Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in
part to support an MS level course in nonparametric statistical methods. Methods
include adjustments for multiple comparisons, implementation of multivariate
Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence
region, some permutation tests for linear models, and some algorithms for
calculating exact probabilities associated with one- and two- stage testing
involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2.3 dated 2016-08-28 and 1.2.5 dated 2016-10-20
DESCRIPTION | 17 ++++++++++---- MD5 | 18 ++++++++------- NAMESPACE | 4 +-- R/aov.P.R | 14 ++++++++++- R/page.test.unbalanced.R |only R/probest.R | 8 ++++-- man/MultNonParam-package.Rd | 46 -------------------------------------- man/page.test.unbalanced.Rd |only man/probest.Rd | 5 ++-- src/aovp.f90 | 13 ++++++----- src/probest.f90 | 52 ++++++++++++++++++++++++++++++++++++++------ 11 files changed, 97 insertions(+), 80 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de> with contributions
from Sebastian Krey, Olaf Mersmann, Sarah Schnackenberg, Guillaume Guenard,
Andrea Preusser, Anita Thieler, Johanna Mielke and Claus Weihs, as well as code fragments
and ideas from the former package 'sound' by Matthias Heymann
and functions from 'rastamat' by Daniel P. W. Ellis.
The included parts of the libmad MPEG audio decoder library are
authored by Underbit Technologies.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.3.0 dated 2016-09-15 and 1.3.1 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/readMidi.R | 47 +++++++++++++++++++++++++---------------------- R/readWave.R | 16 +++++++++++++--- 4 files changed, 45 insertions(+), 32 deletions(-)
Title: Tree Ring Analysis of Disturbance Events in R
Description: Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data.
Author: Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between TRADER versions 1.2-1 dated 2016-02-10 and 1.2-2 dated 2016-10-20
DESCRIPTION | 8 +- MD5 | 30 +++---- NAMESPACE | 2 R/trader.R | 172 +++++++++++++++++++++++---------------------- man/TRADER-package.Rd | 4 - man/abrams.Rd | 2 man/absoluteIncreaseALL.Rd | 2 man/boundaryLineALL.Rd | 2 man/doAll.Rd | 38 ++++++++- man/growthAveragingALL.Rd | 2 man/plotBoundary.Rd | 2 man/plotFirstYears.Rd | 2 man/plotGrowth.Rd | 2 man/plotNORelease.Rd | 2 man/splechtna.Rd | 2 man/splechtnaALL.Rd | 2 16 files changed, 151 insertions(+), 123 deletions(-)
Title: Infrastructure for Running and Cycling Data from GPS-Enabled
Tracking Devices
Description: The aim of this package is to provide infrastructure for handling running and cycling
data from GPS-enabled tracking devices. After extraction and appropriate
manipulation of the training or competition attributes, the data are placed
into session-based and unit-aware data objects of class trackeRdata (S3 class). The
information in the resulting data objects can then be visualised, summarised,
and analysed through corresponding flexible and extensible methods.
Author: Hannah Frick [aut, cre],
Ioannis Kosmidis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between trackeR versions 0.0.3 dated 2016-06-23 and 0.0.4 dated 2016-10-20
DESCRIPTION | 12 MD5 | 47 - NAMESPACE | 1 NEWS | 9 R/Wprime.R | 5 R/read.R | 20 R/trackeRdata.R | 39 R/trackeRdata_summary.R | 16 R/trackeRdata_zones.R | 4 build/vignette.rds |binary data/run.rda |binary data/runs.rda |binary inst/doc/TourDetrackeR.Rmd | 50 - inst/doc/TourDetrackeR.html | 46 - inst/doc/trackeR.R | 176 ---- inst/doc/trackeR.Rnw | 1725 ++++++++++++++++++++++++++------------------ inst/doc/trackeR.pdf |binary man/GC2trackeRdata.Rd | 4 man/readContainer.Rd | 4 man/readDirectory.Rd | 4 man/sanityChecks.Rd |only man/trackeRdata.Rd | 4 vignettes/TourDetrackeR.Rmd | 50 - vignettes/trackeR.Rnw | 1725 ++++++++++++++++++++++++++------------------ vignettes/trackeR.bib | 52 - 25 files changed, 2293 insertions(+), 1700 deletions(-)
Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal
image video files, plotting and converting binary raw data into estimates of
temperature. First published 2015-03-26. Written primarily for research purposes
in biological applications of thermal images. v1 included the base calculations
for converting thermal image binary values to temperatures. v2 included additional
equations for providing heat transfer calculations and an import function for thermal
image files (v2.2.3 fixed error importing jpg to windows OS).
