Mon, 29 Jun 2015

New package pequod with initial version 0.0-4
Package: pequod
Type: Package
Title: Moderated Regression Package
Version: 0.0-4
Date: 2015-6-29
Author: Alberto Mirisola & Luciano Seta
Depends: ggplot2, car
Imports: methods
Maintainer: Alberto Mirisola <alberto.mirisola@gmail.com>
Description: Moderated regression with mean and residual centering and simple slopes analysis.
License: GPL-2
LazyLoad: yes
Packaged: 2015-06-29 17:55:39 UTC; alberto
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-30 01:50:23

More information about pequod at CRAN
Permanent link

Package stochvol updated to version 1.1.2 with previous version 1.1.1 dated 2015-05-22

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>

Diff between stochvol versions 1.1.1 dated 2015-05-22 and 1.1.2 dated 2015-06-29

 stochvol-1.1.1/stochvol/inst/doc/heavytails.R    |only
 stochvol-1.1.1/stochvol/inst/doc/heavytails.Rnw  |only
 stochvol-1.1.1/stochvol/inst/doc/heavytails.pdf  |only
 stochvol-1.1.1/stochvol/vignettes/heavytails.Rnw |only
 stochvol-1.1.2/stochvol/DESCRIPTION              |   10 +++++-----
 stochvol-1.1.2/stochvol/MD5                      |   22 ++++++++++------------
 stochvol-1.1.2/stochvol/NAMESPACE                |    3 +++
 stochvol-1.1.2/stochvol/NEWS                     |    3 +++
 stochvol-1.1.2/stochvol/build/vignette.rds       |binary
 stochvol-1.1.2/stochvol/data/exrates.RData       |binary
 stochvol-1.1.2/stochvol/inst/doc/article.pdf     |binary
 stochvol-1.1.2/stochvol/src/sampler.cpp          |    4 ++--
 stochvol-1.1.2/stochvol/vignettes/Makefile       |    2 +-
 stochvol-1.1.2/stochvol/vignettes/heavytails.R   |only
 stochvol-1.1.2/stochvol/vignettes/heavytails.pdf |only
 15 files changed, 24 insertions(+), 20 deletions(-)

More information about stochvol at CRAN
Permanent link

Package MKmisc updated to version 0.99 with previous version 0.98 dated 2015-03-30

Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

Diff between MKmisc versions 0.98 dated 2015-03-30 and 0.99 dated 2015-06-29

 DESCRIPTION            |   14 +++++++-------
 MD5                    |   10 ++++++----
 NAMESPACE              |   11 ++++++++---
 NEWS                   |   25 ++++++++++++++++++-------
 R/mi.t.test.R          |only
 man/0MKmisc-package.Rd |   14 ++++++++------
 man/mi.t.test.Rd       |only
 7 files changed, 47 insertions(+), 27 deletions(-)

More information about MKmisc at CRAN
Permanent link

Package HelpersMG updated to version 1.2 with previous version 1.1 dated 2015-05-17

Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 1.1 dated 2015-05-17 and 1.2 dated 2015-06-29

