pcalg: pcAlgo-class – R documentation

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pcAlgo-class

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

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)

pcalg

Methods for Graphical Models and Causal Inference

v2.7-2

GPL (>= 2)

Authors

Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb], Marco Eigenmann [ctb], Leonard Henckel [ctb], Joris Mooij [ctb]

Initial release

2021-4-20