Title: Helper Functions for Rmd Documents
Description: A series of functions to aid in repeated tasks for Rmd documents. All details are to my personal preference, though I am happy to add flexibility if there are use cases I am missing. I will continue updating with new functions as I add utility functions for myself.
Author: Mark Peterson
Maintainer: Mark Peterson <mark.phillip.peterson@gmail.com>
Diff between rmdHelpers versions 1.0 dated 2016-04-11 and 1.2 dated 2016-07-11
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++------ NAMESPACE | 1 + R/formatEffectTable.R |only R/myFrac.R | 11 +++++++++-- R/toSetGlobalVariables.R |only README.md |only build/partial.rdb |binary man/formatEffectTable.Rd |only man/myFrac.Rd | 18 +++++++++++++++--- man/refNote.Rd | 46 +++++++++++++++++++++++++++++++++++++++++++++- 11 files changed, 85 insertions(+), 17 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>
Diff between piecewiseSEM versions 1.1.2 dated 2016-06-06 and 1.1.3 dated 2016-07-11
DESCRIPTION | 8 +-- MD5 | 28 +++++++------ NAMESPACE | 16 ++++--- NEWS.md | 8 +++ R/endogenous.reverse.R |only R/get.scaled.data.R | 12 +++-- R/sem.basis.set.R | 4 - R/sem.coefs.R | 36 +++++++++-------- R/sem.missing.paths.R | 89 +++++++++++++++++--------------------------- R/sem.model.fits.R | 53 +++++++++++++++----------- README.md | 2 build/vignette.rds |binary inst/doc/piecewiseSEM.html | 10 ++-- man/endogenous.reverse.Rd |only man/piecewiseSEM-package.Rd | 8 --- man/sem.coefs.Rd | 6 ++ 16 files changed, 145 insertions(+), 135 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.0-1 dated 2016-06-06 and 3.0-2 dated 2016-07-11
DESCRIPTION | 10 ++-- MD5 | 36 +++++++++-------- NEWS | 7 +++ R/grpreg.R | 97 +++++++++++++++++++--------------------------- R/grpsurv.R | 65 +++++++++--------------------- R/predict.cv.R | 2 R/reorderGroups.R |only build/vignette.rds |binary data/Birthwt.RData |binary data/Lung.RData |binary inst/doc/penalties.pdf |binary inst/doc/quick-start.Rnw | 4 - inst/doc/quick-start.pdf |binary inst/tests/coerce.R |only man/grpreg-package.Rd | 42 ++++++++++--------- man/grpreg.Rd | 5 -- man/grpsurv.Rd | 5 -- man/predict.Rd | 2 tests/test.R | 1 vignettes/quick-start.Rnw | 4 - 20 files changed, 125 insertions(+), 155 deletions(-)
Title: Generate Data Summary in a Tidy Format
Description: Functions that simplify the process of generating print-ready data summary using 'dplyr' syntax.
Author: Hao Zhu [aut, cre],
Thomas Travison [ctb],
Timothy Tsai [ctb],
Akhmed Umyarov [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between ezsummary versions 0.2.0 dated 2016-07-03 and 0.2.1 dated 2016-07-11
DESCRIPTION | 12 ++++--- MD5 | 14 ++++----- R/ezsummary_categorical.r | 3 + R/ezsummary_quantitative.r | 3 + inst/doc/intro_to_ezsummary_0.2.0.R | 2 - inst/doc/intro_to_ezsummary_0.2.0.Rmd | 2 - inst/doc/intro_to_ezsummary_0.2.0.html | 50 ++++++++++++++++----------------- vignettes/intro_to_ezsummary_0.2.0.Rmd | 2 - 8 files changed, 46 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-26 0.1.4.2
2014-05-02 0.1.4.1
2013-08-28 0.1.4
2012-09-19 0.1.1
2012-05-23 0.1.0
2012-04-27 0.0.8
2012-04-23 0.0.2
Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized
queries.
