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rconstants

Removal of constant columns in R

I was using the prcomp function when I received this error

Error in prcomp.default(x, ...) : 
cannot rescale a constant/zero column to unit variance

I know I can scan my data manually but is there any function or command in R that can help me remove these constant variables? I know this is a very simple task, but I have never been across any function that does this.

Thanks,

Solution

  • The problem here is that your column variance is equal to zero. You can check which column of a data frame is constant this way, for example :

    df <- data.frame(x=1:5, y=rep(1,5))
df
#   x y
# 1 1 1
# 2 2 1
# 3 3 1
# 4 4 1
# 5 5 1

# Supply names of columns that have 0 variance
names(df[, sapply(df, function(v) var(v, na.rm=TRUE)==0)])
# [1] "y"

    So if you want to exclude these columns, you can use :

    df[,sapply(df, function(v) var(v, na.rm=TRUE)!=0)]

    EDIT : In fact it is simpler to use apply instead. Something like this :

    df[,apply(df, 2, var, na.rm=TRUE) != 0]