Title: Clean Covariance Matrices Using Random Matrix Theory and
Shrinkage Estimators for Portfolio Optimization
Description: Portfolio optimization typically requires an estimate of a covariance matrix of asset returns. There are many approaches for constructing such a covariance matrix, some using the sample covariance matrix as a starting point. This package provides implementations for two such methods: random matrix theory and shrinkage estimation. Each method attempts to clean or remove noise related to the sampling process from the sample covariance matrix.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between tawny versions 2.1.2 dated 2014-05-07 and 2.1.6 dated 2016-07-10
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NAMESPACE | 2 ++ R/divergence.R | 1 + R/shrinkage.R | 37 +++++++++++++------------------------ README.md |only man/divergence.Rd | 6 ++++-- man/tawny-package.Rd | 8 ++++---- 8 files changed, 37 insertions(+), 42 deletions(-)
Title: Time-Weighted Dynamic Time Warping for Satellite Image Time
Series Analysis
Description: Provides an implementation of the Time-Weighted Dynamic Time
Warping (TWDTW) method for land use and land cover mapping using satellite
image time series. TWDTW is based on the Dynamic Time Warping technique and
has achieved high accuracy for land use and land cover classification using
satellite data. The method is based on comparing unclassified satellite image
time series with a set of known temporal patterns (e.g. phenological cycles associated
with the vegetation). Using 'dtwSat' the user can build temporal patterns for land
cover types, apply the TWDTW analysis for satellite datasets, visualize the
results of the time series analysis, produce land cover maps, and
create temporal plots for land cover change analysis.
Author: Victor Maus [aut, cre]
Maintainer: Victor Maus <vwmaus1@gmail.com>
Diff between dtwSat versions 0.1.0 dated 2015-10-09 and 0.2.0 dated 2016-07-10
dtwSat-0.1.0/dtwSat/R/class-dtwSat.R |only dtwSat-0.1.0/dtwSat/R/plot-dtwSat.R |only dtwSat-0.1.0/dtwSat/data/query.list.RData |only dtwSat-0.1.0/dtwSat/data/template.RData |only dtwSat-0.1.0/dtwSat/man/classfyIntervals.Rd |only dtwSat-0.1.0/dtwSat/man/createTimeSequence.Rd |only dtwSat-0.1.0/dtwSat/man/dtwSat-class.Rd |only dtwSat-0.1.0/dtwSat/man/dtwSat.Rd |only dtwSat-0.1.0/dtwSat/man/getAlignments.Rd |only dtwSat-0.1.0/dtwSat/man/getInternals.Rd |only dtwSat-0.1.0/dtwSat/man/getMatches.Rd |only dtwSat-0.1.0/dtwSat/man/getModisTimeIndex.Rd |only dtwSat-0.1.0/dtwSat/man/mtwdtw.Rd |only dtwSat-0.1.0/dtwSat/man/plot-dtwSat-method.Rd |only dtwSat-0.1.0/dtwSat/man/plotAlignment.Rd |only dtwSat-0.1.0/dtwSat/man/plotClassify.Rd |only dtwSat-0.1.0/dtwSat/man/plotPath.Rd |only dtwSat-0.1.0/dtwSat/man/query.list.Rd |only dtwSat-0.1.0/dtwSat/man/template.Rd |only dtwSat-0.1.0/dtwSat/man/twdtw.Rd |only dtwSat-0.1.0/dtwSat/man/waveletSmoothing.Rd |only dtwSat-0.1.0/dtwSat/tests |only dtwSat-0.2.0/dtwSat/DESCRIPTION | 48 +- dtwSat-0.2.0/dtwSat/MD5 | 129 +++++- dtwSat-0.2.0/dtwSat/NAMESPACE | 137 +++++-- dtwSat-0.2.0/dtwSat/NEWS.md |only dtwSat-0.2.0/dtwSat/R/class-twdtwMatches.R |only dtwSat-0.2.0/dtwSat/R/class-twdtwRaster.R |only dtwSat-0.2.0/dtwSat/R/class-twdtwTimeSeries.R |only dtwSat-0.2.0/dtwSat/R/createPatterns.R |only