NEWS

---

tglkmeans 0.6.4

• Fix: match_clusters() mapped only one cluster (leaving the rest NA) unless all per-cluster overlap counts tied; mapping is now per cluster.
• Fix: hclust_intra_clusters = TRUE errored when the id column was not named "id" (e.g. a named or auto-detected id column).
• Fix: predict_tgl_kmeans() crashed (pearson/spearman) or silently used the first center (euclid) for observations with no overlap; these now return NA.
• Removed the unused future/doFuture dependency; the package no longer overrides the user's future plan on load.
• No longer prints internal debugging; verbose = TRUE shows concise per-iteration progress. Default threads cap at 2 under R CMD check.
• Performance: k-means++ seeding uses nth_element instead of a full sort per seed. Cluster assignments are unchanged.

tglkmeans 0.6.3

• Fix: metric = "spearman" ignored missing values. Ranking tested the wrong missing-value sentinel, so NAs were ranked as the largest value and included in the rank correlation instead of being dropped. Spearman now excludes missing values pairwise, matching euclid/pearson. Clustering results for Spearman on data with NAs change (and are now correct); results on complete data are unchanged.
• Fix: predict_tgl_kmeans() with metric = "euclid" used a plain Euclidean distance, which disagreed with the training metric sqrt(sum_sq) / n when a cluster center had a missing dimension. Prediction now reproduces the training distance exactly. Predictions on data whose centers have no missing dimensions are unchanged.
• Performance: removed the dense k x n per-thread vote matrix in the reassignment step. Memory and per-iteration work no longer scale with the number of clusters; cluster assignments are unchanged.
• Performance: metric = "spearman" no longer computes a discarded p-value on every point-to-center comparison, and uses a contiguous sort buffer instead of a linked list. Results are unchanged.
• Performance: predict_tgl_kmeans() uses smaller internal chunks, cutting redundant distance/correlation computation on large inputs. Results are unchanged.
• Fix: hclust_intra_clusters = TRUE returned a scrambled within-cluster ordering. The order/intra_clust_order columns now follow the hclust dendrogram leaf order as documented.
• Removed unused internal code (reduce_coclust/reduce_num_trials and dead rank-sum / incomplete-beta helpers).

tglkmeans 0.6.2

• Fix: predict_tgl_kmeans() crashed with 'from' contains NAs / NAs introduced by coercion to integer range on inputs of ~46K rows or more. The one-shot as.matrix(tgs_dist(.)) overflowed integer indexing inside stats:::as.matrix.dist. The prediction now processes observations in chunks (#21).

tglkmeans 0.6.1 (2026-03-04)

• Added predict_tgl_kmeans() function to assign new observations to existing k-means cluster centers (#5).
• Exported match_clusters() and test_clustering() functions.
• Auto-detect character/factor first column as ID column.
• Parallelized k-means initialization.
• Fix: Pearson distance was not negated, causing incorrect cluster assignments when using metric = "pearson".
• Fix: memory leak in k-means core.
• Fix: k-means seeding crash when k is large relative to data size.
• Fix: race condition in parallel workers.
• Fix: package failed to load on machines where detectCores() returns NA.
• Fix: downsample_matrix used identical random seed for all columns.
• Removed plyr dependency. Moved ggplot2 from Imports to Suggests.

tglkmeans 0.5.8 (2026-01-14)

• Fix: Registered "id" as a global variable to maintain compatibility with future versions of dplyr (addressing the removal of dplyr::id()).

tglkmeans 0.5.7

• Bug fix: crashed on some machines when id_column=TRUE and data had a single column.

tglkmeans 0.5.6

• Removed parallelization for hclust_intra_clusters - it was causing hangs in some systems. The parallel parameter was removed from TGL_kmeans and TGL_kmeans_tidy.

tglkmeans 0.5.5 (2024-05-15)

• Fix: clustering crashed when hclust_intra_clusters was TRUE and input was a matrix.

tglkmeans 0.5.4 (2024-01-09)

• Fixed usage of more than 2 cores when testing on CRAN.

tglkmeans 0.5.3

• Fix: colnames and rownames were removed in downsample_matrix function.

tglkmeans 0.5.2

• Fixed docs.

tglkmeans 0.5.1

• Fix: cluster slot ids were corrupted when data was a tibble and id_column was TRUE.
• Fix: ids were not used when id_column was FALSE and data had rownames.

tglkmeans 0.5.0

• Added dowsample_matrix function to downsample the columns of a count matrix to a target number.

tglkmeans 0.4.0

• Default of id_column parameter was changed to FALSE. Note that this is a breaking change, and if you want to use an id column, you need to set it explicitly to TRUE.
• Use R random number generator instead of C++11 random number generator. For backwards compatibility, the old random number generator can be used by setting use_cpp_random to TRUE.
• Added parallelization using RcppParallel.

tglkmeans 0.3.12

• Added validity checks for k and the number of observations.

tglkmeans 0.3.11 (2023-08-21)

• Changed pkgdoc, see: https://github.com/r-lib/roxygen2/issues/1491.

tglkmeans 0.3.10 (2023-06-26)

• Removed broken link to one of the references in the description.

tglkmeans 0.3.9

• Remove empty clusters. This may happen when the number of clusters is larger than the number of observations, and currently caused an error in the reordering step.

tglkmeans 0.3.8 (2023-03-21)

• Removed C++11 specification + require R >= 4.0.0.

tglkmeans 0.3.6

• Fixed error on debian systems.

tglkmeans 0.3.5 (2022-08-28)

• Changed errors from cpp to 1 based indexing.
• fix: loading the package failed on machines with a single core.

tglkmeans 0.3.4 (2022-04-20)

• First CRAN release.

tglkmeans 0.3.3

• Set NA values to zeros in correlation matrix when reordering clusters (avoid crashing on some datasets with NA's in the dist object)

tglkmeans 0.3.1

• Use rownames when exist.
• Do not fail when "id" column doesn't exist (warn instead).

tglkmeans 0.3.0

• Removed bootstrapping (it was causing a lot of problems in travis testing and almost wasn't used).
• Added a NEWS.md file to track changes to the package.