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>
Diff between RODBCext versions 0.2.5 dated 2015-07-12 and 0.2.6 dated 2016-07-11
DESCRIPTION | 8 - MD5 | 14 +- NEWS | 7 + build/vignette.rds |binary inst/doc/Parameterized_SQL_queries.Rmd | 3 inst/doc/Parameterized_SQL_queries.html | 191 +++++++++++++++++++++----------- src/RODBCext.c | 5 vignettes/Parameterized_SQL_queries.Rmd | 3 8 files changed, 153 insertions(+), 78 deletions(-)
Title: Kernel k Nearest Neighbors
Description: Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between KernelKnn versions 1.0 dated 2016-07-09 and 1.0.1 dated 2016-07-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Makevars | 4 ++-- src/distance_metrics.cpp | 2 ++ 4 files changed, 10 insertions(+), 8 deletions(-)
Title: A Two-Stage Approach to Maximize Interpretability of Drug
Response Models Based on Multiple Molecular Data Types
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016, in press), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>
Diff between TANDEM versions 0.9.1 dated 2016-06-13 and 0.9.2 dated 2016-07-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/functions.R | 36 +++++++++++++++++++++++++++++------- inst/doc/my-vignette.html | 8 ++++---- man/nested.cv.Rd | 12 ++++++++++-- man/tandem.Rd | 6 +++++- 6 files changed, 57 insertions(+), 23 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 2.1.1 dated 2016-07-03 and 2.2 dated 2016-07-11
DESCRIPTION | 8 ++--- MD5 | 10 +++++- R/CV.CondPoisson.R |only R/Performance.CondPoisson.R |only R/SampleSize.CondPoisson.R |only man/CV.CondPoisson.Rd |only man/Performance.CondPoisson.Rd |only man/SampleSize.CondPoisson.Rd |only man/Sequential-package.Rd | 64 +++++++++++++++++++++++++++++++++-------- 9 files changed, 64 insertions(+), 18 deletions(-)
Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au],
Caroline Simonis [au], Laurent Lellouch [main ctrb],
Ethan C. Brown [ctrb], Marion Depraetere [ctrb],
Camille Desjonqueres [ctrb], Francois Fabianek [ctrb],
Amandine Gasc [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb],
Jean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz [ctrb],
Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],
Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>
Diff between seewave versions 2.0.2 dated 2015-07-28 and 2.0.4 dated 2016-07-11
DESCRIPTION | 16 MD5 | 88 +- NEWS | 45 + R/seewave.r | 1242 ++++++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/seewave_IO.pdf |binary inst/doc/seewave_analysis.R | 4 inst/doc/seewave_analysis.pdf |binary inst/doc/seewave_analysis.rnw | 36 - man/Q.Rd | 3 man/SAX.Rd | 2 man/TKEO.Rd | 17 man/afilter.Rd | 3 man/attenuation.Rd | 4 man/bwfilter.Rd |only man/ceps.Rd | 11 man/cepstro.Rd | 4 man/combfilter.Rd | 7 man/cutspec.Rd | 2 man/dBscale.Rd | 2 man/fdoppler.Rd | 3 man/ffilter.Rd | 5 man/fir.Rd | 7 man/fpeaks.Rd | 9 man/ftwindow.Rd | 8 man/ifreq.Rd | 6 man/lfs.Rd | 2 man/listen.Rd | 2 man/meanspec.Rd | 13 man/mel.Rd | 2 man/melfilterbank.Rd |only man/phaseplot.Rd | 10 man/phaseplot2.Rd |only man/preemphasis.Rd |only man/rugo.Rd | 2 man/seewave.internal.Rd | 1 man/seewave.package.Rd | 26 man/songmeter.Rd | 8 man/sox.Rd | 2 man/spec.Rd | 19 man/spectro.Rd | 16 man/spectro3D.Rd | 8 man/squarefilter.Rd | 2 man/symba.Rd | 8 man/synth2.Rd | 4 man/zcr.Rd | 11 vignettes/seewave_analysis.rnw | 36 - 47 files changed, 1010 insertions(+), 686 deletions(-)
Title: An Interface for MIXMOD
Description: Supervised and unsupervised classification with MIXture MODelling.
Author: Florent Langrognet [aut, cre],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [ctb],
C. Biernacki [ctb],
G. Celeux [ctb],
G. Govaert [ctb]
Maintainer: Florent Langrognet <florent.langrognet@univ-fcomte.fr>
Diff between Rmixmod versions 2.0.3 dated 2015-10-06 and 2.1.0 dated 2016-07-11
Rmixmod-2.0.3/Rmixmod/inst/CITATION |only Rmixmod-2.1.0/Rmixmod/DESCRIPTION | 34 Rmixmod-2.1.0/Rmixmod/MD5 | 551 ++++++---- Rmixmod-2.1.0/Rmixmod/NAMESPACE | 19 Rmixmod-2.1.0/Rmixmod/R/CompositeModel.R | 7 Rmixmod-2.1.0/Rmixmod/R/CompositeParameter.R | 7 Rmixmod-2.1.0/Rmixmod/R/GaussianModel.R | 5 Rmixmod-2.1.0/Rmixmod/R/GaussianParameter.R | 6 Rmixmod-2.1.0/Rmixmod/R/Mixmod.R | 194 +++ Rmixmod-2.1.0/Rmixmod/R/MixmodCluster.R | 111 +- Rmixmod-2.1.0/Rmixmod/R/MixmodLearn.R | 101 + Rmixmod-2.1.0/Rmixmod/R/MixmodPredict.R | 29 Rmixmod-2.1.0/Rmixmod/R/MixmodResults.R | 26 Rmixmod-2.1.0/Rmixmod/R/MultinomialModel.R | 7 Rmixmod-2.1.0/Rmixmod/R/Parameter.R | 7 Rmixmod-2.1.0/Rmixmod/R/Rmixmod.R | 9 Rmixmod-2.1.0/Rmixmod/R/Strategy.R | 141 +- Rmixmod-2.1.0/Rmixmod/R/global.R | 1 Rmixmod-2.1.0/Rmixmod/R/zzz.R | 2 Rmixmod-2.1.0/Rmixmod/configure |only Rmixmod-2.1.0/Rmixmod/configure.ac |only Rmixmod-2.1.0/Rmixmod/inst/XML_specs |only Rmixmod-2.1.0/Rmixmod/man/MixmodXmlInput-class.Rd |only Rmixmod-2.1.0/Rmixmod/man/Rmixmod-package.Rd | 8 Rmixmod-2.1.0/Rmixmod/man/barplot-methods.Rd | 10 Rmixmod-2.1.0/Rmixmod/man/histCluster.Rd | 4 Rmixmod-2.1.0/Rmixmod/man/mixmodCluster.Rd | 9 Rmixmod-2.1.0/Rmixmod/man/mixmodCompositeModel.Rd | 2 Rmixmod-2.1.0/Rmixmod/man/mixmodGaussianModel.Rd | 2 Rmixmod-2.1.0/Rmixmod/man/mixmodLearn.Rd | 9 Rmixmod-2.1.0/Rmixmod/man/mixmodMultinomialModel.Rd | 2 Rmixmod-2.1.0/Rmixmod/man/mixmodPredict.Rd | 5 Rmixmod-2.1.0/Rmixmod/man/mixmodStrategy.Rd | 26 Rmixmod-2.1.0/Rmixmod/man/mixmodXmlInput.Rd |only Rmixmod-2.1.0/Rmixmod/src/ClusteringInputHandling.cpp | 78 + Rmixmod-2.1.0/Rmixmod/src/ClusteringOutputHandling.cpp | 34 Rmixmod-2.1.0/Rmixmod/src/ClusteringOutputHandling.h | 7 Rmixmod-2.1.0/Rmixmod/src/Makevars | 15 Rmixmod-2.1.0/Rmixmod/src/Makevars.UNIX |only Rmixmod-2.1.0/Rmixmod/src/Makevars.old |only Rmixmod-2.1.0/Rmixmod/src/Makevars.static |only Rmixmod-2.1.0/Rmixmod/src/Makevars.win |only Rmixmod-2.1.0/Rmixmod/src/OutputHandling.cpp | 15 Rmixmod-2.1.0/Rmixmod/src/XmlMakevars |only Rmixmod-2.1.0/Rmixmod/src/XmlMakevars.in |only Rmixmod-2.1.0/Rmixmod/src/clusteringMain.cpp | 286 +++-- Rmixmod-2.1.0/Rmixmod/src/get_symbolic_link.sh |only Rmixmod-2.1.0/Rmixmod/src/learnMain.cpp | 13 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringInput.cpp | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringInput.h | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringMain.cpp | 108 + Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringMain.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringModelOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringModelOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringOutput.cpp | 323 ++++- Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringOutput.h | 9 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringStrategy.cpp | 64 - Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringStrategy.h | 11 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringStrategyInit.cpp | 5 Rmixmod-2.1.0/Rmixmod/src/mixmod/Clustering/ClusteringStrategyInit.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnInput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnInput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnMain.cpp | 35 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnMain.