prcomp

From stats v3.3 by R-core R-core@R-project.org

Principal Components Analysis

Performs a principal components analysis on the given data matrix and returns the results as an object of class prcomp.

Keywords: multivariate

Usage

prcomp(x, ...)
## S3 method for class 'formula':
prcomp(formula, data = NULL, subset, na.action, \dots)
## S3 method for class 'default':
prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE,
       tol = NULL, \dots)
## S3 method for class 'prcomp':
predict(object, newdata, \dots)

Arguments

formula: a formula with no response variable, referring only to numeric variables.
data: an optional data frame (or similar: see model.frame) containing the variables in the formula formula. By default the variables are taken from environment(formula).
subset: an optional vector used to select rows (observations) of the data matrix x.
na.action: a function which indicates what should happen when the data contain NAs. The default is set by the na.action setting of options, and is na.fail if that is unset. The factory-fresh default is na.omit.
...: arguments passed to or from other methods. If x is a formula one might specify scale. or tol.
x: a numeric or complex matrix (or data frame) which provides the data for the principal components analysis.
retx: a logical value indicating whether the rotated variables should be returned.
center: a logical value indicating whether the variables should be shifted to be zero centered. Alternately, a vector of length equal the number of columns of x can be supplied. The value is passed to scale.
scale.: a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. The default is FALSE for consistency with S, but in general scaling is advisable. Alternatively, a vector of length equal the number of columns of x can be supplied. The value is passed to scale.
tol: a value indicating the magnitude below which components should be omitted. (Components are omitted if their standard deviations are less than or equal to tol times the standard deviation of the first component.) With the default null setting, no components are omitted. Other settings for tol could be tol = 0 or tol = sqrt(.Machine$double.eps), which would omit essentially constant components.
object: Object of class inheriting from "prcomp"
newdata: An optional data frame or matrix in which to look for variables with which to predict. If omitted, the scores are used. If the original fit used a formula or a data frame or a matrix with column names, newdata must contain columns with the same names. Otherwise it must contain the same number of columns, to be used in the same order.

Details

The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using eigen on the covariance matrix. This is generally the preferred method for numerical accuracy. The print method for these objects prints the results in a nice format and the plot method produces a scree plot.

Unlike princomp, variances are computed with the usual divisor $N - 1$.

Note that scale = TRUE cannot be used if there are zero or constant (for center = TRUE) variables.

Value

prcomp returns a list with class "prcomp" containing the following components:
sdevthe standard deviations of the principal components (i.e., the square roots of the eigenvalues of the covariance/correlation matrix, though the calculation is actually done with the singular values of the data matrix).
rotationthe matrix of variable loadings (i.e., a matrix whose columns contain the eigenvectors). The function princomp returns this in the element loadings.
xif retx is true the value of the rotated data (the centred (and scaled if requested) data multiplied by the rotation matrix) is returned. Hence, cov(x) is the diagonal matrix diag(sdev^2). For the formula method, napredict() is applied to handle the treatment of values omitted by the na.action.
center, scalethe centering and scaling used, or FALSE.

Note

The signs of the columns of the rotation matrix are arbitrary, and so may differ between different programs for PCA, and even between different builds of R.

concept

PCA

References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

Mardia, K. V., J. T. Kent, and J. M. Bibby (1979) Multivariate Analysis, London: Academic Press.

Venables, W. N. and B. D. Ripley (2002) Modern Applied Statistics with S, Springer-Verlag.

Examples

library(stats)

## signs are random
require(graphics)

## the variances of the variables in the
## USArrests data vary by orders of magnitude, so scaling is appropriate
prcomp(USArrests)  # inappropriate
prcomp(USArrests, scale = TRUE)
prcomp(~ Murder + Assault + Rape, data = USArrests, scale = TRUE)
plot(prcomp(USArrests))
summary(prcomp(USArrests, scale = TRUE))
biplot(prcomp(USArrests, scale = TRUE))

Documentation reproduced from package stats, version 3.3, License: Part of R 3.3

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