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>
Diff between Thermimage versions 2.2.1 dated 2016-08-04 and 2.2.3 dated 2016-10-20
DESCRIPTION | 10 +++--- MD5 | 10 +++--- R/freeparameters.R | 2 - R/hconv.R | 3 + R/readflirJPG.R | 84 +++++++++++++++++++++++++++++------------------------ man/readflirJPG.Rd | 3 + 6 files changed, 63 insertions(+), 49 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color
from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-5 dated 2016-03-08 and 0.5-6 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 +++++ R/internal.R | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book
"Numerical Methods and Optimization in Finance" by M.
'Gilli', D. 'Maringer' and E. Schumann (2011), ISBN
978-0123756626. The package provides implementations of
several optimisation heuristics, such as Differential
Evolution, Genetic Algorithms and Threshold Accepting.
There are also functions for the valuation of financial
instruments, such as bonds and options, and functions that
help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 0.36-2 dated 2015-10-20 and 0.40-0 dated 2016-10-20
NMOF-0.36-2/NMOF/R/randomp.R |only NMOF-0.36-2/NMOF/inst/unitTests/report.txt |only NMOF-0.40-0/NMOF/DESCRIPTION | 25 NMOF-0.40-0/NMOF/MD5 | 103 +-- NMOF-0.40-0/NMOF/NAMESPACE | 10 NMOF-0.40-0/NMOF/NEWS | 98 +++ NMOF-0.40-0/NMOF/R/DEopt.R | 21 NMOF-0.40-0/NMOF/R/GAopt.R | 6 NMOF-0.40-0/NMOF/R/LSopt.R | 6 NMOF-0.40-0/NMOF/R/TAopt.R | 101 ++- NMOF-0.40-0/NMOF/R/bracket.R | 6 NMOF-0.40-0/NMOF/R/gridSearch.R | 2 NMOF-0.40-0/NMOF/R/integrate.R | 2 NMOF-0.40-0/NMOF/R/internals.R | 4 NMOF-0.40-0/NMOF/R/mc.R | 12 NMOF-0.40-0/NMOF/R/pm.R | 13 NMOF-0.40-0/NMOF/R/portfolio.R |only NMOF-0.40-0/NMOF/R/repairMatrix.R | 9 NMOF-0.40-0/NMOF/R/restartOpt.R | 12 NMOF-0.40-0/NMOF/R/testFun.R | 73 +- NMOF-0.40-0/NMOF/R/xtContractValue.R |only NMOF-0.40-0/NMOF/build/vignette.rds |binary NMOF-0.40-0/NMOF/inst/CITATION | 30 - NMOF-0.40-0/NMOF/inst/NMOFex/NMOFman.R | 661 ++++++++++++----------- NMOF-0.40-0/NMOF/inst/doc/An_overview.R | 16 NMOF-0.40-0/NMOF/inst/doc/An_overview.Rnw | 45 + NMOF-0.40-0/NMOF/inst/doc/An_overview.pdf |binary NMOF-0.40-0/NMOF/inst/doc/DEnss.pdf |binary NMOF-0.40-0/NMOF/inst/doc/LSselect.pdf |binary NMOF-0.40-0/NMOF/inst/doc/PSlms.pdf |binary NMOF-0.40-0/NMOF/inst/doc/TAportfolio.pdf |binary NMOF-0.40-0/NMOF/inst/doc/qTableEx.pdf |binary NMOF-0.40-0/NMOF/inst/doc/repair.pdf |binary NMOF-0.40-0/NMOF/inst/doc/vectorise.pdf |binary NMOF-0.40-0/NMOF/inst/unitTests/runTests.R | 28 NMOF-0.40-0/NMOF/inst/unitTests/test_results.txt |only NMOF-0.40-0/NMOF/inst/unitTests/unitTests2.R | 413 +++++++------- NMOF-0.40-0/NMOF/inst/unitTests/unitTestsDEopt.R | 19 NMOF-0.40-0/NMOF/inst/unitTests/unitTests_mc.R |only NMOF-0.40-0/NMOF/man/DEopt.Rd | 459 ++++++++------- NMOF-0.40-0/NMOF/man/GAopt.Rd | 1 NMOF-0.40-0/NMOF/man/LSopt.Rd | 7 NMOF-0.40-0/NMOF/man/PSopt.Rd | 1 NMOF-0.40-0/NMOF/man/TA.info.Rd | 1 NMOF-0.40-0/NMOF/man/TAopt.Rd | 23 NMOF-0.40-0/NMOF/man/bracketing.Rd | 8 NMOF-0.40-0/NMOF/man/callHestoncf.Rd | 1 NMOF-0.40-0/NMOF/man/gridSearch.Rd | 1 NMOF-0.40-0/NMOF/man/mc.Rd | 30 + NMOF-0.40-0/NMOF/man/options.Rd | 12 NMOF-0.40-0/NMOF/man/pm.Rd | 5 NMOF-0.40-0/NMOF/man/repairMatrix.Rd | 8 NMOF-0.40-0/NMOF/man/testFunctions.Rd | 19 NMOF-0.40-0/NMOF/man/xtContractValue.Rd |only NMOF-0.40-0/NMOF/tests/README | 2 NMOF-0.40-0/NMOF/vignettes/An_overview.Rnw | 45 + 56 files changed, 1335 insertions(+), 1003 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.4.8 dated 2016-09-21 and 1.5.0 dated 2016-10-20
