Changelog

Source: NEWS.md

diceR 3.1.0

• Remove deprecated helper functions package clv currently pending archival
• Improve documentation for parameter k.method in consensus_evaluation()

diceR 3.0.0

CRAN release: 2025-02-05

• There were errors running tests on clang-UBSAN and gcc-UBSAN builds, due to usage of functions from clusterSim. Reinstate internal and external functions from clusterCrit package, which is no longer archived.
• Use new parameter verbose in dice() to control console printouts of main tasks being performed instead of using progress
• Refactor graph_heatmap() to use pheatmap::pheatmap() since NMF::aheatmap() throws a gridPLT() error whenever it is run in a script or interactively, but not in R markdown documents. Thus there are run time errors when used in unit tests and examples. See renozao/NMF#65
• Remove deprecated function usage

diceR 2.2.0

CRAN release: 2024-01-22

• 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

CRAN release: 2023-09-28

• 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

CRAN release: 2023-03-11

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

CRAN release: 2022-09-29

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

diceR 1.2.1

CRAN release: 2022-08-16

• 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

CRAN release: 2022-05-13

• 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

CRAN release: 2021-07-23

• Reinstate blockcluster package as it is under active maintenance again

diceR 1.0.4

CRAN release: 2021-06-04

• Suppress new names messages from transformed NMF data

• Flattened matrices include 4th dimension of clustering array

diceR 1.0.3

CRAN release: 2021-04-17

• Add package logo using hexSticker

• Package blockcluster has been archived, remove from Suggests

diceR 1.0.2

CRAN release: 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

CRAN release: 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

CRAN release: 2020-07-07

Decreased dependencies

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

• Removed cli and RColorBrewer from Imports

• Moved apcluster, blockcluster, cluster, dbscan, e1071, kernlab, and kohonen to Suggests, use their specific clustering algorithms conditionally. mclust needs to be in Imports because mclust::mclustBIC() needs to be imported

• Moved sigclust to Suggests, use within sigclust() conditionally

• Moved progress to Suggests, use within consensus_cluster() conditionally

• Moved poLCA to Suggests, use within dice() conditionally

• Moved Rtsne to Suggests, use within prepare_data() conditionally

• Removed old dependency grDevices from Imports

• Set minimum version to R (>= 3.5) for klaR dependency questionr

• In ev_confmat(), use yardstick::conf_mat() instead of caret::confusionMatrix(). caret has many dependencies, so best to avoid using it

• In graph_heatmap(), use NMF::aheatmap() instead of gplots::heatmap.2(). gplots depends on caTools, which now relies on R (>= 3.6)

• In consensus_cluster(), use stringr::str_to_title() instead of Hmisc::capitalize(). Hmisc depends on latticeExtra, which now relies on R (>= 3.6)

• In graph_delta_area(), use base solution instead of flux::auc(). flux also depends on caTools

• In prepare_data(), use own implementation of quantable::robustscale() with all of the former function’s defaults. quantable also depends on caTools

• Specify Bioconductor installation on Travis and AppVeyor since NMF now Imports Biobase

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

CRAN release: 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

CRAN release: 2019-03-08

• 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)

diceR 0.5.1

CRAN release: 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

CRAN release: 2018-05-05

• Revert back to using NMF since NNLM has been archived and NMF is back in active maintenance.

• Choose fuzzifier m in cmeans using Equation 5 from https://academic.oup.com/bioinformatics/article/26/22/2841/227572 (thanks @Asduveneck)

diceR 0.4.0

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 2017-11-29

• Updated object output names in consensus_evaluate()

• Fix unit test in test-dice.R for R-devel

• Add internal function: ranked algorithms vs internal validity indices heatmap graph

• Fix bugs in graph_cdf(), graph_tracking() when only one k selected

• Progress messages in dice()

• Fix bug in consensus_evaluate() when algorithm has NA for all PAC values

diceR 0.2.0

CRAN release: 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

CRAN release: 2017-06-21

• New submission to CRAN accepted on June 21, 2017