Title: Odds Ratio Estimation for the Trend in Trend Model
Description: Estimation of causal odds ratio given trends in exposure prevalence
and outcome frequencies of stratified data.
Author: Xinyao Ji [aut, cre]
Maintainer: Xinyao Ji <xinyaoji@wharton.upenn.edu>
Diff between TrendInTrend versions 1.0.0 dated 2016-06-06 and 1.0.1 dated 2017-01-09
DESCRIPTION | 12 +++++----- MD5 | 8 +++--- NAMESPACE | 14 +++++------ man/GenData.Rd | 24 ++++++++++---------- man/OR.Rd | 68 ++++++++++++++++++++++++++++----------------------------- 5 files changed, 63 insertions(+), 63 deletions(-)
Title: Bayesian Tensor Factorization
Description: Bayesian Tensor Factorization for decomposition of tensor data sets using the trilinear CANDECOMP/PARAFAC (CP) factorization, with automatic component selection. The complete data analysis pipeline is provided, including functions and recommendations for data normalization and model definition, as well as missing value prediction and model visualization. The method performs factorization for three-way tensor datasets and the inference is implemented with Gibbs sampling.
Author: Suleiman A Khan [aut, cre],
Muhammad Ammad-ud-din [aut]
Maintainer: Suleiman A Khan <suleiman.khan@helsinki.fi>
Diff between tensorBF versions 1.0.0 dated 2016-12-29 and 1.0.1 dated 2017-01-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 1 + R/normalize.R | 4 ++-- R/plot.R | 6 +++--- R/reconstruct.R | 40 +++++++++++----------------------------- R/tensorBF.R | 10 +++++++++- demo/demoTensorBF.R | 2 +- 8 files changed, 37 insertions(+), 46 deletions(-)
Title: Fitting Linear and Generalized Linear Models to Large Data Sets
Description: Fitting linear models and generalized linear models to large data sets by updating algorithms.
Author: Marco Enea [aut, cre], Ronen Meiri [ctb] (on behalf of DMWay Analytics LTD), Tomer Kalimi [ctb] (on behalf of DMWay Analytics LTD)
Maintainer: Marco Enea <emarco76@libero.it>
Diff between speedglm versions 0.3-1 dated 2015-09-21 and 0.3-2 dated 2017-01-09
speedglm-0.3-1/speedglm/R/speedlm.r |only speedglm-0.3-1/speedglm/R/summary.speedlm.r |only speedglm-0.3-2/speedglm/DESCRIPTION | 8 speedglm-0.3-2/speedglm/MD5 | 22 - speedglm-0.3-2/speedglm/NAMESPACE | 12 speedglm-0.3-2/speedglm/NEWS | 12 speedglm-0.3-2/speedglm/R/speedglm.r | 3 speedglm-0.3-2/speedglm/R/speedlm.R |only speedglm-0.3-2/speedglm/R/summary.speedglm.r | 522 ++++++++++++++++++------ speedglm-0.3-2/speedglm/R/summary.speedlm.R |only speedglm-0.3-2/speedglm/man/add1&drop1.Rd | 38 + speedglm-0.3-2/speedglm/man/speedglm.Rd | 2 speedglm-0.3-2/speedglm/man/speedlm.Rd | 4 speedglm-0.3-2/speedglm/man/summary.speedglm.Rd | 6 14 files changed, 482 insertions(+), 147 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis in R
Description: An implementation of Quantitative Fatty Acid Signature
Analysis (QFASA) in R. QFASA is a method of estimating the diet
composition of predators. The fundamental unit of information in
QFASA is a fatty acid signature (signature), which is a vector of
proportions describing the composition of fatty acids within lipids.
Signature data from at least one predator and from samples of all
potential prey types are required. Calibration coefficients, which
adjust for the differential metabolism of individual fatty acids by
predators, are also required. Given those data inputs, a predator
signature is modeled as a mixture of prey signatures and its diet
estimate is obtained as the mixture that minimizes a measure of
distance between the observed and modeled signatures. A variety of
estimation options and simulation capabilities are implemented.
Please refer to the vignette for additional details and references.
Author: Jeffrey F. Bromaghin [aut, cre]
Maintainer: Jeffrey F. Bromaghin <jbromaghin@usgs.gov>
Diff between qfasar versions 1.1.1 dated 2016-12-02 and 1.2.0 dated 2017-01-09
DESCRIPTION | 8 +- MD5 | 14 +-- R/cc_aug.R | 1 R/est_diet.R | 191 ++++++++++++++++++++++++++++++++++----------------- inst/doc/qfasar.Rmd | 11 ++ inst/doc/qfasar.html | 11 +- man/est_diet.Rd | 23 +++--- vignettes/qfasar.Rmd | 11 ++ 8 files changed, 180 insertions(+), 90 deletions(-)
Title: Markov-Switching GARCH Models
Description: The MSGARCH package offers methods to fit (by Maximum Likelihood or Bayesian), simulate, and forecast various Markov-Switching GARCH processes.
Author: David Ardia [aut],
Keven Bluteau [aut, cre],
Kris Boudt [ctb],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between MSGARCH versions 0.17 dated 2016-10-29 and 0.17.7 dated 2017-01-09
MSGARCH-0.17.7/MSGARCH/DESCRIPTION | 30 - MSGARCH-0.17.7/MSGARCH/MD5 | 116 ++-- MSGARCH-0.17.7/MSGARCH/NAMESPACE | 199 +++---- MSGARCH-0.17.7/MSGARCH/NEWS | 36 - MSGARCH-0.17.7/MSGARCH/R/AIC.R | 90 +-- MSGARCH-0.17.7/MSGARCH/R/BIC.R | 92 +-- MSGARCH-0.17.7/MSGARCH/R/DIC.R | 109 ++-- MSGARCH-0.17.7/MSGARCH/R/MSGARCH.R | 4 MSGARCH-0.17.7/MSGARCH/R/Pstate.R | 108 ++-- MSGARCH-0.17.7/MSGARCH/R/bayes.R | 234 ++++---- MSGARCH-0.17.7/MSGARCH/R/cdf.R | 212 +++---- MSGARCH-0.17.7/MSGARCH/R/create.spec.R | 337 ++++++------ MSGARCH-0.17.7/MSGARCH/R/crps.R |only MSGARCH-0.17.7/MSGARCH/R/f.theta.IndDist.R | 110 ++-- MSGARCH-0.17.7/MSGARCH/R/f.theta.mixture.R | 58 +- MSGARCH-0.17.7/MSGARCH/R/findParameters.R | 42 - MSGARCH-0.17.7/MSGARCH/R/ht.R | 96 +-- MSGARCH-0.17.7/MSGARCH/R/kernel.R | 120 ++-- MSGARCH-0.17.7/MSGARCH/R/mle.R | 250 ++++----- MSGARCH-0.17.7/MSGARCH/R/pdf.R | 222 ++++---- MSGARCH-0.17.7/MSGARCH/R/pit.R | 189 +++---- MSGARCH-0.17.7/MSGARCH/R/pred.R | 177 +++--- MSGARCH-0.17.7/MSGARCH/R/print.R | 744 ++++++++++++++-------------- MSGARCH-0.17.7/MSGARCH/R/risk.R | 318 ++++++----- MSGARCH-0.17.7/MSGARCH/R/sim.R | 136 ++--- MSGARCH-0.17.7/MSGARCH/R/simahead.R | 162 +++--- MSGARCH-0.17.7/MSGARCH/R/spec.R | 249 ++++----- MSGARCH-0.17.7/MSGARCH/R/transmat.R | 148 ++--- MSGARCH-0.17.7/MSGARCH/R/unc.vol.R | 113 ++-- MSGARCH-0.17.7/MSGARCH/R/utils.R | 425 ++++++++------- MSGARCH-0.17.7/MSGARCH/R/zzz.R | 10 MSGARCH-0.17.7/MSGARCH/THANKS | 2 MSGARCH-0.17.7/MSGARCH/inst/CITATION | 50 + MSGARCH-0.17.7/MSGARCH/inst/COPYRIGHTS | 20 MSGARCH-0.17.7/MSGARCH/man/AIC.Rd | 76 +- MSGARCH-0.17.7/MSGARCH/man/AMZN.Rd | 24 MSGARCH-0.17.7/MSGARCH/man/BIC.Rd | 76 +- MSGARCH-0.17.7/MSGARCH/man/DIC.Rd | 102 +-- MSGARCH-0.17.7/MSGARCH/man/Pstate.Rd | 90 +-- MSGARCH-0.17.7/MSGARCH/man/cdf.Rd | 130 ++-- MSGARCH-0.17.7/MSGARCH/man/create.spec.Rd | 202 +++---- MSGARCH-0.17.7/MSGARCH/man/crps.Rd |only MSGARCH-0.17.7/MSGARCH/man/fit.bayes.Rd | 176 +++--- MSGARCH-0.17.7/MSGARCH/man/fit.mle.Rd | 167 +++--- MSGARCH-0.17.7/MSGARCH/man/ht.Rd | 88 +-- MSGARCH-0.17.7/MSGARCH/man/kernel.Rd | 112 ++-- MSGARCH-0.17.7/MSGARCH/man/pdf.Rd | 134 ++--- MSGARCH-0.17.7/MSGARCH/man/pit.Rd | 142 ++--- MSGARCH-0.17.7/MSGARCH/man/pred.Rd | 134 ++--- MSGARCH-0.17.7/MSGARCH/man/risk.Rd | 137 ++--- MSGARCH-0.17.7/MSGARCH/man/sim.Rd | 96 +-- MSGARCH-0.17.7/MSGARCH/man/simahead.Rd | 114 ++-- MSGARCH-0.17.7/MSGARCH/man/sp500.Rd | 24 MSGARCH-0.17.7/MSGARCH/man/transmat.Rd | 84 +-- MSGARCH-0.17.7/MSGARCH/man/unc.vol.Rd | 64 +- MSGARCH-0.17.7/MSGARCH/src/Egarch.cpp |only MSGARCH-0.17.7/MSGARCH/src/Gas.cpp |only MSGARCH-0.17.7/MSGARCH/src/Tgarch.cpp |only MSGARCH-0.17.7/MSGARCH/src/spec.h | 8 MSGARCH-0.17/MSGARCH/inst/doc |only MSGARCH-0.17/MSGARCH/man/MSGARCH-package.Rd |only MSGARCH-0.17/MSGARCH/src/GAS.cpp |only MSGARCH-0.17/MSGARCH/src/eGARCH.cpp |only MSGARCH-0.17/MSGARCH/src/tGARCH.cpp |only 64 files changed, 3736 insertions(+), 3652 deletions(-)
Title: Package for Plotting Categorical Longitudinal and Time-Series
Data
Description: Methods for plotting categorical longitudinal and time-series data by mapping individuals to the vertical space (each horizontal line represents a participant), time (or repeated measures) to the horizontal space, categorical (or discrete) states as facets using color or shade, and events to points using plotting characters. Sorting individuals in the vertical space and (or) stratifying them by groups can reveal patterns in the changes over time.
Author: Stephen Tueller. Funded by the National Institute on Drug Abuse (NIDA) Award number 1R03DA030850, the National Institute on Alcohol Abuse and Alcoholism (NIAAA) Award Number R03 AA019775, and the National Institute of Justic Award Number 2011-RY-BX-0003.