DESCRIPTION | 8 ++-- MD5 | 33 +++++++++-------- R/RcppExports.R | 4 ++ R/gmm.R | 27 ++++++-------- inst/CITATION | 2 - inst/add/cvNAM.R | 13 ++++--- inst/add/sparseGMM.R | 79 +++++++++++++++++++++---------------------- inst/doc/gwa_description.pdf |binary inst/doc/vignette1.Rmd | 12 ++++-- inst/doc/vignette1.html | 16 +++++--- inst/doc/vignette2.Rmd | 4 +- inst/doc/vignette2.html | 8 ++-- man/Internals.Rd | 3 + man/NAM-package.Rd | 4 +- src/RcppExports.cpp | 15 ++++++++ src/emBL.cpp |only vignettes/vignette1.Rmd | 12 ++++-- vignettes/vignette2.Rmd | 4 +- 18 files changed, 138 insertions(+), 106 deletions(-)
Title: Reproducible Data Retrieval from the ICPSR Archive
Description: Reproducible, programmatic retrieval of datasets from the
Inter-university Consortium for Political and Social Research archive.
Author: Frederick Solt [aut, cre],
Kellen Gracey [aut],
Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between icpsrdata versions 0.1.1 dated 2016-07-24 and 0.2.0 dated 2016-10-20
DESCRIPTION | 10 +- MD5 | 20 ++--- NAMESPACE | 9 ++ NEWS.md | 9 ++ R/icpsrdownload.R | 142 ++++++++++++++++++--------------------- README.md | 3 build/vignette.rds |binary inst/doc/icpsrdata-vignette.Rmd | 13 ++- inst/doc/icpsrdata-vignette.html | 15 ++-- man/icpsr_download.Rd | 14 ++- vignettes/icpsrdata-vignette.Rmd | 13 ++- 11 files changed, 135 insertions(+), 113 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.7 dated 2016-10-19 and 1.8 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/barnard.test.R | 5 +++-- man/barnard.test.Rd | 2 +- src/Barnard.c | 21 ++++++++++++++++----- 5 files changed, 28 insertions(+), 16 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.0.3 dated 2016-10-14 and 0.0.4 dated 2016-10-20
ChangeLog | 39 +++++++++++++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 23 ++++++++------- R/anytime.R | 20 +++++++++++-- R/init.R | 4 +- README.md | 75 +++++++++++++++++++++++++--------------------------- build/partial.rdb |binary cleanup |only inst/NEWS.Rd | 24 +++++++++++++--- man/anytime.Rd | 22 ++++++++++++--- src/RcppExports.cpp | 4 +- src/anytime.cpp | 72 ++++++++++++++++++++++++++++++++++--------------- tests/allFormats.R | 14 ++++++++- 13 files changed, 211 insertions(+), 94 deletions(-)
Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided.
The first, Alternative Conditional Expectations (ACE),
is an algorithm to find the fixed point of maximal
correlation, i.e. it finds a set of transformed response variables that maximizes R^2
using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations
for Multiple Regression and Correlation". Journal of the American Statistical Association.
80:580-598. <doi:10.1080/01621459.1985.10478157>].
Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity
and Variance Stabilization". Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>].
