plot-abn: Plot an ABN graphic
In abn: Modelling Multivariate Data with Additive Bayesian Networks

plotabn

R Documentation

Plot an ABN graphic

Description

Plot an ABN DAG using formula statement or a matrix in using Rgraphviz through the graphAM class.

Usage

plotAbn(dag, data.dists=NULL, markov.blanket.node=NULL, fitted.values=NULL,
        digits=2, edge.strength=NULL, edge.strength.lwd=5, edge.direction="pc",
        edge.color="black", edge.linetype="solid", edge.arrowsize=0.6,
        edge.fontsize=node.fontsize, node.fontsize=12, node.fillcolor=c(
        "lightblue", "brown3", "chartreuse3"), node.fillcolor.list=NULL,
        node.shape=c("circle", "box", "ellipse", "diamond"), plot=TRUE , ...)

Arguments

`dag`	a matrix or a formula statement (see details for format) defining the network structure, a Directed Acyclic Graph (DAG). Note that rownames must be set or given in `data.dists`.
`data.dists`	a named list giving the distribution for each node in the network, see details.
`markov.blanket.node`	name of variables to display its Markov blanket.
`fitted.values`	modes or coefficents outputted from `fitAbn`.
`digits`	number of digits to display the `fitted.values`.
`edge.strength`	a named matrix containing evaluations of edge strength which will change the arcs width (could be Mutual information, p-values, number of bootstrap retrieve samples or the outcome of the `link.strength`).
`edge.strength.lwd`	maximum line width for `edge.strength`.
`edge.direction`	character giving the direction in which arcs should be plotted, `pc` (parent to child) or `cp` (child to parent) or `undirected`.
`node.fillcolor`	the colour of the node. Second and third element is used for the Markov blanket and node of the Markov blanket.
`node.shape`	the shape of the nodes according the Gaussian, binomial, Poisson and multinomial distributions.
`edge.color`	the colour of the edge.
`edge.linetype`	the linetype of the edge. Defaults to `"solid"`. Valid values are the same as for the R's base graphic parameter `lty`.
`edge.arrowsize`	the thickness of the arrows. Not relevant if `arc.strength` is provided.
`node.fontsize`	the font size of the nodes names.
`edge.fontsize`	the font size of the arcs fitted values.
`plot`	logical variable, if set to `TRUE` then the graph is plotted.
`node.fillcolor.list`	the list of node that should be coloured.
`...`	arguments passed to the plotting function.

Details

By default binomial nodes are squares, multinoial nodes are empty, Gaussian nodes are circles and poison nodes are ellipses.

The dag can be provided using a formula statement (similar to glm). A typical formula is ~ node1|parent1:parent2 + node2:node3|parent3.

The construction is based on the graph package. Properties of the graph can be changend after the construction, see ‘Examples’.

Value

A rendered graph, if plot=TRUE. The graphAM object is returned invisibly.

Author(s)

Gilles Kratzer, Reinhard Furrer

References

Further information about abn can be found at:
http://r-bayesian-networks.org

Examples

#Define distribution list
dist <- list(a="gaussian", b="gaussian", c="gaussian", d="gaussian", e="binomial", f="binomial")

#Define a matrix formulation
edge.strength <- matrix(c(0,0.5,0.5,0.7,0.1,0,
                              0,0,0.3,0.1,0,0.8,
                              0,0,0,0.35,0.66,0,
                              0,0,0,0,0.9,0,
                              0,0,0,0,0,0.8,
                              0,0,0,0,0,0),nrow = 6L, ncol = 6L, byrow = TRUE)

## Naming of the matrix
colnames(edge.strength) <- rownames(edge.strength) <- names(dist)

## Plot form a matrix
plotAbn(dag = edge.strength, data.dists = dist)

## Edge strength
plotAbn(dag = ~a|b:c:d:e+b|c:d:f+c|d:e+d|e+e|f, data.dists = dist, edge.strength = edge.strength)

## Plot from a formula for a different DAG!
plotAbn(dag = ~a|b:c:e+b|c:d:f+e|f, data.dists = dist)

## Markov blanket
plotAbn(dag = ~a|b:c:e+b|c:d:f+e|f, data.dists = dist, markov.blanket.node = "e")

## Change col for all edges
tmp <- plotAbn(dag = ~a|b:c:e+b|c:d:f+e|f, data.dists = dist, plot=FALSE)
graph::edgeRenderInfo(tmp) <- list(col="blue")
Rgraphviz::renderGraph(tmp)

## Change lty for individual ones. Named vector is necessary
tmp <- plotAbn(dag = ~a|b:c:e+b|c:d:f+e|f, data.dists = dist, plot=FALSE)
edgelty <- rep(c("solid","dotted"), c(6,1))
names(edgelty) <- names( graph::edgeRenderInfo(tmp, "col"))
graph::edgeRenderInfo(tmp) <- list(lty=edgelty)
Rgraphviz::renderGraph(tmp)

abn documentation built on April 25, 2022, 9:06 a.m.