Maintainer: Stephen Tueller <stueller@rti.org>
Diff between longCatEDA versions 0.17 dated 2014-02-21 and 0.21 dated 2017-01-09
longCatEDA-0.17/longCatEDA/R/longCatEDA_0.17.r |only longCatEDA-0.17/longCatEDA/man/dimCheck.Rd |only longCatEDA-0.21/longCatEDA/DESCRIPTION | 15 +- longCatEDA-0.21/longCatEDA/MD5 | 36 +++---- longCatEDA-0.21/longCatEDA/NAMESPACE | 5 longCatEDA-0.21/longCatEDA/NEWS | 8 + longCatEDA-0.21/longCatEDA/R/longCatEDA_0.21.r |only longCatEDA-0.21/longCatEDA/man/alignTime.Rd |only longCatEDA-0.21/longCatEDA/man/clean.events.Rd |only longCatEDA-0.21/longCatEDA/man/colChoose.Rd | 4 longCatEDA-0.21/longCatEDA/man/example3.Rd | 2 longCatEDA-0.21/longCatEDA/man/levelCheck.Rd | 2 longCatEDA-0.21/longCatEDA/man/longCat-class.Rd | 21 ++-- longCatEDA-0.21/longCatEDA/man/longCat.Rd | 96 ++++++++++++------- longCatEDA-0.21/longCatEDA/man/longCatEDA-package.Rd | 9 - longCatEDA-0.21/longCatEDA/man/longCatPlot.Rd | 37 +++++-- longCatEDA-0.21/longCatEDA/man/longContPlot.Rd | 2 longCatEDA-0.21/longCatEDA/man/lunique.Rd | 2 longCatEDA-0.21/longCatEDA/man/makePatterns.Rd | 10 - longCatEDA-0.21/longCatEDA/man/norpt.Rd | 2 longCatEDA-0.21/longCatEDA/man/sort1.Rd |only longCatEDA-0.21/longCatEDA/man/sorter.Rd | 50 +++++++-- 22 files changed, 199 insertions(+), 102 deletions(-)
Title: Regression Subset Selection
Description: Regression subset selection, including exhaustive search.
Author: Thomas Lumley based on Fortran code by Alan Miller
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between leaps versions 2.9 dated 2009-05-05 and 3.0 dated 2017-01-09
DESCRIPTION | 16 ++++++++-------- MD5 |only NAMESPACE | 3 +++ NEWS | 7 +++++++ R/leaps.R | 46 ++++++++++++++++++++++++++++++++++------------ README | 14 +++----------- man/leaps.Rd | 3 ++- man/leaps.setup.Rd | 8 +++++--- man/plot.regsubsets.Rd | 3 ++- man/regsubsets.Rd | 32 +++++++++++++++++++++++++++----- tests |only 11 files changed, 91 insertions(+), 41 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration.
Author: Robert B. Gramacy <rbg@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.3-1 dated 2017-01-05 and 1.3-2 dated 2017-01-09
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/gp_sep.R | 2 +- build/vignette.rds |binary inst/doc/laGP.pdf |binary 6 files changed, 17 insertions(+), 10 deletions(-)
Title: Distributed-Lag Structural Equation Modelling
Description: Inference functionalities for structural equation models with constrained lag shapes.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.5 dated 2016-11-23 and 1.7 dated 2017-01-09
dlsem-1.5/dlsem/man/EM.imputation.Rd |only dlsem-1.5/dlsem/man/applyDiff.Rd |only dlsem-1.5/dlsem/man/fitIndices.Rd |only dlsem-1.7/dlsem/DESCRIPTION | 12 dlsem-1.7/dlsem/MD5 | 45 dlsem-1.7/dlsem/NAMESPACE | 12 dlsem-1.7/dlsem/R/dlsem.r | 1849 +++++++++++++-------------- dlsem-1.7/dlsem/build/vignette.rds |binary dlsem-1.7/dlsem/data/industry.rda |binary dlsem-1.7/dlsem/inst/doc/dlsem_tutorial.R | 42 dlsem-1.7/dlsem/inst/doc/dlsem_tutorial.Rnw | 305 ++-- dlsem-1.7/dlsem/inst/doc/dlsem_tutorial.pdf |binary dlsem-1.7/dlsem/man/auto.lagPlot.Rd |only dlsem-1.7/dlsem/man/causalEff.Rd | 29 dlsem-1.7/dlsem/man/dlsem-package.Rd | 13 dlsem-1.7/dlsem/man/dlsem.Rd | 130 + dlsem-1.7/dlsem/man/edgeCoeff.Rd | 18 dlsem-1.7/dlsem/man/industry.Rd | 4 dlsem-1.7/dlsem/man/isIndep.Rd | 13 dlsem-1.7/dlsem/man/lagPlot.Rd | 21 dlsem-1.7/dlsem/man/modelFit.Rd |only dlsem-1.7/dlsem/man/unirootTest.Rd | 14 dlsem-1.7/dlsem/vignettes/dlsem_tutorial.Rnw | 305 ++-- dlsem-1.7/dlsem/vignettes/figures/lagsh1.pdf |binary dlsem-1.7/dlsem/vignettes/figures/lagsh2.pdf |binary dlsem-1.7/dlsem/vignettes/figures/lagsh3.pdf |binary 26 files changed, 1451 insertions(+), 1361 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with both continuous and discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.31 dated 2016-12-20 and 2.32 dated 2017-01-09
DESCRIPTION | 8 - MD5 | 12 +- R/bdgraph.R | 2 src/ggm_bd.cpp | 245 +++++++++++++++++++++++++-------------------------------- src/matrix.cpp | 170 ++++++++++++++++++++++++++++----------- src/matrix.h | 14 +-- src/rgwish.cpp | 39 ++++----- 7 files changed, 271 insertions(+), 219 deletions(-)
More information about stormwindmodel at CRAN
Permanent link
Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <mdo.statmatch@gmail.com>
Diff between StatMatch versions 1.2.4 dated 2016-01-13 and 1.2.5 dated 2017-01-09
StatMatch-1.2.4/StatMatch/R/Frechet.bounds.cat.2.R |only StatMatch-1.2.5/StatMatch/DESCRIPTION | 10 StatMatch-1.2.5/StatMatch/MD5 | 62 - StatMatch-1.2.5/StatMatch/NEWS | 9 StatMatch-1.2.5/StatMatch/R/Fbwidths.by.x.R | 19 StatMatch-1.2.5/StatMatch/R/Frechet.bounds.cat.R |only StatMatch-1.2.5/StatMatch/R/NND.hotdeck.R | 480 +++++----- StatMatch-1.2.5/StatMatch/R/RANDwNND.hotdeck.R | 4 StatMatch-1.2.5/StatMatch/R/gower.dist.R | 199 ++-- StatMatch-1.2.5/StatMatch/build/vignette.rds |binary StatMatch-1.2.5/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.Rnw | 14 StatMatch-1.2.5/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.pdf |binary StatMatch-1.2.5/StatMatch/man/Fbwidths.by.x.Rd | 4 StatMatch-1.2.5/StatMatch/man/Frechet.bounds.cat.Rd | 2 StatMatch-1.2.5/StatMatch/man/NND.hotdeck.Rd | 27 StatMatch-1.2.5/StatMatch/man/RANDwNND.hotdeck.Rd | 2 StatMatch-1.2.5/StatMatch/man/StatMatch-package.Rd | 12 StatMatch-1.2.5/StatMatch/man/comb.samples.Rd | 2 StatMatch-1.2.5/StatMatch/man/comp.prop.Rd | 2 StatMatch-1.2.5/StatMatch/man/create.fused.Rd | 2 StatMatch-1.2.5/StatMatch/man/fact2dummy.Rd | 2 StatMatch-1.2.5/StatMatch/man/gower.dist.Rd | 7 StatMatch-1.2.5/StatMatch/man/harmonize.x.Rd | 2 StatMatch-1.2.5/StatMatch/man/mahalanobis.dist.Rd | 2 StatMatch-1.2.5/StatMatch/man/maximum.dist.Rd | 2 StatMatch-1.2.5/StatMatch/man/mixed.mtc.Rd | 4 StatMatch-1.2.5/StatMatch/man/pBayes.Rd | 2 StatMatch-1.2.5/StatMatch/man/pw.assoc.Rd | 2 StatMatch-1.2.5/StatMatch/man/rankNND.hotdeck.Rd | 2 StatMatch-1.2.5/StatMatch/man/samp.A.Rd | 2 StatMatch-1.2.5/StatMatch/man/samp.B.Rd | 2 StatMatch-1.2.5/StatMatch/man/samp.C.Rd | 2 StatMatch-1.2.5/StatMatch/vignettes/Statistical_Matching_with_StatMatch.Rnw | 14 33 files changed, 470 insertions(+), 425 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the 'CVODES' library, but it is not accessible from R. 'StanHeaders' is only useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.14.0 dated 2016-12-28 and 2.14.0-1 dated 2017-01-09
DESCRIPTION | 10 +-- MD5 | 4 - inst/include/stan/math/prim/mat/fun/LDLT_factor.hpp | 62 ++++++++++---------- 3 files changed, 41 insertions(+), 35 deletions(-)
Title: Loading Facebook and Instagram Advertising Data from
'Smartly.io'
Description: Aims at loading Facebook and Instagram advertising data from
'Smartly.io' into R. 'Smartly.io' is an online advertising service that enables
advertisers to display commercial ads on social media networks (see <http://www.smartly.io/> for more information).
