MPSEM-generics: Generic Function (Methods)

In guenardg/MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps

Generic Function (Methods)

Description

A set of non-standard generic functions used by package MPSEM.

Usage

nedge(x)

edge(x)

edge(x) <- value

edgenames(x)

edgenames(x) <- value

geometry(x)

geometry(x) <- value

labels(object) <- value

as.graph(x, ...)

locate(x, target, ...)

evolution.model(object, y, ..., x = NULL)

## S3 method for class 'graph'
edge(x)

## S3 replacement method for class 'graph'
edge(x) <- value

## S3 method for class 'graph'
edgenames(x)

## S3 replacement method for class 'graph'
edgenames(x) <- value

Arguments

x	A graph-class object or an object of any class that can be converted into a graph-class object, or a numeric vector or numeric matrix of auxiliary trait(s) to help in estimating the parameters of the trait evolution model. In the second case, the default is NULL, which entails that no auxiliary trait is used.
value	A two-column data.frame giving the coordinates (e.g., x, y, z) to be applied to the graph-class object.
object	A graph-class object or an object of any class that can be converted into a graph-class object.
...	Further arguments of the particular conversion method that is being implemented.
target	A numeric or character vector specifying one or more target species in graph x.
y	A numeric vector or numeric matrix of trait(s) against which to estimate the parameters of the trait evolution model.

Value

The return value depends on the implementation of the methods for a particular S3 class.

Functions

• nedge(): Number of Edges

  A method to access the number of edges

• edge(): Edge Extraction

  A method to extract edges from an object.

• edge(x) <- value: Edge Assignment

  A method to assign edges to an object.

• edgenames(): Edge Names Extraction

  A method to extract edge names from an object.

• edgenames(x) <- value: Edge Assignment

  A method to assign edges to an object.

• geometry(): Geometry Extraction

  A method to obtain an object's geometry.

• geometry(x) <- value: Geometry Assignment

  A method to assign a geometry to an object.

• labels(object) <- value: Labels Assignment

  A method to assign labels to an object.

• as.graph(): Graph-class Conversion

  A method to convert an object into a graph-class object.

• locate(): Locate Targets

  A method to locate a set of targets species from a graph-class object.

• evolution.model(): Estimate Evolution Model

  Estimate the parameters of an evolution model on a PEM2-class object.

• edge(graph): Edge Extraction

  Extracts the edges of a graph-class object.

• edge(graph) <- value: Edge Assignment

  Assigns edges to a graph-class object.

• edgenames(graph): Edge Names Extraction

  Extracts the edge names of a graph-class object.

• edgenames(graph) <- value: Edge Names Assignment

  Assigns edge names to a graph-class object.

guenardg/MPSEM documentation built on April 14, 2025, 3:53 p.m.