Author: Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley, Shawn Garbett, Jonathan Baron
Maintainer: Shawn Garbett <shawn.garbett@vanderbilt.edu>
Diff between acepack versions 1.3-3.3 dated 2013-05-03 and 1.4.0 dated 2016-10-20
acepack-1.3-3.3/acepack/CHANGES |only acepack-1.3-3.3/acepack/README |only acepack-1.3-3.3/acepack/README.ace |only acepack-1.3-3.3/acepack/README.avas |only acepack-1.3-3.3/acepack/ace.doc |only acepack-1.4.0/acepack/DESCRIPTION | 26 + acepack-1.4.0/acepack/LICENSE | 153 --------- acepack-1.4.0/acepack/LICENSE.note |only acepack-1.4.0/acepack/MD5 | 25 - acepack-1.4.0/acepack/NEWS |only acepack-1.4.0/acepack/inst |only acepack-1.4.0/acepack/man/ace.Rd | 16 - acepack-1.4.0/acepack/src/ace.f | 210 ++++++------- acepack-1.4.0/acepack/src/avas.f | 499 ++++++++++++++++--------------- acepack-1.4.0/acepack/src/rlsmo.f | 573 ++++++++++++++++++------------------ acepack-1.4.0/acepack/tests |only 16 files changed, 703 insertions(+), 799 deletions(-)
Title: Generalized and Safe-Bayesian Ridge and Lasso Regression
Description: Functions for Generalized and Safe-Bayesian Ridge and Lasso Regression models with both fixed and varying variance.
Author: Rianne de Heide [aut, cre],
Gustavo de los Campos [ctb],
Paulino Perez Rodriguez [ctb],
Bob Wheeler [ctb]
Maintainer: Rianne de Heide <r.de.heide@cwi.nl>
Diff between SafeBayes versions 1.0 dated 2016-05-23 and 1.1 dated 2016-10-20
DESCRIPTION | 8 ++++---- MD5 | 37 +++++++++++++++++++++---------------- NEWS |only R/GBRidgeFV.R |only R/GBlassoFV.R |only R/SBLassoISq.R | 7 +++++++ R/SBLassoRSq.R | 7 +++++++ R/SBRidgeISq.R | 7 +++++++ R/SBRidgeRSq.R | 7 +++++++ man/GBLasso.Rd | 4 ++-- man/GBLassoFV.Rd |only man/GBRidge.Rd | 4 ++-- man/GBRidgeFV.Rd |only man/SBLassoISq.Rd | 7 ++++--- man/SBLassoIlog.Rd | 8 ++++---- man/SBLassoRSq.Rd | 7 ++++--- man/SBLassoRlog.Rd | 7 ++++--- man/SBRidgeISq.Rd | 7 ++++--- man/SBRidgeIlog.Rd | 7 ++++--- man/SBRidgeRSq.Rd | 7 ++++--- man/SBRidgeRlog.Rd | 7 ++++--- src/dists.cc | 11 +++++------ 22 files changed, 94 insertions(+), 55 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.1.6 dated 2016-09-10 and 1.2.3 dated 2016-10-20
yuima-1.1.6/yuima/man/info.Output.Rd |only yuima-1.1.6/yuima/man/param.Output.Rd |only yuima-1.1.6/yuima/man/yuima.Output-class.Rd |only yuima-1.2.3/yuima/DESCRIPTION | 6 yuima-1.2.3/yuima/MD5 | 43 - yuima-1.2.3/yuima/NAMESPACE | 23 yuima-1.2.3/yuima/NEWS | 2 yuima-1.2.3/yuima/R/FunctionAndOperators.R | 21 yuima-1.2.3/yuima/R/MethodForLaw.R |only yuima-1.2.3/yuima/R/NewClasses.R | 26 yuima-1.2.3/yuima/R/PointProcessClasses.R | 4 yuima-1.2.3/yuima/R/qmle.R | 584 +++++++-------- yuima-1.2.3/yuima/R/setMultiModel.R | 2 yuima-1.2.3/yuima/R/sim.euler.R | 5 yuima-1.2.3/yuima/R/simulate.R | 59 - yuima-1.2.3/yuima/R/simulateForMapsIntegralAndOperator.R | 10 yuima-1.2.3/yuima/R/yuima.data.R | 10 yuima-1.2.3/yuima/R/yuima.law.r |only yuima-1.2.3/yuima/R/yuima.model.R | 3 yuima-1.2.3/yuima/man/LawMethods.Rd |only yuima-1.2.3/yuima/man/info.Map.Rd |only yuima-1.2.3/yuima/man/param.Map.Rd |only yuima-1.2.3/yuima/man/setLaw.Rd |only yuima-1.2.3/yuima/man/setMap.Rd | 8 yuima-1.2.3/yuima/man/yuima.Map-class.Rd |only yuima-1.2.3/yuima/man/yuima.law-class.rd |only yuima-1.2.3/yuima/src/RcppExports.cpp | 6 yuima-1.2.3/yuima/src/qmlecpp.cpp | 134 +-- 28 files changed, 510 insertions(+), 436 deletions(-)