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnModelOutput.cpp | 8 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnModelOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnStrategy.cpp | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Learn/LearnStrategy.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictInput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictInput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictMain.cpp | 11 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictMain.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictModelOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictModelOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictStrategy.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/DiscriminantAnalysis/Predict/PredictStrategy.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/Algo.cpp | 82 + Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/Algo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/CEMAlgo.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/CEMAlgo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/EMAlgo.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/EMAlgo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/MAPAlgo.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/MAPAlgo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/MAlgo.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/MAlgo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/SEMAlgo.cpp | 12 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Algo/SEMAlgo.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/BICCriterion.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/BICCriterion.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/CVCriterion.cpp | 25 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/CVCriterion.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/Criterion.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/Criterion.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/CriterionOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/CriterionOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/ICLCriterion.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/ICLCriterion.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/NECCriterion.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Criterion/NECCriterion.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/BinaryData.cpp | 5 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/BinaryData.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/BinarySample.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/BinarySample.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/CompositeData.cpp | 14 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/CompositeData.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/CompositeSample.cpp | 14 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/CompositeSample.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Data.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Data.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/DataDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/DataDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Description.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Description.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/GaussianData.cpp | 11 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/GaussianData.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/GaussianSample.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/GaussianSample.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/IndividualColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/IndividualColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Input.cpp | 15 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Input.h | 8 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Label.cpp | 56 - Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Label.h | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/LabelDescription.cpp | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/LabelDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/LikelihoodOutput.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/LikelihoodOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ModelOutput.cpp | 35 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ModelOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ParameterDescription.cpp | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ParameterDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Partition.cpp | 54 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Partition.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Proba.cpp | 11 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Proba.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ProbaDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ProbaDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ProbaOutput.cpp | 38 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/ProbaOutput.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/QualitativeColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/QualitativeColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/QuantitativeColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/QuantitativeColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Sample.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/Sample.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/UnusedColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/UnusedColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/WeightColumnDescription.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/IO/WeightColumnDescription.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/BinaryModel.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/BinaryModel.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/Model.cpp | 198 +++ Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/Model.h | 8 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/ModelType.cpp | 7 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Model/ModelType.h | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEParameter.cpp | 28 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEjParameter.cpp | 60 - Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEjParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkParameter.cpp | 36 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkjParameter.cpp | 35 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkjParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkjhParameter.cpp | 83 - Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryEkjhParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryParameter.cpp | 42 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/BinaryParameter.h | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/CompositeParameter.