Load the package, the example dataset for clustering complex shapes and we define a vector of correct labels.

data("complex.shapes", package = "pdc")
truth <- rep(c("fish", "bottle", "glasses"), c(5, 4, 5))

We set a larger minimum time-delay of 5 to increase robustness over discretization errors when searching for the optimal delay.

ent <- entropyHeuristic(complex.shapes, t.min = 5, t.max = 10)
#> Embedding dimension:  3 [ 3,4,5,6,7 ]   
#> Time delay:  5 [ 5,6,7,8,9,10 ]

This is a plot of the entropy heuristic over time-delays and embedding dimensions.


Now, we apply the clustering algorithm.

clust <- pdclust(complex.shapes, m = ent$m, t = ent$t)

Using the function rasterPlot, we get a dendrogram of the clustering solution with the images as leafs.

data("complex.shapes.raw", package = "pdc")
rasterPlot(clust, complex.shapes.raw$images)

And, finally, this is the multi-dimensional scaling projection onto two dimensions:

mdsPlot(clust, labels=truth, col=c("blue","green","red"))

Now, what if we use some sub-optimal clustering:

clust <- pdclust(complex.shapes, 3, t = 1)
rasterPlot(clust, complex.shapes.raw$images)

mdsPlot(clust, labels=truth, col=c("blue","green","red"))