For the simple example below, you can see that there are certain points that are identified in the ensuing plots. How can I extract the row numbers identified in these plots, especially the Normal Q-Q plot?
maya <- data.frame(rnorm(100))
names(maya) <- "a"
maya$b <- rnorm(100)
mara <- lm(b~a, data=maya)
I have edited your question using
set.seed(2016) for reproducibility. To answer your question, I need to explain how to produce the Q-Q plot you see.
se <- sqrt(sum(mara$residuals^2) / mara$df.residual) ## Pearson residual standard error hii <- lm.influence(mara, do.coef = FALSE)$hat ## leverage std.resi <- mara$residuals / (se * sqrt(1 - hii)) ## standardized residuals ## these three lines can be replaced by: std.resi <- rstandard(mara)
Now, let's compare the Q-Q plot we generate ourselves and that generated by
par(mfrow = c(1,2)) qqnorm(std.resi, main = "my Q-Q"); qqline(std.resi, lty = 2) plot(mara, which = 2) ## only display Q-Q plot
The same, right?
Now, the only issue left is how the numbers are labelled. Those labelled points mark the largest 3 absolute standardised residuals. Consider:
x <- sort(abs(std.resi), decreasing = TRUE) id <- as.integer(names(x)) id[1:3] #  23 8 12
Now, if you look at the graph closely, you can see that those three numbers are exactly what is shown. Knowing this, you can also check out, for example,