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/CompositeParameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianDiagParameter.cpp | 51 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianDiagParameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianEDDAParameter.cpp | 37 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianEDDAParameter.h | 3 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianGeneralParameter.cpp | 79 + Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianGeneralParameter.h | 10 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianHDDAParameter.cpp | 36 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianHDDAParameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianParameter.cpp | 21 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianParameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianSphericalParameter.cpp | 33 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/GaussianSphericalParameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/Parameter.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Kernel/Parameter/Parameter.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/DiagMatrix.cpp | 20 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/DiagMatrix.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/GeneralMatrix.cpp | 17 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/GeneralMatrix.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/Matrix.cpp | 7 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/Matrix.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/SphericalMatrix.cpp | 12 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/SphericalMatrix.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/SymmetricMatrix.cpp | 15 Rmixmod-2.1.0/Rmixmod/src/mixmod/Matrix/SymmetricMatrix.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Error.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Error.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/ExampleDataUtil.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/ExampleDataUtil.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Random.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Random.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Util.cpp | 62 + Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/Util.h | 77 + Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/DCVException.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/DCVException.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/ErrorEnumerations.h | 9 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/Exception.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/Exception.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/InputException.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/InputException.h | 6 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/NumericException.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/NumericException.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/OtherException.cpp | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/exceptions/OtherException.h | 10 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/Armadillo.h |only Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/Eigen.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/GSL.h |only Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/ITpp.h |only Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/NEWMAT.h | 11 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/maths/SelectLibrary.h | 28 Rmixmod-2.1.0/Rmixmod/src/mixmod/Utilities/mixmod.h | 2 Rmixmod-2.1.0/Rmixmod/src/mixmod/mixmod_r.mk | 4 Rmixmod-2.1.0/Rmixmod/src/mixmod_iostream |only Rmixmod-2.1.0/Rmixmod/src/myClusteringOutputHandling.h.txt |only Rmixmod-2.1.0/Rmixmod/src/myClusteringOutputHandling.txt |only Rmixmod-2.1.0/Rmixmod/src/myclusteringMain.txt |only Rmixmod-2.1.0/Rmixmod/src/predictMain.cpp | 12 Rmixmod-2.1.0/Rmixmod/tests/Rplots.pdf |only Rmixmod-2.1.0/Rmixmod/tests/clustering1test.R |only Rmixmod-2.1.0/Rmixmod/tests/clusteringParametertest.R |only Rmixmod-2.1.0/Rmixmod/tests/clusteringPartitiontest.R |only Rmixmod-2.1.0/Rmixmod/tests/heterogeneousDAtest.R | 2 Rmixmod-2.1.0/Rmixmod/tests/init-param+partition |only Rmixmod-2.1.0/Rmixmod/tests/init-param+partition. |only Rmixmod-2.1.0/Rmixmod/tests/init-param+partition.tar |only Rmixmod-2.1.0/Rmixmod/tests/mass |only Rmixmod-2.1.0/Rmixmod/tests/ssupervised.R |only Rmixmod-2.1.0/Rmixmod/tests/test.R | 2 245 files changed, 2803 insertions(+), 1292 deletions(-)
Title: Multivariate Peaks-over-Threshold Modelling for Spatial Extreme
Events
Description: Tools for high-dimensional peaks-over-threshold inference and simulation
of spatial extremal processes.
Author: Raphael de Fondeville [aut, cre]
Maintainer: Raphael de Fondeville <raphael.de-fondeville@epfl.ch>
Diff between mvPot versions 0.1.0 dated 2016-06-23 and 0.1.1 dated 2016-07-11
DESCRIPTION | 11 +++++---- MD5 | 35 +++++++++++++++--------------- NEWS.md |only R/censored_likelihood.R | 27 ++++++++++++----------- R/generating_vector.R | 6 ++--- R/gradient_score.R | 22 +++++++++---------- R/mvNormQMC.R | 16 +++++++------- R/rBrownResnick.R | 27 ++++++++++++----------- R/rMvtPar.R | 19 ++++++++-------- R/spectral_likelihood.R | 18 +++++++-------- man/censoredLikelihood.Rd | 27 ++++++++++++----------- man/genVecQMC.Rd | 6 ++--- man/mvPot-package.Rd | 48 ++++++++++++++++++++---------------------- man/mvtNormQuasiMonteCarlo.Rd | 16 +++++++------- man/scoreEstimation.Rd | 22 +++++++++---------- man/simulBrownResnick.Rd | 27 ++++++++++++----------- man/simulPareto.Rd | 19 ++++++++-------- man/spectralLikelihood.Rd | 18 +++++++-------- src/mvnCppAdaptedSTL.cpp | 2 - 19 files changed, 186 insertions(+), 180 deletions(-)
Title: Utility Functions by Youyi, Krisz and Others
Description: A miscellaneous set of functions for printing, plotting, kernels, etc. Additional contributors are acknowledged on individual function help pages.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between kyotil versions 2016.7-7 dated 2016-07-08 and 2016.7-9 dated 2016-07-11
DESCRIPTION | 10 +-- MD5 | 8 +- R/print.R | 178 +++++++++++++++++++++++++++++----------------------------- R/string.R | 48 +++++++-------- man/random.Rd | 7 +- 5 files changed, 129 insertions(+), 122 deletions(-)
Title: Generalized Non-negative Matrix Factorization Based on Renyi
Divergence
Description: This package performs generalized non-negative matrix factorization based on Renyi divergence.
Author: Jose M. Maisog, Guoli Wang, Karthik Devarajan
Maintainer: Jose M. Maisog <bravas02@gmail.com>
Diff between gnmf versions 0.7 dated 2014-01-25 and 0.7.1 dated 2016-07-11
DESCRIPTION | 6 +++--- MD5 | 3 ++- src/Makevars |only 3 files changed, 5 insertions(+), 4 deletions(-)
Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Maintainer: Han Zhang <han.zhang2@nih.gov>
Diff between ARTP2 versions 0.9.30 dated 2016-07-11 and 0.9.30.1 dated 2016-07-11
ARTP2-0.9.30.1/ARTP2/DESCRIPTION | 10 +++++----- ARTP2-0.9.30.1/ARTP2/MD5 | 6 ++++-- ARTP2-0.9.30.1/ARTP2/configure |only ARTP2-0.9.30.1/ARTP2/configure.ac |only ARTP2-0.9.30.1/ARTP2/src/Makevars.in |only ARTP2-0.9.30/ARTP2/src/Makevars |only 6 files changed, 9 insertions(+), 7 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform and the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library.
