R: Canonical Correlation Analysis

cancor {candisc}

R Documentation

Canonical Correlation Analysis

Description

The function cancor generalizes and regularizes computation for canonical correlation analysis in a way conducive to visualization using methods in the heplots package.

The package provides the following display, extractor and plotting methods for "cancor" objects

print(), summary(): Print and summarise the CCA
coef(): Extract coefficients for X, Y, or both
scores(): Extract observation scores on the canonical variables
redundancy(): Redundancy analysis: proportion of variances of the variables in each set (X and Y) accounted for by the variables in the other set through the canonical variates
plot(): Plot pairs of canonical scores with a data ellipse and regression line
heplot(): HE plot of the Y canonical variables showing effects of the X variables and projections of the Y variables in this space.

As well, the function provides for observation weights, which may be useful in some situations, as well as providing a basis for robust methods in which potential outliers can be down-weighted.

Usage

cancor(x, ...)

## S3 method for class 'formula'
cancor(formula, data, subset, weights, na.rm = TRUE, method = "gensvd", ...)

## Default S3 method:
cancor(
  x,
  y,
  weights,
  X.names = colnames(x),
  Y.names = colnames(y),
  row.names = rownames(x),
  xcenter = TRUE,
  ycenter = TRUE,
  xscale = FALSE,
  yscale = FALSE,
  ndim = min(p, q),
  set.names = c("X", "Y"),
  prefix = c("Xcan", "Ycan"),
  na.rm = TRUE,
  use = if (na.rm) "complete" else "pairwise",
  method = "gensvd",
  ...
)

## S3 method for class 'cancor'
print(x, digits = max(getOption("digits") - 2, 3), ...)

## S3 method for class 'cancor'
summary(object, digits = max(getOption("digits") - 2, 3), ...)

## S3 method for class 'cancor'
scores(x, type = c("x", "y", "both", "list", "data.frame"), ...)

## S3 method for class 'cancor'
coef(object, type = c("x", "y", "both", "list"), standardize = FALSE, ...)

Arguments

`x`	Varies depending on method. For the `cancor.default` method, this should be a matrix or data.frame whose columns contain the X variables
`...`	Other arguments, passed to methods
`formula`	A two-sided formula of the form `cbind(y1, y2, y3, ...) ~ x1 + x2 + x3 + ...`
`data`	The data.frame within which the formula is evaluated
`subset`	an optional vector specifying a subset of observations to be used in the calculations.
`weights`	Observation weights. If supplied, this must be a vector of length equal to the number of observations in X and Y, typically within [0,1]. In that case, the variance-covariance matrices are computed using `cov.wt`, and the number of observations is taken as the number of non-zero weights.
`na.rm`	logical, determining whether observations with missing cases are excluded in the computation of the variance matrix of (X,Y). See Notes for details on missing data.
`method`	the method to be used for calculation; currently only `method = "gensvd"` is supported;
`y`	For the `cancor.default` method, a matrix or data.frame whose columns contain the Y variables
`X.names`, `Y.names`	Character vectors of names for the X and Y variables.
`row.names`	Observation names in `x`, `y`
`xcenter`, `ycenter`	logical. Center the X, Y variables? [not yet implemented]
`xscale`, `yscale`	logical. Scale the X, Y variables to unit variance? [not yet implemented]
`ndim`	Number of canonical dimensions to retain in the result, for scores, coefficients, etc.
`set.names`	A vector of two character strings, giving names for the collections of the X, Y variables.
`prefix`	A vector of two character strings, giving prefixes used to name the X and Y canonical variables, respectively.
`use`	argument passed to `var` determining how missing data are handled. Only the default, `use="complete"` is allowed when observation weights are supplied.
`digits`	Number of digits passed to `print` and `summary` methods
`object`	A `cancor` object for related methods.
`type`	For the `coef` method, the type of coefficients returned, one of `"x"`, `"y"`, `"both"`. For the `scores` method, the same list, or `"data.frame"`, which returns a data.frame containing the X and Y canonical scores.
`standardize`	For the `coef` method, whether coefficients should be standardized by dividing by the standard deviations of the X and Y variables.

