Question

library(MASS)
example(lda)
plot(z)

How can I access all the points in z? I want to know the values of every point along LD1 and LD2 depending on their Sp (c,s,v).

Answer 1

What you are looking for is computed as part of the predict() method of objects of class "lda" (see ?predict.lda). It is returned as component x of the object produced by predict(z):

## follow example from ?lda
Iris <- data.frame(rbind(iris3[,,1], iris3[,,2], iris3[,,3]),
                   Sp = rep(c("s","c","v"), rep(50,3)))
set.seed(1) ## remove this line if you want it to be pseudo random
train <- sample(1:150, 75)
table(Iris$Sp[train])
## your answer may differ
##  c  s  v
## 22 23 30
z <- lda(Sp ~ ., Iris, prior = c(1,1,1)/3, subset = train)

## get the whole prediction object
pred <- predict(z)
## show first few sample scores on LDs
head(z$x)

the last line shows the first few rows of the object scores on the linear discriminants

> head(pred$x)
          LD1        LD2
40  -8.334664  0.1348578
56   2.462821 -1.5758927
85   2.998319 -0.6648073
134  4.030165 -1.4724530
30  -7.511226 -0.6519301
131  6.779570 -0.8675742

These scores can be plotted like so

plot(LD2 ~ LD1, data = pred$x)

producing the following plot (for this training sample!)