compareGraphs: Compare two graphs in terms of TPR, FPR and TDR

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/pcalg.R

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

1

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 (in true graph)

tdr

True Discovery Rate: Number of correctly found edges divided by number of found edges (both in estimated graph)

Author(s)

Markus Kalisch ([email protected]) and Martin Maechler

See Also

randomDAG for generating a random DAG.

Examples

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

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

}

pcalg documentation built on June 5, 2018, 1:05 a.m.