InflMat-class: Influence Matrix

In guenardg/MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps

Influence Matrix

Description

Functions and methods calculate and manipulate graph influence matrix.

Usage

InflMat(x)

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

## S3 method for class 'InflMat'
nedge(x)

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

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

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

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

Arguments

x	A graph-class or InflMat-class object.
...	Further arguments to be passed internally to other functions or methods.
value	A vector or data.frame containing the values to be given to the InflMat-class object.

Value

The returned value depends on the function:

InflMat

A binary influence matrix of the graph with as many rows as its number of vertices and as many columns as its number of edges.

Functions

• InflMat(): Influence Matrix

  Calculates the influence matrix of a phylogenetic graph. The influence matrix is a binary matrix whose rows and columns correspond to the vertices and edges of the phylogenetic graph, respectively, and whose elements describe whether a given edge had been taken by any ancestors of a vertex (representing extinct of extant species) during evolution (value = 1) or not (value = 0).

• print(InflMat): Print Graph

  A print method for InflMat-class objects.

• nedge(InflMat): Number of Edges

  Get the number of edges in an InflMat-class object.

• edge(InflMat): Edge Extraction

  Extracts the edges of an InflMat-class object.

• edge(InflMat) <- value: Edge Assignment

  Assigns edges to an InflMat-class object.

• edgenames(InflMat): Edge Names Extraction

  Extracts the edge names of an InflMat-class object.

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

  Assigns edge names to an InflMat-class object.

Author(s)

Guillaume Guénard [aut, cre] (<https://orcid.org/0000-0003-0761-3072>), Pierre Legendre [ctb] (<https://orcid.org/0000-0002-3838-3305>) – Maintainer: Guillaume Guénard <[e-mail]>

References

Guénard, G., Legendre, P., and Peres-Neto, P. 2013. Phylogenetic eigenvector maps: a framework to model and predict species traits. Methods in Ecology and Evolution. 4: 1120–1131

Makarenkov, V., Legendre, L. & Desdevise, Y. 2004. Modelling phylogenetic relationships using reticulated networks. Zoologica Scripta 33: 89–96

Blanchet, F. G., Legendre, P. & Borcard, D. 2008. Modelling directional spatial processes in ecological data. Ecological Modelling 215: 325–336

See Also

PEM-class PEM-functions

Examples

 ## Exemplary graph:
data.frame(
  species = as.logical(c(0,0,1,0,0,0,0,0,0,0,1,1,1)),
  type = c(2,2,3,1,2,2,2,2,2,2,3,3,3),
  x = c(1,3,4,0,1.67,4,1,1.33,2.33,3.33,4.33,4,5),
  y = c(1,1,1,0,0.5,0,-1,0,0,-0.5,-1,-0.5,-0.5),
  row.names = sprintf("V%d",1:13)
) %>%
  st_as_sf(
    coords=c("x","y"),
    crs = NA
  ) %>%
  graph %>%
  add.edge(
    from = c(1,2,1,5,4,4,5,9,4,8,9,4,7,7,6,6,9,10,10),
    to = c(2,3,5,2,1,5,9,2,8,9,6,7,8,9,3,13,10,12,11),
    data = data.frame(
      distance = c(4.2,4.7,3.9,3.0,3.6,2.7,4.4,3.4,3.6,3.3,
                   4.8,3.2,3.5,4.4,2.5,3.4,4.3,3.1,2.2),
      row.names = sprintf("E%d",1:19)
    )
  ) -> x

## Calculation of the influence matrix:
y <- InflMat(x)

## Obtain the number of edges:
nedge(y)

## Obtain the edge names:
edgenames(y)

## Obtain the edge data frame:
edge(y)

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