The package offers an interface to query the 'Smartly.io' API and loads data directly into R for further data processing and data analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Diff between RSmartlyIO versions 0.1.0 dated 2016-07-06 and 0.1.1 dated 2017-01-09
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- NAMESPACE | 1 - R/getSmartlyData.R | 11 ++++++++++- man/getSmartlyData.Rd | 5 ++++- 5 files changed, 27 insertions(+), 16 deletions(-)
Title: Microsoft Word and PowerPoint Documents Generation
Description: Create 'Microsoft Word' document (>=2007) and
'Microsoft PowerPoint' document (>=2007) from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document. You can use the package as a tool for fast reporting
and as a tool for reporting automation. The package does not require
any installation of Microsoft product to be able to write Microsoft files.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between ReporteRs versions 0.8.7 dated 2016-11-05 and 0.8.8 dated 2017-01-09
ReporteRs-0.8.7/ReporteRs/R/addMarkdown.bsdoc.R |only ReporteRs-0.8.7/ReporteRs/R/addMarkdown.docx.R |only ReporteRs-0.8.7/ReporteRs/R/addSubtitle.pptx.R |only ReporteRs-0.8.7/ReporteRs/R/bootstrap.copy.R |only ReporteRs-0.8.7/ReporteRs/R/bsdoc.R |only ReporteRs-0.8.7/ReporteRs/R/markdown.api.R |only ReporteRs-0.8.7/ReporteRs/R/setHeaderStyle.docx.R |only ReporteRs-0.8.7/ReporteRs/inst/COPYRIGHTS |only ReporteRs-0.8.7/ReporteRs/inst/bootstrap |only ReporteRs-0.8.7/ReporteRs/man/addJavascript.Rd |only ReporteRs-0.8.7/ReporteRs/man/addMarkdown.Rd |only ReporteRs-0.8.7/ReporteRs/man/addMarkdown.bsdoc.Rd |only ReporteRs-0.8.7/ReporteRs/man/addMarkdown.docx.Rd |only ReporteRs-0.8.7/ReporteRs/man/addSubtitle.pptx.Rd |only ReporteRs-0.8.7/ReporteRs/man/as.html.RScript.Rd |only ReporteRs-0.8.7/ReporteRs/man/as.html.bsdoc.Rd |only ReporteRs-0.8.7/ReporteRs/man/bsdoc.Rd |only ReporteRs-0.8.7/ReporteRs/man/declareTitlesStyles.Rd |only ReporteRs-0.8.7/ReporteRs/man/declareTitlesStyles.docx.Rd |only ReporteRs-0.8.7/ReporteRs/man/doc-list-settings.Rd |only ReporteRs-0.8.7/ReporteRs/man/docx-bookmark.Rd |only ReporteRs-0.8.7/ReporteRs/man/knit_print.pot.Rd |only ReporteRs-0.8.7/ReporteRs/man/print.bsdoc.Rd |only ReporteRs-0.8.7/ReporteRs/man/print.pot.Rd |only ReporteRs-0.8.7/ReporteRs/man/toc.options.docx.Rd |only ReporteRs-0.8.8/ReporteRs/DESCRIPTION | 26 - ReporteRs-0.8.8/ReporteRs/MD5 | 256 ++++------ ReporteRs-0.8.8/ReporteRs/NAMESPACE | 28 - ReporteRs-0.8.8/ReporteRs/NEWS | 14 ReporteRs-0.8.8/ReporteRs/R/00_AllGeneric.R | 82 --- ReporteRs-0.8.8/ReporteRs/R/01_tools.R | 11 ReporteRs-0.8.8/ReporteRs/R/CodeBlock.R | 2 ReporteRs-0.8.8/ReporteRs/R/FlexCell.R | 43 + ReporteRs-0.8.8/ReporteRs/R/FlexRow.R | 18 ReporteRs-0.8.8/ReporteRs/R/FlexTable.R | 122 ++++ ReporteRs-0.8.8/ReporteRs/R/FlexTablePublicAPI.R | 225 +++++++- ReporteRs-0.8.8/ReporteRs/R/FlexTable_theme.R | 40 - ReporteRs-0.8.8/ReporteRs/R/Footnote.R | 48 + ReporteRs-0.8.8/ReporteRs/R/Lists.R | 72 ++ ReporteRs-0.8.8/ReporteRs/R/RScript.R | 23 ReporteRs-0.8.8/ReporteRs/R/ReporteRs.R | 41 - ReporteRs-0.8.8/ReporteRs/R/Section.R | 30 + ReporteRs-0.8.8/ReporteRs/R/addCodeBlock.R | 32 - ReporteRs-0.8.8/ReporteRs/R/addColumnBreak.R | 4 ReporteRs-0.8.8/ReporteRs/R/addDate.pptx.R | 16 ReporteRs-0.8.8/ReporteRs/R/addDocument.R | 2 ReporteRs-0.8.8/ReporteRs/R/addFlexTable.R | 36 - ReporteRs-0.8.8/ReporteRs/R/addFooter.pptx.R | 2 ReporteRs-0.8.8/ReporteRs/R/addImage.R | 55 -- ReporteRs-0.8.8/ReporteRs/R/addPageBreak.docx.R | 2 ReporteRs-0.8.8/ReporteRs/R/addPageNumber.pptx.R | 17 ReporteRs-0.8.8/ReporteRs/R/addParagraph.R | 233 ++++----- ReporteRs-0.8.8/ReporteRs/R/addPlot.R | 58 -- ReporteRs-0.8.8/ReporteRs/R/addRScript.R | 43 - ReporteRs-0.8.8/ReporteRs/R/addSlide.R | 36 + ReporteRs-0.8.8/ReporteRs/R/addSubtitle.R |only ReporteRs-0.8.8/ReporteRs/R/addTOC.R | 68 ++ ReporteRs-0.8.8/ReporteRs/R/addTitle.R | 81 +-- ReporteRs-0.8.8/ReporteRs/R/as.FlexTable.sessionInfo.R | 17 ReporteRs-0.8.8/ReporteRs/R/as.html.FlexTable.R | 10 ReporteRs-0.8.8/ReporteRs/R/as_link.R |only ReporteRs-0.8.8/ReporteRs/R/cellProperties.R | 18 ReporteRs-0.8.8/ReporteRs/R/chprop.FlexTable.R | 4 ReporteRs-0.8.8/ReporteRs/R/docx.R | 143 +++++ ReporteRs-0.8.8/ReporteRs/R/map_title.R |only ReporteRs-0.8.8/ReporteRs/R/parProperties.R | 19 ReporteRs-0.8.8/ReporteRs/R/pot.R | 59 +- ReporteRs-0.8.8/ReporteRs/R/pptx.R | 95 +++ ReporteRs-0.8.8/ReporteRs/R/pptx.graphic.R | 8 ReporteRs-0.8.8/ReporteRs/R/slide.layouts.pptx.R | 15 ReporteRs-0.8.8/ReporteRs/R/styles.docx.R | 2 ReporteRs-0.8.8/ReporteRs/R/textProperties.R | 29 - ReporteRs-0.8.8/ReporteRs/R/text_extract.R | 18 ReporteRs-0.8.8/ReporteRs/R/toc.options.R | 15 ReporteRs-0.8.8/ReporteRs/R/writeDoc.R | 50 - ReporteRs-0.8.8/ReporteRs/inst/java/ReporteRs-0.8.jar |binary ReporteRs-0.8.8/ReporteRs/inst/templates/bookmark_example.docx |binary ReporteRs-0.8.8/ReporteRs/java/ReporteRs-0.8-src.jar |binary ReporteRs-0.8.8/ReporteRs/man/CodeBlock.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/FlexCell.Rd | 18 ReporteRs-0.8.8/ReporteRs/man/FlexRow-alter.Rd | 9 ReporteRs-0.8.8/ReporteRs/man/FlexRow.Rd | 20 ReporteRs-0.8.8/ReporteRs/man/FlexTable-alter.Rd | 49 - ReporteRs-0.8.8/ReporteRs/man/FlexTable.Rd | 181 ++----- ReporteRs-0.8.8/ReporteRs/man/Footnote.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/RScript.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/ReporteRs-package.Rd | 24 ReporteRs-0.8.8/ReporteRs/man/addCodeBlock.Rd | 12 ReporteRs-0.8.8/ReporteRs/man/addColumnBreak.Rd | 3 ReporteRs-0.8.8/ReporteRs/man/addDate.Rd | 20 ReporteRs-0.8.8/ReporteRs/man/addDocument.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/addFlexTable.Rd | 22 ReporteRs-0.8.8/ReporteRs/man/addFooter.pptx.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/addFooterRow.Rd | 36 - ReporteRs-0.8.8/ReporteRs/man/addHeaderRow.Rd | 46 - ReporteRs-0.8.8/ReporteRs/man/addImage.Rd | 28 - ReporteRs-0.8.8/ReporteRs/man/addPageBreak.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/addPageNumber.pptx.Rd | 30 - ReporteRs-0.8.8/ReporteRs/man/addParagraph.Rd | 224 +------- ReporteRs-0.8.8/ReporteRs/man/addPlot.Rd | 20 ReporteRs-0.8.8/ReporteRs/man/addRScript.Rd | 35 - ReporteRs-0.8.8/ReporteRs/man/addSection.Rd | 23 ReporteRs-0.8.8/ReporteRs/man/addSlide.Rd | 36 - ReporteRs-0.8.8/ReporteRs/man/addSubtitle.Rd | 25 ReporteRs-0.8.8/ReporteRs/man/addTOC.Rd | 19 ReporteRs-0.8.8/ReporteRs/man/addTitle.Rd | 56 -- ReporteRs-0.8.8/ReporteRs/man/as.FlexTable.sessionInfo.Rd | 5 ReporteRs-0.8.8/ReporteRs/man/as.html.FlexTable.Rd | 28 - ReporteRs-0.8.8/ReporteRs/man/cellProperties.Rd | 55 -- ReporteRs-0.8.8/ReporteRs/man/chprop.FlexTable.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/docx.Rd | 10 ReporteRs-0.8.8/ReporteRs/man/light.table.Rd | 8 ReporteRs-0.8.8/ReporteRs/man/list.settings.Rd |only ReporteRs-0.8.8/ReporteRs/man/list_bookmarks.Rd | 5 ReporteRs-0.8.8/ReporteRs/man/map_title.Rd |only ReporteRs-0.8.8/ReporteRs/man/office_web_viewer.Rd |only ReporteRs-0.8.8/ReporteRs/man/parProperties.Rd | 22 ReporteRs-0.8.8/ReporteRs/man/pot.Rd | 31 - ReporteRs-0.8.8/ReporteRs/man/pptx.Rd | 20 ReporteRs-0.8.8/ReporteRs/man/setColumnsColors.Rd | 11 ReporteRs-0.8.8/ReporteRs/man/setFlexTableBackgroundColors.Rd | 93 ++- ReporteRs-0.8.8/ReporteRs/man/setFlexTableBorders.Rd | 17 ReporteRs-0.8.8/ReporteRs/man/setFlexTableWidths.Rd | 8 ReporteRs-0.8.8/ReporteRs/man/setRowsColors.Rd | 11 ReporteRs-0.8.8/ReporteRs/man/setZebraStyle.Rd | 12 ReporteRs-0.8.8/ReporteRs/man/slide.layouts.pptx.Rd | 13 ReporteRs-0.8.8/ReporteRs/man/spanFlexTableColumns.Rd | 15 ReporteRs-0.8.8/ReporteRs/man/spanFlexTableRows.Rd | 15 ReporteRs-0.8.8/ReporteRs/man/styles.Rd | 2 ReporteRs-0.8.8/ReporteRs/man/textProperties.Rd | 44 - ReporteRs-0.8.8/ReporteRs/man/text_extract.Rd | 5 ReporteRs-0.8.8/ReporteRs/man/toc.options.Rd | 25 ReporteRs-0.8.8/ReporteRs/man/vanilla.table.Rd | 8 ReporteRs-0.8.8/ReporteRs/man/writeDoc.Rd | 6 ReporteRs-0.8.8/ReporteRs/tests/testthat/get_relationship.R |only ReporteRs-0.8.8/ReporteRs/tests/testthat/test-docx-bookmarks.R |only ReporteRs-0.8.8/ReporteRs/tests/testthat/test-flextable.R |only ReporteRs-0.8.8/ReporteRs/tests/testthat/test-formatting-props.R |only ReporteRs-0.8.8/ReporteRs/tests/testthat/test-pptx-img.R | 17 ReporteRs-0.8.8/ReporteRs/tests/testthat/test-pptx-plot.R | 52 ++ 140 files changed, 1951 insertions(+), 1805 deletions(-)
Title: Functions to Support the Multicriteria Decision Aiding Process
Description: Functions which can be useful to support the analyst in the Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting criteria.
