Changelog
Source:NEWS.md
diceR 2.2.0
- New
abs
argument inconsensus_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 ofmixedClust
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
andseed.data
arguments todice()
(#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 fromclv
. Previously only the total separation between clusters was returned. - S_Dbw index now calculated using
clv::clv.SDbw()
and helper functions fromclv
- 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
andupper
parameters 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
@examplesIf
andrlang::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 testsAdd
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, amatrix
object also inherits from classarray
In
algii_heatmap()
, the objectii
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
andRColorBrewer
from ImportsMoved
apcluster
,blockcluster
,cluster
,dbscan
,e1071
,kernlab
, andkohonen
toSuggests
, use their specific clustering algorithms conditionally.mclust
needs to be inImports
becausemclust::mclustBIC()
needs to be importedMoved
sigclust
toSuggests
, use withinsigclust()
conditionallyMoved
progress
toSuggests
, use withinconsensus_cluster()
conditionallyMoved
poLCA
toSuggests
, use withindice()
conditionallyMoved
Rtsne
toSuggests
, use withinprepare_data()
conditionallyRemoved old dependency
grDevices
fromImports
Set minimum version to R (>= 3.5) for
klaR
dependencyquestionr
In
ev_confmat()
, useyardstick::conf_mat()
instead ofcaret::confusionMatrix()
.caret
has many dependencies, so best to avoid using itIn
graph_heatmap()
, useNMF::aheatmap()
instead ofgplots::heatmap.2()
.gplots
depends oncaTools
, which now relies on R (>= 3.6)In
consensus_cluster()
, usestringr::str_to_title()
instead ofHmisc::capitalize()
.Hmisc
depends onlatticeExtra
, which now relies on R (>= 3.6)In
graph_delta_area()
, use base solution instead offlux::auc()
.flux
also depends oncaTools
In
prepare_data()
, use own implementation ofquantable::robustscale()
with all of the former function’s defaults.quantable
also depends oncaTools
Specify Bioconductor installation on Travis and AppVeyor since
NMF
now 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
Inf
entries forconsensus_reweigh()
Use a cleaner, more robust method of removing
Rplots.pdf
after runningtest-graphs.R
Ensure 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
dplyr
functions and use.data
pronounk-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 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
.covrignore
to excludezzz.R
from being considered in code coverageUse
dplyr
version >= 0.7.5 to ensurebind_rows()
worksFixed bug where scaled matrix using the “robust” method in
prepare_data()
was nested in thedata
element (@AlineTalhouk, #134)
diceR 0.5.1
CRAN release: 2018-06-11
Add parameter
hc.method
indice
andconsensus_cluster
to pass tomethod
parameter 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
NMF
sinceNNLM
has been archived andNMF
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
withNNLM
andpheatmap
: CRAN notified thatNMF
will be archived because of inactive maintenanceUpdate
.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()
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.R
for 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 hasNA
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
packageSpeed up the operation that transforms a matrix to become “NMF-ready”
Simplify saving mechanism in
consensus_cluster()
such that onlyfile.name
needs to be specified, and thesave
parameter 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