• Reinstate blockcluster package as it is under active maintenance again
  • Suppress new names messages from transformed NMF data

  • Flattened matrices include 4th dimension of clustering array

  • Add package logo using hexSticker

  • Package blockcluster has been archived, remove from Suggests

  • Remove deprecated context() in tests

  • Add RColorBrewer to Suggests because it is cross referenced in ?graphs

  • Add trailing slash for URLs in DESCRIPTION

  • Remove tibble from Imports, no longer used

  • Suppress warnings when clValid::connectivity() is called regarding comparison with more than one class. Since R-4.0.0, a matrix object also inherits from class array

  • In algii_heatmap(), the object ii already has row names passed from columns which are named vectors (issue also identified in #148, thanks @romainfrancois)

Decreased dependencies

The following steps were taken to minimize dependencies and ensure that diceR can still run on R 3.5:

Minor improvements and bug fixes

  • Remove suppressWarnings(RNGversion("3.5.0")) after updating R version

  • Run LCA() unit test on imputed clustering object

  • Remove internal validity measures with any Inf entries for consensus_reweigh()

  • Use a cleaner, more robust method of removing Rplots.pdf after running test-graphs.R

  • Ensure column binding with purrr::map_dfc() in consensus_rank()

  • Replaced dplyr::bind_cols() with purrr::flatten_dfc() to suppress warning “Outer names are only allowed for unnamed scalar” in get_cdf()

  • update roxygen and docs

  • Remove deprecated dplyr functions and use .data pronoun

  • k-means clustering should not support distance matrices as input (@jerryji1993, #139)

  • Add LCA as a consensus function (@philstraforelli, #137)

  • Fix length > 1 in coercion to logical error in consensus_evaluate() due to comparisons using || operator

  • Add suppressWarnings(RNGversion("3.5.0")) before call to set.seed() in examples, tests, and vignette to use old RNG sampling

  • Use .covrignore to exclude zzz.R from being considered in code coverage

  • Use dplyr version >= 0.7.5 to ensure bind_rows() works

  • Fixed bug where scaled matrix using the “robust” method in prepare_data() was nested in the data element (@AlineTalhouk, #134)

  • Add parameter hc.method in dice and consensus_cluster to pass to method parameter in stats::hclust (@JakeNel28, #130)

  • Remove dependencies on largeVis: package will be archived

  • Replace all code that depended on NMF with NNLM and pheatmap: CRAN notified that NMF will be archived because of inactive maintenance

  • Update .yml files default templates

  • Fix bug in consensus_cluster() when custom algorithms were excluded from output (thanks @phiala)

  • Use markdown language for documentation

  • Various performance improvements and code simplifications

  • Suppress success/fail message printout and fix input data to be matrix for block clustering

  • Fix bug in algii_heatmap() when k.method = "all" in dice()

  • Fix bug in calculating internal indices when data has categorical variables (thanks Kurt Salmela)

  • New dimension reduction methods: t-SNE, largeVis (@dustin21)

  • Better annotated progress bar using progress package

  • Speed up the operation that transforms a matrix to become “NMF-ready”

  • Simplify saving mechanism in consensus_cluster() such that only file.name needs to be specified, and the save parameter has been removed

  • New algorithms: SOM, Fuzzy C-Means, DBSCAN (@dustin21, #118)

  • Added significance testing section to vignette

  • Fixed direction of optimization: compactness and connectivity should be minimized

  • New submission to CRAN accepted on June 21, 2017