Author: Patrick Meyer, Sébastien Bigaret, Richard Hodgett, Alexandru-Liviu Olteanu
Maintainer: Patrick Meyer <patrick.meyer@telecom-bretagne.eu>
Diff between MCDA versions 0.0.14 dated 2016-12-16 and 0.0.15 dated 2017-01-09
DESCRIPTION | 12 MD5 | 192 +++--- NAMESPACE | 3 R/AHP.R | 40 - R/LPDMRSort.R | 40 - R/LPDMRSortIdentifyIncompatibleAssignments.R | 40 - R/LPDMRSortInferenceExact.R | 40 - R/MARE.R | 264 +++----- R/MRSort.R | 39 - R/MRSortIdentifyIncompatibleAssignments.R | 40 - R/MRSortInferenceApprox.R | 40 - R/MRSortInferenceExact.R | 40 - R/TOPSIS.R | 40 - R/UTA.R | 39 - R/UTADIS.R | 39 - R/UTASTAR.R | 39 - R/additiveValueFunctionElicitation.R | 39 - R/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R | 39 - R/assignAlternativesToCategoriesByThresholds.R | 39 - R/normalizePerformanceTable.R | 39 - R/pairwiseConsistencyMeasures.R | 301 ++++------ R/plotAlternativesValuesPreorder.R | 39 - R/plotMRSortSortingProblem.R | 240 +++++-- R/plotPiecewiseLinearValueFunctions.R | 39 - R/plotRadarPerformanceTable.R | 39 - R/weightedSum.R | 40 - inst/extdata/MRSortDIdentifyInvalidAssignmentsSet.gmpl | 4 inst/extdata/MRSortDIdentifyMinimalInvalidAssignmentsSet.gmpl | 4 inst/extdata/MRSortDInferenceModel.gmpl | 4 inst/extdata/MRSortDInferenceModelLPD.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadProfiles.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadProfilesLPD.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadWeights.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadWeightsLPD.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadWeightsProfiles.gmpl | 4 inst/extdata/MRSortDInferenceModelSpreadWeightsProfilesLPD.gmpl | 4 inst/extdata/MRSortDV1IdentifyInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV1IdentifyMinimalInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV1InferenceModel.gmpl | 8 inst/extdata/MRSortDV1InferenceModelLPD.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadProfiles.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadProfilesLPD.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadWeights.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadWeightsLPD.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadWeightsProfiles.gmpl | 8 inst/extdata/MRSortDV1InferenceModelSpreadWeightsProfilesLPD.gmpl | 8 inst/extdata/MRSortDV2IdentifyInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV2IdentifyMinimalInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV2InferenceModel.gmpl | 8 inst/extdata/MRSortDV2InferenceModelLPD.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadProfiles.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadProfilesLPD.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadWeights.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadWeightsLPD.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadWeightsProfiles.gmpl | 8 inst/extdata/MRSortDV2InferenceModelSpreadWeightsProfilesLPD.gmpl | 8 inst/extdata/MRSortDV3IdentifyInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV3IdentifyMinimalInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV3InferenceModel.gmpl | 8 inst/extdata/MRSortDV3InferenceModelLPD.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadProfiles.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadProfilesLPD.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadWeights.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadWeightsLPD.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadWeightsProfiles.gmpl | 8 inst/extdata/MRSortDV3InferenceModelSpreadWeightsProfilesLPD.gmpl | 8 inst/extdata/MRSortDV4IdentifyInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV4IdentifyMinimalInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV4InferenceModel.gmpl | 8 inst/extdata/MRSortDV4InferenceModelLPD.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadProfiles.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadProfilesLPD.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadWeights.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadWeightsLPD.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadWeightsProfiles.gmpl | 8 inst/extdata/MRSortDV4InferenceModelSpreadWeightsProfilesLPD.gmpl | 8 inst/extdata/MRSortDV5IdentifyInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV5IdentifyMinimalInvalidAssignmentsSet.gmpl | 8 inst/extdata/MRSortDV5InferenceModel.gmpl | 8 inst/extdata/MRSortDV5InferenceModelLPD.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadProfiles.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadProfilesLPD.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadWeights.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadWeightsLPD.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadWeightsProfiles.gmpl | 8 inst/extdata/MRSortDV5InferenceModelSpreadWeightsProfilesLPD.gmpl | 8 inst/extdata/MRSortVIdentifyInvalidAssignmentsSet.gmpl | 4 inst/extdata/MRSortVIdentifyMinimalInvalidAssignmentsSet.gmpl | 4 inst/extdata/MRSortVInferenceModel.gmpl | 4 inst/extdata/MRSortVInferenceModelLPD.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadProfiles.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadProfilesLPD.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadWeights.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadWeightsLPD.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadWeightsProfiles.gmpl | 4 inst/extdata/MRSortVInferenceModelSpreadWeightsProfilesLPD.gmpl | 4 man/plotMRSortSortingProblem.Rd | 16 97 files changed, 879 insertions(+), 1418 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Peter Li [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.8-0 dated 2016-12-17 and 0.8-1 dated 2017-01-09
DESCRIPTION | 21 +++--- MD5 | 16 ++-- NAMESPACE | 8 ++ NEWS | 7 ++ R |only data/Snow.polygons.RData |binary data/Snow.pumps.RData |binary inst/doc/Snow_deaths-duplicates.html | 4 - man/Snow.Rd | 121 +++++++---------------------------- man/SnowMap.Rd |only 10 files changed, 63 insertions(+), 114 deletions(-)
Title: Java Executable .jar Files for 'RKEEL'
Description: KEEL is a popular Java software for a large number of different knowledge data discovery tasks. Furthermore, 'RKEEL' is a package with a R code layer between R and KEEL, for using KEEL in R code. This package downloads and install the .jar files necessary for 'RKEEL' algorithms execution. For more information about KEEL, see <http://www.keel.es/>.
Author: Jose Moyano [aut, cre], Luciano Sanchez Ramos [aut]
Maintainer: Jose Moyano <i02momuj@uco.es>
Diff between RKEELjars versions 1.0.11 dated 2016-02-02 and 1.0.14 dated 2017-01-09
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/getExePath.R | 14 +++---- R/getJarList.R | 23 +++++++++++ R/zzz.R | 110 ++++++++++++++++++++++++++++----------------------------- 5 files changed, 92 insertions(+), 71 deletions(-)
Title: Download Aggregate Trial Information and Results from
ClinicalTrials.gov
Description: ClinicalTrials.gov is a registry and results database of publicly
and privately supported clinical studies of human participants conducted
around the world (see <https://clinicaltrials.gov/> for more information).
Users can search for information about and results from
those trials. This provides a set of functions to interact with the search
and download features. Results are downloaded to temporary directories and
returned as R objects.
Author: Michael C Sachs <sachsmc@gmail.com>
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between rclinicaltrials versions 1.4.6 dated 2017-01-02 and 1.4.7 dated 2017-01-09
DESCRIPTION | 8 +- MD5 | 8 +- NEWS | 5 + R/clinicaltrials_download.R | 11 +- inst/doc/basics.html | 164 ++++++++++++++++++++++++++------------------ 5 files changed, 118 insertions(+), 78 deletions(-)
More information about rclinicaltrials at CRAN
Permanent link
Title: The Residual-Based Predictiveness Curve
Description: The RBP curve is a visual tool to assess the
performance of prediction models.
Author: Giuseppe Casalicchio, Bernd Bischl
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between RBPcurve versions 1.0-33 dated 2015-11-23 and 1.1 dated 2017-01-09
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- README.md |only tests/testthat/helper_objects.R | 10 ++++------ tests/testthat/test_makeRBPObj.R | 2 +- 5 files changed, 15 insertions(+), 16 deletions(-)
Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets. Through
the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker <Alexander.Walker1989@gmail.com>
Diff between openxlsx versions 3.0.0 dated 2015-07-03 and 4.0.0 dated 2017-01-09
openxlsx-3.0.0/openxlsx/src/cppFunctions.cpp |only openxlsx-3.0.0/openxlsx/tests/testthat/test-load_read_file_read_equality.R |only openxlsx-3.0.0/openxlsx/tests/testthat/test-load_read_file_read_equality2.R |only openxlsx-3.0.0/openxlsx/tests/testthat/test-load_read_file_read_equality4.R |only openxlsx-3.0.0/openxlsx/tests/testthat/test-load_read_file_read_equality5.R |only openxlsx-4.0.0/openxlsx/DESCRIPTION | 24 openxlsx-4.0.0/openxlsx/MD5 | 221 - openxlsx-4.0.0/openxlsx/NAMESPACE | 20 openxlsx-4.0.0/openxlsx/NEWS | 45 openxlsx-4.0.0/openxlsx/R/CommentClass.R | 13 openxlsx-4.0.0/openxlsx/R/HyperlinkClass.R |only openxlsx-4.0.0/openxlsx/R/RcppExports.R | 198 - openxlsx-4.0.0/openxlsx/R/StyleClass.R | 27 openxlsx-4.0.0/openxlsx/R/WorkbookClass.R | 1611 ++++------ openxlsx-4.0.0/openxlsx/R/baseXML.R | 128 openxlsx-4.0.0/openxlsx/R/borderFunctions.R | 10 openxlsx-4.0.0/openxlsx/R/chartsheet_class.R |only openxlsx-4.0.0/openxlsx/R/class_definitions.R |only openxlsx-4.0.0/openxlsx/R/helperFunctions.R | 286 + openxlsx-4.0.0/openxlsx/R/loadWorkbook.R | 290 + openxlsx-4.0.0/openxlsx/R/openXL.R | 4 openxlsx-4.0.0/openxlsx/R/openxlsx.R | 5 openxlsx-4.0.0/openxlsx/R/openxlsxCoerce.R | 24 openxlsx-4.0.0/openxlsx/R/readWorkbook.R | 571 +-- openxlsx-4.0.0/openxlsx/R/sheet_data_class.R |only openxlsx-4.0.0/openxlsx/R/workbook_column_widths.R |only openxlsx-4.0.0/openxlsx/R/workbook_read_workbook.R |only openxlsx-4.0.0/openxlsx/R/workbook_write_data.R |only openxlsx-4.0.0/openxlsx/R/worksheet_class.R |only openxlsx-4.0.0/openxlsx/R/wrappers.R | 1217 +++++-- openxlsx-4.0.0/openxlsx/R/writeData.R | 146 openxlsx-4.0.0/openxlsx/R/writeDataTable.R | 90 openxlsx-4.0.0/openxlsx/R/writexlsx.R | 155 openxlsx-4.0.0/openxlsx/README.md | 18 openxlsx-4.0.0/openxlsx/build/vignette.rds |binary openxlsx-4.0.0/openxlsx/inst/build_font_size_lookup.R |only openxlsx-4.0.0/openxlsx/inst/conditional_formatting_testing.R |only openxlsx-4.0.0/openxlsx/inst/doc/Introduction.Rnw | 6 openxlsx-4.0.0/openxlsx/inst/doc/Introduction.pdf |binary openxlsx-4.0.0/openxlsx/inst/doc/formatting.Rnw | 5 openxlsx-4.0.0/openxlsx/inst/doc/formatting.pdf |binary openxlsx-4.0.0/openxlsx/inst/doc/installation.Rnw |only openxlsx-4.0.0/openxlsx/inst/doc/installation.pdf |only openxlsx-4.0.0/openxlsx/inst/loadExample.xlsx |binary openxlsx-4.0.0/openxlsx/inst/load_xlsx_testing.R |only openxlsx-4.0.0/openxlsx/inst/readTest.xlsx |binary openxlsx-4.0.0/openxlsx/inst/stack_style_testing.R |only