tcherry_CL: Determines a t-cherry tree from a Chow-Liu tree

In nvihrs14/tcherry: Learning the structure of tcherry trees

Description

Determines the structure of a t-cherry tree by expanding a Chow-Liu tree.

Usage

tcherry_CL(data, ...)

Arguments

data	The data the tree structure should be based on.
...	Additional arguments passed to MI2 and MI3.

Details

This function i mainly kept for historical purposes, and it is recommended to use increase_order2 instead.

The algorithm for constructing the t-cherry tree from a Chow-Liu tree is as described in \insertRefEKTStcherry.

The algorithm is greedy in the sence that it always attempts to use the three variables with highest mutual information as the next cherry.

Value

A list containing the following components:

• adj_matrix The adjacency matrix for the t-cherry tree.

• cliques A list containing the cliques of the t-cherry tree.

• separators A list containing the separators of a junction tree for the t-cherry tree.

Author(s)

Katrine Kirkeby, [e-mail]

Maria Knudsen, [e-mail]

Ninna Vihrs, [e-mail]

References

\insertRef

EKTStcherry

See Also

ChowLiu for construction of Chow-Liu trees and MI3 for mutual information of three variables.

Examples

set.seed(43)
var1 <- c(sample(c(1, 2), 100, replace = TRUE))
var2 <- var1 + c(sample(c(1, 2), 100, replace = TRUE))
var3 <- var1 + c(sample(c(0, 1), 100, replace = TRUE,
                        prob = c(0.9, 0.1)))
var4 <- c(sample(c(1, 2), 100, replace = TRUE))
var5 <- var2 + var3
var6 <- var1 - var4 + c(sample(c(1, 2), 100, replace = TRUE))
var7 <- c(sample(c(1, 2), 100, replace = TRUE))

data <- data.frame("var1" = as.character(var1),
                   "var2" = as.character(var2),
                   "var3" = as.character(var3),
                   "var4" = as.character(var4),
                   "var5" = as.character(var5),
                   "var6" = as.character(var6),
                   "var7" = as.character(var7))

# smooth used in both MI2 and MI3
(tch <- tcherry_CL(data, smooth = 0.1))

nvihrs14/tcherry documentation built on Aug. 1, 2020, 6:25 p.m.