Details

Canonical correlation analysis (CCA), as traditionally presented is used to identify and measure the associations between two sets of quantitative variables, X and Y. It is often used in the same situations for which a multivariate multiple regression analysis (MMRA) would be used.

However, CCA is is “symmetric” in that the sets X and Y have equivalent status, and the goal is to find orthogonal linear combinations of each having maximal (canonical) correlations. On the other hand, MMRA is “asymmetric”, in that the Y set is considered as responses, each one to be explained by separate linear combinations of the Xs.

Let \mathbf{Y}_{n \times p} and \mathbf{X}_{n \times q} be two sets of variables over which CCA is computed. We find canonical coefficients \mathbf{A}_{p \times k} and \mathbf{B}_{q \times k}, k=\min(p,q) such that the canonical variables

\mathbf{U}_{n \times k} = \mathbf{Y} \mathbf{A} \quad \text{and} \quad \mathbf{V}_{n \times k} = \mathbf{X} \mathbf{B}

have maximal, diagonal correlation structure. That is, the coefficients \mathbf{A} and \mathbf{B} are chosen such that the (canonical) correlations between each pair r_i = \text{cor}(\mathbf{u}_i, \mathbf{v}_i), i=1, 2, \dots , k are maximized and all other pairs are uncorrelated, r_{ij} = \text{cor}(\mathbf{u}_i, \mathbf{v}_j) = 0, i \ne j. Thus, all correlations between the X and Y variables are channeled through the correlations between the pairs of canonical variates.

For visualization using HE plots, it is most natural to consider plots representing the relations among the canonical variables for the Y variables in terms of a multivariate linear model predicting the Y canonical scores, using either the X variables or the X canonical scores as predictors. Such plots, using heplot.cancor provide a low-rank (1D, 2D, 3D) visualization of the relations between the two sets, and so are useful in cases when there are more than 2 or 3 variables in each of X and Y.

The connection between CCA and HE plots for MMRA models can be developed as follows. CCA can also be viewed as a principal component transformation of the predicted values of one set of variables from a regression on the other set of variables, in the metric of the error covariance matrix.

For example, regress the Y variables on the X variables, giving predicted values \hat{Y} = X (X'X)^{-1} X' Y and residuals R = Y - \hat{Y}. The error covariance matrix is E = R'R/(n-1). Choose a transformation Q that orthogonalizes the error covariance matrix to an identity, that is, (RQ)'(RQ) = Q' R' R Q = (n-1) I, and apply the same transformation to the predicted values to yield, say, Z = \hat{Y} Q. Then, a principal component analysis on the covariance matrix of Z gives eigenvalues of E^{-1} H, and so is equivalent to the MMRA analysis of lm(Y ~ X) statistically, but visualized here in canonical space.

Value

An object of class cancorr, a list with the following components:

`cancor`	Canonical correlations, i.e., the correlations between each canonical variate for the Y variables with the corresponding canonical variate for the X variables.
`names`	Names for various items, a list of 4 components: `X`, `Y`, `row.names`, `set.names`
`ndim`	Number of canonical dimensions extracted, `<= min(p,q)`
`dim`	Problem dimensions, a list of 3 components: `p` (number of X variables), `q` (number of Y variables), `n` (sample size)
`coef`	Canonical coefficients, a list of 2 components: `X`, `Y`
`scores`	Canonical variate scores, a list of 2 components: `X`, `Y`
`scores`	Canonical variate scores, a list of 2 components: `X` Canonical variate scores for the X variables `Y` Canonical variate scores for the Y variables
`X`	The matrix X
`Y`	The matrix Y
`weights`	Observation weights, if supplied, else `NULL`
`structure`	Structure correlations, a list of 4 components: `X.xscores`, `Y.xscores`, `X.yscores`, `Y.yscores`
`structure`	Structure correlations ("loadings"), a list of 4 components: X.xscores Structure correlations of the X variables with the Xcan canonical scores Y.xscores Structure correlations of the Y variables with the Xcan canonical scores X.yscores Structure correlations of the X variables with the Ycan canonical scores Y.yscores Structure correlations of the Y variables with the Ycan canonical scores The formula method also returns components `call` and `terms`