openxlsx-4.0.0/openxlsx/man/addFilter.Rd | 6 openxlsx-4.0.0/openxlsx/man/addStyle.Rd | 8 openxlsx-4.0.0/openxlsx/man/addWorksheet.Rd | 21 openxlsx-4.0.0/openxlsx/man/all.equal.Rd | 2 openxlsx-4.0.0/openxlsx/man/conditionalFormat.Rd | 63 openxlsx-4.0.0/openxlsx/man/conditionalFormatting.Rd | 29 openxlsx-4.0.0/openxlsx/man/convertFromExcelRef.Rd | 7 openxlsx-4.0.0/openxlsx/man/convertToDate.Rd | 6 openxlsx-4.0.0/openxlsx/man/convertToDateTime.Rd | 4 openxlsx-4.0.0/openxlsx/man/copyWorkbook.Rd |only openxlsx-4.0.0/openxlsx/man/createComment.Rd | 10 openxlsx-4.0.0/openxlsx/man/createNamedRegion.Rd |only openxlsx-4.0.0/openxlsx/man/createStyle.Rd | 16 openxlsx-4.0.0/openxlsx/man/createWorkbook.Rd | 4 openxlsx-4.0.0/openxlsx/man/dataValidation.Rd |only openxlsx-4.0.0/openxlsx/man/deleteData.Rd | 14 openxlsx-4.0.0/openxlsx/man/freezePane.Rd | 4 openxlsx-4.0.0/openxlsx/man/getBaseFont.Rd | 6 openxlsx-4.0.0/openxlsx/man/getCellRefs.Rd | 2 openxlsx-4.0.0/openxlsx/man/getDateOrigin.Rd | 6 openxlsx-4.0.0/openxlsx/man/getNamedRegions.Rd | 44 openxlsx-4.0.0/openxlsx/man/getSheetNames.Rd | 5 openxlsx-4.0.0/openxlsx/man/getStyles.Rd | 9 openxlsx-4.0.0/openxlsx/man/insertImage.Rd | 6 openxlsx-4.0.0/openxlsx/man/insertPlot.Rd | 6 openxlsx-4.0.0/openxlsx/man/int2col.Rd | 2 openxlsx-4.0.0/openxlsx/man/loadWorkbook.Rd | 4 openxlsx-4.0.0/openxlsx/man/makeHyperlinkString.Rd |only openxlsx-4.0.0/openxlsx/man/mergeCells.Rd | 2 openxlsx-4.0.0/openxlsx/man/modifyBaseFont.Rd | 6 openxlsx-4.0.0/openxlsx/man/names.Rd | 3 openxlsx-4.0.0/openxlsx/man/openXL.Rd | 3 openxlsx-4.0.0/openxlsx/man/openxlsx.Rd | 8 openxlsx-4.0.0/openxlsx/man/pageBreak.Rd |only openxlsx-4.0.0/openxlsx/man/pageSetup.Rd | 96 openxlsx-4.0.0/openxlsx/man/read.xlsx.Rd | 48 openxlsx-4.0.0/openxlsx/man/readWorkbook.Rd | 33 openxlsx-4.0.0/openxlsx/man/removeCellMerge.Rd | 2 openxlsx-4.0.0/openxlsx/man/removeColWidths.Rd | 6 openxlsx-4.0.0/openxlsx/man/removeComment.Rd | 4 openxlsx-4.0.0/openxlsx/man/removeFilter.Rd | 6 openxlsx-4.0.0/openxlsx/man/removeRowHeights.Rd | 4 openxlsx-4.0.0/openxlsx/man/removeWorksheet.Rd | 6 openxlsx-4.0.0/openxlsx/man/renameWorksheet.Rd | 7 openxlsx-4.0.0/openxlsx/man/replaceStyle.Rd | 9 openxlsx-4.0.0/openxlsx/man/saveWorkbook.Rd | 6 openxlsx-4.0.0/openxlsx/man/setColWidths.Rd | 6 openxlsx-4.0.0/openxlsx/man/setFooter.Rd | 4 openxlsx-4.0.0/openxlsx/man/setHeader.Rd | 4 openxlsx-4.0.0/openxlsx/man/setHeaderFooter.Rd | 10 openxlsx-4.0.0/openxlsx/man/setRowHeights.Rd | 4 openxlsx-4.0.0/openxlsx/man/sheetVisibility.Rd |only openxlsx-4.0.0/openxlsx/man/sheetVisible.Rd |only openxlsx-4.0.0/openxlsx/man/sheets.Rd | 6 openxlsx-4.0.0/openxlsx/man/showGridLines.Rd | 2 openxlsx-4.0.0/openxlsx/man/worksheetOrder.Rd | 6 openxlsx-4.0.0/openxlsx/man/write.xlsx.Rd | 46 openxlsx-4.0.0/openxlsx/man/writeComment.Rd | 4 openxlsx-4.0.0/openxlsx/man/writeData.Rd | 67 openxlsx-4.0.0/openxlsx/man/writeDataTable.Rd | 47 openxlsx-4.0.0/openxlsx/man/writeFormula.Rd | 12 openxlsx-4.0.0/openxlsx/src/RcppExports.cpp | 826 +---- openxlsx-4.0.0/openxlsx/src/helper_functions.cpp |only openxlsx-4.0.0/openxlsx/src/load_workbook.cpp |only openxlsx-4.0.0/openxlsx/src/openxlsx.h |only openxlsx-4.0.0/openxlsx/src/read_workbook.cpp |only openxlsx-4.0.0/openxlsx/src/write_data.cpp |only openxlsx-4.0.0/openxlsx/src/write_file.cpp |only openxlsx-4.0.0/openxlsx/src/write_file_2.cpp |only openxlsx-4.0.0/openxlsx/tests/testthat/Rplots.pdf |binary openxlsx-4.0.0/openxlsx/tests/testthat/test-freeze_pane.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-loading_workbook.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-named_regions.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-read_from_created_wb.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-read_from_loaded_workbook.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-read_sources.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-read_write_logicals.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-trying_to_break_openxlsx.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-v3_0_0_bugs.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-validate_table_name.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-worksheet_renaming.R | 2 openxlsx-4.0.0/openxlsx/tests/testthat/test-write_data_to_sheetData.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-write_data_to_sheetData_NAs.R |only openxlsx-4.0.0/openxlsx/tests/testthat/test-write_read_equality.R | 39 openxlsx-4.0.0/openxlsx/vignettes/Introduction.Rnw | 6 openxlsx-4.0.0/openxlsx/vignettes/formatting.Rnw | 5 openxlsx-4.0.0/openxlsx/vignettes/installation.Rnw |only openxlsx-4.0.0/openxlsx/vignettes/rtools_installation_path.PNG |only 135 files changed, 3725 insertions(+), 3018 deletions(-)
Title: Normalisation of Multiple Variables in Large-Scale Datasets
Description: The robustness of many of the statistical techniques, such as factor analysis, applied in
the social sciences rests upon the assumption of item-level normality. However, when dealing
with real data, these assumptions are often not met. The Box-Cox transformation (Box & Cox, 1964)
<http://www.jstor.org/stable/2984418> provides an optimal transformation for non-normal variables. Yet, for
large datasets of continuous variables, its application in current software programs is cumbersome
with analysts having to take several steps to normalise each variable. We present an R package
'normalr' that enables researchers to make convenient optimal transformations of multiple variables
in datasets. This R package enables users to quickly and accurately: (1) anchor all of their
variables at 1.00, (2) select the desired precision with which the optimal lambda is estimated,
(3) apply each unique exponent to its variable, (4) rescale resultant values to within their
original X1 and X(n) ranges, and (5) provide original and transformed estimates of skewness,
kurtosis, and other inferential assessments of normality.
Author: Kevin Chang [aut, cre],
Matthew Courtney [aut]
Maintainer: Kevin Chang <k.chang@auckland.ac.nz>
Diff between normalr versions 0.0.1 dated 2016-12-20 and 0.0.2 dated 2017-01-09
DESCRIPTION | 12 ++++++------ MD5 | 21 ++++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/getLambda.R | 38 ++++++++++++++++++++++++-------------- R/normalise.R | 21 ++++++++++++++------- R/normaliseData.R | 8 ++++---- R/normalrShiny.R |only README.md | 14 ++++++++++++++ inst |only man/getLambda.Rd | 4 ++-- man/normaliseData.Rd | 4 ++-- man/normalrShiny.Rd |only 13 files changed, 85 insertions(+), 44 deletions(-)
Title: Microbial Pan-Genome Analysis
Description: A collection of functions for computations and visualizations of
microbial pan-genomes.
Author: Lars Snipen and Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between micropan versions 1.1 dated 2016-12-06 and 1.1.1 dated 2017-01-09
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/blasting.R | 2 +- R/entrez.R | 8 ++++---- R/prodigal.R | 2 +- man/blastAllAll.Rd | 2 +- man/entrezDownload.Rd | 4 ++-- man/prodigalPredict.Rd | 2 +- 8 files changed, 22 insertions(+), 22 deletions(-)
Title: Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria
Description: Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between JADE versions 1.9-93 dated 2015-08-14 and 2.0-0 dated 2017-01-09
JADE-1.9-93/JADE/inst/vignette |only JADE-2.0-0/JADE/DESCRIPTION | 9 ++-- JADE-2.0-0/JADE/MD5 | 58 +++++++++++++------------- JADE-2.0-0/JADE/R/AMUSE.R | 4 + JADE-2.0-0/JADE/R/rjd.fortran.R | 5 -- JADE-2.0-0/JADE/build/vignette.rds |binary JADE-2.0-0/JADE/data |only JADE-2.0-0/JADE/inst/CITATION |only JADE-2.0-0/JADE/inst/ChangeLog | 8 +++ JADE-2.0-0/JADE/inst/datafiles |only JADE-2.0-0/JADE/inst/doc/JADE-BSSasymp.pdf |binary JADE-2.0-0/JADE/man/AMUSE.Rd | 2 JADE-2.0-0/JADE/man/CPPdata.Rd |only JADE-2.0-0/JADE/man/FG.Rd | 4 - JADE-2.0-0/JADE/man/FOBI.Rd | 7 ++- JADE-2.0-0/JADE/man/JADE-package.Rd | 9 +++- JADE-2.0-0/JADE/man/JADE.Rd | 5 ++ JADE-2.0-0/JADE/man/MD.Rd | 6 ++ JADE-2.0-0/JADE/man/NSS.JD.Rd | 6 +- JADE-2.0-0/JADE/man/NSS.SD.Rd | 6 +- JADE-2.0-0/JADE/man/NSS.TD.JD.Rd | 6 +- JADE-2.0-0/JADE/man/SOBI.Rd | 9 +++- JADE-2.0-0/JADE/man/amari.error.Rd | 4 + JADE-2.0-0/JADE/man/djd.Rd | 6 +- JADE-2.0-0/JADE/man/k_JADE.Rd | 2 JADE-2.0-0/JADE/man/plot.bss.Rd | 4 - JADE-2.0-0/JADE/man/rjd.Rd | 2 JADE-2.0-0/JADE/vignettes/JADE-references.bib | 10 ++-- 28 files changed, 110 insertions(+), 62 deletions(-)
Title: RStudio Addins for Data Copy-Pasta
Description: RStudio addins to make copy-pasting vectors and tables into source painless.
Author: Miles McBain [aut, cre],
Jonathan Carroll [aut]
Maintainer: Miles McBain <miles.mcbain@gmail.com>
Diff between datapasta versions 1.0.0 dated 2016-11-29 and 1.1.0 dated 2017-01-09
DESCRIPTION | 17 LICENSE | 4 MD5 | 69 +-- NAMESPACE | 11 NEWS.md | 42 +- R/df_paste.R |only R/tribble_paste.R | 443 +++++++++++----------- R/vector_paste.R | 224 +++++------ README.md | 113 +++-- build/vignette.rds |binary inst/doc/how-to-datapasta.R | 99 ++--- inst/doc/how-to-datapasta.Rmd | 237 ++++++------ inst/doc/how-to-datapasta.html | 471 ++++++++++++------------ inst/media/df_paste.gif |only inst/rstudio/addins.dcf | 33 - man/df_paste.Rd |only man/guess_sep.Rd | 42 +- man/pad_to.Rd | 40 +- man/parse_vector.Rd | 34 - man/read_clip_tbl_guess.Rd | 44 +- man/render_type.Rd | 44 +- man/render_type_pad_to.Rd | 48 +- man/tortellini.Rd |only man/tribble_paste.Rd | 30 - man/vector_paste.Rd | 32 - man/vector_paste_vertical.Rd | 32 - tests/testthat.R | 8 tests/testthat/brisbane_weather.txt | 22 - tests/testthat/brisbane_weather_empty_lines.txt |only tests/testthat/dates_currency.txt | 4 tests/testthat/pipe_delim.txt | 4 tests/testthat/route_length.txt |only tests/testthat/semi_colon_delim.txt | 4 tests/testthat/tab_with_blank.txt | 8 tests/testthat/test_dfpaste.R |only tests/testthat/test_rstudio.R | 18 tests/testthat/test_tribble.R | 184 +++++---- tests/testthat/test_vector.R | 213 +++++----- vignettes/how-to-datapasta.Rmd | 237 ++++++------ 39 files changed, 1474 insertions(+), 1337 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert <marius.hofert@uwaterloo.ca>,
Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>, and
Jun Yan <jun.yan@uconn.edu>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 0.999-15 dated 2016-07-24 and 0.999-16 dated 2017-01-09
