registry_for_seriaiton_methods {seriation}

Registry for Seriation Methods

Description

A registry to manage methods used by seriate().

Usage

registry_seriate

list_seriation_methods(kind, names_only = TRUE)

get_seriation_method(kind, name)

set_seriation_method(
  kind,
  name,
  definition,
  description = NULL,
  control = list(),
  randomized = FALSE,
  optimizes = NA_character_,
  verbose = FALSE,
  ...
)

## S3 method for class 'seriation_method'
print(x, ...)

Arguments

kind

the data type the method works on. For example, "dist", "matrix" or "array". If missing, then methods for any type are shown.

names_only

logical; return only the method name. FALSE returns also the method descriptions.

name

the name for the method used to refer to the method in seriate().

definition

a function containing the method's code.

description

a description of the method. For example, a long name.

control

a list with control arguments and default values.

randomized

logical; does the algorithm use randomization and re-running the algorithm several times will lead to different results (see: seriate_rep()).

optimizes

what criterion does the algorithm try to optimize (see: list_criterion_methods()).

verbose

logical; print a message when a new method is registered.

...

further information that is stored for the method in the registry.

x

an object of class "seriation_method" to be printed.

Format

An object of class seriation_registry (inherits from registry) of length 57.

Details

The functions below are convenience function for the registry registry_seriate.

list_seriation_method() lists all available methods for a given data type (kind) (e.g., "dist", "matrix"). The result is a vector of character strings with the method names that can be used in function seriate(). If kind is missing, then a list of methods is returned.

get_seriation_method() returns detailed information for a given method in form of an object of class "seriation_method". The information includes a description, parameters and the implementing function.

With set_seriation_method() new seriation methods can be added by the user. The implementing function (definition) needs to have the formal arguments x, control and, for arrays and matrices margin, where x is the data object and control contains a list with additional information for the method passed on from seriate(), and margin is a vector specifying what dimensions should be seriated. The implementation has to return a list of objects which can be coerced into ser_permutation_vector objects (e.g., integer vectors). The elements in the list have to be in corresponding order to the dimensions of x.

Value

• list_seriation_method() result is a vector of character strings with the names of the methods. These names are used for methods in seriate().

• get_seriation_method() returns a given method in form of an object of class "seriation_method".

Author(s)

Michael Hahsler

See Also

This registry uses registry::registry.

Other seriation: register_DendSer(), register_GA(), register_optics(), register_smacof(), register_tsne(), register_umap(), seriate(), seriate_best()

Examples

# Registry
registry_seriate

# List all seriation methods by type
list_seriation_methods()

# List methods for matrix seriation
list_seriation_methods("matrix")

get_seriation_method(name = "BEA")

# Example for defining a new seriation method (reverse identity function for matrix)

# 1. Create the seriation method
#    (with margin since it is for arrays; NA means no seriation is applied)
seriation_method_reverse <- function(x, control = NULL,
                                     margin = seq_along(dim(x))) {
 lapply(seq_along(dim(x)), function(i)
   if (i %in% margin) rev(seq(dim(x)[i]))
   else NA)
}

# 2. Register new method
set_seriation_method("matrix", "Reverse", seriation_method_reverse,
    description = "Reverse identity order", control = list())

list_seriation_methods("matrix")
get_seriation_method("matrix", "reverse")

# 3. Use the new seriation methods
seriate(matrix(1:12, ncol=3), "reverse")