dtwSat-0.2.0/dtwSat/R/data.R | 134 +++++-- dtwSat-0.2.0/dtwSat/R/dtw.R |only dtwSat-0.2.0/dtwSat/R/getInternals.R |only dtwSat-0.2.0/dtwSat/R/getTimeSeries.R |only dtwSat-0.2.0/dtwSat/R/linearWeight.R |only dtwSat-0.2.0/dtwSat/R/logisticWeight.R |only dtwSat-0.2.0/dtwSat/R/methods.R |only dtwSat-0.2.0/dtwSat/R/miscellaneous.R | 376 ++++++++------------ dtwSat-0.2.0/dtwSat/R/plot.R |only dtwSat-0.2.0/dtwSat/R/plotAlignments.R |only dtwSat-0.2.0/dtwSat/R/plotArea.R |only dtwSat-0.2.0/dtwSat/R/plotChanges.R |only dtwSat-0.2.0/dtwSat/R/plotClassification.R |only dtwSat-0.2.0/dtwSat/R/plotCostMatrix.R |only dtwSat-0.2.0/dtwSat/R/plotDistance.R |only dtwSat-0.2.0/dtwSat/R/plotMaps.R |only dtwSat-0.2.0/dtwSat/R/plotMatches.R |only dtwSat-0.2.0/dtwSat/R/plotPaths.R |only dtwSat-0.2.0/dtwSat/R/plotPatterns.R |only dtwSat-0.2.0/dtwSat/R/plotTimeSeries.R |only dtwSat-0.2.0/dtwSat/R/resampleTimeSeries.R |only dtwSat-0.2.0/dtwSat/R/subset.R |only dtwSat-0.2.0/dtwSat/R/twdtw.R | 410 ++++++---------------- dtwSat-0.2.0/dtwSat/R/twdtwApply.R |only dtwSat-0.2.0/dtwSat/R/twdtwClassify.R |only dtwSat-0.2.0/dtwSat/R/zzz.R | 37 + dtwSat-0.2.0/dtwSat/build |only dtwSat-0.2.0/dtwSat/data/example_ts.RData |only dtwSat-0.2.0/dtwSat/data/example_ts.list.RData |only dtwSat-0.2.0/dtwSat/data/example_ts_labels.RData |only dtwSat-0.2.0/dtwSat/data/patterns.list.RData |only dtwSat-0.2.0/dtwSat/data/yearly_patterns_mt.RData |only dtwSat-0.2.0/dtwSat/inst |only dtwSat-0.2.0/dtwSat/man/Assessment.Rd |only dtwSat-0.2.0/dtwSat/man/createPatterns.Rd |only dtwSat-0.2.0/dtwSat/man/example_ts.Rd |only dtwSat-0.2.0/dtwSat/man/example_ts.list.Rd |only dtwSat-0.2.0/dtwSat/man/example_ts_labels.Rd |only dtwSat-0.2.0/dtwSat/man/get.Rd |only dtwSat-0.2.0/dtwSat/man/getDatesFromDOY.Rd | 19 - dtwSat-0.2.0/dtwSat/man/getTimeSeries.Rd |only dtwSat-0.2.0/dtwSat/man/linearWeight.Rd |only dtwSat-0.2.0/dtwSat/man/logisticWeight.Rd |only dtwSat-0.2.0/dtwSat/man/patterns.list.Rd |only dtwSat-0.2.0/dtwSat/man/plot.Rd |only dtwSat-0.2.0/dtwSat/man/plotAlignments.Rd |only dtwSat-0.2.0/dtwSat/man/plotArea.Rd |only dtwSat-0.2.0/dtwSat/man/plotChanges.Rd |only dtwSat-0.2.0/dtwSat/man/plotClassification.Rd |only dtwSat-0.2.0/dtwSat/man/plotCostMatrix.Rd | 54 +- dtwSat-0.2.0/dtwSat/man/plotDistance.Rd |only dtwSat-0.2.0/dtwSat/man/plotMaps.Rd |only dtwSat-0.2.0/dtwSat/man/plotMatches.Rd |only dtwSat-0.2.0/dtwSat/man/plotPaths.Rd |only dtwSat-0.2.0/dtwSat/man/plotPatterns.Rd |only dtwSat-0.2.0/dtwSat/man/plotTimeSeries.Rd |only dtwSat-0.2.0/dtwSat/man/reexports.Rd |only dtwSat-0.2.0/dtwSat/man/resampleTimeSeries.Rd |only dtwSat-0.2.0/dtwSat/man/shiftDates.Rd |only dtwSat-0.2.0/dtwSat/man/subset.Rd |only dtwSat-0.2.0/dtwSat/man/twdtwApply.Rd |only dtwSat-0.2.0/dtwSat/man/twdtwClassify.Rd |only dtwSat-0.2.0/dtwSat/man/twdtwMatches-class.Rd |only dtwSat-0.2.0/dtwSat/man/twdtwRaster-class.Rd |only dtwSat-0.2.0/dtwSat/man/twdtwTimeSeries-class.Rd |only dtwSat-0.2.0/dtwSat/man/yearly_patterns_mt.Rd |only dtwSat-0.2.0/dtwSat/src |only dtwSat-0.2.0/dtwSat/vignettes |only 98 files changed, 684 insertions(+), 660 deletions(-)
Title: Survey Sampling Procedures
Description: Sampling procedures from the book 'Stichproben - Methoden
und praktische Umsetzung mit R' by Goeran Kauermann and Helmut
Kuechenhoff (2010).