DESCRIPTION | 36 - MD5 | 320 ++++++------ NAMESPACE | 76 +-- R/AllClass.R | 10 R/AllGeneric.R |only R/Auxiliaries.R | 83 +++ R/Classes.R | 43 + R/Copula.R | 55 +- R/K.R | 113 ++-- R/amhCopula.R | 30 - R/archmCopula.R | 15 R/asymCopula.R | 655 ++++++++++++-------------- R/aux-acopula.R | 73 +- R/cCopula.R | 80 +-- R/claytonCopula.R | 85 +-- R/cop_objects.R | 155 +++--- R/dC-dc.R | 265 +++++++--- R/ellipCopula.R | 34 + R/empcop.R | 44 + R/estimation.R | 2 R/evTests.R | 88 ++- R/exchTests.R | 263 ++++++++-- R/fgmCopula.R | 15 R/fitCopula.R | 332 ++++++++----- R/fitMvdc.R | 132 ++--- R/fixedPar.R | 96 ++- R/frankCopula.R | 101 ++-- R/galambosCopula.R | 6 R/gofCopula.R | 101 ++-- R/gofEVTests.R | 11 R/graphics.R | 402 ++++++++-------- R/gumbelCopula.R | 91 +-- R/huslerReissCopula.R | 8 R/indepCopula.R | 64 +- R/indepTests.R | 37 - R/joeCopula.R | 41 + R/matrix_tools.R | 2 R/mixCopula.R |only R/mvdc.R | 5 R/nacopula.R | 23 R/normalCopula.R | 29 - R/pairsRosenblatt.R | 2 R/plackettCopula.R | 6 R/prob.R | 3 R/rotCopula.R | 181 ++++++- R/safeUroot.R | 2 R/schlatherCopula.R | 2 R/tCopula.R | 55 +- R/tawnCopula.R | 23 R/tevCopula.R | 7 R/wrapper.R | 12 R/xvCopula.R | 3 R/zzz.R | 7 TODO | 108 ++-- build/partial.rdb |binary build/vignette.rds |binary demo/estimation_via_HAC.R | 118 ++-- inst/CITATION | 2 inst/NEWS.Rd | 70 ++ inst/Rsource/cops.R | 8 inst/Rsource/estim-gof-fn.R | 4 inst/Rsource/utils.R | 22 inst/doc/AC_Liouville.html | 343 ++++--------- inst/doc/AR_Clayton.Rmd | 3 inst/doc/AR_Clayton.html | 456 ++++++------------ inst/doc/Frank-Rmpfr.Rnw | 4 inst/doc/Frank-Rmpfr.pdf |binary inst/doc/GIG.html | 707 ++++++++++------------------ inst/doc/NALC.Rmd | 21 inst/doc/NALC.html | 640 +++++++++---------------- inst/doc/copula_GARCH.html | 447 +++++------------ inst/doc/dNAC.html | 594 ++++++++--------------- inst/doc/logL_visualization.Rmd | 9 inst/doc/logL_visualization.html | 979 ++++++++++++++------------------------- inst/doc/nacopula-pkg.Rnw | 4 inst/doc/nacopula-pkg.pdf |binary inst/doc/qrng.Rmd | 196 +++---- inst/doc/qrng.html | 890 ++++++++++++----------------------- inst/doc/rhoAMH-dilog.Rnw | 11 inst/doc/rhoAMH-dilog.pdf |binary inst/doc/tail_compatibility.html | 728 +++++++++++------------------ inst/doc/wild_animals.Rmd | 8 inst/doc/wild_animals.html | 759 ++++++++++++------------------ man/Copula.Rd | 9 man/K.Rd | 168 +++--- man/Mvdc.Rd | 47 + man/RSpobs.Rd | 20 man/acR.Rd | 4 man/acopula-class.Rd | 8 man/archmCopula-class.Rd | 6 man/archmCopula.Rd | 8 man/assocMeasures.Rd | 5 man/asymCopula-class.Rd | 6 man/asymCopula.Rd | 78 ++- man/beta.Blomqvist.Rd | 12 man/cCopula.Rd | 69 +- man/cloud2-methods.Rd | 15 man/contour-methods.Rd | 4 man/contourplot2-methods.Rd | 10 man/copFamilies.Rd | 4 man/copula-class.Rd | 3 man/copula-package.Rd | 2 man/describeCop.Rd |only man/ellipCopula-class.Rd | 2 man/ellipCopula.Rd | 9 man/emle.Rd | 2 man/empcop.Rd | 57 +- man/evCopula.Rd | 59 +- man/evTestA.Rd | 12 man/evTestC.Rd | 10 man/evTestK.Rd | 18 man/exchEVTest.Rd | 44 - man/exchTest.Rd | 40 - man/fitCopula.Rd | 116 ++-- man/fitMvdc.Rd | 90 +-- man/fixedPar.Rd | 22 man/generator-methods.Rd | 11 man/getTheta.Rd |only man/gofCopula.Rd | 81 +-- man/gofEVCopula.Rd | 40 - man/gofOtherTstat.Rd | 14 man/indepCopula-class.Rd | 2 man/indepTest.Rd | 6 man/log1mexp.Rd | 2 man/matrix_tools.Rd | 6 man/mixCopula-class.Rd |only man/mixCopula.Rd |only man/multIndepTest.Rd | 6 man/multSerialIndepTest.Rd | 6 man/onacopula.Rd | 4 man/persp-methods.Rd | 20 man/plot-methods.Rd | 4 man/pobs.Rd | 5 man/qqplot2.Rd | 17 man/radSymTest.Rd |only man/rnacopula.Rd | 8 man/rotCopula.Rd | 28 - man/serialIndepTest.Rd | 9 man/setTheta.Rd | 42 + man/show-methods.Rd | 6 man/splom2-methods.Rd | 13 man/wireframe2-methods.Rd | 56 +- src/copula.h | 3 src/empcop.c | 77 ++- src/empcop.h | 5 src/exchtest.c | 48 + src/init.c | 7 tests/copula-play.R | 109 ++-- tests/dC-dc-ex.R | 66 -- tests/explicitCop-ex.R |only tests/fitting-ex.R | 150 ++++- tests/fixedPar-ex.R | 24 tests/khoudraji-ex.R |only tests/mixCop-tst.R |only tests/moments.R | 9 tests/nac-experi.R | 81 ++- tests/tail-pcopula.Rout.save | 18 vignettes/AR_Clayton.Rmd | 3 vignettes/Frank-Rmpfr.Rnw | 4 vignettes/NALC.Rmd | 21 vignettes/logL_visualization.Rmd | 9 vignettes/nacopula-pkg.Rnw | 4 vignettes/nacopula.bib | 4 vignettes/qrng.Rmd | 196 +++---- vignettes/rhoAMH-dilog.Rnw | 11 vignettes/wild_animals.Rmd | 8 166 files changed, 6751 insertions(+), 6906 deletions(-)
Title: Estimation, Gene Selection, and Survival Prediction Based on the
Compound Covariate Method Under the Cox Proportional Hazard
Model
Description: Estimation, gene selection, and survival prediction based on the compound covariate method under the Cox model with high-dimensional gene expressions.
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627> and
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.0 dated 2016-11-28 and 3.1 dated 2017-01-09
DESCRIPTION | 21 +++++++++++---------- MD5 | 18 +++++++++--------- R/CG.Clayton.R | 2 +- R/compound.reg.R | 10 +++++----- data/Lung.rda |binary man/Lung.Rd | 14 ++++++++++++-- man/compound.Cox-package.Rd | 13 ++++++------- man/compound.reg.Rd | 32 +++++++++++++++----------------- man/dependCox.reg.CV.Rd | 33 +++++++-------------------------- man/dependCox.reg.Rd | 36 +++++++++--------------------------- 10 files changed, 75 insertions(+), 104 deletions(-)
Title: Learning Causal Cyclic Graphs from Unknown Shift Interventions
Description: Code for 'backShift', an algorithm to estimate the connectivity
matrix of a directed (possibly cyclic) graph with hidden variables. The
underlying system is required to be linear and we assume that observations
under different shift interventions are available. For more details,
see <http://arxiv.org/abs/1506.02494>.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between backShift versions 0.1.3 dated 2015-10-13 and 0.1.4.1 dated 2017-01-09
DESCRIPTION | 28 - MD5 | 43 +- NAMESPACE | 10 R/backShift.R | 17 - R/bootstrap.R |only R/checkDiagonalization.R | 28 + R/computeDelta.R | 1 R/generateA.R | 10 R/permuteAndScale.R | 26 - R/plotGraph.R | 11 R/plotInterventionVar.R | 8 build/vignette.rds |binary inst/doc/exampleBackShift.Rmd | 4 inst/doc/exampleBackShift.html | 639 ++++++++++++++--------------------------- man/backShift.Rd | 103 +++--- man/bootstrapBackShift.Rd |only man/computeDiagonalization.Rd |only man/generateA.Rd | 16 - man/metricsThreshold.Rd | 12 man/plotDiagonalization.Rd | 4 man/plotGraphEdgeAttr.Rd | 34 +- man/plotInterventionVars.Rd | 14 man/simulateInterventions.Rd | 18 - vignettes/exampleBackShift.Rmd | 4 24 files changed, 449 insertions(+), 581 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.2.8 dated 2016-10-22 and 1.2.9 dated 2017-01-09
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.txt | 6 ++++++ inst/doc/ssizeRNA.R | 21 +++++++++------------ inst/doc/ssizeRNA.Rnw | 9 ++++----- inst/doc/ssizeRNA.pdf |binary vignettes/ssizeRNA.Rnw | 9 ++++----- 8 files changed, 35 insertions(+), 34 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut],
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-28 dated 2015-09-28 and 0.6-29 dated 2017-01-09
ChangeLog | 338 +++++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 - MD5 | 12 - build/vignette.rds |binary inst/ChangeLog | 338 +++++++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/GWR.pdf |binary src/gwe.c | 3 7 files changed, 688 insertions(+), 11 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.6-8 dated 2016-09-21 and 0.6-9 dated 2017-01-09
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/vignette.rds |binary inst/ChangeLog | 16 ++++++++++++++++ inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/sids.pdf |binary man/bhicv.Rd | 4 +++- src/dnn.c | 3 ++- 11 files changed, 51 insertions(+), 16 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks when working with
data : 1) Reading and writing data between R and other statistical software
packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this
includes easy ways to get and set label attributes, to convert labelled
vectors into factors (and vice versa), or to deal with multiple declared
missing values etc. 2) Data transformation tasks like recoding,
dichotomizing or grouping variables, setting and replacing missing values.
The data transformation functions also support labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.2.0 dated 2016-12-21 and 2.2.1 dated 2017-01-09
DESCRIPTION | 8 MD5 | 16 - NEWS | 5 NEWS.md | 6 R/frq.R | 502 +++++++++++++++++++++++++------------------------- R/spread_coef.R | 4 build/partial.rdb |binary man/sjmisc-package.Rd | 4 man/spread_coef.Rd | 4 9 files changed, 280 insertions(+), 269 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by
Translation And Rotation) growth curve models. SITAR is a shape-invariant model
with a regression B-spline mean curve and subject-specific random effects on
both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.0.8 dated 2016-10-17 and 1.0.9 dated 2017-01-09
DESCRIPTION | 8 - MD5 | 26 ++--- NEWS | 17 +++ R/ifun.R | 276 ++++++++++++++++++++++++++---------------------------- R/plot.sitar.R | 45 ++++---- R/predict.sitar.R | 18 +-- R/sitar.R | 82 ++++++---------- R/sitarlib.R | 2 R/timegap.R | 38 ++++--- R/xyadj.R | 28 +++-- man/ifun.Rd | 155 +++++++++++++----------------- man/sitar.Rd | 29 ++--- man/timegap.Rd | 26 +++-- man/xyadj.Rd | 11 +- 14 files changed, 381 insertions(+), 380 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 0.3-21 dated 2016-10-20 and 0.3-22 dated 2017-01-09
ChangeLog | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ configure | 18 +++++++++--------- inst/ChangeLog | 12 ++++++++++++ inst/SVN_VERSION | 2 +- src/init.c | 2 ++ 7 files changed, 46 insertions(+), 20 deletions(-)
Title: A Platform for the Study of Macro-Ecology of Life History Traits
Description: Tools for easy generation of (life-history) traits maps based on
species range (extent-of-occurrence) maps.
Author: Mihai Valcu [aut, cre],
James Dale [aut],
Joan Maspons [ctb]
Maintainer: Mihai Valcu <valcu@orn.mpg.de>
Diff between rangeMapper versions 0.3-0 dated 2016-01-03 and 0.3-1 dated 2017-01-09
DESCRIPTION | 16 +- MD5 | 58 ++++---- NAMESPACE | 2 R/AAA.R | 4 R/AllClasses.R | 2 R/GUI.R | 2 R/MapCanvas-methods.R | 60 +++------ R/MapProcess-methods.R | 43 ++++-- R/MapSave-methods.R | 50 ++++--- R/MapShow-methods.R | 4 R/metadataUpdate-methods.R | 4 R/projectINI-methods.R | 8 - R/utils.R | 2 build/vignette.rds |binary inst/doc/Appendix_S2_Valcu_et_al_2012.R | 6 inst/doc/Appendix_S2_Valcu_et_al_2012.Rmd | 6 inst/doc/Appendix_S2_Valcu_et_al_2012.html | 187 +++++++++++++++-------------- inst/doc/Appendix_S3_Valcu_et_al_2012.html | 120 ++++++++++-------- inst/doc/Appendix_S4_Valcu_et_al_2012.html | 76 +++++++---- inst/doc/Appendix_S5_Valcu_et_al_2012.R | 2 inst/doc/Appendix_S5_Valcu_et_al_2012.Rmd | 2 inst/doc/Appendix_S5_Valcu_et_al_2012.html | 111 +++++++++-------- man/metadata.update.Rd | 2 man/processRanges.Rd | 5 man/ramp.Rd | 2 tests/testthat/test-1_projectINI.R | 29 ++++ tests/testthat/test-2_processRanges.R | 32 ++-- tests/testthat/test-4_save.R | 38 +++-- vignettes/Appendix_S2_Valcu_et_al_2012.Rmd | 6 vignettes/Appendix_S5_Valcu_et_al_2012.Rmd | 2 30 files changed, 499 insertions(+), 382 deletions(-)
Title: Fast and Stable Estimation of the Probability of Informed
Trading (PIN)
Description: Utilities for fast and stable estimation of the probability of
informed trading (PIN) in the model introduced by Easley et al. (2002)
<DOI:10.1111/1540-6261.00493> are implemented. Since the basic model developed
by Easley et al. (1996) <DOI:10.1111/j.1540-6261.1996.tb04074.x> is nested in the
former due to equating the intensity of uninformed buys and sells, functions
can also be applied to this simpler model structure, if needed.