Author: Lampros Mouselimis [aut, cre],
Sight Machine [cph] (findHOGFeatures function of the SimpleCV computer
vision platform),
Johannes Buchner [cph] (average_hash, dhash and phash functions of the
ImageHash python library)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.0.1 dated 2016-07-09 and 1.0.2 dated 2016-07-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 24 +++++++++++++++++++----- README.md | 8 +++----- inst/doc/The_OpenImageR_package.html | 18 +++++++++--------- src/Makevars | 4 ++-- src/Makevars.win | 4 ++-- src/dilation_erosion_rgb2gray.cpp | 6 +++++- src/hog_features.cpp | 18 +++++++++++++----- src/image_hashing.cpp | 16 ++++++++++++++++ src/utils.cpp | 9 ++++++++- 11 files changed, 91 insertions(+), 44 deletions(-)
Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'.
Provides 'ggplot2' themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata',
'Excel', and 'The Wall Street Journal', among others.
Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre],
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb, cph] (Code from the ggplot2 package.),
Justin Talbot [ctb] (Code from the labeling package),
Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 3.0.3 dated 2016-04-09 and 3.2.0 dated 2016-07-11
DESCRIPTION | 14 +- MD5 | 35 ++--- NAMESPACE | 4 NEWS | 15 ++ R/banking.R | 171 ++++++------------------- R/economist.R | 14 +- R/gdocs.R | 2 R/ggthemes-data.R | 265 +++++++++++++++++++++------------------- R/hc.R | 4 R/ptol.R |only R/shapes.R | 3 R/stata.R | 4 build/vignette.rds |binary inst/doc/ggthemes.R | 11 + inst/doc/ggthemes.html | 28 +++- man/bank_slopes.Rd | 90 +------------ man/ptol_pal.Rd |only man/scale_ptol.Rd |only vignettes/children/examples.Rmd | 17 ++ vignettes/children/intro.Rmd | 1 20 files changed, 309 insertions(+), 369 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear and Logistic Mixed Models (AIREML
Algorithm), Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.4.5 dated 2016-03-30 and 1.4.6 dated 2016-07-11
DESCRIPTION | 17 ++-- MD5 | 55 +++++++++----- NAMESPACE | 13 +-- NEWS | 8 ++ R/bm.r | 4 - R/bm_bind.r | 4 - R/bm_files.r | 32 +++----- R/bm_product.r | 12 +-- R/gwas.r | 75 ++++++++++++++----- R/lmm_aireml.r | 152 ++++++++++++++++++++-------------------- R/lmm_diago.r | 12 +-- R/logistic_mm_aireml.r |only R/score.r |only TODO |only man/LD.Rd | 2 man/association.test.Rd | 81 +++++++++++++++------ man/lmm.aireml.Rd | 6 + man/logistic.mm.aireml.Rd |only man/score.fixed.Rd |only man/score.variance.Rd |only src/ai-reml-1k-covar.h | 4 - src/ai-reml-1k.h | 4 - src/ai-reml-logit-1k-covar.h |only src/ai-reml-logit-1k.h |only src/ai-reml-logit-nk-covar.h |only src/ai-reml-logit-nk.h |only src/ai-reml-nk-covar.h | 4 - src/ai-reml-nk.h | 3 src/export-aireml-1k.cpp | 154 ++++++++++++++++++++--------------------- src/export-aireml-logit-1k.cpp |only src/export-aireml-logit-nk.cpp |only src/export-aireml-nk.cpp | 153 ++++++++++++++++++++-------------------- src/gwas_lmm_score.cpp |only src/m4_read_vcf.cpp | 36 ++++++--- vignettes/gaston.Rnw | 43 +++++++++-- 35 files changed, 504 insertions(+), 370 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.991-1 dated 2016-05-31 and 5.0-0 dated 2016-07-11
DESCRIPTION | 11 +- MD5 | 51 +++++++----- NAMESPACE | 114 +++++++++++++-------------- R/WaldTest.R | 2 R/abs_approx.R |only R/calc_posterior.R | 65 ++++++++------- R/coef.R | 10 +- R/deltaMethod.R |only R/gdd.R | 20 ++-- R/gdina.R | 35 ++++++-- R/gdina_proc_noninvariance_multiple_groups.R |only R/gdina_proc_sequential_items.R |only R/item_by_group.R |only R/mcdina.R | 7 + R/numerical_Hessian.R | 66 +++++++-------- R/osink.R | 4 R/slca.R | 2 R/summary_sink.R |only data/data.cdm04.rda |only inst/NEWS | 30 +++++++ man/CDM-package.Rd | 102 +++++++++++++----------- man/abs_approx.Rd |only man/data.cdm.Rd | 34 +++++++- man/deltaMethod.Rd |only man/din.Rd | 3 man/gdina.Rd | 91 ++++++++++++++++----- man/item_by_group.Rd |only man/numerical_Hessian.Rd | 3 man/osink.Rd | 5 - man/sequential.items.Rd | 14 +++ man/slca.Rd | 60 ++++++++------ man/summary_sink.Rd |only 32 files changed, 460 insertions(+), 269 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 by Baoxun Xu, Joshua Zhexue Huang, Graham Williams, Qiang