Author: Juliane Manitz <r@manitz.org>, contributions by Mark
Hempelmann <mark.hempelmann@o2online.de>, Goeran Kauermann
<gkauermann@wiwi.uni-bielefeld.de>, Helmut Kuechenhoff
<kuechenhoff@stat.uni-muenchen.de>, Shuai Shao
<shuai.shao@campus.lmu.de>, Cornelia Oberhauser
<conny.oberhauser@gmx.de>, Nina Westerheide
<nwesterheide@wiwi.uni-bielefeld.de>, Manuel Wiesenfarth
<m.wiesenfarth@uni-goettingen.de>
Maintainer: Juliane Manitz <r@manitz.org>
Diff between samplingbook versions 1.2.0 dated 2013-01-14 and 1.2.1 dated 2016-07-10
DESCRIPTION | 17 +++++++++-------- MD5 | 6 +++--- NAMESPACE | 5 ++++- man/samplingbook-package.Rd | 10 +++++----- 4 files changed, 21 insertions(+), 17 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 0.9.2 dated 2016-07-05 and 0.9.3 dated 2016-07-10
MXM-0.9.2/MXM/R/mmhc.skel2.R |only MXM-0.9.3/MXM/DESCRIPTION | 10 MXM-0.9.3/MXM/MD5 | 53 +- MXM-0.9.3/MXM/NAMESPACE | 6 MXM-0.9.3/MXM/R/MMPC.R | 680 ++++++++++++++++++++--------------- MXM-0.9.3/MXM/R/SES.R | 392 +++++++++++++++++--- MXM-0.9.3/MXM/R/cv.mmpc.R | 40 +- MXM-0.9.3/MXM/R/cv.ses.R | 87 ++++ MXM-0.9.3/MXM/R/cvmmpc.par.R |only MXM-0.9.3/MXM/R/cvses.par.R |only MXM-0.9.3/MXM/R/glm.fsreg.R | 353 +++++++++++++++++- MXM-0.9.3/MXM/R/glm.fsreg_2.R | 371 +++++++++++++++++++ MXM-0.9.3/MXM/R/mmpc.model.R | 5 MXM-0.9.3/MXM/R/partialcor.R |only MXM-0.9.3/MXM/R/reg.fit.R | 10 MXM-0.9.3/MXM/R/ridge.plot.R | 2 MXM-0.9.3/MXM/R/ridge.reg.R | 4 MXM-0.9.3/MXM/R/ridgereg.cv.R | 4 MXM-0.9.3/MXM/R/ses.model.R | 23 - MXM-0.9.3/MXM/R/testIndBinom.R | 4 MXM-0.9.3/MXM/R/testIndGLMM.R | 4 MXM-0.9.3/MXM/man/MXM-internal.Rd | 5 MXM-0.9.3/MXM/man/MXM-package.Rd | 8 MXM-0.9.3/MXM/man/MXMCondIndTests.Rd | 5 MXM-0.9.3/MXM/man/cv.ses.Rd | 12 MXM-0.9.3/MXM/man/partialcor.Rd |only MXM-0.9.3/MXM/man/reg.fit.Rd | 2 MXM-0.9.3/MXM/man/testIndBeta.Rd | 2 MXM-0.9.3/MXM/man/testIndBinom.Rd | 2 MXM-0.9.3/MXM/man/testIndGLMM.Rd | 2 30 files changed, 1677 insertions(+), 409 deletions(-)
Title: Modeling Data with Functional Programming
Description: A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between lambda.r versions 1.1.7 dated 2015-03-20 and 1.1.9 dated 2016-07-10
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 1 + R/framework.R | 13 ++++++++----- inst/unitTests/runit.parse_transforms.3.R |only man/lambda.r-package.Rd | 4 ++-- 6 files changed, 20 insertions(+), 15 deletions(-)
Title: Hosmer-Lemeshow Test for Binary and Multinomial Logistic Models
Description: Contains a sole function that performs the Hosmer-Lemeshow test for binary and multinomial logistic regression models. It
implements the classic Hosmer-Lemeshow test as well as its multinomial generalisation, both of which are described in Hosmer, Lemeshow
and Sturdivant (2013).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>
Diff between generalhoslem versions 1.0 dated 2016-07-03 and 1.0.1 dated 2016-07-10
DESCRIPTION | 12 ++++---- MD5 | 8 ++--- R/logitgof.R | 76 +++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/logitgof.Rd | 25 +++++++++++++++-- 5 files changed, 72 insertions(+), 49 deletions(-)
Title: Random Matrix Generation and Manipulation
Description: A collection of functions for manipulating matrices and generating
ensembles of random matrices. Used primarily to identify the cutoff point
for the noise portion of the eigenvalue spectrum.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between futile.matrix versions 1.2.2 dated 2014-05-07 and 1.2.6 dated 2016-07-10