 HelpersMG-1.1/HelpersMG/R/getTide.R                 |only
 HelpersMG-1.1/HelpersMG/R/moon_phase.R              |only
 HelpersMG-1.1/HelpersMG/R/temperature.periodic.R    |only
 HelpersMG-1.1/HelpersMG/man/getTide.Rd              |only
 HelpersMG-1.1/HelpersMG/man/moon_phase.Rd           |only
 HelpersMG-1.1/HelpersMG/man/temperature.periodic.Rd |only
 HelpersMG-1.2/HelpersMG/DESCRIPTION                 |   10 -
 HelpersMG-1.2/HelpersMG/MD5                         |   49 +++++----
 HelpersMG-1.2/HelpersMG/NAMESPACE                   |   14 ++
 HelpersMG-1.2/HelpersMG/NEWS                        |   11 +-
 HelpersMG-1.2/HelpersMG/R/HelpersMG-package.R       |    7 -
 HelpersMG-1.2/HelpersMG/R/LD50.R                    |only
 HelpersMG-1.2/HelpersMG/R/LD50_fit.R                |only
 HelpersMG-1.2/HelpersMG/R/MHalgoGen.R               |    2 
 HelpersMG-1.2/HelpersMG/R/compare_AIC.R             |    5 
 HelpersMG-1.2/HelpersMG/R/ind_long_lat.R            |    8 -
 HelpersMG-1.2/HelpersMG/R/index.periodic.R          |only
 HelpersMG-1.2/HelpersMG/R/logLik.LD50.R             |only
 HelpersMG-1.2/HelpersMG/R/minmax.periodic.R         |  104 +++++++++++++-------
 HelpersMG-1.2/HelpersMG/R/moon.info.R               |only
 HelpersMG-1.2/HelpersMG/R/plot.LD50.R               |only
 HelpersMG-1.2/HelpersMG/R/predict.LD50.R            |only
 HelpersMG-1.2/HelpersMG/R/sun.info.R                |    7 -
 HelpersMG-1.2/HelpersMG/R/tide.info.R               |only
 HelpersMG-1.2/HelpersMG/man/HelpersMG-package.Rd    |    7 -
 HelpersMG-1.2/HelpersMG/man/LD50.Rd                 |only
 HelpersMG-1.2/HelpersMG/man/compare_AIC.Rd          |    5 
 HelpersMG-1.2/HelpersMG/man/ind_long_lat.Rd         |    8 -
 HelpersMG-1.2/HelpersMG/man/index.periodic.Rd       |only
 HelpersMG-1.2/HelpersMG/man/logLik.LD50.Rd          |only
 HelpersMG-1.2/HelpersMG/man/minmax.periodic.Rd      |   46 +++++---
 HelpersMG-1.2/HelpersMG/man/moon.info.Rd            |only
 HelpersMG-1.2/HelpersMG/man/plot.LD50.Rd            |only
 HelpersMG-1.2/HelpersMG/man/predict.LD50.Rd         |only
 HelpersMG-1.2/HelpersMG/man/sun.info.Rd             |   11 +-
 HelpersMG-1.2/HelpersMG/man/tide.info.Rd            |only
 36 files changed, 192 insertions(+), 102 deletions(-)

More information about HelpersMG at CRAN
Permanent link

Package FunChisq updated to version 2.1.0 with previous version 2.0.2 dated 2015-03-04

Title: Chi-Square and Exact Tests for Non-Parametric Functional Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal causality based on evidence from functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

Diff between FunChisq versions 2.0.2 dated 2015-03-04 and 2.1.0 dated 2015-06-29

 FunChisq-2.0.2/FunChisq/src/AdjustPvalue.cpp           |only
 FunChisq-2.0.2/FunChisq/src/ChisqDirTest.cpp           |only
 FunChisq-2.0.2/FunChisq/src/ChisqTests.cpp             |only
 FunChisq-2.0.2/FunChisq/src/ChisqTests.h               |only
 FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.cpp    |only
 FunChisq-2.0.2/FunChisq/src/ExactMultiTableTest.h      |only
 FunChisq-2.0.2/FunChisq/src/StatDistributions.cpp      |only
 FunChisq-2.0.2/FunChisq/src/StatDistributions.h        |only
 FunChisq-2.0.2/FunChisq/src/TransitionTable.cpp        |only
 FunChisq-2.0.2/FunChisq/src/TransitionTable.h          |only
 FunChisq-2.1.0/FunChisq/DESCRIPTION                    |   15 
 FunChisq-2.1.0/FunChisq/MD5                            |   37 
 FunChisq-2.1.0/FunChisq/NAMESPACE                      |    1 
 FunChisq-2.1.0/FunChisq/NEWS                           |   12 
 FunChisq-2.1.0/FunChisq/R/FunChisq.R                   |   17 
 FunChisq-2.1.0/FunChisq/inst/CITATION                  |    4 
 FunChisq-2.1.0/FunChisq/man/FunChisq-package.Rd        |   13 
 FunChisq-2.1.0/FunChisq/man/cp.fun.chisq.test.Rd       |    6 
 FunChisq-2.1.0/FunChisq/man/fun.chisq.test.Rd          |    2 
 FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.cpp    |  918 +++++++++++------
 FunChisq-2.1.0/FunChisq/src/ExactFunctionalTest.h      |  180 ++-
 FunChisq-2.1.0/FunChisq/src/Makevars                   |only
 FunChisq-2.1.0/FunChisq/src/Makevars.win               |only
 FunChisq-2.1.0/FunChisq/src/define.h                   |only
 FunChisq-2.1.0/FunChisq/src/main.cpp                   |   22 
 FunChisq-2.1.0/FunChisq/tests/testthat/test_FunChisq.R |    9 
 26 files changed, 820 insertions(+), 416 deletions(-)