Wang, and Yunming Ye (2012) <DOI:10.4018/jdwm.2012040103>. 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 1.5.29 dated 2015-10-10 and 1.5.47 dated 2016-07-11
DESCRIPTION | 26 ++++++++++--------- MD5 | 32 ++++++++++++------------ R/wsrf.R | 2 + R/wsrf.R.in | 2 + build/vignette.rds |binary configure | 14 +++++++++- inst/NEWS.Rd | 24 ++++++++++++++++++ inst/doc/wsrf-guide.html | 27 ++++++++++---------- src/c4_5_var_selector.cpp | 24 ++++++++++-------- src/dataset.h | 12 ++++----- src/meta_data.cpp | 13 ++++++--- src/meta_data.h | 61 ++++++++++++++++++++++++---------------------- src/node.h | 15 ++++++----- src/rforest.cpp | 2 - src/utility.h | 4 +-- src/var_selector.h | 4 +-- src/wsrf.cpp | 2 - 17 files changed, 160 insertions(+), 104 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero-or-One Inflated
Beta Regression
Description: Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu <fang.liu.131@nd.edu> with contributions from Yunchuan Kong
Maintainer: Fang Liu <fang.liu.131@nd.edu>
Diff between zoib versions 1.3.4 dated 2016-05-21 and 1.4.0 dated 2016-07-11
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/zoib.R | 104 +++++++++++++++++++++++++++++++++++++++++----------- man/zoib-package.Rd | 4 +- tests/test1.R | 2 - 5 files changed, 94 insertions(+), 32 deletions(-)
Title: R Interface to the Protocol Buffers API
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our paper
in the Journal of Statistical Software (2016, v71i02).
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.3 dated 2015-08-25 and 0.4.4 dated 2016-07-11
ChangeLog | 46 ++++++++++++++++++++++++++++++++ DESCRIPTION | 17 +++++------- MD5 | 53 +++++++++++++++++++++++--------------- R/rexp_obj.R | 5 ++- R/serialize_pb.R | 30 ++++++++++----------- README.md | 6 ++-- build/vignette.rds |binary inst/CITATION | 44 +++++++++++++++++++------------ inst/NEWS.Rd | 24 +++++++++++++++++ inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.R |only inst/doc/RProtoBuf-paper.Rnw |only inst/doc/RProtoBuf-paper.pdf |only inst/doc/RProtoBuf-quickref.pdf |binary inst/doc/RProtoBuf-unitTests.R | 12 ++++---- inst/doc/RProtoBuf-unitTests.Rnw | 12 ++++---- inst/doc/RProtoBuf-unitTests.pdf |binary man/EnumDescriptor-class.Rd | 2 - man/Message-class.Rd | 2 - man/MethodDescriptor-class.Rd | 2 - man/ServiceDescriptor-class.Rd | 2 - man/serialize_pb.Rd | 41 +++++++++++++---------------- src/Makevars.win | 12 ++------ vignettes/RProtoBuf-paper.Rnw |only vignettes/RProtoBuf-paper.bib |only vignettes/RProtoBuf-unitTests.Rnw | 12 ++++---- vignettes/figures |only vignettes/jss.cls |only vignettes/proto |only 29 files changed, 205 insertions(+), 117 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut, cre],
Julia Wrobel [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb],
So Young Park [ctb],
David L. Miller [ctb],
Ana-Maria Staicu [ctb]
Maintainer: Lei Huang <huangracer@gmail.com>
Diff between refund versions 0.1-14 dated 2016-01-28 and 0.1-15 dated 2016-07-11