Title: Wavelets Statistics and Transforms
Description: Performs 1, 2 and 3D real and complex-valued wavelet transforms,
nondecimated transforms, wavelet packet transforms, nondecimated
wavelet packet transforms, multiple wavelet transforms,
complex-valued wavelet transforms, wavelet shrinkage for
various kinds of data, locally stationary wavelet time series,
nonstationary multiscale transfer function modeling, density
estimation.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <G.P.Nason@bristol.ac.uk>
Diff between wavethresh versions 4.6.6 dated 2013-10-21 and 4.6.8 dated 2016-10-20
DESCRIPTION | 12 +-- MD5 | 12 +-- NAMESPACE | 13 +++ R/function.r | 170 ++++++++++++++++++++++++++++++++++++++++----------- R/wavde.r | 20 ------ inst/CHANGES | 22 ++++++ man/filter.select.rd | 8 ++ 7 files changed, 190 insertions(+), 67 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 1.4.6 dated 2016-07-11 and 1.4.7 dated 2016-10-20
gaston-1.4.6/gaston/TODO |only gaston-1.4.6/gaston/vignettes/gaston-015.pdf |only gaston-1.4.6/gaston/vignettes/gaston-026.pdf |only gaston-1.4.6/gaston/vignettes/gaston-028.pdf |only gaston-1.4.6/gaston/vignettes/gaston-030.pdf |only gaston-1.4.6/gaston/vignettes/gaston-032.pdf |only gaston-1.4.6/gaston/vignettes/gaston-037.pdf |only gaston-1.4.6/gaston/vignettes/gaston-039.pdf |only gaston-1.4.6/gaston/vignettes/gaston-041.pdf |only gaston-1.4.6/gaston/vignettes/gaston-043.pdf |only gaston-1.4.6/gaston/vignettes/gaston-045.pdf |only gaston-1.4.6/gaston/vignettes/gaston-047.pdf |only gaston-1.4.6/gaston/vignettes/gaston-051.pdf |only gaston-1.4.6/gaston/vignettes/gaston-052.pdf |only gaston-1.4.6/gaston/vignettes/gaston-053.pdf |only gaston-1.4.7/gaston/DESCRIPTION | 12 - gaston-1.4.7/gaston/MD5 | 95 +++----- gaston-1.4.7/gaston/NAMESPACE | 11 gaston-1.4.7/gaston/NEWS | 15 + gaston-1.4.7/gaston/R/bm.r | 8 gaston-1.4.7/gaston/R/bm_as_bm.r | 1 gaston-1.4.7/gaston/R/bm_bind.r | 127 ++++++++-- gaston-1.4.7/gaston/R/bm_genomic_sex.r | 48 ++-- gaston-1.4.7/gaston/R/bm_grm.r | 14 - gaston-1.4.7/gaston/R/bm_ld_thinner.r | 11 gaston-1.4.7/gaston/R/bm_select.r | 11 gaston-1.4.7/gaston/R/bm_stats.r | 211 ++++++++++++----- gaston-1.4.7/gaston/R/bm_subsetting.r | 8 gaston-1.4.7/gaston/R/ld_plot.r |only gaston-1.4.7/gaston/R/ld_plot_exemple.r |only gaston-1.4.7/gaston/R/score.r | 79 ++++-- gaston-1.4.7/gaston/R/zzz.r |only gaston-1.4.7/gaston/inst/doc/gaston.R | 159 ++++++++----- gaston-1.4.7/gaston/inst/doc/gaston.Rnw | 173 +++++++++++--- gaston-1.4.7/gaston/inst/doc/gaston.pdf |binary gaston-1.4.7/gaston/man/GRM.Rd | 4 gaston-1.4.7/gaston/man/LD.Rd | 7 gaston-1.4.7/gaston/man/LD.plot.Rd |only gaston-1.4.7/gaston/man/LD.thin.Rd | 2 gaston-1.4.7/gaston/man/score.variance.Rd | 29 +- gaston-1.4.7/gaston/man/select.inds.Rd | 4 gaston-1.4.7/gaston/man/select.snps.Rd | 5 gaston-1.4.7/gaston/man/set.genomic.sex.Rd | 9 gaston-1.4.7/gaston/man/set.stats.Rd | 39 ++- gaston-1.4.7/gaston/src/Makevars |only gaston-1.4.7/gaston/src/Makevars.win |only gaston-1.4.7/gaston/src/ai-reml-1k-covar.h | 1 gaston-1.4.7/gaston/src/ai-reml-logit-1k-covar.h | 1 gaston-1.4.7/gaston/src/davies.c |only gaston-1.4.7/gaston/src/gwas_lmm_diago_wald.cpp | 