futile.matrix-1.2.2/futile.matrix/man/density.Rd |only futile.matrix-1.2.6/futile.matrix/DESCRIPTION | 19 - futile.matrix-1.2.6/futile.matrix/MD5 | 40 +- futile.matrix-1.2.6/futile.matrix/NAMESPACE | 8 futile.matrix-1.2.6/futile.matrix/R/cutoff.R | 63 +++- futile.matrix-1.2.6/futile.matrix/R/density.R | 37 ++ futile.matrix-1.2.6/futile.matrix/R/ensemble.R | 130 +++++--- futile.matrix-1.2.6/futile.matrix/R/futile.matrix-package.R |only futile.matrix-1.2.6/futile.matrix/R/io.R | 71 ++++ futile.matrix-1.2.6/futile.matrix/R/manip.R | 155 ++++++++-- futile.matrix-1.2.6/futile.matrix/man/RandomMatrixModel.Rd | 78 ++--- futile.matrix-1.2.6/futile.matrix/man/arrange.Rd | 48 +-- futile.matrix-1.2.6/futile.matrix/man/assign_matrix_dense.Rd |only futile.matrix-1.2.6/futile.matrix/man/ct.Rd |only futile.matrix-1.2.6/futile.matrix/man/cutoff.Rd |only futile.matrix-1.2.6/futile.matrix/man/dmatrix.Rd |only futile.matrix-1.2.6/futile.matrix/man/domain.Rd |only futile.matrix-1.2.6/futile.matrix/man/expand.Rd | 94 +++--- futile.matrix-1.2.6/futile.matrix/man/fit.density.Rd |only futile.matrix-1.2.6/futile.matrix/man/futile.matrix-package.Rd | 74 ++-- futile.matrix-1.2.6/futile.matrix/man/peek.Rd | 33 +- futile.matrix-1.2.6/futile.matrix/man/print.Ensemble.Rd |only futile.matrix-1.2.6/futile.matrix/man/rcomp.Rd |only futile.matrix-1.2.6/futile.matrix/man/read.matrix.Rd | 116 ++++--- futile.matrix-1.2.6/futile.matrix/man/rmatrix.Rd | 74 ++-- futile.matrix-1.2.6/futile.matrix/man/select.Rd | 67 ++-- 26 files changed, 708 insertions(+), 399 deletions(-)
Title: A Logging Utility for R
Description: Provides a simple yet powerful logging utility. Based loosely on
log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between futile.logger versions 1.4.1 dated 2015-04-20 and 1.4.3 dated 2016-07-10
DESCRIPTION | 14 +-- MD5 | 32 +++---- NAMESPACE | 3 R/futile.logger-package.R | 6 - README.md | 18 +--- man/flog.appender.Rd | 80 +++++++++-------- man/flog.carp.Rd | 34 ++++--- man/flog.layout.Rd | 104 ++++++++++++----------- man/flog.logger.Rd | 193 +++++++++++++++++++------------------------ man/flog.remove.Rd | 17 ++- man/flog.threshold.Rd | 33 +++---- man/ftry.Rd | 19 ++-- man/futile.logger-package.Rd | 190 ++++++++++++++++++++---------------------- man/logger.options.Rd | 23 ++--- man/scat.Rd | 25 ++--- tests/testthat.R | 3 tests/testthat/test_debug.R | 4 17 files changed, 399 insertions(+), 399 deletions(-)
Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a
wide range of frailty distributions using a consistent and
asymptotically-normal estimator. Currently supports: gamma, power variance
function, log-normal, and inverse Gaussian frailty models.
Author: John V. Monaco [aut, cre],
Malka Gorfine [aut],
Li Hsu [aut]
Maintainer: John V. Monaco <vincent@vmonaco.com>
Diff between frailtySurv versions 1.2.2 dated 2015-09-30 and 1.2.2.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/distributions.cpp | 24 ++++++++++++------------ 3 files changed, 17 insertions(+), 17 deletions(-)
Title: Elliptic Distribution and Lambda Option Pricing Model
Description: An implementation of the univariate elliptic distribution, and
lambda option pricing model. It provides detailed functionality and data
sets for the distribution and modelling. Especially, it contains functions
for the computation of density, probability, quantile, fitting procedures,
option prices, volatility smile. It also comes with sample financial data,
and plotting routines.