DESCRIPTION | 63 +++-- MD5 | 272 ++++++++++++------------ NAMESPACE | 19 + R/DTI-data.R | 2 R/DTI2-data.R | 8 R/GLS_CS.R | 5 R/Gibbs_CS_FPCA.R | 7 R/Gibbs_CS_Wish.R | 82 +++---- R/Gibbs_Mult_FPCA.R | 11 R/Gibbs_Mult_Wish.R | 95 ++++---- R/OLS_CS.R | 5 R/VB_CS_FPCA.R | 35 ++- R/VB_CS_Wish.R | 7 R/VB_Mult_FPCA.R | 41 ++- R/VB_Mult_Wish.R | 9 R/bayes_fosr.R | 6 R/coefficients.pfr.R | 150 ++++++------- R/dt_basis.R | 2 R/fgam.R | 9 R/fosr.vs.R | 4 R/fpca.face.R | 283 +++++++++++++------------ R/fpca.sc.R | 350 ++++++++++++++++--------------- R/fpca.ssvd.R | 193 ++++++++++------- R/fpca2s.R | 165 ++++++++------ R/pffr-ff.R | 223 +++++++++++-------- R/pffr-ffpc.R | 105 ++++----- R/pffr-methods.R | 2 R/pffr-utilities.R | 46 ++-- R/pffr.R | 129 ++++++----- R/pfr.R | 13 - R/poridge.R |only R/predict.pfr.R | 2 R/summary.pfr.R | 32 +- R/vis.pfr.R | 5 man/DTI.Rd | 4 man/DTI2.Rd | 9 man/PEER.Sim.Rd | 2 man/Predict.matrix.dt.smooth.Rd | 2 man/Predict.matrix.fpc.smooth.Rd | 2 man/Predict.matrix.pcre.random.effect.Rd | 2 man/Predict.matrix.peer.smooth.Rd | 2 man/Predict.matrix.pi.smooth.Rd | 2 man/Xt_siginv_X.Rd | 2 man/af.Rd | 2 man/af_old.Rd | 2 man/amc.Rd | 2 man/bayes_fosr.Rd | 8 man/ccb.fpc.Rd | 2 man/cd4.Rd | 2 man/cmdscale_lanczos.Rd |only man/coef.pffr.Rd | 2 man/coefboot.pffr.Rd | 2 man/coefficients.pfr.Rd | 2 man/create.prep.func.Rd | 2 man/expand.call.Rd | 2 man/f_sum.Rd | 2 man/f_sum2.Rd | 2 man/f_sum4.Rd | 2 man/f_trace.Rd | 2 man/fbps.Rd | 2 man/ff.Rd | 41 ++- man/ffpc.Rd | 2 man/ffpcplot.Rd | 2 man/fgam.Rd | 2 man/fosr.Rd | 2 man/fosr.perm.Rd | 2 man/fosr.vs.Rd | 6 man/fosr2s.Rd | 2 man/fpc.Rd | 2 man/fpca.face.Rd | 151 +++++++------ man/fpca.lfda.Rd | 2 man/fpca.sc.Rd | 22 + man/fpca.ssvd.Rd | 108 +++++---- man/fpca2s.Rd | 58 +++-- man/fpcr.Rd | 2 man/gasoline.Rd | 2 man/getTF.Rd | 2 man/gibbs_cs_fpca.Rd | 7 man/gibbs_cs_wish.Rd | 7 man/gibbs_mult_fpca.Rd | 7 man/gibbs_mult_wish.Rd | 7 man/gls_cs.Rd | 7 man/lf.Rd | 2 man/lf.vd.Rd | 2 man/lf_old.Rd | 2 man/lofocv.Rd | 2 man/lpeer.Rd | 2 man/lpfr.Rd | 2 man/mfpca.sc.Rd | 2 man/model.matrix.pffr.Rd | 2 man/ols_cs.Rd | 7 man/pco_predict_preprocess.Rd |only man/pcre.Rd | 2 man/peer.Rd | 2 man/peer_old.Rd | 2 man/pffr.Rd | 105 +++++---- man/pffr.check.Rd | 2 man/pffrGLS.Rd | 2 man/pffrSim.Rd | 2 man/pfr.Rd | 2 man/pfr_old.Rd | 2 man/pfr_plot.gam.Rd | 2 man/plot.fosr.Rd | 2 man/plot.fosr.vs.Rd | 2 man/plot.fpcr.Rd | 2 man/plot.lpeer.Rd | 2 man/plot.peer.Rd | 2 man/plot.pffr.Rd | 2 man/plot.pfr.Rd | 2 man/predict.fbps.Rd | 2 man/predict.fgam.Rd | 2 man/predict.fosr.vs.Rd | 2 man/predict.pffr.Rd | 2 man/predict.pfr.Rd | 2 man/print.summary.pffr.Rd | 2 man/pwcv.Rd | 2 man/qq.pffr.Rd | 7 man/quadWeights.Rd | 2 man/re.Rd | 2 man/refund-package.Rd | 4 man/residuals.pffr.Rd | 2 man/rlrt.pfr.Rd | 2 man/sff.Rd | 2 man/smooth.construct.dt.smooth.spec.Rd | 2 man/smooth.construct.fpc.smooth.spec.Rd | 2 man/smooth.construct.pco.smooth.spec.Rd |only man/smooth.construct.pcre.smooth.spec.Rd | 2 man/smooth.construct.peer.smooth.spec.Rd | 2 man/smooth.construct.pi.smooth.spec.Rd | 2 man/smooth.construct.pss.smooth.spec.Rd | 2 man/sofa.Rd | 2 man/summary.pffr.Rd | 2 man/summary.pfr.Rd | 4 man/vb_cs_fpca.Rd | 12 - man/vb_cs_wish.Rd | 7 man/vb_mult_fpca.Rd | 11 man/vb_mult_wish.Rd | 7 man/vis.fgam.Rd | 2 man/vis.pfr.Rd | 2 139 files changed, 1759 insertions(+), 1385 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.4 dated 2016-05-23 and 0.6.4.1 dated 2016-07-11
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- R/nhanes.R | 9 ++++--- build/vignette.rds |binary inst/doc/Introducing_nhanesA.Rmd | 5 +++ inst/doc/Introducing_nhanesA.html | 48 +++++++++++++++++++++++++------------- vignettes/Introducing_nhanesA.Rmd | 5 +++ 7 files changed, 56 insertions(+), 31 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt [aut],
Yue Hu [aut, cre],
Oliver Keyes [ctb],
Ben Bolker [ctb]
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.5 dated 2016-03-04 and 0.2.1 dated 2016-07-11
