diceR 1.2.2
- Pass
lowerandupperparameters fromPAC()toconsensus_evaluate()(#160)
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
@examplesIfandrlang::is_installed()to run examples conditionally when using packages in Suggests
diceR 1.1.0
CRAN release: 2021-07-23
- Reinstate
blockclusterpackage 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
hexStickerPackage
blockclusterhas been archived, remove from Suggests
diceR 1.0.2
CRAN release: 2021-03-18
Remove deprecated
context()in testsAdd
RColorBrewerto Suggests because it is cross referenced in?graphsAdd trailing slash for URLs in DESCRIPTION
Remove
tibblefrom 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, amatrixobject also inherits from classarrayIn
algii_heatmap(), the objectiialready 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
cliandRColorBrewerfrom ImportsMoved
apcluster,blockcluster,cluster,dbscan,e1071,kernlab, andkohonentoSuggests, use their specific clustering algorithms conditionally.mclustneeds to be inImportsbecausemclust::mclustBIC()needs to be importedMoved
sigclusttoSuggests, use withinsigclust()conditionallyMoved
progresstoSuggests, use withinconsensus_cluster()conditionallyMoved
poLCAtoSuggests, use withindice()conditionallyMoved
RtsnetoSuggests, use withinprepare_data()conditionallyRemoved old dependency
grDevicesfromImportsSet minimum version to R (>= 3.5) for
klaRdependencyquestionrIn
ev_confmat(), useyardstick::conf_mat()instead ofcaret::confusionMatrix().carethas many dependencies, so best to avoid using itIn
graph_heatmap(), useNMF::aheatmap()instead ofgplots::heatmap.2().gplotsdepends oncaTools, which now relies on R (>= 3.6)In
consensus_cluster(), usestringr::str_to_title()instead ofHmisc::capitalize().Hmiscdepends onlatticeExtra, which now relies on R (>= 3.6)In
graph_delta_area(), use base solution instead offlux::auc().fluxalso depends oncaToolsIn
prepare_data(), use own implementation ofquantable::robustscale()with all of the former function’s defaults.quantablealso depends oncaToolsSpecify Bioconductor installation on Travis and AppVeyor since
NMFnow ImportsBiobase
Minor improvements and bug fixes
Remove
suppressWarnings(RNGversion("3.5.0"))after updating R versionRun
LCA()unit test on imputed clustering objectRemove internal validity measures with any
Infentries forconsensus_reweigh()Use a cleaner, more robust method of removing
Rplots.pdfafter runningtest-graphs.REnsure column binding with
purrr::map_dfc()inconsensus_rank()Replaced
dplyr::bind_cols()withpurrr::flatten_dfc()to suppress warning “Outer names are only allowed for unnamed scalar” inget_cdf()update roxygen and docs
diceR 0.6.0
CRAN release: 2019-07-25
Remove deprecated
dplyrfunctions and use.datapronounk-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 logicalerror inconsensus_evaluate()due to comparisons using||operatorAdd
suppressWarnings(RNGversion("3.5.0"))before call toset.seed()in examples, tests, and vignette to use old RNG samplingUse
.covrignoreto excludezzz.Rfrom being considered in code coverageUse
dplyrversion >= 0.7.5 to ensurebind_rows()worksFixed bug where scaled matrix using the “robust” method in
prepare_data()was nested in thedataelement (@AlineTalhouk, #134)
diceR 0.5.1
CRAN release: 2018-06-11
Add parameter
hc.methodindiceandconsensus_clusterto pass tomethodparameter instats::hclust(@JakeNel28, #130)Remove dependencies on
largeVis: package will be archived
diceR 0.5.0
CRAN release: 2018-05-05
Revert back to using
NMFsinceNNLMhas been archived andNMFis back in active maintenance.Choose fuzzifier m in
cmeansusing 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
NMFwithNNLMandpheatmap: CRAN notified thatNMFwill be archived because of inactive maintenanceUpdate
.ymlfiles 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()whenk.method = "all"indice()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.Rfor R-develAdd internal function: ranked algorithms vs internal validity indices heatmap graph
Fix bugs in
graph_cdf(),graph_tracking()when only one k selectedProgress messages in
dice()Fix bug in
consensus_evaluate()when algorithm hasNAfor 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
progresspackageSpeed up the operation that transforms a matrix to become “NMF-ready”
Simplify saving mechanism in
consensus_cluster()such that onlyfile.nameneeds to be specified, and thesaveparameter has been removedNew algorithms: SOM, Fuzzy C-Means, DBSCAN (@dustin21, #118)
Added significance testing section to vignette
Fixed direction of optimization: compactness and connectivity should be minimized
