pca example.R

set.seed(2)
x <- 1:100

y <- 20 + 3 * x
e <- rnorm(100, 0, 60)
y <- 20 + 3 * x + e

plot(x,y)
yx.lm <- lm(y ~ x)
lines(x, predict(yx.lm), col="red")

xy.lm <- lm(x ~ y)
lines(predict(xy.lm), y, col="blue")

# so lm() depends on which variable is x and wich is y
# lm minimizes y distance (the error term is y-yhat)

#normalize means and cbind together
xyNorm <- cbind(x=x-mean(x), y=y-mean(y))
plot(xyNorm)

#covariance
xyCov <- cov(xyNorm)
eigenValues <- eigen(xyCov)$values
eigenVectors <- eigen(xyCov)$vectors
eigenValues
eigenVectors

plot(xyNorm, ylim=c(-200,200), xlim=c(-200,200))
lines(xyNorm[x], eigenVectors[2,1]/eigenVectors[1,1] * xyNorm[x])
lines(xyNorm[x], eigenVectors[2,2]/eigenVectors[1,2] * xyNorm[x])

# the largest eigenValue is the first one
# so that's our principal component.
# but the principal component is in normalized terms (mean=0)
# and we want it back in real terms like our starting data
# so let's denormalize it
plot(x,y)
lines(x, (eigenVectors[2,1]/eigenVectors[1,1] * xyNorm[x]) + mean(y))
# that looks right. line through the middle as expected

# what if we bring back our other two regressions?
lines(x, predict(yx.lm), col="red")
lines(predict(xy.lm), y, col="blue")

And Josh Ulrich provided an answer in under 20 minutes. Hive mind FTW!

http://stackoverflow.com/questions/3737165/drop-lines-from-actual-to-modeled-points-in-r/3737183#3737183

-JD

Thanks a lot!

I really enjoyed the blog post and thanks for sharing the code. I have been trying to figure out how to generate the orange (drop) lines on this plot(and below). I tried the segments() function as suggested by Josh Ulrich's posts...but keep going in circles. Any help is appreciated.