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Diff between ecd versions 0.6.4 dated 2015-12-23 and 0.8.2 dated 2016-07-10
ecd-0.6.4/ecd/tests/testthat/test-ecd11-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-ecd25-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-high-kurt-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-quadpack-cusp-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-quadpack-j0plus-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-sged-ecd.R |only ecd-0.6.4/ecd/tests/testthat/test-taylor-expansion-ecd.R |only ecd-0.8.2/ecd/DESCRIPTION | 52 +++--- ecd-0.8.2/ecd/MD5 | 115 +++++++-------- ecd-0.8.2/ecd/NAMESPACE | 46 ++++++ ecd-0.8.2/ecd/NEWS.md | 20 ++ ecd-0.8.2/ecd/R/ecd-data-config-internal.R | 87 +++++++---- ecd-0.8.2/ecd/R/ecd-erfq-method.R |only ecd-0.8.2/ecd/R/ecd-mpfr-method.R | 49 ++++++ ecd-0.8.2/ecd/R/ecd-read-csv-by-symbol-method.R | 38 +++- ecd-0.8.2/ecd/R/ecd-solve-generic.R | 19 -- ecd-0.8.2/ecd/R/ecd-uniroot-method.R | 2 ecd-0.8.2/ecd/R/ecld-cdf-method.R | 8 - ecd-0.8.2/ecd/R/ecld-class.R | 9 + ecd-0.8.2/ecd/R/ecld-constructor.R | 46 +++++- ecd-0.8.2/ecd/R/ecld-gamma-method.R | 52 ++++++ ecd-0.8.2/ecd/R/ecld-imgf-method.R | 69 ++++++++- ecd-0.8.2/ecd/R/ecld-ivol-ogf-star-method.R | 9 - ecd-0.8.2/ecd/R/ecld-mgf-term-method.R | 2 ecd-0.8.2/ecd/R/ecld-moment-method.R | 62 ++++++-- ecd-0.8.2/ecd/R/ecld-mu-D-method.R | 99 +++++++++--- ecd-0.8.2/ecd/R/ecld-ogf-method.R | 99 +++++++++++- ecd-0.8.2/ecd/R/ecld-ogf-star-method.R | 31 ++++ ecd-0.8.2/ecd/R/ecld-op-V-method.R | 62 ++++++-- ecd-0.8.2/ecd/R/ecld-solve-method.R | 108 +++++++++++++- ecd-0.8.2/ecd/R/ecld.quartic-Qp-method.R |only ecd-0.8.2/ecd/R/ecld.quartic-RN0-method.R |only ecd-0.8.2/ecd/R/ecld.quartic_Qp_atm_attr.R |only ecd-0.8.2/ecd/R/ecop-constructor.R | 21 ++ ecd-0.8.2/ecd/R/ecop-opt-class.R | 7 ecd-0.8.2/ecd/R/ecop-plot-option-method.R | 37 +++- ecd-0.8.2/ecd/R/ecop-read-csv-by-symbol.R | 17 +- ecd-0.8.2/ecd/R/ecop-term-master-calculator-method.R |only ecd-0.8.2/ecd/R/ecop-term-plot-3x3-method.R |only ecd-0.8.2/ecd/inst/extdata/data_conf.yml |only ecd-0.8.2/ecd/inst/extdata/spx_archive_7.csv.zip |only ecd-0.8.2/ecd/inst/extdata/vix_archive_7.csv.zip |binary ecd-0.8.2/ecd/man/ecd.erfq.Rd |only ecd-0.8.2/ecd/man/ecd.mpfr.Rd | 28 +++ ecd-0.8.2/ecd/man/ecd.read_csv_by_symbol.Rd | 10 - ecd-0.8.2/ecd/man/ecd.uniroot.Rd | 2 ecd-0.8.2/ecd/man/ecld-class.Rd | 7 ecd-0.8.2/ecd/man/ecld.Rd | 20 ++ ecd-0.8.2/ecd/man/ecld.gamma.Rd | 8 - ecd-0.8.2/ecd/man/ecld.imgf.Rd | 3 ecd-0.8.2/ecd/man/ecld.ivol_ogf_star.Rd | 4 ecd-0.8.2/ecd/man/ecld.mgf_term.Rd | 2 ecd-0.8.2/ecd/man/ecld.moment.Rd | 6 ecd-0.8.2/ecd/man/ecld.mu_D.Rd | 9 + ecd-0.8.2/ecd/man/ecld.ogf.Rd | 6 ecd-0.8.2/ecd/man/ecld.ogf_star.Rd | 3 ecd-0.8.2/ecd/man/ecld.op_V.Rd | 31 +++- ecd-0.8.2/ecd/man/ecld.quartic_Qp.Rd |only ecd-0.8.2/ecd/man/ecld.quartic_Qp_atm_attr.Rd |only ecd-0.8.2/ecd/man/ecld.quartic_SN0_atm_ki.Rd |only ecd-0.8.2/ecd/man/ecld.solve.Rd | 9 + ecd-0.8.2/ecd/man/ecop.from_symbol_conf.Rd | 4 ecd-0.8.2/ecd/man/ecop.opt-class.Rd | 2 ecd-0.8.2/ecd/man/ecop.plot_option.Rd | 7 ecd-0.8.2/ecd/man/ecop.read_csv_by_symbol.Rd | 11 + ecd-0.8.2/ecd/man/ecop.term_master_calculator.Rd |only ecd-0.8.2/ecd/man/ecop.term_plot_3x3.Rd |only ecd-0.8.2/ecd/tests/testthat/test-lambda-gamma-ecd.R | 13 + ecd-0.8.2/ecd/tests/testthat/test-option-ecop.R | 85 +++++++++++ 69 files changed, 1164 insertions(+), 272 deletions(-)
Title: Derivative-Free Optimization
Description: Derivative-Free optimization algorithms. These algorithms do not require gradient information. More importantly, they can be used to solve non-smooth optimization problems.