State-of-the-art factorization of the model likelihood function as well as
most recent algorithms for generating initial values for optimization routines are implemented.
In total, two likelihood factorizations and three methodologies for
starting values are included.
Furthermore, functions for simulating datasets of daily aggregated buys and sells,
calculating confidence intervals for the probability of informed trading and posterior probabilities
of trading days' conditions are available.
Author: Andreas Recktenwald [aut, cre]
Maintainer: Andreas Recktenwald <a.recktenwald@mx.uni-saarland.de>
Diff between pinbasic versions 0.2.0 dated 2016-12-02 and 1.0.0 dated 2017-01-09
pinbasic-0.2.0/pinbasic/man/qpin_plot.Rd |only pinbasic-0.2.0/pinbasic/vignettes/Examples.Rmd |only pinbasic-1.0.0/pinbasic/DESCRIPTION | 19 + pinbasic-1.0.0/pinbasic/MD5 | 100 ++++++---- pinbasic-1.0.0/pinbasic/NAMESPACE | 20 +- pinbasic-1.0.0/pinbasic/NEWS | 38 ++- pinbasic-1.0.0/pinbasic/NEWS.md | 19 + pinbasic-1.0.0/pinbasic/R/day_probs.R |only pinbasic-1.0.0/pinbasic/R/initialCAR.R | 12 - pinbasic-1.0.0/pinbasic/R/pin_confint.R | 12 - pinbasic-1.0.0/pinbasic/R/pin_est.R | 9 pinbasic-1.0.0/pinbasic/R/pin_ll_CAR.R | 4 pinbasic-1.0.0/pinbasic/R/pin_max.R | 5 pinbasic-1.0.0/pinbasic/R/pinbasic.R | 11 - pinbasic-1.0.0/pinbasic/R/plot_post_states.R |only pinbasic-1.0.0/pinbasic/R/qpin_plot.R | 54 +++-- pinbasic-1.0.0/pinbasic/R/quarterly_pin.R | 6 pinbasic-1.0.0/pinbasic/R/summary.R | 1 pinbasic-1.0.0/pinbasic/build/partial.rdb |binary pinbasic-1.0.0/pinbasic/build/vignette.rds |binary pinbasic-1.0.0/pinbasic/inst/doc/pinbasicVignette.R | 25 ++ pinbasic-1.0.0/pinbasic/inst/doc/pinbasicVignette.Rmd | 7 pinbasic-1.0.0/pinbasic/inst/doc/pinbasicVignette.html | 94 ++++++++- pinbasic-1.0.0/pinbasic/man/ggplot.posterior.Rd |only pinbasic-1.0.0/pinbasic/man/ggplot.qpin.Rd |only pinbasic-1.0.0/pinbasic/man/initial_vals.Rd | 3 pinbasic-1.0.0/pinbasic/man/pin_calc.Rd | 2 pinbasic-1.0.0/pinbasic/man/pin_confint.Rd | 2 pinbasic-1.0.0/pinbasic/man/pin_est.Rd | 8 pinbasic-1.0.0/pinbasic/man/pin_ll.Rd | 4 pinbasic-1.0.0/pinbasic/man/pinbasic.Rd | 11 - pinbasic-1.0.0/pinbasic/man/posterior.Rd |only pinbasic-1.0.0/pinbasic/man/qpin.Rd | 10 - pinbasic-1.0.0/pinbasic/man/simulateBS.Rd | 2 pinbasic-1.0.0/pinbasic/vignettes/Examples/Examples.Rmd | 36 +++ pinbasic-1.0.0/pinbasic/vignettes/Introduction/Introduction.Rmd | 3 pinbasic-1.0.0/pinbasic/vignettes/PostProbs |only pinbasic-1.0.0/pinbasic/vignettes/RDSfiles/pin_bsheavy.rds |binary pinbasic-1.0.0/pinbasic/vignettes/RDSfiles/qpin2015.rds |binary pinbasic-1.0.0/pinbasic/vignettes/pinbasicVignette.Rmd | 7 pinbasic-1.0.0/pinbasic/vignettes/references.bib | 7 pinbasic-1.0.0/pinbasic/vignettes/tikzfigs |only 42 files changed, 393 insertions(+), 138 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis <arelli4@uky.edu>
Diff between npmv versions 2.3.0 dated 2015-08-30 and 2.4.0 dated 2017-01-09
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- inst |only man/npmv-package.Rd | 11 ++++++++--- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Tools for Reading and Handling Spatial Objects
Description: Set of tools for manipulating and reading geographic data, in particular 'ESRI Shapefiles'; C code used from 'shapelib'. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', 'Stata tmap', 'WinBUGS', 'Mondrian', and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Kent Johnson [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 0.8-40 dated 2016-11-15 and 0.8-41 dated 2017-01-09
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 2 ++ R/as.linnet.SL.R |only inst/ChangeLog | 14 ++++++++++++++ inst/doc/combine_maptools.pdf |binary man/as.linnet.SpatialLines.Rd |only 8 files changed, 41 insertions(+), 9 deletions(-)
Title: Imperialist Competitive Algorithm for Optimal Designs
Description: Finding locally D-optimal, minimax D-optimal, standardized maximin D-optimal, optim-on-the-average and multiple objective optimal designs for nonlinear models. Different Fisher information matrices can also be set by user. There are also useful functions for verifying the optimality of the designs with respect to different criteria by equivalence theorem. ICA is a meta-heuristic evolutionary algorithm inspired from the socio-political process of humans. See Masoudi et al. (2016) <doi:10.1016/j.csda.2016.06.014>.
Author: Ehsan Masoudi [aut, cre],
Heinz Holling [aut],
Weng Kee Wong [aut]
Maintainer: Ehsan Masoudi <ehsan.masoudi@wwu.de>
Diff between ICAOD versions 0.9.1 dated 2016-08-09 and 0.9.2 dated 2017-01-09
ICAOD-0.9.1/ICAOD/R/ICA_on_average_ica.R |only ICAOD-0.9.1/ICAOD/R/common_equivalence_on_average.R |only ICAOD-0.9.1/ICAOD/man/equivalence_on_average.Rd |only ICAOD-0.9.1/ICAOD/man/on_average_ica.Rd |only ICAOD-0.9.2/ICAOD/DESCRIPTION | 6 ICAOD-0.9.2/ICAOD/MD5 | 67 ICAOD-0.9.2/ICAOD/NAMESPACE | 5 ICAOD-0.9.2/ICAOD/R/ICAOD.R |only ICAOD-0.9.2/ICAOD/R/ICA_Calculate_Cost.R | 128 - ICAOD-0.9.2/ICAOD/R/ICA_ave.R |only ICAOD-0.9.2/ICAOD/R/ICA_iterate.R | 1713 ++++++++++---------- ICAOD-0.9.2/ICAOD/R/ICA_mica.R | 173 -- ICAOD-0.9.2/ICAOD/R/ICA_multica_4pl.R | 52 ICAOD-0.9.2/ICAOD/R/ICA_plot.R | 266 +-- ICAOD-0.9.2/ICAOD/R/ICA_print.R | 114 - ICAOD-0.9.2/ICAOD/R/RcppExports.R | 4 ICAOD-0.9.2/ICAOD/R/check_inner.R |only ICAOD-0.9.2/ICAOD/R/common_PlotDLB.R | 64 ICAOD-0.9.2/ICAOD/R/common_Psi_x.R | 100 - ICAOD-0.9.2/ICAOD/R/common_equivalence.R | 1288 +++++++-------- ICAOD-0.9.2/ICAOD/R/common_equivalence_ave.R |only ICAOD-0.9.2/ICAOD/R/common_equivalence_multiple.R | 408 ++-- ICAOD-0.9.2/ICAOD/R/common_iterate_methods.R | 25 ICAOD-0.9.2/ICAOD/R/common_make_vertices.R | 34 ICAOD-0.9.2/ICAOD/R/common_print_equivalnce.R | 66 ICAOD-0.9.2/ICAOD/man/FIM_logisitic_1par.Rd | 2 ICAOD-0.9.2/ICAOD/man/ICAOD.Rd |only ICAOD-0.9.2/ICAOD/man/ave.Rd |only ICAOD-0.9.2/ICAOD/man/equivalence.Rd | 139 - ICAOD-0.9.2/ICAOD/man/equivalence_ave.Rd |only ICAOD-0.9.2/ICAOD/man/equivalence_multiple.Rd | 36 ICAOD-0.9.2/ICAOD/man/iterate.ICA.Rd | 2 ICAOD-0.9.2/ICAOD/man/iterate.Rd | 7 ICAOD-0.9.2/ICAOD/man/mica.Rd | 166 - ICAOD-0.9.2/ICAOD/man/multica_4pl.Rd | 44 ICAOD-0.9.2/ICAOD/man/plot.ICA.Rd | 2 ICAOD-0.9.2/ICAOD/man/print.ICA.Rd | 2 ICAOD-0.9.2/ICAOD/man/print.equivalence.Rd | 2 ICAOD-0.9.2/ICAOD/src/FIM_logistic_1par.cpp | 2 ICAOD-0.9.2/ICAOD/src/RcppExports.cpp | 114 - 40 files changed, 2522 insertions(+), 2509 deletions(-)
Title: Simplify Analysis and Annotation of Human Microarray Datasets
Description: Utilises GRanges, data.frame or IRanges objects. Integrates gene annotation for ImmunoChip (or your custom chip) with function calls. Intuitive wrappers for annotation lookup (gene lists, exon ranges, etc) and conversion (e.g, between build 36 and 37 coordinates). Conversion between ensembl and HGNC gene ids, chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and position for gene, band or SNP-ids, or reverse lookup. Simulation functions for ranges objects.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>
Diff between humarray versions 1.0.2 dated 2016-07-15 and 1.1 dated 2017-01-09
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NAMESPACE | 4 +++- R/humarray.R | 38 +++++++++++++++++++++++++++++++++----- man/get.immunobase.snps.Rd | 5 ++++- man/get.t1d.regions.Rd | 1 + man/humarray-internal.Rd | 1 + man/humarray-package.Rd | 4 ++-- 8 files changed, 59 insertions(+), 24 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code
inspection using various strategies, e.g. conservative or liberal. The objective
of this package is to make it as simple as possible to identify global objects
for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.7.1 dated 2016-10-14 and 0.7.2 dated 2017-01-09
DESCRIPTION | 6 +- MD5 | 8 +- NEWS | 151 +++++++++++++++++++++++++++++++++++++----------------- R/Globals-class.R | 3 + tests/Globals.R | 14 ++++- 5 files changed, 127 insertions(+), 55 deletions(-)
Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides empirical Bayes estimator of Fst, Nei's Gst, Nei & Chesser's Gst, and Weir & Cockerham's theta adapted for pairwise comparison. It also provides interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi@affrc.go.jp>
Diff between FinePop versions 1.2.0 dated 2016-12-05 and 1.2.1 dated 2017-01-09
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- R/EBFST.R | 14 +++++++++++--- R/GstN.R | 3 ++- R/GstNC.R | 3 ++- R/thetaWC.pair.R | 3 ++- build/partial.rdb |binary data/data.JSM.rda |binary man/EBFST.Rd | 9 +++++++-- man/GstN.Rd | 7 ++++++- man/GstNC.Rd | 7 ++++++- man/clip.genepop.Rd | 2 +- man/read.frequency.Rd | 11 +++++++---- man/read.genepop.Rd | 8 +++++--- man/thetaWC.pair.Rd | 7 ++++++- 16 files changed, 75 insertions(+), 39 deletions(-)
Title: Extract and Visualize the Results of Multivariate Data Analyses
Description: Provides some easy-to-use functions to extract and visualize the
output of multivariate data analyses, including 'PCA' (Principal Component
Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence
Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple
Factor Analysis) functions from different R packages. It contains also functions
for simplifying some clustering analysis steps and provides 'ggplot2' - based
elegant data visualization.
