R: Arc strength plot

strength.plot {bnlearn} | R Documentation

## Arc strength plot

### Description

Plot a Bayesian network and format its arcs according to the strength of the dependencies they represent. Requires the Rgraphviz package.

### Usage

    strength.plot(x, strength, threshold, cutpoints, highlight = NULL, groups,
      layout = "dot", shape = "circle", main = NULL, sub = NULL, render = TRUE,
      debug = FALSE)

### Arguments

`x` | an object of class `bn`.
`strength` | an object of class `bn.strength` computed from the object of class `bn` corresponding to the `x` argument.
`threshold` | a numeric value. See below.
`cutpoints` | an array of numeric values. See below.
`highlight` | a list, see `graphviz.plot` for details.
`groups` | a list of character vectors, representing groups of node labels of nodes that should be plotted close to each other.
`layout` | a character string, the layout argument that will be passed to Rgraphviz. Possible values are `dots`, `neato`, `twopi`, `circo` and `fdp`. See Rgraphviz documentation for details.
`shape` | a character string, the shape of the nodes. Can be `circle`, `ellipse` or `rectangle`.
`main` | a character string, the main title of the graph. It's plotted at the top of the graph.
`sub` | a character string, a subtitle which is plotted at the bottom of the graph.
`debug` | a boolean value. If `TRUE` a lot of debugging output is printed; otherwise the function is completely silent.
`render` | a logical value. If `TRUE`, `strength.plot()` actually draws the figure in addition to returning the corresponding `graph` object. If `FALSE`, no figure is produced.

### Details

The `threshold` argument is used to determine which arcs are supported strongly enough by the data to be deemed significant:

- if arc strengths have been computed using conditional independence tests, any strength coefficient (which is the p-value of the test) lesser than or equal to the threshold is considered significant.

- if arc strengths have been computed using network scores, any strength coefficient (which is the increase/decrease of the network score caused by the removal of the arc) lesser than the threshold is considered significant.

- if arc strengths have been computed using bootstrap or using Bayes factors, any strength coefficient (which can be interpreted as a probability for inclusion) greater or equal than the threshold is considered significant.

The default value is the value of the `strength` attribute of the `bn.strength` object passed via the `strength` argument.

Non-significant arcs are plotted as dashed lines.

The `cutpoints` argument is an array of numeric values used to divide the range of the strength coefficients into intervals. The interval each strength coefficient falls into determines the line width of the corresponding arc in the plot. The default intervals are delimited by

`unique(c(0, threshold/c(10, 5, 2, 1.5, 1), 1))`

if the coefficients are computed from conditional independence tests, by

`unique(c(0, (1 - threshold)/c(10, 5, 2, 1.5, 1), 1))`

for bootstrap estimates or by the quantiles

`quantile(s[s < threshold], 1 - c(0.50, 0.75, 0.90, 0.95, 1))`

of the significant differences if network scores are used.

### Value

`graphviz.plot()` returns invisibly the `graph` object produced by Rgraphviz. It can be further modified using the commands present in the graph and Rgraphviz packages, and it contains the arc strengths in the edge weight attribute.

### Author(s)

Marco Scutari

### Examples

    ## Not run:
    # plot the network learned by hc().
    res = hc(learning.test)
    strength = arc.strength(res, learning.test, criterion = "x2")
    \dontrun{strength.plot(res, strength)}
    # add another (non-significant) arc and plot the network again.
    res = set.arc(res, "A", "C")
    strength = arc.strength(res, learning.test, criterion = "x2")
    \dontrun{strength.plot(res, strength)}

    ## End(Not run)

[Package bnlearn version 4.7 Index]