Author: Ravi Varadhan, Johns Hopkins University, and Hans W. Borchers,
ABB Corporate Research.
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between dfoptim versions 2011.8-1 dated 2011-08-12 and 2016.7-1 dated 2016-07-10
DESCRIPTION | 17 +- MD5 | 16 +- NAMESPACE | 18 +- NEWS | 3 R/hjk.R | 25 ++- R/hjkb.R | 36 +++-- R/nmk.R | 348 ++++++++++++++++++++++++------------------------- man/dfoptim-package.Rd | 8 - man/nmkb.Rd | 3 9 files changed, 245 insertions(+), 229 deletions(-)
Title: Diagnostics for Fine and Gray Model
Description: Provides the implementation of analytical and graphical approaches for checking the assumptions of the Fine and Gray model.
Author: Jianing Li
Maintainer: Jianing Li <kinger198549@gmail.com>
Diff between crskdiag versions 1.0 dated 2015-10-02 and 1.0.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/diag.cc | 36 ++++++++++++++++++------------------ src/matrix.h | 2 +- src/util.cc | 30 +++++++++++++++--------------- src/util.h | 14 +++++++------- 6 files changed, 49 insertions(+), 49 deletions(-)
Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Compositional versions 1.4 dated 2016-07-08 and 1.5 dated 2016-07-10
DESCRIPTION | 10 ++++---- MD5 | 52 +++++++++++++++++++++---------------------- NAMESPACE | 2 - R/alfa.reg.R | 2 - R/alfa.tune.R | 4 +-- R/glm.pcr.R | 2 - R/glmpcr.tune.R | 4 +-- R/hotel1T2.R | 4 +-- R/hotel2T2.R | 4 +-- R/james.R | 4 +-- R/js.compreg.R | 4 +-- R/kl.compreg.R | 4 +-- R/maovjames.R | 2 - R/mix.compnorm.R | 2 - R/mkde.R | 4 +-- R/multivreg.R | 6 ++-- R/multivt.R | 2 - R/ols.compreg.R | 4 +-- R/pcr.R | 2 - R/pcr.tune.R | 2 - R/rda.R | 4 +-- R/rda.tune.R | 8 +++--- R/ridge.reg.R | 4 +-- R/ridge.tune.R | 4 +-- R/spat.med.R | 2 - man/Compositional-package.Rd | 6 ++-- man/alfa.Rd | 2 - 27 files changed, 75 insertions(+), 75 deletions(-)
Title: Weighted summary of cumulative incidence functions
Description: Estimate of cumulative incidence function in two samples. Provide weighted summary statistics based on various methods and weights.
Author: Jianing Li
Maintainer: Jianing Li <jili@mcw.edu>
Diff between CIFsmry versions 1.0.1 dated 2013-10-31 and 1.0.1.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/newplt.cc | 5 +++-- src/newuseplt.cc | 3 ++- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph],
Leblois Raphaël [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.0.8 dated 2016-05-25 and 1.0.8.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/qr.h | 16 ++++++++-------- src/smooth.cpp | 8 +++++--- src/smooth.h | 4 ++-- src/smoothFriends.h | 10 +++++----- 6 files changed, 28 insertions(+), 26 deletions(-)
Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.06 dated 2016-04-18 and 2.06.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/bmn5.cc | 24 ++++++++++++------------ 3 files changed, 17 insertions(+), 17 deletions(-)
Title: Genetic Rare Variants Tests
Description: Tests for genetic rare variants.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between thgenetics versions 0.3-4 dated 2013-03-30 and 0.3-4.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/raremethods.cpp | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: SemiParametric Transformation Model Methods
Description: Implements semiparametric transformation model two-phase estimation using calibration weights.
Author: Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between sptm versions 14.10-11 dated 2014-10-13 and 16.7-9 dated 2016-07-10
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- NAMESPACE | 12 +++++++++++- 3 files changed, 19 insertions(+), 10 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
Dirk Eddelbuettel [ctb] (ziggurat rnorm sources),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 1.9.0 dated 2016-05-24 and 1.9.0.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/COMPoisson.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Some Algorithms for Mixed Models
Description: Programs for fitting Gaussian linear mixed models (LMM).
