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Order variables according to canonical structure or other criteria

Source: R/varOrder.R
varOrder.Rd

The varOrder function implements some features of “effect ordering” (Friendly & Kwan (2003) for variables in a multivariate data display to make the displayed relationships more coherent.

This can be used in pairwise HE plots, scatterplot matrices, parallel coordinate plots, plots of multivariate means, and so forth.

For a numeric data frame, the most useful displays often order variables according to the angles of variable vectors in a 2D principal component analysis or biplot. For a multivariate linear model, the analog is to use the angles of the variable vectors in a 2D canonical discriminant biplot.

Usage

varOrder(x, ...)

# S3 method for mlm
varOrder(
  x,
  term,
  variables,
  type = c("can", "pc"),
  method = c("angles", "dim1", "dim2", "alphabet", "data", "colmean"),
  names = FALSE,
  descending = FALSE,
  ...
)

# S3 method for data.frame
varOrder(
  x,
  variables,
  method = c("angles", "dim1", "dim2", "alphabet", "data", "colmean"),
  names = FALSE,
  descending = FALSE,
  ...
)

# S3 method for default
varOrder(x, ...)

Arguments

x

A multivariate linear model or a numeric data frame

...

Arguments passed to methods

term

For the mlm method, one term in the model for which the canonical structure coefficients are found.

variables

indices or names of the variables to be ordered; defaults to all response variables an MLM or all numeric variables in a data frame.

type

For an MLM, type="can" uses the canonical structure coefficients for the given term; type="pc" uses the principal component variable eigenvectors.

method

One of c("angles", "dim1", "dim2", "alphabet", "data", "colmean") giving the effect ordering method.

"angles"

Orders variables according to the angles their vectors make with dimensions 1 and 2, counter-clockwise starting from the lower-left quadrant in a 2D biplot or candisc display.

"dim1"

Orders variables in increasing order of their coordinates on dimension 1

"dim2"

Orders variables in increasing order of their coordinates on dimension 2

"alphabet"

Orders variables alphabetically

"data"

Uses the order of the variables in the data frame or the list of responses in the MLM

"colmean"

Uses the order of the column means of the variables in the data frame or the list of responses in the MLM

names

logical; if TRUE the effect ordered names of the variables are returned; otherwise, their indices in variables are returned.

descending

If TRUE, the ordered result is reversed to a descending order.

Value

A vector of integer indices of the variables or a character vector of their names.

Methods (by class)

  • varOrder(mlm): "mlm" method.

  • varOrder(data.frame): "data.frame" method.

  • varOrder(default): "default" method.

References

Friendly, M. & Kwan, E. (2003). Effect Ordering for Data Displays, Computational Statistics and Data Analysis, 43, 509-539. doi:10.1016/S0167-9473(02)00290-6

Author

Michael Friendly

Examples


data(Wine, package="candisc")
Wine.mod <- lm(as.matrix(Wine[, -1]) ~ Cultivar, data=Wine)
Wine.can <- candisc(Wine.mod)
plot(Wine.can, ellipse=TRUE)
#> Vector scale factor set to 5.168


# pairs.mlm HE plot, variables in given order
pairs(Wine.mod, fill=TRUE, fill.alpha=.1, var.cex=1.5)


order <- varOrder(Wine.mod)
pairs(Wine.mod, variables=order, fill=TRUE, fill.alpha=.1, var.cex=1.5)