More information about FunChisq at CRAN
Permanent link

Package agridat updated to version 1.12 with previous version 1.11 dated 2015-03-03

Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture. Example analyses are included. Includes functions for plotting field designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright <kw.stat@gmail.com>

Diff between agridat versions 1.11 dated 2015-03-03 and 1.12 dated 2015-06-29

 DESCRIPTION                      |   10 +--
 MD5                              |   98 +++++++++++++++++++++------------------
 NAMESPACE                        |    3 +
 NEWS                             |   23 ++++++---
 R/desplot.r                      |   27 ++++++----
 R/gge.r                          |    4 -
 build/vignette.rds               |binary
 data/cochran.beets.txt.gz        |only
 data/cochran.lattice.txt.gz      |only
 data/datalist                    |    4 +
 data/jansen.apple.txt.gz         |only
 data/jansen.carrot.txt.gz        |only
 data/karcher.turfgrass.txt.gz    |binary
 inst/doc/agridat_examples.Rnw    |   16 +++---
 inst/doc/agridat_examples.pdf    |binary
 man/agridat.Rd                   |   36 +++++++++++---
 man/beall.webworms.Rd            |    4 -
 man/besag.bayesian.Rd            |    2 
 man/besag.beans.Rd               |    2 
 man/besag.triticale.Rd           |    2 
 man/bliss.borers.Rd              |    2 
 man/burgueno.alpha.Rd            |    2 
 man/burgueno.rowcol.Rd           |    3 +
 man/burgueno.unreplicated.Rd     |    3 +
 man/cochran.beets.Rd             |only
 man/cochran.latin.Rd             |    2 
 man/cochran.lattice.Rd           |only
 man/cochran.wireworms.Rd         |   11 +++-
 man/connolly.potato.Rd           |   10 ++-
 man/crowder.seeds.Rd             |   27 +++++-----
 man/cullis.earlygen.Rd           |    6 +-
 man/diggle.cow.Rd                |    2 
 man/hayman.tobacco.Rd            |    2 
 man/ilri.sheep.Rd                |    2 
 man/jansen.apple.Rd              |only
 man/jansen.carrot.Rd             |only
 man/jansen.strawberry.Rd         |   21 +++++---
 man/jenkyn.mildew.Rd             |    4 -
 man/karcher.turfgrass.Rd         |    9 +--
 man/keen.potatodamage.Rd         |    9 +++
 man/kempton.barley.uniformity.Rd |    2 
 man/lasrosas.corn.Rd             |   12 ++--
 man/lonnquist.maize.Rd           |    2 
 man/mercer.wheat.uniformity.Rd   |   30 ++++++++---
 man/snijders.fusarium.Rd         |    2 
 man/stroup.nin.Rd                |   21 ++++++--
 man/theobald.covariate.Rd        |    6 +-
 man/turner.herbicide.Rd          |   45 ++++++++++++++++-
 man/vold.longterm.Rd             |   36 +++++++-------
 man/wallace.iowaland.Rd          |    2 
 man/wedderburn.barley.Rd         |    2 
 man/welch.bermudagrass.Rd        |   14 +++--
 man/wiebe.wheat.uniformity.Rd    |   29 ++++++-----
 vignettes/agridat_examples.Rnw   |   16 +++---
 54 files changed, 363 insertions(+), 202 deletions(-)

