tests/test.R

In filosi/nettools: A Network Comparison Framework

##--------------------------------------------------
## Testing nettools usage
##--------------------------------------------------

library(nettools)

## Create toy dataset
a <- matrix(rnorm(1000),ncol=100)
b <- matrix(rnorm(1000),ncol=100)

## Compute adjacency matrix!
## For different methods check the mat2adj help page!
aadj <- mat2adj(a, infer.method="MINE", n.cores=1)
badj <- mat2adj(b, infer.method="MINE", n.cores=1)

## Compute the him distance between the 2 matrix

## Him distance
netdist(aadj,badj, d="HIM", components=FALSE, n.cores=1)
## HIM distance using list of matrices as input
netdist(list(aadj,badj), d="HIM", components=FALSE, n.cores=1)


## Hamming distance
dd <- netdist(aadj, badj, d="ham", n.cores=1)
## [1] 0.2134906
##

## Ipsen distance
netdist(aadj, badj, d="ips",gamma=0.09, n.cores=1)
## [1] 0.1358396
##

##-------------------------------------------------
## Using igraph
##-------------------------------------------------
## require(igraph)

## g1 <- barabasi.game(200,0.8)
## g2 <- barabasi.game(200,0.2)

## a1 <- get.adjacency(g1,type="both",sparse=TRUE)
## a2 <- get.adjacency(g2,type="both",sparse=TRUE)

## HIM distance
## netdist(g1,g2,d="HIM", n.cores=1)


##-------------------------------------------------
## Computing stability indicators
##-------------------------------------------------
ssind <- netSI(a, n.cores=1, use="pair")