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between SAMM versions 0.0 dated 2016-05-12 and 0.0.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/SAMM.cpp | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.0.4 dated 2016-04-17 and 0.0.5 dated 2016-07-10
ChangeLog | 29 +++++++++++++++++++++++++- DESCRIPTION | 22 +++++++++++--------- MD5 | 21 +++++++++++-------- R/RcppExports.R | 48 ++++++++++++++++++++++++++++++++++++++++++++ inst/include/time_zone_if.h | 2 - man/RcppCCTZ-package.Rd | 32 +++++++++++++++-------------- man/toTz.Rd |only man/tzDiff.Rd |only src/RcppExports.cpp | 37 +++++++++++++++++++++++++++++++++ src/examples.cpp | 24 +++++++++++++++++++--- src/time_zone_info.cc | 16 +------------- src/time_zone_libc.cc | 4 --- src/utilities.cpp |only 13 files changed, 178 insertions(+), 57 deletions(-)
Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre],
Kouros Owzar [aut],
Gregory D. Sempowski [aut],
Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between permPATH versions 0.7 dated 2016-07-06 and 0.7.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/permPATH.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Multi-Resolution Scanning for Cross-Sample Differences
Description: An implementation of the MRS algorithm for comparison across distributions.
The model is based on a nonparametric process taking the form of a Markov model
that transitions between a "null" and an "alternative" state
on a multi-resolution partition tree of the sample space.
MRS effectively detects and characterizes a variety of underlying differences.
These differences can be visualized using several plotting functions.
Author: Jacopo Soriano and Li Ma
Maintainer: Jacopo Soriano <jsoriano.stat@gmail.com>
Diff between MRS versions 1.1 dated 2016-01-25 and 1.1.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/helpers.cpp | 6 +++--- src/recursion.cpp | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Kernel Based Regression Models
Description: Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence.
Author: Youyi Fong <youyifong@gmail.com>, Saheli Datta, Krisztian Sebestyen
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between krm versions 2015.3-4 dated 2015-03-04 and 2016.7-9 dated 2016-07-10
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- NAMESPACE | 8 ++++++-- 3 files changed, 12 insertions(+), 7 deletions(-)
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-1 dated 2014-03-22 and 1.0-1.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/cgFbat.cpp | 52 ++++++++++++++++++++++++++-------------------------- src/fbatdist.cpp | 4 ++-- src/fbatmeev.cpp | 2 +- src/nuclify.cpp | 2 +- 6 files changed, 38 insertions(+), 38 deletions(-)
Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you
run 'Domino' commands (e.g., "run", "upload", "download") directly from your
R environment. Under the hood, it uses R's system function to run the 'Domino'
executable, which must be installed as a prerequisite. 'Domino' is a service
that makes it easy to run your code on scalable hardware, with integrated
version control and collaboration features designed for analytical workflows
(see <http://www.dominodatalab.com> for more information).
Author: Jacek Glodek <jacek@theiterators.com>
Maintainer: Nick Elprin <nick@dominodatalab.com>
Diff between domino versions 0.2-7 dated 2015-06-10 and 0.3.0 dated 2016-07-10
DESCRIPTION | 23 +++-- LICENSE | 4 MD5 | 57 ++++++++---- NAMESPACE | 32 ++++--- R/domino-package.R |only R/domino.R | 209 +---------------------------------------------- R/domino.create.R |only R/domino.debug.R |only R/domino.diff.R |only R/domino.download.R |only R/domino.dump.R |only R/domino.get.R |only R/domino.init.R |only R/domino.login.R |only R/domino.reset.R |only R/domino.run.R |only R/domino.runCommand.R |only R/domino.snapshot.R |only R/domino.status.R |only R/domino.sync.R |only R/domino.upload.R |only man/domino-package.Rd | 53 +++++------ man/domino.create.Rd | 26 ++--- man/domino.debug.Rd | 13 +- man/domino.diff.Rd | 13 +- man/domino.download.Rd | 13 +- man/domino.dump.Rd |only man/domino.get.Rd | 39 ++++---- man/domino.init.Rd | 31 +++--- man/domino.login.Rd | 54 ++++++------ man/domino.reset.Rd | 13 +- man/domino.run.Rd | 33 +++---- man/domino.runCommand.Rd | 63 ++++++-------- man/domino.snapshot.Rd |only man/domino.status.Rd | 17 +-- man/domino.sync.Rd | 17 +-- man/domino.upload.Rd | 19 +--- tests |only 38 files changed, 271 insertions(+), 458 deletions(-)
Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>
Diff between D3M versions 0.41 dated 2015-08-03 and 0.41.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/funcs.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Change Point Regression
Description: Change point regression models are also called two-phase regression, break-point regression, split-point regression, structural change models and threshold regression models. Hypothesis testing in change point logistic regression with or without interaction terms. Several options are provided for testing in models with interaction, including a maximum of likelihood ratios test that determines p-value through Monte Carlo. Estimation under change point model is also included, but less developed at this point.