More information about agridat at CRAN
Permanent link

Package spatial updated to version 7.3-10 with previous version 7.3-9 dated 2015-02-11

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between spatial versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 NAMESPACE   |   11 +++--------
 R/pp.R      |    2 +-
 4 files changed, 11 insertions(+), 16 deletions(-)

More information about spatial at CRAN
Permanent link

Package rpart updated to version 4.1-10 with previous version 4.1-9 dated 2015-02-11

Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between rpart versions 4.1-9 dated 2015-02-11 and 4.1-10 dated 2015-06-29

 ChangeLog                         |    2 ++
 DESCRIPTION                       |    8 ++++----
 MD5                               |   14 +++++++-------
 NAMESPACE                         |    7 ++++---
 build/vignette.rds                |binary
 inst/doc/longintro.pdf            |binary
 inst/doc/usercode.pdf             |binary
 tests/Examples/rpart-Ex.Rout.save |   13 ++++++-------
 8 files changed, 23 insertions(+), 21 deletions(-)

More information about rpart at CRAN
Permanent link

Package nnet updated to version 7.3-10 with previous version 7.3-9 dated 2015-02-11

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between nnet versions 7.3-9 dated 2015-02-11 and 7.3-10 dated 2015-06-29

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 NAMESPACE   |   11 +++--------
 3 files changed, 9 insertions(+), 14 deletions(-)

More information about nnet at CRAN
Permanent link

Package nlme updated to version 3.1-121 with previous version 3.1-120 dated 2015-02-20

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

Diff between nlme versions 3.1-120 dated 2015-02-20 and 3.1-121 dated 2015-06-29

 DESCRIPTION             |    8 ++++----
 MD5                     |    6 +++---
 NAMESPACE               |    7 ++-----
 tests/missing.Rout.save |    2 +-
 4 files changed, 10 insertions(+), 13 deletions(-)

More information about nlme at CRAN
Permanent link

Package KernSmooth updated to version 2.23-15 with previous version 2.23-14 dated 2015-02-11

Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between KernSmooth versions 2.23-14 dated 2015-02-11 and 2.23-15 dated 2015-06-29

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 NAMESPACE   |    3 ++-
 PORTING     |    5 +++++
 4 files changed, 14 insertions(+), 8 deletions(-)

More information about KernSmooth at CRAN
Permanent link

Package class updated to version 7.3-13 with previous version 7.3-12 dated 2015-02-11

Title: Functions for Classification
Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between class versions 7.3-12 dated 2015-02-11 and 7.3-13 dated 2015-06-29

 DESCRIPTION |   11 ++++++-----
 MD5         |    6 +++---
 NAMESPACE   |    2 +-
 man/knn1.Rd |    4 ++--
 4 files changed, 12 insertions(+), 11 deletions(-)

More information about class at CRAN
Permanent link

Package boot updated to version 1.3-17 with previous version 1.3-16 dated 2015-06-07

Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Applications" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between boot versions 1.3-16 dated 2015-06-07 and 1.3-17 dated 2015-06-29

 ChangeLog         |    4 ++++
 DESCRIPTION       |    8 ++++----
 INDEX             |    7 +------
 MD5               |   10 +++++-----
 NAMESPACE         |    6 ++++--
 man/print.boot.Rd |    3 ++-
 6 files changed, 20 insertions(+), 18 deletions(-)

