pcAlgo-class {pcalg}

Class "pcAlgo" of PC Algorithm Results, incl. Skeleton

Description

This class of objects is returned by the functions skeleton and pc to represent the (skeleton) of an estimated CPDAG. Objects of this class have methods for the functions plot, show and summary.

Usage

## S4 method for signature 'pcAlgo,ANY'
plot(x, y, main = NULL,
     zvalue.lwd = FALSE, lwd.max = 7, labels = NULL, ...)
## S3 method for class 'pcAlgo'
print(x, amat = FALSE, zero.print = ".", ...)

## S4 method for signature 'pcAlgo'
summary(object, amat = TRUE, zero.print = ".", ...)
## S4 method for signature 'pcAlgo'
show(object)

Arguments

x, object

a "pcAlgo" object.

y

(generic plot() argument; unused).

main

main title for the plot (with an automatic default).

zvalue.lwd

logical indicating if the line width (lwd) of the edges should be made proportional to the entries of matrix zMin (originally) or derived from matrix pMax.

lwd.max

maximal lwd to be used, if zvalue.lwd is true.

labels

if non-NULL, these are used to define node attributes nodeAttrs and attrs, passed to agopen() from package Rgraphviz.

amat

logical indicating if the adjacency matrix should be shown (printed) as well.

zero.print

string for printing 0 (‘zero’) entries in the adjacency matrix.

...

optional further arguments (passed from and to methods).

Creation of objects

Objects are typically created as result from skeleton() or pc(), but could be be created by calls of the form new("pcAlgo", ...).

Slots

The slots call, n, max.ord, n.edgetests, sepset, and pMax are inherited from class "gAlgo", see there.

In addition, "pcAlgo" has slots

graph:

Object of class "graph": the undirected or partially directed graph that was estimated.

zMin:

Deprecated.

Extends

Class "gAlgo".

Methods

plot

signature(x = "pcAlgo"): Plot the resulting graph. If argument "zvalue.lwd" is true, the linewidth an edge reflects zMin, so that thicker lines indicate more reliable dependencies. The argument "lwd.max" controls the maximum linewidth.

show

signature(object = "pcAlgo"): Show basic properties of the fitted object

summary

signature(object = "pcAlgo"): Show details of the fitted object

Author(s)

Markus Kalisch and Martin Maechler

See Also

pc, skeleton, fciAlgo

Examples

  showClass("pcAlgo")

## generate a pcAlgo object
p <- 8
set.seed(45)
myDAG <- randomDAG(p, prob = 0.3)
n <- 10000
d.mat <- rmvDAG(n, myDAG, errDist = "normal")
suffStat <- list(C = cor(d.mat), n = n)
pc.fit <- pc(suffStat, indepTest = gaussCItest, alpha = 0.01, p = p)

## use methods of class pcAlgo
show(pc.fit)
if(require(Rgraphviz))
  plot(pc.fit, main = "Fitted graph")
summary(pc.fit)

## access slots of this object
(g  <- pc.fit@graph)
str(ss <- pc.fit@sepset, max=1)