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Revert back to using NMF since NNLM has been archived and NMF is back in active maintenance.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