Author: Youyi Fong
Maintainer: Youyi Fong <yfong@fhcrc.org>
Diff between chngpt versions 2015.9-5 dated 2015-09-09 and 2016.7-9 dated 2016-07-10
ChangeLog | 30 - DESCRIPTION | 10 MD5 | 24 NAMESPACE | 19 R/chngpt.test.R | 229 +++++---- R/chngptm.R | 903 +++++++++++++++++++++++++++++-------- R/sim.chngpt.R | 83 ++- data/dat.mtct.rda |only inst/unitTests/runit.chngpt.test.R | 37 + inst/unitTests/runit.chngptm.R | 117 +++- man/chngpt.test.Rd | 38 + man/chngptm.Rd | 47 + man/dat.mtct.Rd |only man/sim.chngpt.Rd | 26 - 14 files changed, 1130 insertions(+), 433 deletions(-)
Title: Methods for Temporal Disaggregation and Interpolation of Time
Series
Description: Temporal disaggregation methods are used to disaggregate and
interpolate a low frequency time series to a higher frequency series, where
either the sum, the average, the first or the last value of the resulting
high frequency series is consistent with the low frequency series. Temporal
disaggregation can be performed with or without one or more high frequency
indicator series. Contains the methods of Chow-Lin, Santos-Silva-Cardoso,
Fernandez, Litterman, Denton and Denton-Cholette.
Author: Christoph Sax [aut, cre],
Peter Steiner [aut],
Tommaso Di Fonzo [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between tempdisagg versions 0.24.0 dated 2014-12-07 and 0.25.0 dated 2016-07-10
DESCRIPTION | 23 ++- MD5 | 33 ++--- NAMESPACE | 4 NEWS | 20 +++ R/ta.R | 60 ++++++++++ R/td.R | 36 +++++- R/td.calc.R | 18 +++ R/td.output.R | 1 R/td.sub.R | 35 +++++- README.md | 15 ++ man/exports.m.Rd | 5 man/plot.td.Rd | 10 + man/predict.td.Rd | 8 - man/summary.td.Rd | 22 ++- man/ta.Rd | 18 +-- man/td.Rd | 267 ++++++++++++++++++++++++---------------------- man/tempdisagg-package.Rd | 17 +- tests |only 18 files changed, 393 insertions(+), 199 deletions(-)
Title: Variational Bayes (VB) Approximation of Gibbs Posteriors with
Hinge Losses
Description: Variational Bayesian approximations of Gibbs measures with hinge losses for classification and ranking.
Author: James Ridgway
Maintainer: James Ridgway <james.ridgway@bristol.ac.uk>
Diff between PACVB versions 1.1 dated 2016-02-04 and 1.1.1 dated 2016-07-10
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- man/PACVB-package.Rd | 2 +- src/PAC.cpp | 4 ---- src/Random.h | 8 ++++---- 5 files changed, 15 insertions(+), 19 deletions(-)
Title: Non-Negative Matrix Factorization (NMF) using CUDA
Description: Wrapper package for the nmfgpu library, which implements several
Non-negative Matrix Factorization (NMF) algorithms for CUDA platforms.
By using the acceleration of GPGPU computing, the NMF can be used for
real-world problems inside the R environment. All CUDA devices starting with
Kepler architecture are supported by the library.
Author: Sven Koitka [aut, cre, cph],
Christoph M. Friedrich [ctb]
Maintainer: Sven Koitka <sven.koitka@fh-dortmund.de>
Diff between nmfgpu4R versions 0.2.5 dated 2016-05-30 and 0.2.5.1 dated 2016-07-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Helper.h | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.3 dated 2016-06-06 and 2.4 dated 2016-07-10
DESCRIPTION | 8 - MD5 | 64 +++++------ NAMESPACE | 2 NEWS | 20 +++ R/DJL-internal.R | 250 +++++++++++++++++++++++----------------------- R/dm.ddf.R | 16 ++ R/dm.dea.R | 12 +- R/dm.sbm.R | 31 ++++- R/dm.sf.R | 16 ++ R/ma.aps.reg.R | 41 +++++++ R/map.soa.ddf.R | 6 - R/map.soa.dea.R | 6 - R/map.soa.sbm.R | 6 - R/map.soa.sf.R | 6 - R/roc.dea.R | 13 +- R/roc.sf.R | 21 ++- R/target.arrival.dea.R | 13 +- R/target.arrival.sf.R | 21 ++- R/target.spec.dea.R | 17 ++- man/dm.ddf.Rd | 13 +- man/dm.dea.Rd | 23 ++-- man/dm.sbm.Rd | 11 +- man/dm.sf.Rd | 15 +- man/ma.aps.reg.Rd | 6 - man/map.soa.ddf.Rd | 15 +- man/map.soa.dea.Rd | 14 +- man/map.soa.sbm.Rd | 15 +- man/map.soa.sf.Rd | 19 ++- man/roc.dea.Rd | 26 ++-- man/roc.sf.Rd | 15 +- man/target.arrival.dea.Rd | 15 +- man/target.arrival.sf.Rd | 21 ++- man/target.spec.dea.Rd | 14 +- 33 files changed, 488 insertions(+), 303 deletions(-)