dotwhisker-0.2.0.5/dotwhisker/README.md |only dotwhisker-0.2.1/dotwhisker/DESCRIPTION | 22 dotwhisker-0.2.1/dotwhisker/LICENSE | 4 dotwhisker-0.2.1/dotwhisker/MD5 | 67 dotwhisker-0.2.1/dotwhisker/NAMESPACE | 2 dotwhisker-0.2.1/dotwhisker/NEWS.md | 11 dotwhisker-0.2.1/dotwhisker/R/add_brackets.R | 225 - dotwhisker-0.2.1/dotwhisker/R/by_2sd.R | 7 dotwhisker-0.2.1/dotwhisker/R/dwplot.R | 146 dotwhisker-0.2.1/dotwhisker/R/relabel_predictors.R | 64 dotwhisker-0.2.1/dotwhisker/R/relabel_y_axis.R | 36 dotwhisker-0.2.1/dotwhisker/R/secret_weapon.R | 137 dotwhisker-0.2.1/dotwhisker/R/small_multiple.R | 34 dotwhisker-0.2.1/dotwhisker/build/vignette.rds |binary dotwhisker-0.2.1/dotwhisker/inst/CITATION | 32 dotwhisker-0.2.1/dotwhisker/inst/doc/dotwhisker-vignette.R | 24 dotwhisker-0.2.1/dotwhisker/inst/doc/dotwhisker-vignette.Rmd | 35 dotwhisker-0.2.1/dotwhisker/inst/doc/dotwhisker-vignette.html | 109 dotwhisker-0.2.1/dotwhisker/inst/doc/dwplot-vignette.R | 426 +- dotwhisker-0.2.1/dotwhisker/inst/doc/kl2007_examples.R | 10 dotwhisker-0.2.1/dotwhisker/inst/doc/kl2007_examples.Rmd | 1468 +++++----- dotwhisker-0.2.1/dotwhisker/inst/doc/kl2007_examples.html | 33 dotwhisker-0.2.1/dotwhisker/inst/doc/vignette.bib | 94 dotwhisker-0.2.1/dotwhisker/inst/doc/vignette_dwplot.bib | 120 dotwhisker-0.2.1/dotwhisker/man/add_brackets.Rd | 96 dotwhisker-0.2.1/dotwhisker/man/by_2sd.Rd | 80 dotwhisker-0.2.1/dotwhisker/man/dwplot.Rd | 36 dotwhisker-0.2.1/dotwhisker/man/relabel_predictors.Rd | 74 dotwhisker-0.2.1/dotwhisker/man/relabel_y_axis.Rd | 48 dotwhisker-0.2.1/dotwhisker/man/secret_weapon.Rd | 95 dotwhisker-0.2.1/dotwhisker/man/small_multiple.Rd | 184 - dotwhisker-0.2.1/dotwhisker/vignettes/dotwhisker-vignette.Rmd | 35 dotwhisker-0.2.1/dotwhisker/vignettes/kl2007_examples.Rmd | 1468 +++++----- dotwhisker-0.2.1/dotwhisker/vignettes/vignette.bib | 96 dotwhisker-0.2.1/dotwhisker/vignettes/vignette_dwplot.bib | 122 35 files changed, 2768 insertions(+), 2672 deletions(-)
Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang
Maintainer: Han Zhang <han.zhang2@nih.gov>
Diff between ARTP2 versions 0.9.22 dated 2016-02-11 and 0.9.30 dated 2016-07-11
DESCRIPTION | 8 +-- MD5 | 80 +++++++++++++++++++++------------------ NAMESPACE | 3 - NEWS.md | 3 + R/complete.sum.stat.R | 9 +++- R/data.parse.R | 4 - R/exclude.snps.R |only R/extract.position.information.R |only R/filter.raw.geno.R | 24 +++++------ R/filter.reference.geno.R | 2 R/find.snps.in.regions.R | 3 + R/gen.stat.miss.R |only R/generate.normal.statistics.R | 15 ++++++- R/generate.pathway.pvalue.stat.R | 2 R/inflation.R |only R/load.pathway.definition.R | 11 +++++ R/load.summary.files.R | 14 +++++- R/load.summary.statistics.R | 2 R/merge.stat.R | 9 +++- R/meta.R | 4 + R/multiple.pathways.setup.R | 4 - R/norm.stat.test.R | 2 R/onAttach.R |only R/options.default.R | 4 + R/rawData.dataframe.setup.R | 4 - R/rawData.genofiles.setup.R | 8 +-- R/rawData.plinkfiles.setup.R | 8 +-- R/read.bed.R | 2 R/recover.stat.R | 8 +++ R/summaryData.setup.R | 17 ++++++-- R/update.direction.R |only R/update.raw.geno.R | 2 R/validate.outcome.R | 21 ++++++---- R/validate.plinkfiles.R | 2 R/validate.reference.R | 2 R/warm.start.R | 3 - README.md | 6 ++ man/exclude.snps.Rd |only man/inflation.Rd |only man/meta.Rd | 4 - man/options.Rd | 5 +- man/rARTP.Rd | 6 +- man/read.bed.Rd | 4 - man/warm.start.Rd | 2 src/artp2.cpp | 54 +++++++++++++++++++++----- 45 files changed, 248 insertions(+), 113 deletions(-)
Title: Comparison of Alternative Multiple Sequence Alignments
Description: Methods for comparing two alternative multiple
sequence alignments (MSAs) to determine whether they align homologous residues in
the same columns as one another. It then classifies similarities and differences
into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative
to the other. Summarising these categories for each MSA column yields information
on which sequence regions are agreed upon my both MSAs, and which differ. Several
plotting functions enable easily visualisation of the comparison data for analysis.
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>
Diff between AlignStat versions 1.2.1 dated 2016-05-24 and 1.2.2 dated 2016-07-11
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- R/compare_alignments.R | 13 ++++++++----- src/rcpp_align.cpp | 2 +- 4 files changed, 16 insertions(+), 12 deletions(-)