Description Usage Arguments Examples
create_adjacency
creates an n-by-n sparse adjacency matrix from the matrix of centroid differences.
1 | create_adjacency(V, w, n, method = "ama")
|
V |
Matrix of centroid differences |
w |
Weights vector |
n |
Number of points to cluster |
method |
'ama' or 'admm' |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Clusterpaths for Mammal Dentition
data(mammals)
X <- as.matrix(mammals[,-1])
X <- t(scale(X,center=TRUE,scale=FALSE))
n <- ncol(X)
## Pick some weights and a sequence of regularization parameters.
k <- 5
phi <- 0.5
w <- kernel_weights(X,phi)
w <- knn_weights(w,k,n)
gamma <- seq(0.0,43, length.out=100)
## Perform clustering
nu <- AMA_step_size(w,n)
sol <- cvxclust_path_ama(X,w,gamma,nu=nu)
## Construct adjacency matrix
A <- create_adjacency(sol$V[[10]],w,n)
G <- graph.adjacency(A, mode = 'upper')
plot(G,vertex.label=as.character(mammals[,1]),vertex.label.cex=0.65,vertex.label.font=2)
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