diceR 2.2.0

• New abs argument in consensus_cluster(): control whether to apply absolute value to Spearman and Pearson correlation matrices before subtracting from one (@tiagochst, #161)
• New distance matrix option, distance = "pearson"
• Use blockcluster instead of mixedClust as the latter is now archived
• Update tests in consensus_cluster() that skip when suggested packages are not installed

diceR 2.1.0

• Sort cluster sizes k correctly in relative change in area under CDF curve (@IgnatiusPang, #167) and consensus matrix CDF graphs
• Replace deprecated aes_ calls with tidyeval idioms
• Pass p.item and seed.data arguments to dice() (#162, #165)

diceR 2.0.0

Internal and external validity indices were refactored to avoid using helper functions from the clusterCrit package, which is scheduled to be archived. Please adapt your code if it extracts deprecated validity indices, as described below.

• Calinski-Harabasz index now calculated using clusterSim::index.G1()
• Dunn index now calculated using clValid::dunn()
• Gamma index now calculated using clusterSim::index.G2()
• C-index now calculated using clusterSim::index.C()
• Davies-Bouldin now calculated using clusterSim::index.DB()
• SD index now calculated correctly using clv::clv.SD() and helper functions from clv. Previously only the total separation between clusters was returned.
• S_Dbw index now calculated using clv::clv.SDbw() and helper functions from clv
• Rousseeuw's Silhouette now calculated using clusterSim::index.S()
• PBM, Tau, McClain-Rao, Ray-Turi, and G-plus indices were removed as equivalent implementations from other packages were not found. They may be reinstated in the future.
• All external validity indices are now calculated manually using counts from the concordance matrix (Hubert, Jaccard, McNemar, and Rand indices)
• Best index value (maximum or minimum) now calculated manually

diceR 1.2.2

• Pass lower and upper parameters from PAC() to consensus_evaluate() (#160)

diceR 1.2.1

• References added for k_modes() and CSPA() consensus functions (#157)
• Update roxygen2 to avoid HTML5 documentation notes
• Use mixedClust instead of blockcluster for co-clustering since the latter keeps getting archived

diceR 1.2.0

• Use testthat::skip_if_not_installed() to run tests conditionally when using packages in Suggests
• Use roxygen tag @examplesIf and rlang::is_installed() to run examples conditionally when using packages in Suggests

diceR 1.1.0

• Reinstate blockcluster package as it is under active maintenance again

diceR 1.0.4

• Suppress new names messages from transformed NMF data

• Flattened matrices include 4th dimension of clustering array

diceR 1.0.3

• Add package logo using hexSticker

• Package blockcluster has been archived, remove from Suggests

diceR 1.0.2

• 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