Identification of near zero variance predictors
Description
nearZeroVar
diagnoses predictors that have one unique value (i.e. are
zero variance predictors) or predictors that are have both of the following
characteristics: they have very few unique values relative to the number of
samples and the ratio of the frequency of the most common value to the
frequency of the second most common value is large. checkConditionalX
looks at the distribution of the columns of x
conditioned on the
levels of y
and identifies columns of x
that are sparse within
groups of y
.
Usage
1 2 3 4 5 6 
Arguments
x 
a numeric vector or matrix, or a data frame with all numeric data 
freqCut 
the cutoff for the ratio of the most common value to the second most common value 
uniqueCut 
the cutoff for the percentage of distinct values out of the number of total samples 
saveMetrics 
a logical. If false, the positions of the zero or nearzero predictors is returned. If true, a data frame with predictor information is returned. 
names 
a logical. If false, column indexes are returned. If true, column names are returned. 
foreach 
should the foreach package be used for the
computations? If 
allowParallel 
should the parallel processing via the foreach
package be used for the computations? If 
y 
a factor vector with at least two levels 
index 
a list. Each element corresponds to the training set samples in

Details
For example, an example of near zero variance predictor is one that, for 1000 samples, has two distinct values and 999 of them are a single value.
To be flagged, first the frequency of the most prevalent value over the
second most frequent value (called the “frequency ratio”) must be above
freqCut
. Secondly, the “percent of unique values,” the number of
unique values divided by the total number of samples (times 100), must also
be below uniqueCut
.
In the above example, the frequency ratio is 999 and the unique value percentage is 0.0001.
Checking the conditional distribution of x
may be needed for some
models, such as naive Bayes where the conditional distributions should have
at least one data point within a class.
nzv
is the original version of the function.
Value
For nearZeroVar
: if saveMetrics = FALSE
, a vector of
integers corresponding to the column positions of the problematic
predictors. If saveMetrics = TRUE
, a data frame with columns:
freqRatio 
the ratio of frequencies for the most common value over the second most common value 
percentUnique 
the percentage of unique data points out of the total number of data points 
zeroVar 
a vector of logicals for whether the predictor has only one distinct value 
nzv

a vector of logicals for whether the predictor is a near zero variance predictor 
For checkResamples
or checkConditionalX
, a vector of column
indicators for predictors with empty conditional distributions in at least
one class of y
.
Author(s)
Max Kuhn, with speed improvements to nearZeroVar by Allan Engelhardt
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  nearZeroVar(iris[, 5], saveMetrics = TRUE)
data(BloodBrain)
nearZeroVar(bbbDescr)
nearZeroVar(bbbDescr, names = TRUE)
set.seed(1)
classes < factor(rep(letters[1:3], each = 30))
x < data.frame(x1 = rep(c(0, 1), 45),
x2 = c(rep(0, 10), rep(1, 80)))
lapply(x, table, y = classes)
checkConditionalX(x, classes)
folds < createFolds(classes, k = 3, returnTrain = TRUE)
x$x3 < x$x1
x$x3[folds[[1]]] < 0
checkResamples(folds, x, classes)
