Support nEig > nL

ms609 · Aug 14, 2024 · 908cd46 · 908cd46
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.8.0
+Version: 2.8.0.9000
 Authors@R: c(person("Martin R.", "Smith",
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# TreeDist 2.8.0.9000 (development)
+
+- `SpectralEigens()` survives values of nEig larger than the input
+
 # TreeDist 2.8.0 (2024-07-25)
 
 - `Islands()` allows the identification of islands of trees.

diff --git a/R/spectral_clustering.R b/R/spectral_clustering.R
@@ -60,8 +60,14 @@ SpectralEigens <- function(D, nn = 10L, nEig = 2L) {
   L <- GraphLaplacian(W) # 2. compute graph laplacian
   ei <- eigen(L, symmetric = TRUE) # 3. Compute the eigenvectors and values of L
 
-  # Return the eigenvectors of the n_eig smallest eigenvalues:
-  ei[["vectors"]][, nrow(L) - rev(seq_len(nEig))]
+  nL <- dim(L)[[1]]
+
+  if (nL > nEig) {
+    # Return the eigenvectors of the n_eig smallest eigenvalues:
+    ei[["vectors"]][, nL - rev(seq_len(nEig))]
+  } else {
+    ei[["vectors"]]
+  }
 }
 
 #' @export