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Principal Components Analysis

Source: R/AllGenerics.R, R/pca.R
pca.Rd

Computes a principal components analysis based on the singular value decomposition.

Usage

pca(object, ...)

# S4 method for data.frame
pca(
  object,
  center = TRUE,
  scale = TRUE,
  rank = NULL,
  sup_row = NULL,
  sup_col = NULL,
  weight_row = NULL,
  weight_col = NULL
)

# S4 method for matrix
pca(
  object,
  center = TRUE,
  scale = TRUE,
  rank = NULL,
  sup_row = NULL,
  sup_col = NULL,
  weight_row = NULL,
  weight_col = NULL
)

Arguments

object

A \(m \times p\) numeric matrix or a data.frame.

...

Currently not used.

center

A logical scalar: should the variables be shifted to be zero centered?

scale

A logical scalar: should the variables be scaled to unit variance?

rank

An integer value specifying the maximal number of components to be kept in the results. If NULL (the default), \(p - 1\) components will be returned.

sup_row

A vector specifying the indices of the supplementary rows.

sup_col

A vector specifying the indices of the supplementary columns.

weight_row

A numeric vector specifying the active row (individual) weights. If NULL (the default), uniform weights are used. Row weights are internally normalized to sum 1

weight_col

A numeric vector specifying the active column (variable) weights. If NULL (the default), uniform weights (1) are used.

Value

A PCA object.

References

Lebart, L., Piron, M. and Morineau, A. Statistique exploratoire multidimensionnelle: visualisation et inférence en fouille de données. Paris: Dunod, 2006.

See also

svd()

Other multivariate analysis: ca(), mca(), predict()

Author

N. Frerebeau

Examples

## Load data
data("iris")

## Compute principal components analysis
X <- pca(iris, scale = TRUE, sup_row = sample(150, 10), sup_col = 2)
#> 1 qualitative variable was removed: Species.

## Get row coordinates
head(get_coordinates(X, margin = 1))
#>          F1          F2  .sup
#> 1 -2.071210  0.30628230 FALSE
#> 2 -2.205873  0.11088123 FALSE
#> 3 -2.374237 -0.07036696 FALSE
#> 4 -2.374166 -0.19637325 FALSE
#> 5 -2.138542  0.20858176 FALSE
#> 6 -1.613606  0.41615798 FALSE

## Get column coordinates
head(get_coordinates(X, margin = 2))
#>                      F1         F2  .sup
#> Sepal.Length  0.9306562  0.3647468 FALSE
#> Petal.Length  0.9849858 -0.1117255 FALSE
#> Petal.Width   0.9655250 -0.2375970 FALSE
#> Sepal.Width  -0.3327152  0.4554679  TRUE

## Get correlations between variables and dimensions
head(get_correlations(X))
#>                      F1         F2  .sup
#> Sepal.Length  0.9306562  0.3647468 FALSE
#> Petal.Length  0.9849858 -0.1117255 FALSE
#> Petal.Width   0.9655250 -0.2375970 FALSE
#> Sepal.Width  -0.3327152  0.4554679  TRUE

## Get eigenvalues
get_eigenvalues(X)
#>    eigenvalues  variance cumulative
#> F1   2.7685566 93.200706   93.20071
#> F2   0.2019752  6.799294  100.00000