compareGraphs {pcalg}R Documentation

Compare two graphs in terms of TPR, FPR and TDR

Description

Compares the true undirected graph with an estimated undirected graph in terms of True Positive Rate (TPR), False Positive Rate (FPR) and True Discovery Rate (TDR).

Usage

compareGraphs(gl, gt)

Arguments

gl estimated graph (graph object)
gt true graph (graph object)

Details

If the input graph is directed, the directions are omitted. Special cases:

Value

a named numeric vector with three numbers

tpr True Positive Rate: Number of correctly found edges (in estimated graph) divided by number of true edges (in true graph)
fpr False Positive Rate: Number of incorrectly found edges divided by number of true gaps
tdr True Discovery Rate: Number of correctly found edges divided by number of found edges (both in estimated graph)

Author(s)

Markus Kalisch (kalisch@stat.math.ethz.ch) and Martin Maechler

See Also

randomDAG for generating a random DAG.

Examples

## generate a graph with 4 nodes
V <- LETTERS[1:4]
edL2 <- vector("list", length=4)
names(edL2) <- V
edL2[[1]] <- list(edges= 2)
edL2[[2]] <- list(edges= c(1,3,4))
edL2[[3]] <- list(edges= c(2,4))
edL2[[4]] <- list(edges= c(2,3))
gt <- new("graphNEL", nodes=V, edgeL=edL2, edgemode="undirected")

## change graph
gl <- addEdge("A","C", gt,1)

## compare the two graphs
par(mfrow=c(2,1))
plot(gt) ; title("True graph")
plot(gl) ; title("Estimated graph")
(cg <- compareGraphs(gl,gt))


[Package pcalg version 0.1-9 Index]