Nothing
small.world <- function(wave.adj.mat,dat="reduced",distance="norm",coord=0, export.data=FALSE)
{
n.regions<-dim(wave.adj.mat)[1]
if(distance=="euclid"){
euclid <- 2 * dist(t(coord), method = "euclidean")
x.euclid <- as.matrix(euclid)
}
# For the computation of Cp and Lp
if(distance=="euclid"){
dist.mat<-x.euclid
}else{
dist.mat<-matrix(1,n.regions,n.regions)
}
mat<-wave.adj.mat
# Test : diagonal of mat.
if(sum(diag(mat)>0)>0) stop("terms on the diagonal of the adjacency matrix are not all equal to 0")
z<-.C("Rkfun",
as.integer(n.regions),
as.integer(mat),
deg=double(n.regions), PACKAGE="brainwaver")
deg<-z$deg
if(dat=="all") in.degree<-deg
in.degree.mean<-mean(deg)
z<-.C("Rlpfun",
as.integer(n.regions),
as.integer(mat),
as.double(dist.mat),
lp=double(n.regions), PACKAGE="brainwaver")
lp<-z$lp
if(dat=="all") Lp<-lp
lp<-lp[lp>-1]
mlp=mean(lp)
if(mlp=='NaN'){
Lp.mean<- NaN
}else{
Lp.mean<-mlp
}
z<-.C("Rcpfun",
as.integer(n.regions),
as.integer(mat),
cp=double(n.regions), PACKAGE="brainwaver")
cp<-z$cp
if(dat=="all") Cp<-cp
cp<-cp[cp>-1]
mcp<-mean(cp)
if(mcp=='NaN'){
Cp.mean<- NaN
}else{
Cp.mean<-mcp
}
z<-.C("Rconnex_components",
as.integer(n.regions),
as.integer(mat),
acc=double(n.regions+3), PACKAGE="brainwaver")
size.large.connex<-z$acc[n.regions+2]
#small-world parameters
if(export.data==TRUE){
if(dat == "all"){
write.table(in.degree,"in_degree.txt")
write.table(Lp,"Lp_txt")
write.table(Cp,"Cp_txt")
}
write.table(in.degree.mean,"in_degree_mean.txt")
write.table(Lp.mean,"Lp_mean.txt")
write.table(Cp.mean,"Cp_mean.txt")
}
if(dat=="all"){
list(in.degree.mean=in.degree.mean,in.degree=in.degree, Cp=Cp, Cp.mean=Cp.mean,Lp.mean=Lp.mean, Lp=Lp, size.large.connex=size.large.connex)
}else{
list(in.degree.mean=in.degree.mean,Cp.mean=Cp.mean,Lp.mean=Lp.mean,size.large.connex=size.large.connex)
}
}
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