then once you run a prediction, you can calculate a prediction interval based on the prediction like so:
upper = predAll$fit + 1.96 * predAll$se.fit
lower = predAll$fit - 1.96 * predAll$se.fit
You are simply taking the prediction (at any given point if you use a single set of predictor variables) and adding and subtracting 1.96 * absolute value of the standard error. (1.96 se includes 97.5% of the normal distribution and represents the 95% interval as it does for the standard deviation in the normal distribution)
This is the same formula that you would use for a traditional confidence interval except that using the standard error (as opposed to the standard deviation) makes the interval wider to account for the uncertainty in prediction itself.
Update:
Method for plotting prediction invervals courtesy of Rstudio!
As requested...though not done by me!