seriation (version 1.5.4)

get_order: Extracting Order Information from a Permutation Object

Description

Method to get the order information from an object of class ser_permutation or ser_permutation_vector. Order information can be extracted as a permutation vector, a vector containing each object's rank or a permutation matrix.

Usage

get_order(x, ...)
# S3 method for ser_permutation_vector
get_order(x, ...)
# S3 method for ser_permutation
get_order(x, dim = 1, ...)
# S3 method for hclust
get_order(x, ...)
# S3 method for dendrogram
get_order(x, ...)
# S3 method for integer
get_order(x, ...)
# S3 method for numeric
get_order(x, ...)
get_rank(x, ...)
get_permutation_matrix(x, ...)

Value

Returns an integer permutation vector/a permutation matrix.

Arguments

x

an object of class ser_permutation or ser_permutation_vector.

...

further arguments are ignored for get_order(). For get_rank() and for get_permutation_matrix() the additional arguments are passed on to get_order() (e.g., as dim).

dim

order information for which dimension should be returned?

Author

Michael Hahsler

Details

get_order() returns the permutation as an integer vector which arranges the objects in the seriation order. That is, a vector with the index of the first, second, \(..., n\)-th object in the order defined by the permutation. These permutation vectors can directly be used to reorder objects using subsetting with "[". Note: In seriation we usually use these order-based permutation vectors. Note on names: While R's order() returns an unnamed vector, get_order() returns names (if available). The names are the object label corresponding to the index at that position. Therefore, the names in the order are in the order after the permutation.

get_rank() returns the seriation as an integer vector containing the rank/position for each objects after the permutation is applied. That is, a vector with the position of the first, second, \(..., n\)-th object after permutation. Note: Use order() to convert ranks back to an order.

get_permutation_matrix() returns a \(n \times n\) permutation matrix.

See Also

Other permutation: permutation_vector2matrix(), permute(), ser_dist(), ser_permutation_vector(), ser_permutation()

Examples

## create a random ser_permutation_vector
## Note that ser_permutation_vector is a single permutation vector
x <- structure(1:10, names = paste0("X", 1:10))
o <- sample(x)
o

p <- ser_permutation_vector(o)
p

get_order(p)
get_rank(p)
get_permutation_matrix(p)

## reorder objects using subsetting, the provided permute function or by
## multiplying the with the permutation matrix. We use here
x[get_order(p)]
permute(x, p)
drop(get_permutation_matrix(p) %*%  x)

## ser_permutation contains one permutation vector for each dimension
p2 <- ser_permutation(p, sample(5))
p2

get_order(p2, dim = 2)
get_rank(p2, dim = 2)
get_permutation_matrix(p2, dim = 2)