Methods (by class)

cancor(formula): "formula" method.
cancor(default): "default" method.

Methods (by generic)

print(cancor): print() method for "cancor" objects.
summary(cancor): summary() method for "cancor" objects.
scores(cancor): scores() method for "cancor" objects.
coef(cancor): coef() method for "cancor" objects.

Note

Not all features of CCA are presently implemented: standardized vs. raw scores, more flexible handling of missing data, other plot methods, ...

Author(s)

Michael Friendly

References

Gittins, R. (1985). Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer.

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

Examples


data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10])  # the PA tests
Y <- as.matrix(Rohwer[,3:5])   # the aptitude/ability variables

# visualize the correlation matrix using corrplot()
if (require(corrplot)) {
M <- cor(cbind(X,Y))
corrplot(M, method="ellipse", order="hclust", addrect=2, addCoef.col="black")
}


(cc <- cancor(X, Y, set.names=c("PA", "Ability")))

## Canonical correlation analysis of:
##       5   PA  variables:  n, s, ns, na, ss 
##   with        3   Ability  variables:  SAT, PPVT, Raven 
## 
##     CanR  CanRSQ   Eigen percent    cum                          scree
## 1 0.6703 0.44934 0.81599   77.30  77.30 ******************************
## 2 0.3837 0.14719 0.17260   16.35  93.65 ******                        
## 3 0.2506 0.06282 0.06704    6.35 100.00 **                            
## 
## Test of H0: The canonical correlations in the 
## current row and all that follow are zero
## 
##      CanR  WilksL      F df1   df2  p.value
## 1 0.67033 0.44011 3.8961  15 168.8 0.000006
## 2 0.38366 0.79923 1.8379   8 124.0 0.076076
## 3 0.25065 0.93718 1.4078   3  63.0 0.248814


# formula method
cc <- cancor(cbind(SAT, PPVT, Raven) ~  n + s + ns + na + ss, data=Rohwer, 
    set.names=c("PA", "Ability"))

# using observation weights
set.seed(12345)
wts <- sample(0:1, size=nrow(Rohwer), replace=TRUE, prob=c(.05, .95))
(ccw <- cancor(X, Y, set.names=c("PA", "Ability"), weights=wts) )

# show correlations of the canonical scores 
zapsmall(cor(scores(cc, type="x"), scores(cc, type="y")))

# standardized coefficients
coef(cc, type="both", standardize=TRUE)

# plot canonical scores
plot(cc, 
     smooth=TRUE, pch=16, id.n = 3)
text(-2, 1.5, paste("Can R =", round(cc$cancor[1], 3)), pos = 4)
plot(cc, which = 2,
     smooth=TRUE, pch=16, id.n = 3)
text(-2.2, 2.5, paste("Can R =", round(cc$cancor[2], 3)), pos = 4)

##################
data(schooldata)
##################

#fit the MMreg model
school.mod <- lm(cbind(reading, mathematics, selfesteem) ~ 
education + occupation + visit + counseling + teacher, data=schooldata)
car::Anova(school.mod)
pairs(school.mod)

# canonical correlation analysis
school.cc <- cancor(cbind(reading, mathematics, selfesteem) ~ 
education + occupation + visit + counseling + teacher, data=schooldata)
school.cc
heplot(school.cc, xpd=TRUE, scale=0.3)

[Package candisc version 0.9.0 Index]