inst/unitTests/test_evaluate.R

In netbenchmark: Benchmarking of several gene network inference methods

test_evaluate<-function(){
    alg1<-matrix(0,6,6)
    alg1[1,2]<-0.7
    alg1[1,3]<-0.69
    alg1[1,6]<-0.65
    alg1[2,3]<-0.63
    alg1[3,6]<-0.6
    alg1[1,5]<-0.55
    alg1[3,5]<-0.53
    alg1[4,5]<-0.5
    alg1[2,4]<-0.4
    alg1[4,6]<-0.32
    alg1[5,6]<-0.3
    gs<-matrix(0,6,6)
    gs[6,5]<-1
    gs[4,5]<-1
    gs[2,5]<-1
    gs[3,5]<-1
    gs[1,4]<-1
    gs[1,2]<-1
    gs[3,2]<-1
    res<-c(1,1,1,2,2,2,3,4,4,4,5,0,1,2,2,3,4,4,4,5,6,6,8,7,6,6,5,4,4,
        4,3,2,2,6,6,6,5,5,5,4,3,3,3,2)
    res<-matrix(res,11,4)
    colnames(res)<-c("TP","FP","TN","FN")
    checkEquals(res,evaluate(alg1,gs))
    G<-pmax(gs,t(gs))
    G<-1-G
    diag(G)<-0
    r<-evaluate(G,gs)
    checkEquals(r[,1],rep(0,8))
    checkEquals(r[,2],1:8)
}