More information about boot at CRAN
Permanent link

Package WaterML updated to version 1.2.3 with previous version 1.0.0 dated 2015-05-05

Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service from any hydroserver. To see list of available hydroservers, see http://hiscentral.cuahsi.org. The package has five data download functions: GetServices(): show all public HydroServers from the HIS Central Catalog. HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or time series from the HIS Central catalog based on geographic bounding box, server, or keyword. GetVariables(): Show a data.frame with all variables on the server. GetSites(): Show a data.frame with all sites on the server. GetSiteInfo(): Show what variables, methods and quality control levels are available at the specific site. GetValues(): Given a site code, variable code, start time and endtime, fetch a data.frame of all the observation time series data values. The data.frame has two columns: time and DataValue. This function has an optional "daily" parameter, you can set daily="max", daily="min" or daily="mean" to get aggregated daily values. The package also has five data upload functions: AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues(). These functions can be used for uploading data to a HydroServer Lite ODM database via the JSON data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>

Diff between WaterML versions 1.0.0 dated 2015-05-05 and 1.2.3 dated 2015-06-29

 DESCRIPTION                        |   21 -
 MD5                                |   44 +-
 NAMESPACE                          |    4 
 R/AddMethods.R                     |    2 
 R/GetServices.R                    |    1 
 R/GetSiteInfo.R                    |  748 ++++++++++++++++++++++++++-----------
 R/GetSites.R                       |  365 +++++++++++++-----
 R/GetValues.R                      |  425 +++++++++++++++++----
 R/GetVariables.R                   |  174 +++++++-
 R/HISCentral_GetSeriesCatalog.R    |only
 R/HISCentral_GetSites.R            |only
 R/MakeSOAPEnvelope.R               |    6 
 R/PackageDocumentation.R           |only
 R/WaterOneFlowNamespace.R          |only
 README.md                          |   12 
 build                              |only
 inst                               |only
 man/GetSiteInfo.Rd                 |   94 ++++
 man/GetSites.Rd                    |   40 +
 man/GetValues.Rd                   |   43 ++
 man/GetVariables.Rd                |   23 +
 man/HISCentral_GetSeriesCatalog.Rd |only
 man/HISCentral_GetSites.Rd         |only
 man/MakeSOAPEnvelope.Rd            |    3 
 man/WaterML-package.Rd             |only
 man/WaterOneFlowNamespace.Rd       |only
 vignettes                          |only
 27 files changed, 1569 insertions(+), 436 deletions(-)

More information about WaterML at CRAN
Permanent link

Package brms updated to version 0.3.0 with previous version 0.2.0 dated 2015-05-26

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>

Diff between brms versions 0.2.0 dated 2015-05-26 and 0.3.0 dated 2015-06-29

 DESCRIPTION                    |   16 +
 MD5                            |   70 ++++----
 NAMESPACE                      |   12 +
 R/bugs.R                       |   27 +--
 R/data.docu.R                  |   19 +-
 R/extract.old.R                |    2 
 R/main.R                       |  151 +++++++++++-------
 R/parser.R                     |only
 R/s3.correlations.R            |only
 R/s3.generics.R                |  108 +++++++++++-
 R/s3.methods.R                 |  139 ++++++++++++++--
 R/stan.R                       |  342 +++++++++++++++++++++++------------------
 R/support.export.R             |  150 +++++++++++++----
 R/support.internal.R           |  102 ++++--------
 data/kidney.rda                |binary
 man/VarCorr.Rd                 |    3 
 man/brm.Rd                     |  118 +++++++++-----
 man/brm.data.Rd                |   16 +
 man/brm.pars.Rd                |   11 +
 man/brm.plot.Rd                |    3 
 man/brms-package.Rd            |    2 
 man/brmsfit-class.Rd           |    6 
 man/cor.ar.Rd                  |only
 man/cor.arma.Rd                |only
 man/cor.brms.Rd                |only
 man/cor.ma.Rd                  |only
 man/epilepsy.Rd                |    2 
 man/fixef.Rd                   |    3 
 man/hypothesis.Rd              |only
 man/inhaler.Rd                 |    2 
 man/kidney.Rd                  |   15 -
 man/ngrps.Rd                   |    5 
 man/par.names.Rd               |only
 man/plot.brmsfit.Rd            |    3 
 man/posterior.samples.Rd       |only
 man/print.brmsfit.Rd           |    3 
 man/ranef.Rd                   |    7 
 man/summary.brmsfit.Rd         |    3 
 tests/testthat/tests.parser.R  |only
 tests/testthat/tests.stan.R    |   35 +++-
 tests/testthat/tests.support.R |    6 
 41 files changed, 916 insertions(+), 465 deletions(-)