63 ++--- gaston-1.4.7/gaston/src/gwas_lmm_diago_wald_mt.cpp | 43 ++- gaston-1.4.7/gaston/src/m4_bind_inds.cpp | 146 ++++++++++++ gaston-1.4.7/gaston/src/m4_kinship.cpp | 71 +++++- gaston-1.4.7/gaston/src/m4_kinship_p.cpp | 65 ++++- gaston-1.4.7/gaston/src/m4_ldthin_left.cpp | 59 ++-- gaston-1.4.7/gaston/src/m4_ldthin_random.cpp | 60 ++--- gaston-1.4.7/gaston/src/m4_ldthin_right.cpp | 59 ++-- gaston-1.4.7/gaston/src/m4_recode.cpp |only gaston-1.4.7/gaston/src/m4_stats.cpp | 248 +++++++++++++++------ gaston-1.4.7/gaston/vignettes/gaston.Rnw | 130 ++++++++--- 60 files changed, 1428 insertions(+), 600 deletions(-)
Title: Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Diff between Rsurrogate versions 1.0 dated 2015-10-23 and 2.0 dated 2016-10-20
DESCRIPTION | 10 MD5 | 30 ++ NAMESPACE | 3 R/Functions_Rsurrogate.R | 431 +++++++++++++++++++++++++++++++++++++++++-- man/Aug.R.s.surv.estimate.Rd |only man/R.s.estimate.Rd | 103 +++++----- man/R.s.surv.estimate.Rd |only man/R.t.surv.estimate.Rd |only man/augment.est.vector.Rd |only man/censor.weight.Rd |only man/cumsum2.Rd |only man/d_example_surv.Rd | 8 man/delta.estimate.Rd | 24 +- man/delta.s.estimate.Rd | 41 ++-- man/delta.s.surv.estimate.Rd |only man/delta.surv.estimate.Rd |only man/delta.t.surv.estimate.Rd |only man/fieller.ci.Rd | 6 man/helper.si.Rd |only man/perturb.nu.vector.Rd |only man/pred.smooth.Rd | 3 man/pred.smooth.surv.Rd |only 22 files changed, 550 insertions(+), 109 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-20 dated 2016-09-07 and 0.3-21 dated 2016-10-20
ChangeLog | 30 +++++++++++++++++++++++++++++ DESCRIPTION | 16 +++++++-------- MD5 | 28 ++++++++++++++------------- NAMESPACE | 2 - R/rgeos_misc.R | 41 ++++++++++++++++++++++++++++++++++++++++ R/rgeos_spExtensions_Methods.R | 2 - R/rgeos_topology.R | 6 ++--- configure | 18 ++++++++--------- inst/ChangeLog | 30 +++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 - man/misc-gNearestPoints.Rd |only src/init.c | 3 +- src/rgeos.h | 4 ++- src/rgeos_misc.c | 26 +++++++++++++++++++++++++ tests/testthat/test-linearref.R | 21 ++++++++++++-------- tests/testthat/test-misc.R |only 16 files changed, 183 insertions(+), 46 deletions(-)
Title: Estimating Time-Varying Mixed Graphical Models
Description: Estimation of time-varying Mixed Graphical models and mixed VAR models using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-6 dated 2016-06-16 and 1.1-7 dated 2016-10-20
DESCRIPTION | 10 - MD5 | 46 +++-- NAMESPACE | 7 NEWS |only R/RcppExports.R | 2 R/estimation_msg.R |only R/mgmfit.R | 12 - R/mgmfit_core.R | 419 +++++++++++++++++++++++++++++++++++++++------------- R/plot.mgm.R |only R/plot.rs.R |only R/predict.mgm.R | 62 +++++-- R/print.mgm.R | 55 ++++-- R/print.rs.R |only R/rs.mgm.R |only R/startup_msg.R |only R/summary.mgm.R | 154 +++++++++---------- R/summary.rs.R |only R/tv.mgmfit.R | 3 R/tv_var.mgm.R | 4 R/var.mgm.R | 9 - README.md | 30 +-- man/mgmfit.Rd | 4 man/plot.rs.Rd |only man/predict.mgm.Rd | 15 + man/print.rs.Rd |only man/rs.mgm.Rd |only man/summary.mgm.Rd | 3 man/summary.rs.Rd |only man/var.mgm.Rd | 6 src/RcppExports.cpp | 10 - 30 files changed, 581 insertions(+), 270 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.5.0 dated 2016-08-29 and 3.5.1 dated 2016-10-20
