diceR 1.0.4 2021-06-04

  • Suppress new names messages from transformed NMF data

  • Flattened matrices include 4th dimension of clustering array

diceR 1.0.3 2021-04-17

  • Add package logo using hexSticker

  • Package blockcluster has been archived, remove from Suggests

diceR 1.0.2 2021-03-18

  • 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

diceR 1.0.1 2021-01-30

  • 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)

diceR 1.0.0 2020-07-07

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

diceR 0.6.0 2019-07-25

  • 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)

diceR 0.5.2 2019-03-08

diceR 0.5.1 2018-06-11

  • 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

diceR 0.5.0 2018-05-05

diceR 0.4.0 2018-02-22

  • 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

diceR 0.3.2 2018-01-14

  • 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

diceR 0.3.1 2017-12-12

  • 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)

diceR 0.3.0 2017-11-29

diceR 0.2.0 2017-09-29

  • 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

diceR 0.1.0 2017-06-21

  • New submission to CRAN accepted on June 21, 2017