Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-3 dated 2015-05-23 and 1.1-4 dated 2015-05-24
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NAMESPACE | 1 R/DSC_DStream.R | 2 R/DSC_R.R | 3 - build/vignette.rds |binary inst/NEWS | 2 inst/doc/stream.pdf |binary src/DBSTREAM.cpp | 105 +++++++++++++++++++++++++--------------------------- src/DStream.cpp | 67 ++++++++++++++++++--------------- 10 files changed, 108 insertions(+), 100 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.4.0 dated 2014-05-30 and 1.5.0 dated 2015-05-24
wsrf-1.4.0/wsrf/R/merge.wsrf.R |only wsrf-1.4.0/wsrf/R/oobErrorRate.wsrf.R |only wsrf-1.4.0/wsrf/R/summary.wsrf.R |only wsrf-1.4.0/wsrf/man/oobErrorRate.wsrf.Rd |only wsrf-1.4.0/wsrf/man/summary.wsrf.Rd |only wsrf-1.4.0/wsrf/src/RF_deployment.cpp |only wsrf-1.4.0/wsrf/src/RF_deployment.h |only wsrf-1.4.0/wsrf/src/attribute_selection_method.cpp |only wsrf-1.4.0/wsrf/src/attribute_selection_method.h |only wsrf-1.4.0/wsrf/src/attribute_value_mapper.cpp |only wsrf-1.4.0/wsrf/src/attribute_value_mapper.h |only wsrf-1.4.0/wsrf/src/c4_5_attribute_selection_method.cpp |only wsrf-1.4.0/wsrf/src/c4_5_attribute_selection_method.h |only wsrf-1.4.0/wsrf/src/decision_tree.cpp |only wsrf-1.4.0/wsrf/src/decision_tree.h |only wsrf-1.4.0/wsrf/src/node.cpp |only wsrf-1.4.0/wsrf/src/random_forests.cpp |only wsrf-1.4.0/wsrf/src/random_forests.h |only wsrf-1.4.0/wsrf/src/training_set.cpp |only wsrf-1.4.0/wsrf/src/training_set.h |only wsrf-1.4.0/wsrf/src/weighted_random_forest.cpp |only wsrf-1.4.0/wsrf/src/weighted_random_forest.h |only wsrf-1.5.0/wsrf/DESCRIPTION | 42 +- wsrf-1.5.0/wsrf/MD5 | 93 ++--- wsrf-1.5.0/wsrf/NAMESPACE | 10 wsrf-1.5.0/wsrf/R/combine.wsrf.R |only wsrf-1.5.0/wsrf/R/correlation.wsrf.R | 2 wsrf-1.5.0/wsrf/R/importance.wsrf.R |only wsrf-1.5.0/wsrf/R/oob.error.rate.wsrf.R |only wsrf-1.5.0/wsrf/R/predict.wsrf.R | 66 +-- wsrf-1.5.0/wsrf/R/print.wsrf.R | 92 ----- wsrf-1.5.0/wsrf/R/strength.wsrf.R | 4 wsrf-1.5.0/wsrf/R/subset.wsrf.R |only wsrf-1.5.0/wsrf/R/varCounts.wsrf.R | 57 +-- wsrf-1.5.0/wsrf/R/wsrf.R | 259 +++++++------- wsrf-1.5.0/wsrf/R/wsrf.R.in | 259 +++++++------- wsrf-1.5.0/wsrf/README.md | 17 wsrf-1.5.0/wsrf/build/vignette.rds |binary wsrf-1.5.0/wsrf/configure | 18 wsrf-1.5.0/wsrf/inst/NEWS.Rd | 102 ++++- wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.R | 50 -- wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.Rnw | 3 wsrf-1.5.0/wsrf/inst/doc/wsrfGuide.pdf |binary wsrf-1.5.0/wsrf/man/combine.wsrf.Rd |only wsrf-1.5.0/wsrf/man/importance.wsrf.Rd |only wsrf-1.5.0/wsrf/man/oob.error.rate.wsrf.Rd |only wsrf-1.5.0/wsrf/man/print.wsrf.Rd | 13 wsrf-1.5.0/wsrf/man/subset.wsrf.Rd |only wsrf-1.5.0/wsrf/man/wsrf.Rd | 76 ++-- wsrf-1.5.0/wsrf/src/IGR.cpp | 209 ++++++----- wsrf-1.5.0/wsrf/src/IGR.h | 43 +- wsrf-1.5.0/wsrf/src/c4_5_var_selector.cpp |only wsrf-1.5.0/wsrf/src/c4_5_var_selector.h |only wsrf-1.5.0/wsrf/src/dataset.cpp |only wsrf-1.5.0/wsrf/src/dataset.h |only wsrf-1.5.0/wsrf/src/meta_data.cpp |only wsrf-1.5.0/wsrf/src/meta_data.h |only wsrf-1.5.0/wsrf/src/node.h | 289 +++++++++++----- wsrf-1.5.0/wsrf/src/rforest.cpp |only wsrf-1.5.0/wsrf/src/rforest.h |only wsrf-1.5.0/wsrf/src/tree.cpp |only wsrf-1.5.0/wsrf/src/tree.h |only wsrf-1.5.0/wsrf/src/utility.h | 142 ++++--- wsrf-1.5.0/wsrf/src/var_selector.h |only wsrf-1.5.0/wsrf/src/wsrf.cpp |only wsrf-1.5.0/wsrf/src/wsrf.h |only wsrf-1.5.0/wsrf/tests/wsrftest.R | 48 +- wsrf-1.5.0/wsrf/tests/wsrftest.Rout.save | 127 +++---- wsrf-1.5.0/wsrf/vignettes/wsrfGuide.Rnw | 3 69 files changed, 1116 insertions(+), 908 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking (by continents, regions, or countries), data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multi-variate clustering (MVC), cluster validation, and visualization of region maps.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 1.2.0 dated 2015-03-27 and 1.2.1 dated 2015-05-24
DESCRIPTION | 12 +++--- MD5 | 40 +++++++++++----------- R/HiClimR.R | 93 ++++++++++++++++++++++++++++++---------------------- R/coarseR.R | 3 + R/fastCor.R | 3 + R/geogMask.R | 49 ++++++++++++++------------- R/grid2D.R | 3 + R/minSigCor.R | 3 + R/validClimR.R | 25 +++++++------- README.md | 95 +++++++++++++++++++++++++++++++++++++++++++----------- inst/CITATION | 15 +++++--- man/HiClimR.Rd | 29 +++++++++++----- man/TestCase.Rd | 2 - man/WorldMask.Rd | 2 - man/coarseR.Rd | 2 - man/fastCor.Rd | 4 +- man/geogMask.Rd | 18 +++++++--- man/grid2D.Rd | 13 +++---- man/minSigCor.Rd | 2 - man/validClimR.Rd | 13 +++++-- src/HiClimR.f90 | 17 +++++---- 21 files changed, 278 insertions(+), 165 deletions(-)
Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological (developmental) processes to capture evolutionary signals in developmental transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>
Diff between myTAI versions 0.0.2 dated 2014-12-27 and 0.1.0 dated 2015-05-24
myTAI-0.0.2/myTAI/man/combinatorialSignificance.Rd |only myTAI-0.1.0/myTAI/DESCRIPTION | 19 myTAI-0.1.0/myTAI/MD5 | 160 ++-- myTAI-0.1.0/myTAI/NAMESPACE | 7 myTAI-0.1.0/myTAI/R/CollapseReplicates.R |only myTAI-0.1.0/myTAI/R/EarlyConservationTest.R | 60 + myTAI-0.1.0/myTAI/R/FilterRNASeqCT.R |only myTAI-0.1.0/myTAI/R/FlatLineTest.R | 52 + myTAI-0.1.0/myTAI/R/PlotBarRE.R | 12 myTAI-0.1.0/myTAI/R/PlotCorrelation.R | 18 myTAI-0.1.0/myTAI/R/PlotDistribution.R | 6 myTAI-0.1.0/myTAI/R/PlotMeans.R | 4 myTAI-0.1.0/myTAI/R/PlotPattern.R | 186 ++++- myTAI-0.1.0/myTAI/R/PlotRE.R | 2 myTAI-0.1.0/myTAI/R/ReductiveHourglassTest.R | 48 - myTAI-0.1.0/myTAI/R/TAI.R | 7 myTAI-0.1.0/myTAI/R/TDI.R | 4 myTAI-0.1.0/myTAI/R/age.apply.R | 11 myTAI-0.1.0/myTAI/R/base.R | 23 myTAI-0.1.0/myTAI/R/bootMatrix.R | 16 myTAI-0.1.0/myTAI/R/combinatorialSignificance.R | 35 - myTAI-0.1.0/myTAI/R/datasets.R | 16 myTAI-0.1.0/myTAI/R/ecScore.R | 3 myTAI-0.1.0/myTAI/R/pMatrix.R | 5 myTAI-0.1.0/myTAI/R/pStrata.R |only myTAI-0.1.0/myTAI/R/rel_exp.R | 16 myTAI-0.1.0/myTAI/R/tf.R | 10 myTAI-0.1.0/myTAI/README.md | 125 +-- myTAI-0.1.0/myTAI/build/vignette.rds |binary myTAI-0.1.0/myTAI/inst/doc/Advanced.R | 78 -- myTAI-0.1.0/myTAI/inst/doc/Advanced.Rmd | 141 ---- myTAI-0.1.0/myTAI/inst/doc/Advanced.html | 113 --- myTAI-0.1.0/myTAI/inst/doc/Intermediate.R | 66 - myTAI-0.1.0/myTAI/inst/doc/Intermediate.Rmd | 78 +- myTAI-0.1.0/myTAI/inst/doc/Intermediate.html | 79 +- myTAI-0.1.0/myTAI/inst/doc/Introduction.R | 160 ++-- myTAI-0.1.0/myTAI/inst/doc/Introduction.Rmd | 551 ++++++++++------ myTAI-0.1.0/myTAI/inst/doc/Introduction.html | 406 +++++++---- myTAI-0.1.0/myTAI/man/CollapseReplicates.Rd |only myTAI-0.1.0/myTAI/man/CombinatorialSignificance.Rd |only myTAI-0.1.0/myTAI/man/DivergenceExpressionSetExample.Rd | 10 myTAI-0.1.0/myTAI/man/EarlyConservationTest.Rd | 27 myTAI-0.1.0/myTAI/man/FilterRNASeqCT.Rd |only myTAI-0.1.0/myTAI/man/FlatLineTest.Rd | 29 myTAI-0.1.0/myTAI/man/MatchMap.Rd | 9 myTAI-0.1.0/myTAI/man/PhyloExpressionSetExample.Rd | 10 myTAI-0.1.0/myTAI/man/PlotBarRE.Rd | 6 myTAI-0.1.0/myTAI/man/PlotCorrelation.Rd | 13 myTAI-0.1.0/myTAI/man/PlotDistribution.Rd | 6 myTAI-0.1.0/myTAI/man/PlotMeans.Rd | 4 myTAI-0.1.0/myTAI/man/PlotPattern.Rd | 73 +- myTAI-0.1.0/myTAI/man/PlotRE.Rd | 4 myTAI-0.1.0/myTAI/man/RE.Rd | 8 myTAI-0.1.0/myTAI/man/REMatrix.Rd | 9 myTAI-0.1.0/myTAI/man/ReductiveHourglassTest.Rd | 27 myTAI-0.1.0/myTAI/man/TAI.Rd | 8 myTAI-0.1.0/myTAI/man/TDI.Rd | 6 myTAI-0.1.0/myTAI/man/age.apply.Rd | 7 myTAI-0.1.0/myTAI/man/bar.colors.Rd | 8 myTAI-0.1.0/myTAI/man/bootMatrix.Rd | 12 myTAI-0.1.0/myTAI/man/ecScore.Rd | 5 myTAI-0.1.0/myTAI/man/is.ExpressionSet.Rd | 4 myTAI-0.1.0/myTAI/man/omitMatrix.Rd | 6 myTAI-0.1.0/myTAI/man/pMatrix.Rd | 7 myTAI-0.1.0/myTAI/man/pStrata.Rd |only myTAI-0.1.0/myTAI/man/rhScore.Rd | 2 myTAI-0.1.0/myTAI/man/tf.Rd | 12 myTAI-0.1.0/myTAI/src/RcppExports.cpp | 94 +- myTAI-0.1.0/myTAI/src/rcpp_funcs.cpp | 2 myTAI-0.1.0/myTAI/tests |only myTAI-0.1.0/myTAI/vignettes/Advanced.Rmd | 141 ---- myTAI-0.1.0/myTAI/vignettes/Intermediate.Rmd | 78 +- myTAI-0.1.0/myTAI/vignettes/Introduction.Rmd | 551 ++++++++++------ 73 files changed, 2033 insertions(+), 1662 deletions(-)
Title: Penalized Likelihood Estimation under the Joint Cox Models
Between TTP and OS for Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between TTP and OS for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <emura@stat.ncu.edu.tw>