lessR-3.5.0/lessR/R/print.outall.R |only lessR-3.5.0/lessR/R/print.outpiece.R |only lessR-3.5.1/lessR/DESCRIPTION | 8 lessR-3.5.1/lessR/MD5 | 72 ++-- lessR-3.5.1/lessR/NAMESPACE | 4 lessR-3.5.1/lessR/NEWS | 32 + lessR-3.5.1/lessR/R/ANOVAz1.R | 8 lessR-3.5.1/lessR/R/Help.R | 2 lessR-3.5.1/lessR/R/LineChart.R | 19 - lessR-3.5.1/lessR/R/Plot.R | 507 ++++++++++++++++------------- lessR-3.5.1/lessR/R/Regression.R | 2 lessR-3.5.1/lessR/R/bx.zmain.R | 7 lessR-3.5.1/lessR/R/corScree.R | 18 - lessR-3.5.1/lessR/R/cr.data.frame.R | 4 lessR-3.5.1/lessR/R/details.R | 2 lessR-3.5.1/lessR/R/dp.zmain.R | 117 ++++-- lessR-3.5.1/lessR/R/dpmat.zmain.R | 2 lessR-3.5.1/lessR/R/hst.zmain.R | 14 lessR-3.5.1/lessR/R/lc.zmain.R | 48 +- lessR-3.5.1/lessR/R/logit.z4Pred.R | 10 lessR-3.5.1/lessR/R/plt.zmain.R | 451 ++++++++++++++----------- lessR-3.5.1/lessR/R/print.outall.r |only lessR-3.5.1/lessR/R/print.outpiece.r |only lessR-3.5.1/lessR/R/reg.z1anvBasic.R | 2 lessR-3.5.1/lessR/R/reg.z1modelBasic.R | 2 lessR-3.5.1/lessR/R/reg.z2Relations.R | 2 lessR-3.5.1/lessR/R/reg.z3dnResidual.R | 6 lessR-3.5.1/lessR/R/reg.z3resfitResidual.R | 14 lessR-3.5.1/lessR/R/reg.z3txtResidual.R | 4 lessR-3.5.1/lessR/R/reg.z4Pred.R | 2 lessR-3.5.1/lessR/R/reg.z5Plot.R | 16 lessR-3.5.1/lessR/R/tt.z1group.R | 8 lessR-3.5.1/lessR/R/tt.z2group.R | 16 lessR-3.5.1/lessR/R/ttp2zgraph.R | 8 lessR-3.5.1/lessR/R/zzz.R | 89 ++--- lessR-3.5.1/lessR/inst/CITATION | 4 lessR-3.5.1/lessR/man/Plot.Rd | 200 +++++++---- lessR-3.5.1/lessR/man/Read.Rd | 2 lessR-3.5.1/lessR/man/ttest.Rd | 2 39 files changed, 984 insertions(+), 720 deletions(-)
Title: Group Sorted L1 Penalized Estimation
Description: Group SLOPE is a penalized linear regression method that is used
for adaptive selection of groups of significant predictors in a
high-dimensional linear model.
The Group SLOPE method can control the (group) false discovery rate at a
user-specified level (i.e., control the expected proportion of irrelevant
among all selected groups of predictors).
Author: Alexej Gossmann [aut, cre],
Damian Brzyski [aut],
Weijie Su [aut],
Malgorzata Bogdan [aut],
Ewout van den Berg [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3),
Emmanuel Candes [ctb] (A part of the optimization code was obtained
from http://statweb.stanford.edu/~candes/SortedL1/software.html
under GNU GPL-3)
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>
Diff between grpSLOPE versions 0.1.0 dated 2016-04-24 and 0.2.0 dated 2016-10-20
grpSLOPE-0.1.0/grpSLOPE/R/RcppExports.R |only grpSLOPE-0.1.0/grpSLOPE/man/lambdaChiMCAdjustment.Rd |only grpSLOPE-0.1.0/grpSLOPE/man/lambdaMC.Rd |only grpSLOPE-0.1.0/grpSLOPE/man/proxSortedL1.Rd |only grpSLOPE-0.1.0/grpSLOPE/src |only grpSLOPE-0.2.0/grpSLOPE/DESCRIPTION | 13 grpSLOPE-0.2.0/grpSLOPE/MD5 | 46 grpSLOPE-0.2.0/grpSLOPE/NAMESPACE | 11 grpSLOPE-0.2.0/grpSLOPE/R/generics.R |only grpSLOPE-0.2.0/grpSLOPE/R/grpslope.R | 460 ++++----- grpSLOPE-0.2.0/grpSLOPE/R/lambda_seq.R | 136 -- grpSLOPE-0.2.0/grpSLOPE/README.md | 36 grpSLOPE-0.2.0/grpSLOPE/build/vignette.rds |binary grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.R | 51 - grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.Rmd | 138 +- grpSLOPE-0.2.0/grpSLOPE/inst/doc/basic-usage.html | 370 ++++--- grpSLOPE-0.2.0/grpSLOPE/man/coef.