I am constantly getting this error. I am sure the matrix does not have any non-numeric entries. I also tried imputing the matrix, did not work.
Anyone know what the error might be?
fileUrl <- "https://dl.dropboxusercontent.com/u/76668273/kdd.csv";
download.file(fileUrl,destfile="./kdd.csv",method="curl");
kddtrain <- read.csv("kdd.csv");
kddnumeric <- kddtrain[,sapply(kddtrain,is.numeric)];
kddmatrix <- as.matrix(kddnumeric);
svd1 <- svd(scale(kddmatrix));
You have columns composed of all zeroes. Using scale
on a column of all zeroes returns a column composed of NaN
. To solve this, remove columns where you have all zeroes (svd
will not reveal anything new about them), or replace NaN
columns with zero after using scale
.
Reproducible example:
mat <- matrix(c(1,2,3,0,0,0,2,4,6,5,12,13),nrow = 3)
# [,1] [,2] [,3] [,4]
# [1,] 1 0 2 5
# [2,] 2 0 4 12
# [3,] 3 0 6 13
scale(mat)
# [,1] [,2] [,3] [,4]
# [1,] -1 NaN -1 -1.1470787
# [2,] 0 NaN 0 0.4588315
# [3,] 1 NaN 1 0.6882472
# attr(,"scaled:center")
# [1] 2 0 4 10
# attr(,"scaled:scale")
# [1] 1.000000 0.000000 2.000000 4.358899
svd(mat) #fine
svd(scale(mat)) # not fine