Diff between joint.Cox versions 1.0 dated 2015-02-28 and 1.1 dated 2015-05-24
DESCRIPTION | 10 - MD5 | 14 +- R/joint.Cox-internal.R | 250 +++++++++++++++++++++++----------------------- R/jointCox.indep.reg.R |only R/jointCox.reg.R | 229 +++++++++++++++++++++--------------------- data |only man/dataOvarian.Rd |only man/joint.Cox-package.Rd | 11 +- man/jointCox.indep.reg.Rd |only man/jointCox.reg.Rd | 85 +++++++++------ 10 files changed, 315 insertions(+), 284 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts
('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and
supporting most output formats of R graphics including PNG, PDF and
SVG. Text glyphs will be converted into polygons or raster images,
hence after the plot has been created, it no longer relies on the font files.
No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-1 dated 2015-04-27 and 0.4-2 dated 2015-05-24
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- inst/NEWS.Rd | 8 ++++++++ man/showtext.auto.Rd | 2 +- man/showtext.begin.Rd | 2 +- man/showtext.end.Rd | 2 +- man/showtext.opts.Rd | 2 +- src/fonts.c | 44 ++++++++++++++++++++++++++------------------ 8 files changed, 50 insertions(+), 34 deletions(-)
Title: Simulating Data to Study Performance of Clustering Algorithms
Description: The utility of this package is in simulating mixtures of Gaussian
distributions with different levels of overlap between mixture
components. Pairwise overlap, defined as a sum of two
misclassification probabilities, measures the degree of
interaction between components and can be readily employed to
control the clustering complexity of datasets simulated from
mixtures. These datasets can then be used for systematic
performance investigation of clustering and finite mixture
modeling algorithms. Among other capabilities of 'MixSim', there
are computing the exact overlap for Gaussian mixtures,
simulating Gaussian and non-Gaussian data, simulating outliers
and noise variables, calculating various measures of agreement
between two partitionings, and constructing parallel
distribution plots for the graphical display of finite mixture
models.
Author: Volodymyr Melnykov [aut, cre],
Wei-Chen Chen [aut],
Ranjan Maitra [aut]
Maintainer: Volodymyr Melnykov <vmelnykov@cba.ua.edu>
Diff between MixSim versions 1.0-9 dated 2013-12-10 and 1.1-1 dated 2015-05-24
DESCRIPTION | 15 ++-- MD5 | 20 +++-- NAMESPACE | 10 ++ NEWS |only R/main.R | 102 +++++++++++++++++++++++++++--- cleanup |only man/MixGOM.Rd |only man/overlapGOM.Rd |only man/print.summary.Rd | 10 +- src/libEVD.c | 24 +------ src/libMixSim.c | 16 ++-- src/libOverlap.c | 173 +++++++++++++++++++++++++++++++++++++++++++++------ src/overlap.h | 4 - 13 files changed, 296 insertions(+), 78 deletions(-)