diff --git a/DESCRIPTION b/DESCRIPTION index c213e616..86719ef6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: TreeDist Type: Package Title: Calculate and Map Distances Between Phylogenetic Trees -Version: 2.11.0 +Version: 2.11.1 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 index 96d9b193..38a3c936 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# TreeDist 2.11.1 (2025-10-13) + +- Improve robustness of `SpectralEigens()` tests. + + # TreeDist 2.11.0 (2025-09-26) - `HierarchicalMutualInformation()` calculates the information shared between diff --git a/R/spectral_clustering.R b/R/spectral_clustering.R index fe5ff77e..a113ac82 100644 --- a/R/spectral_clustering.R +++ b/R/spectral_clustering.R @@ -77,5 +77,5 @@ SpectralEigens <- function(D, nn = 10L, nEig = 2L) { #' @rdname SpectralEigens SpectralClustering <- function(D, nn = 10L, nEig = 2L) { .Deprecated("SpectralEigens") # 2021-07 - SpectralEigens(D, nn, nEig) + SpectralEigens(D = D, nn = nn, nEig = nEig) } diff --git a/tests/testthat/test-spectral_clustering.R b/tests/testthat/test-spectral_clustering.R index 35c4947b..a3d3defd 100644 --- a/tests/testthat/test-spectral_clustering.R +++ b/tests/testthat/test-spectral_clustering.R @@ -9,7 +9,10 @@ test_that("Spectral clustering works", { expect_equal(dim(allEig), c(40, 40)) expect_equal(abs(SpectralEigens(d, nEig = 2)), abs(allEig[, 40:39]), tolerance = sqrt(.Machine[["double.eps"]])) - - expect_warning(expect_equal(SpectralClustering(d, nEig = Inf), allEig), + + expect_warning(deprecated <- SpectralClustering(d, nEig = Inf), "'SpectralClustering' is deprecated.") + # Can't check raw equality because signs may flip + expect_true(all.equal(crossprod(deprecated), crossprod(allEig), + tolerance = sqrt(.Machine[["double.eps"]]))) })