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/man/grpSLOPE.Rd | 74 - grpSLOPE-0.2.0/grpSLOPE/man/lambdaGroupSLOPE.Rd | 90 - grpSLOPE-0.2.0/grpSLOPE/man/predict.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/man/proxGroupSortedL1.Rd | 19 grpSLOPE-0.2.0/grpSLOPE/man/proximalGradientSolverGroupSLOPE.Rd | 9 grpSLOPE-0.2.0/grpSLOPE/man/sigma.grpSLOPE.Rd |only grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_generics.R |only grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_grpSLOPE.R | 485 +++++++++- grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_lambda.R | 50 - grpSLOPE-0.2.0/grpSLOPE/tests/testthat/test_proximal_gradient_method.R | 35 grpSLOPE-0.2.0/grpSLOPE/vignettes/basic-usage.Rmd | 138 +- 28 files changed, 1253 insertions(+), 908 deletions(-)
Title: Repulsive Text and Label Geoms for 'ggplot2'
Description:
Provides text and label geoms for 'ggplot2' that help to avoid overlapping
text labels. Labels repel away from each other and away from the data
points.
Author: Kamil Slowikowski [aut, cre]
Maintainer: Kamil Slowikowski <kslowikowski@fas.harvard.edu>
Diff between ggrepel versions 0.5 dated 2016-02-08 and 0.6.3 dated 2016-10-20
DESCRIPTION | 8 MD5 | 44 - NEWS | 51 + R/RcppExports.R | 31 R/geom-label-repel.R | 127 ++- R/geom-text-repel.R | 192 ++++- README.md | 8 inst/doc/ggrepel.Rmd | 112 ++- inst/doc/ggrepel.html | 216 ++++-- man/geom_text_repel.Rd | 62 + src/RcppExports.cpp | 56 - src/repel_boxes.cpp | 336 +++++----- vignettes/Makefile | 2 vignettes/figures/ggrepel/animated.gif |binary vignettes/figures/ggrepel/geom_label_repel-1.png |binary vignettes/figures/ggrepel/geom_text-1.png |binary vignettes/figures/ggrepel/geom_text_repel-1.png |binary vignettes/figures/ggrepel/geom_text_repel_empty_string-1.png |only vignettes/figures/ggrepel/geom_text_repel_options-1.png |binary vignettes/figures/ggrepel/geom_text_repel_point_padding_na-1.png |only vignettes/figures/ggrepel/line_plot-1.png |binary vignettes/figures/ggrepel/volcano-1.png |binary vignettes/ggrepel.Rmd | 112 ++- vignettes/ggrepel.md | 122 ++- 24 files changed, 991 insertions(+), 488 deletions(-)
Title: Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic
Regression" (3rd Ed., 2013)
Description: An unofficial companion to "Applied
Logistic Regression" by D.W. Hosmer, S. Lemeshow and
R.X. Sturdivant (3rd ed., 2013) containing the dataset used in the book.
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between aplore3 versions 0.7 dated 2014-12-21 and 0.9 dated 2016-10-20
DESCRIPTION | 19 ++++++++------- MD5 | 52 +++++++++++++++++++++--------------------- R/aplore3.R | 12 ++++----- R/icu.R | 2 - README.md | 22 ++++++++--------- build/vignette.rds |binary data/icu.rda |binary inst/doc/aplore3-examples.pdf |binary man/aplore3.Rd | 15 ++++++------ man/aps.Rd | 8 ++++-- man/burn1000.Rd | 3 +- man/burn13m.Rd | 3 +- man/burn_eval_1.Rd | 3 +- man/burn_eval_2.Rd | 3 +- man/chdage.Rd | 5 ++-- man/glow11m.Rd | 3 +- man/glow500.Rd | 3 +- man/glow_bonemed.Rd | 3 +- man/glow_mis_comp.Rd | 3 +- man/glow_mis_wmissing.Rd | 3 +- man/glow_rand.Rd | 3 +- man/icu.Rd | 5 ++-- man/lowbwt.Rd | 5 ++-- man/myopia.Rd | 3 +- man/nhanes.Rd | 3 +- man/polypharm.Rd | 3 +- man/scale_example.Rd | 3 +- 27 files changed, 103 insertions(+), 84 deletions(-)