scale.datacggm {cglasso}R Documentation

Scaling and Centering of “datacggm” Objects

Description

The method function scale.datacggm centers and/or scales the columns of a numeric matrix storaged in a ‘datacggm’ object.

Usage

## S3 method for class 'datacggm'
scale(x, center = TRUE, scale = TRUE)

Arguments

x

an object of class ‘datacggm’.

center

either a logical value or numeric-alike vector of length equal to the number of columns of x, where ‘numeric-alike’ means that as.numeric(.) will be applied successfully if is.numeric(.) is not true.

scale

either a logical value or a numeric-alike vector of length equal to the number of columns of x.

Details

The value of center determines how column centering is performed. If center is a numeric-alike vector with length equal to the number of columns of x, then each column of x has the corresponding value from center subtracted from it. If center is TRUE then centering is done by subtracting the column means (omitting censoring values) of x$X from their corresponding columns, and if center is FALSE, no centering is done. The same is done for x$lo and x$up.

The value of scale determines how column scaling is performed (after centering). If scale is a numeric-alike vector with length equal to the number of columns of x, then each column of x$X is divided by the corresponding value from scale. If scale is TRUE then scaling is done by dividing the (centered) columns of x$X by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done. The same is done for x$lo and x$up.

The root-mean-square for a (possibly centered) column is defined as sqrt(sum(x^2)/(n-1)), where x is a vector of observed values and n is the number of observed values. In the case center = TRUE, this is the same as the standard deviation, but in general it is not. (To scale by the standard deviations without centering, use scale(x, center = FALSE, scale = apply(x, 2, sd, na.rm = TRUE)).)

Value

The method function ‘scale.datacggm’ returns an object of class datacggm. The numeric centering and scalings used (if any) are returned as attributes "scaled:center" and "scaled:scale".

See Also

datacggm.

Examples

set.seed(123)

n <- 100L
p <- 3L
mu <- rep(1L, p)
X <- rdatacggm(n = n, mu = mu, probr = 0.05, probl = 0.05)
centered.X <- scale(X)
centered.X
attr(centered.X, "scaled:center")
attr(centered.X, "scaled:scale")

[Package cglasso version 1.1.1 Index]