seriation (version 1.3.2)

seriation_methods: Registry for Seriation Methods

Description

A registry to manage methods for seriation.

Usage

list_seriation_methods(kind)
get_seriation_method(kind, name)
set_seriation_method(kind, name, definition, description = NULL, control = list(), ...)
## deprecated
show_seriation_methods(kind)

Arguments

kind

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

name

a short 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.

...

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

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). The result is a vector of character strings with the short names of the methods. If kind is missing, then a list of methods is returned.

get_seriation_method() returns information (including the implementing function) about a given method in form of an object of class "seriation_method".

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, where x is the data object and control contains a list with additional information for the method passed on from seriate(). 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.

Examples

# NOT RUN {
# 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
seriation_method_reverse <- function(x, control) {
   # return a list of order vectors, one for each dimension
   list(seq(nrow(x), 1), seq(ncol(x), 1))
}

# 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")
# }