princomp

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Principal Components Analysis

princomp performs a principal components analysis on the given numeric data matrix and returns the results as an object of class princomp.

Keywords
multivariate
Usage
princomp(x, ...)

## S3 method for class 'formula': princomp(formula, data = NULL, subset, na.action, \dots)

## S3 method for class 'default': princomp(x, cor = FALSE, scores = TRUE, covmat = NULL, subset = rep_len(TRUE, nrow(as.matrix(x))), ...)

## S3 method for class 'princomp': 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.
x
a numeric matrix or data frame which provides the data for the principal components analysis.
cor
a logical value indicating whether the calculation should use the correlation matrix or the covariance matrix. (The correlation matrix can only be used if there are no constant variables.)
scores
a logical value indicating whether the score on each principal component should be calculated.
covmat
a covariance matrix, or a covariance list as returned by cov.wt (and cov.mve or cov.mcd from package MASS). If supplied, this is used rather than the covariance matrix of x.
...
arguments passed to or from other methods. If x is a formula one might specify cor or scores.
object
Object of class inheriting from "princomp"
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

princomp is a generic function with "formula" and "default" methods.

The calculation is done using eigen on the correlation or covariance matrix, as determined by cor. This is done for compatibility with the S-PLUS result. A preferred method of calculation is to use svd on x, as is done in prcomp.

Note that the default calculation uses divisor N for the covariance matrix.

The print method for these objects prints the results in a nice format and the plot method produces a scree plot (screeplot). There is also a biplot method.

If x is a formula then the standard NA-handling is applied to the scores (if requested): see napredict.

princomp only handles so-called R-mode PCA, that is feature extraction of variables. If a data matrix is supplied (possibly via a formula) it is required that there are at least as many units as variables. For Q-mode PCA use prcomp.

Value

  • princomp returns a list with class "princomp" containing the following components:
  • sdevthe standard deviations of the principal components.
  • loadingsthe matrix of variable loadings (i.e., a matrix whose columns contain the eigenvectors). This is of class "loadings": see loadings for its print method.
  • centerthe means that were subtracted.
  • scalethe scalings applied to each variable.
  • n.obsthe number of observations.
  • scoresif scores = TRUE, the scores of the supplied data on the principal components. These are non-null only if x was supplied, and if covmat was also supplied if it was a covariance list. For the formula method, napredict() is applied to handle the treatment of values omitted by the na.action.
  • callthe matched call.
  • na.actionIf relevant.

Note

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

concept

PCA

References

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.

See Also

summary.princomp, screeplot, biplot.princomp, prcomp, cor, cov, eigen.

Aliases
  • princomp
  • princomp.formula
  • princomp.default
  • plot.princomp
  • print.princomp
  • predict.princomp
Examples
library(stats) require(graphics) ## The variances of the variables in the ## USArrests data vary by orders of magnitude, so scaling is appropriate (pc.cr <- princomp(USArrests)) # inappropriate princomp(USArrests, cor = TRUE) # =^= prcomp(USArrests, scale=TRUE) ## Similar, but different: ## The standard deviations differ by a factor of sqrt(49/50) summary(pc.cr <- princomp(USArrests, cor = TRUE)) loadings(pc.cr) # note that blank entries are small but not zero ## The signs of the columns are arbitrary plot(pc.cr) # shows a screeplot. biplot(pc.cr) ## Formula interface princomp(~ ., data = USArrests, cor = TRUE) ## NA-handling USArrests[1, 2] <- NA pc.cr <- princomp(~ Murder + Assault + UrbanPop, data = USArrests, na.action = na.exclude, cor = TRUE) pc.cr$scores[1:5, ] ## (Simple) Robust PCA: ## Classical: (pc.cl <- princomp(stackloss)) ## Robust: (pc.rob <- princomp(stackloss, covmat = MASS::cov.rob(stackloss)))
Documentation reproduced from package stats, version 3.3, License: Part of R 3.3

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