Author: Alboukadel Kassambara [aut, cre],
Fabian Mundt [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between factoextra versions 1.0.3 dated 2016-04-26 and 1.0.4 dated 2017-01-09
DESCRIPTION | 43 - MD5 | 116 ++-- NAMESPACE | 14 NEWS.md | 48 + R/decathlon2.R | 2 R/deprecated.R |only R/dist.R | 24 R/eclust.R | 89 +-- R/eigenvalue.R | 97 +-- R/facto_summarize.R | 125 ++-- R/fviz.R |only R/fviz_add.R | 81 +-- R/fviz_ca.R | 336 ++----------- R/fviz_cluster.R | 276 ++++------ R/fviz_contrib.R | 67 +- R/fviz_cos2.R | 72 +- R/fviz_dend.R | 480 +++++++++++++++++- R/fviz_ellipses.R |only R/fviz_famd.R |only R/fviz_hmfa.R | 1111 +++++-------------------------------------- R/fviz_mca.R | 511 +++----------------- R/fviz_mclust.R |only R/fviz_mfa.R | 1223 ++++++++---------------------------------------- R/fviz_nbclust.R | 30 - R/fviz_pca.R | 517 ++------------------ R/fviz_silhouette.R | 17 R/get_ca.R | 53 +- R/get_famd.R |only R/get_hmfa.R | 116 ++-- R/get_mca.R | 126 +++- R/get_mfa.R | 89 +-- R/get_pca.R | 21 R/hkmeans.R | 15 R/print.factoextra.R | 116 +--- R/utilities.R | 564 ++++++---------------- README.md | 16 man/decathlon2.Rd | 2 man/deprecated.Rd |only man/dist.Rd | 12 man/eclust.Rd | 92 +-- man/eigenvalue.Rd | 64 -- man/facto_summarize.Rd | 53 +- man/fviz.Rd |only man/fviz_add.Rd | 14 man/fviz_ca.Rd | 174 ++---- man/fviz_cluster.Rd | 98 ++- man/fviz_contrib.Rd | 44 - man/fviz_cos2.Rd | 61 +- man/fviz_dend.Rd | 81 ++- man/fviz_ellipses.Rd |only man/fviz_famd.Rd |only man/fviz_hmfa.Rd | 328 +++--------- man/fviz_mca.Rd | 180 ++----- man/fviz_mclust.Rd |only man/fviz_mfa.Rd | 390 ++++----------- man/fviz_nbclust.Rd | 2 man/fviz_pca.Rd | 163 ++---- man/fviz_silhouette.Rd | 14 man/get_famd.Rd |only man/get_hmfa.Rd | 50 - man/get_mca.Rd | 35 - man/get_mfa.Rd | 25 man/get_pca.Rd | 4 man/hkmeans.Rd | 15 man/print.factoextra.Rd | 7 65 files changed, 2812 insertions(+), 5491 deletions(-)
Title: Extended Empirical Saddlepoint Density Approximation
Description: Tools for fitting the Extended Empirical Saddlepoint (EES) density.
Author: Matteo Fasiolo and Simon Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between esaddle versions 0.0.2 dated 2016-11-28 and 0.0.3 dated 2017-01-09
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ NAMESPACE | 2 +- R/dsaddle.R | 2 +- R/selectDecay.R | 2 +- build/vignette.rds |binary src/Makevars | 2 +- 7 files changed, 15 insertions(+), 16 deletions(-)
Title: Dynamic Models for Survival Data
Description: Functions to fit time-varying coefficient models for interval
censored and right censored survival data. Three major approaches are
implemented: 1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data; 2)
Spline based time-varying coefficient Cox model for right censored data; 3)
Transformation model with time-varying coefficients for right censored data
using estimating equations.
Author: Wenjie Wang [cre, aut],
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between dynsurv versions 0.3-4 dated 2016-12-24 and 0.3-5 dated 2017-01-09
ChangeLog | 37 +++++--- DESCRIPTION | 8 - MD5 | 40 ++++----- NAMESPACE | 1 R/bayesCox.R | 207 +++++++++++++++++++++++++++++++---------------- R/coef.R | 2 R/data.R | 2 R/dynsurv-package.R | 2 R/jump.R | 2 R/plot.R | 52 +++++------- R/print.R | 2 R/splineCox.R | 2 R/survCurv.R | 225 ++++++++++++++++++++++++++-------------------------- R/tvTran.R | 2 inst/CITATION | 10 +- man/bayesCox.Rd | 136 ++++++++++++++++++++----------- man/plotCoef.Rd | 1 man/plotJump.Rd | 2 man/plotNu.Rd | 1 man/survCurve.Rd | 2 man/survDiff.Rd | 11 +- 21 files changed, 432 insertions(+), 315 deletions(-)
Title: Dynamic Modeling in R
Description: Dynamic modeling of all kinds in R. These include models of
processes in discrete time or continuous time. They also include processes
that are linear or nonlinear. Latent variables can be continuous (e.g. state
space models) or discrete (e.g. regime-switching models). The general approach
involves maximum likelihood estimation of single- and multi-subject models of
latent time series with the extended Kalman filter and Kim filter. The user
provides recipes and data which are combined into a model that is then cooked to
obtain free parameter estimates.
Author: Lu Ou [aut, cre],
Michael D. Hunter [aut],
Sy-Miin Chow [aut]
Maintainer: Lu Ou <lzo114@psu.edu>
Diff between dynr versions 0.1.7 dated 2016-06-13 and 0.1.8-17 dated 2017-01-09
DESCRIPTION | 28 - MD5 | 116 ++-- NAMESPACE | 2 NEWS |only R/dataDoc.R | 26 + R/dynrCook.R | 257 ++++++++-- R/dynrModel.R | 13 R/dynrModelInternal.R | 2 R/dynrPlot.R | 1024 +++++++++++++++++++++-------------------- R/dynrRecipe.R | 128 +++-- R/dynrVersion.R | 2 build/partial.rdb |binary data/EMG.txt.gz |only data/RSPPsim.txt.gz |binary data/datalist |only demo/00Index | 5 demo/LinearSDE.R | 7 demo/RSLinearDiscrete.R | 83 ++- demo/RSLinearDiscreteYang.R |only demo/RSNonlinearODE.R | 46 - man/EMG.Rd |only man/EMGsim.Rd | 10 man/NonlinearDFAsim.Rd | 16 man/PPsim.Rd | 2 man/RSPPsim.Rd | 4 man/coef.dynrCook.Rd | 2 man/diag-character-method.Rd | 2 man/dynr.cook.Rd | 31 - man/dynr.data.Rd | 14 man/dynr.ggplot.Rd | 2 man/dynr.ldl.Rd | 2 man/dynr.model.Rd | 14 man/dynr.plotFreq.Rd |only man/dynrCook-class.Rd | 2 man/dynrDynamics-class.Rd | 6 man/dynrInitial-class.Rd | 2 man/dynrMeasurement-class.Rd | 2 man/dynrModel-class.Rd | 2 man/dynrNoise-class.Rd | 2 man/dynrRecipe-class.Rd | 16 man/dynrRegimes-class.Rd | 2 man/dynrTrans-class.Rd | 2 man/internalModelPrep.Rd | 2 man/logLik.dynrCook.Rd | 2 man/plot-dynrCook-method.Rd | 2 man/plotFormula.Rd | 8 man/prep.formulaDynamics.Rd | 16 man/prep.initial.Rd | 12 man/prep.loadings.Rd | 22 man/prep.matrixDynamics.Rd | 6 man/prep.measurement.Rd | 4 man/prep.noise.Rd | 4 man/prep.regimes.Rd | 14 man/prep.tfun.Rd | 32 - man/printex.Rd | 50 +- man/summary-dynrCook-method.Rd | 6 man/vcov.dynrCook.Rd | 2 src/brekfis.c | 14 src/estimation.c | 21 src/glue.c | 6 src/mainR.c | 33 - src/mainR.h | 2 62 files changed, 1245 insertions(+), 887 deletions(-)
Title: Species Distribution Modeling
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites and the environment at these sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between dismo versions 1.1-1 dated 2016-06-16 and 1.1-4 dated 2017-01-09
dismo-1.1-1/dismo/R/circularArea.R |only dismo-1.1-4/dismo/DESCRIPTION | 13 ++++++----- dismo-1.1-4/dismo/MD5 | 34 ++++++++++++++++--------------- dismo-1.1-4/dismo/R/boundRect.R | 12 +++++++++- dismo-1.1-4/dismo/R/circleHull.R |only dismo-1.1-4/dismo/R/circleHull.predict.R |only dismo-1.1-4/dismo/R/circles.R | 2 - dismo-1.1-4/dismo/R/convHull.R | 2 - dismo-1.1-4/dismo/R/convHull.predict.R | 2 - dismo-1.1-4/dismo/R/gbif.R | 5 ++++ dismo-1.1-4/dismo/R/hullls.R | 2 - dismo-1.1-4/dismo/R/rectHull.R | 7 ++++-- dismo-1.1-4/dismo/build/vignette.rds |binary dismo-1.1-4/dismo/inst/doc/brt.pdf |binary dismo-1.1-4/dismo/inst/doc/sdm.pdf |binary dismo-1.1-4/dismo/man/circleHull.Rd |only dismo-1.1-4/dismo/man/circles.Rd | 15 ++++++++++++- dismo-1.1-4/dismo/man/convexHull.Rd | 3 -- dismo-1.1-4/dismo/man/predict.Rd | 1 dismo-1.1-4/dismo/man/rectHull.Rd | 8 +++---- 20 files changed, 69 insertions(+), 37 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the Windows,
OS X, and X11 clipboards.
Author: Matthew Lincoln [aut, cre],
Louis Maddox [ctb],
Steve Simpson [ctb],
Jennifer Bryan [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.3.1 dated 2016-12-02 and 0.3.2 dated 2017-01-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/clipboard.R | 4 +--- R/flat_str.R | 8 +++++++- R/linux_clipboard.R | 18 +----------------- R/osx_clipboard.R | 17 ++++++++++++++++- tests/testthat/test_render.R | 22 ++++++++++++++++++++++ 8 files changed, 68 insertions(+), 32 deletions(-)
Title: Easily Download and Visualise Climate Data from CliFlo
Description: CliFlo is a web portal to the New Zealand National Climate
Database and provides public access (via subscription) to around 6,500
various climate stations (see <https://cliflo.niwa.co.nz/> for more
information). Collating and manipulating data from CliFlo
(hence clifro) and importing into R for further analysis, exploration and
visualisation is now straightforward and coherent. The user is required to
have an internet connection, and a current CliFlo subscription (free) if
data from stations, other than the public Reefton electronic weather
station, is sought.
Author: Blake Seers [aut, cre]
Maintainer: Blake Seers <blake.seers@gmail.com>
Diff between clifro versions 3.1-1 dated 2016-12-20 and 3.1-2 dated 2017-01-09
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/cfQuery.R | 3 +++ R/cfUser.R | 21 ++++++++++++--------- inst/doc/cfStation.html | 6 +++--- inst/doc/choose-datatype.html | 4 ++-- inst/doc/choose-station.html | 4 ++-- inst/doc/clifro.html | 4 ++-- man/windrose.Rd | 12 +++++------- 10 files changed, 48 insertions(+), 39 deletions(-)
Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric and squared symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>
Diff between BSSasymp versions 1.1-2 dated 2016-02-11 and 1.2-0 dated 2017-01-09
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- inst/CITATION |only inst/ChangeLog | 23 ++++++++++++++--------- man/BSSasymp-package.Rd | 9 +++++++-- 5 files changed, 29 insertions(+), 18 deletions(-)