space (version 0.1-1.1)

space.neighbor: A function to estimate partial correlations using the neighborhood selection approach

Description

A function to estimate partial correlations using the neighborhood selection approach

Usage

space.neighbor(Y.m, lam1, lam2=0)

Arguments

Y.m

numeric matrix. Each column is for one variable and each row is for one sample. Missing values are not allowed. It's recommended to first standardize each column to have mean 0 and norm 1.

lam1

numeric value. This is the \(l_1\) norm penalty parameeter. If the columns of Y.m have norm one, then the suggested range of lam1 is: \(O(n^{1/2}\Phi^{-1}(1-\alpha/(2p^2)))\) for small \(\alpha\) such as 0.1.

lam2

numeric value. If not specified, lasso regression is used in the neighborhood selection. Otherwise, elastic net regression is used and lam2 serves as the \(l_2\) norm penalty parameter.

Value

A list with two components

ParCor

the estimated partial correlation matrix.

sig.fit

numeric vector of the estimated \(\sigma^{ii}\)

Details

space.neighbor estimate partial correlations using the neighborhood selection approach (Meinshausen and Buhlmann, 2006).

References

J. Peng, P. Wang, N. Zhou, J. Zhu (2007). Partial Correlation Estimation by Joint Sparse Regression Model.

Meinshausen, N., and Buhlmann, P. (2006), High Dimensional Graphs and Variable Selection with the Lasso, Annals of Statistics, 34, 1436-1462.

Examples

# NOT RUN {
#############################################################################################
############################ (A) The simulated Hub.net example in Peng et. al. (2007).
#############################################################################################
data(spaceSimu)

n=nrow(spaceSimu$Y.data)
p=ncol(spaceSimu$Y.data)
true.adj=abs(spaceSimu$ParCor.true)>1e-6

#################### view the network corresponding to the parcial correlation matrix in the simulation example
#################### view the network corresponding to the parcial correlation matrix in the simulation example
########### the following code can run only if the "igraph" is installed in the system.
#library(igraph)
#plot.adj=true.adj
#diag(plot.adj)=0
#temp=graph.adjacency(adjmatrix=plot.adj, mode="undirected")
#temp.degree=apply(plot.adj, 2, sum)
#V(temp)$color=(temp.degree>9)+3
#plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))


#################### estimate the parcial correlation matrix with various methods
alpha=1
l1=1/sqrt(n)*qnorm(1-alpha/(2*p^2))
iter=3


########### the values of lam1 were selected to make the results of different methods comparable. 
#### 1. MB method
result1=space.neighbor(spaceSimu$Y.data, lam1=l1*0.7, lam2=0)
fit.adj=abs(result1$ParCor)>1e-6
sum(fit.adj==1)/2                  ##total number of edges detected      
sum(fit.adj[true.adj==1]==1)/2  ##total number of true edges detected        
 
#### 2. Joint method with no weight
result2=space.joint(spaceSimu$Y.data, lam1=l1*n*1.56, lam2=0, iter=iter)
fit.adj=abs(result2$ParCor)>1e-6
sum(fit.adj==1)/2                  ##total number of edges detected      
sum(fit.adj[true.adj==1]==1)/2  ##total number of true edges detected        

#### 3. Joint method with residue variance based weights
result3=space.joint(spaceSimu$Y.data, lam1=l1*n*1.86, lam2=0, weight=1, iter=iter)
fit.adj=abs(result3$ParCor)>1e-6
sum(fit.adj==1)/2                  ##total number of edges detected      
sum(fit.adj[true.adj==1]==1)/2  ##total number of true edges detected        

#### 4. Joint method with degree based weights
result4=space.joint(spaceSimu$Y.data, lam1=l1*n*1.61, lam2=0, weight=2, iter=iter)
fit.adj=abs(result4$ParCor)>1e-6
sum(fit.adj==1)/2                  ##total number of edges detected      
sum(fit.adj[true.adj==1]==1)/2  ##total number of true edges detected        

# }