More information about brms at CRAN
Permanent link

Package Power2Stage updated to version 0.4-1 with previous version 0.3-1 dated 2015-01-23

Title: Power and Sample-Size Distribution of 2-Stage Bioequivalence Studies
Description: Functions to obtain the operational characteristics of bioequivalence studies with 2-stage designs via simulations - Contains a function to calculate power and sample-size distribution of 2-stage bioequivalence (BE) studies with a 2x2 crossover design according to Potvin et al. / Montague et al. modified to include a futility Nmax and modified to do the sample size estimation step with PE and mse of stage 1. - Contains further a function with the modifications according to Karalis & Macheras which use both point estimate (PE) and mse from stage 1 also for the power monitoring steps. - The third function power.2stage.fC() calculates power and sample-size distribution of 2-stage BE studies with a futility criterion for the PE or CI of T/R from stage 1. - The fourth function power.2stage.GS() calculates power of non-adaptive group sequential (2-stage) BE studies. - The fifth function power.2stage.p() calculates power and sample size distribution of 2-stage BE studies with 2 parallel groups. This function has a sibling power.2stage.pAF(), which performs exactly as described in A.Fuglsang 2014 - Another function power.2stage.ssr() allows the power calculation for 2-stage studies with (blinded) interim sample size re-estimation.
Author: Detlew Labes [aut, cre], Helmut Schuetz [ctb]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

Diff between Power2Stage versions 0.3-1 dated 2015-01-23 and 0.4-1 dated 2015-06-29

 Power2Stage-0.3-1/Power2Stage/R/sampsiz.R                  |only
 Power2Stage-0.4-1/Power2Stage/DESCRIPTION                  |   54 ++---
 Power2Stage-0.4-1/Power2Stage/MD5                          |   41 ++--
 Power2Stage-0.4-1/Power2Stage/NAMESPACE                    |    6 
 Power2Stage-0.4-1/Power2Stage/NEWS                         |   25 ++
 Power2Stage-0.4-1/Power2Stage/R/power.R                    |    6 
 Power2Stage-0.4-1/Power2Stage/R/power_2stage.R             |   71 +++----
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_DL.R          |only
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_GS.R          |   47 +---
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_KM.R          |   61 ++----
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_SSR.R         |   70 ++-----
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_fC.R          |   86 +++-----
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel.R    |  126 +++++--------
 Power2Stage-0.4-1/Power2Stage/R/power_2stage_parallel_AF.R |   81 ++------
 Power2Stage-0.4-1/Power2Stage/R/print_pwrtsd_s3.R          |only
 Power2Stage-0.4-1/Power2Stage/R/sampsiz2.R                 |   28 +-
 Power2Stage-0.4-1/Power2Stage/R/sampsiz_n0.R               |    6 
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.GS.Rd       |   58 +++--
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.KM.Rd       |   23 +-
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.Rd          |   71 +++++--
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.fC.Rd       |   57 ++++-
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.p.Rd        |   35 ++-
 Power2Stage-0.4-1/Power2Stage/man/power.2stage.ssr.Rd      |   30 +--
 23 files changed, 503 insertions(+), 479 deletions(-)

More information about Power2Stage at CRAN
Permanent link

Package tree updated to version 1.0-36 with previous version 1.0-35 dated 2014-03-03

Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between tree versions 1.0-35 dated 2014-03-03 and 1.0-36 dated 2015-06-29

 ChangeLog                        |    6 ++++++
 DESCRIPTION                      |   14 +++++++-------
 MD5                              |    8 ++++----
 NAMESPACE                        |    5 +++++
 tests/Examples/tree-Ex.Rout.save |   12 ++++++------
 5 files changed, 28 insertions(+), 17 deletions(-)

More information about tree at CRAN
Permanent link

Package RODBC updated to version 1.3-12 with previous version 1.3-11 dated 2015-02-26

Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre], Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between RODBC versions 1.3-11 dated 2015-02-26 and 1.3-12 dated 2015-06-29

 ChangeLog                |    4 ++++
 DESCRIPTION              |   10 +++++-----
 MD5                      |   46 +++++++++++++++++++++++-----------------------
 NAMESPACE                |    1 +
 R/RODBC.R                |    3 ++-
 R/sql.R                  |    3 ++-
 build/vignette.rds       |binary
 inst/doc/RODBC.pdf       |binary
 man/odbc.Rd              |    3 ++-
 man/odbcClose.Rd         |    3 ++-
 man/odbcConnect.Rd       |    3 ++-
 man/odbcDataSources.Rd   |    2 +-
 man/odbcGetInfo.Rd       |    3 ++-
 man/odbcSetAutoCommit.Rd |    2 +-
 man/setSqlTypeInfo.Rd    |    2 +-
 man/sqlColumns.Rd        |    3 ++-
 man/sqlCopy.Rd           |    3 ++-
 man/sqlDrop.Rd           |    3 ++-
 man/sqlFetch.Rd          |    3 ++-
 man/sqlQuery.Rd          |    3 ++-
 man/sqlSave.Rd           |    3 ++-
 man/sqlTables.Rd         |    3 ++-
 man/sqlTypeInfo.Rd       |    3 ++-
 src/RODBC.c              |   41 +++++++++++++++++++++++------------------
 24 files changed, 87 insertions(+), 63 deletions(-)

More information about RODBC at CRAN
Permanent link

Package pspline updated to version 1.0-17 with previous version 1.0-16 dated 2013-04-16

Title: Penalized Smoothing Splines
Description: Smoothing splines with penalties on order m derivatives.
Author: S original by Jim Ramsey <ramsay@psych.mcgill.ca>. R port by Brian Ripley <ripley@stats.ox.ac.uk>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between pspline versions 1.0-16 dated 2013-04-16 and 1.0-17 dated 2015-06-29

 ChangeLog   |    5 +++++
 DESCRIPTION |   12 ++++++------
 MD5         |    6 +++---
 NAMESPACE   |    3 +++
 4 files changed, 17 insertions(+), 9 deletions(-)

More information about pspline at CRAN
Permanent link

Package mix updated to version 1.0-9 with previous version 1.0-8 dated 2010-01-03

Title: Estimation/Multiple Imputation for Mixed Categorical and Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical and continuous data.
Author: Original by Joseph L. Schafer <jls@stat.psu.edu>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between mix versions 1.0-8 dated 2010-01-03 and 1.0-9 dated 2015-06-29

 ChangeLog        |    9 +++++++++
 DESCRIPTION      |   17 +++++++++--------
 MD5              |only
 NAMESPACE        |    2 ++
 R/mix.R          |    2 +-
 data/stlouis.rda |binary
 6 files changed, 21 insertions(+), 9 deletions(-)

More information about mix at CRAN
Permanent link

Package gee updated to version 4.13-19 with previous version 4.13-18 dated 2012-03-14

Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and 4.4) and Brian Ripley <ripley@stats.ox.ac.uk> (version 4.13). Note that maintainers are not available to give advice on using a package they did not author.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between gee versions 4.13-18 dated 2012-03-14 and 4.13-19 dated 2015-06-29

 ChangeLog                       |   10 ++++++++++
 DESCRIPTION                     |   21 +++++++++++----------
 MD5                             |   14 +++++++-------
 NAMESPACE                       |    4 +++-
 R/ugee.R                        |    6 ++----
 src/ugee.c                      |   18 ++++++++++++++++++
 src/ugee.h                      |    3 ---
 tests/Examples/gee-Ex.Rout.save |   13 +++++++------
 8 files changed, 58 insertions(+), 31 deletions(-)

More information about gee at CRAN
Permanent link

Package stcm updated to version 0.1.1 with previous version 0.1.0 dated 2015-04-02

Title: Tools for Inference with Set-Theoretic Comparative Methods
Description: Provides a number of functions for carrying out inference with set-theoretic comparative methods, including facilities for examining causal paths, assessing the sensitivity of results to measurement and model specification error, and performing Random Forest Comparative Analysis.
Author: Chris Krogslund [aut, cre]
Maintainer: Chris Krogslund <ckrogslund@berkeley.edu>

Diff between stcm versions 0.1.0 dated 2015-04-02 and 0.1.1 dated 2015-06-29

 DESCRIPTION           |   10 +++++-----
 MD5                   |   32 ++++++++++++++++----------------
 R/caret_infer.R       |    6 +++---
 R/cond_expand.R       |    2 +-
 R/fsqca_sim.R         |    2 +-
 R/fsqca_sim_inclcut.R |    4 ++--
 R/get_qca_datasets.R  |    6 +++---
 R/hicks_20.R          |    2 +-
 R/hicks_29.R          |    2 +-
 R/meas_error.R        |    4 ++--
 R/mod_error.R         |    6 +++---
 R/paths_summary.R     |   21 ++++++++++-----------
 R/rfca.R              |   10 +++++-----
 man/fsqca_sim.Rd      |    2 +-
 man/hicks_20.Rd       |    2 +-
 man/hicks_29.Rd       |    2 +-
 man/rfca.Rd           |    6 +++---
 17 files changed, 59 insertions(+), 60 deletions(-)

More information about stcm at CRAN
Permanent link

Package stringi updated to version 0.5-5 with previous version 0.5-4 dated 2015-06-28

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 0.5-4 dated 2015-06-28 and 0.5-5 dated 2015-06-29

 DESCRIPTION |    6 +++---
 MD5         |    6 +++---
 NEWS        |    6 +++---
 configure   |    6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

More information about stringi at CRAN
Permanent link

Package spatstat updated to version 1.42-2 with previous version 1.42-1 dated 2015-06-05

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>, Rolf Turner <r.turner@auckland.ac.nz> and Ege Rubak <rubak@math.aau.dk>, with substantial contributions of code by Kasper Klitgaard Berthelsen; Abdollah Jalilian; Marie-Colette van Lieshout; Tuomas Rajala; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; A. Bilgrau; L. Bischof; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; A. El-Gabbas; O. Flores; E.D. Ford; P. Forbes; S. Frank; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; M. Genton; S. Ghalandarayeshi; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M.B. Hansen; M. Hazelton; J. Heikkinen; M. Hering; M. Herrmann; K. Hornik; P. Hunziker; J. Hywood; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Khanmohammadi; R. Klaver; P. Kovesi; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; A. Lister; B. Madin; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; E. Miranda; J. Moller; E. Mudrak; G.M. Nair; N. Nava; L.S. Nielsen; F. Nunes; J.R. Nyengaard; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; P. Ramon; X. Raynaud, M. Reiter; I. Renner; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; C. Schank; K. Schladitz; S. Schutte; B.T. Scott; O. Semboli; V. Shcherbakov; G.C. Shen; H.-J. Ship; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; T. Tvedebrink; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; S. Voss; H. Wang; H. Wendrock; J. Wild; C. Witthoft; S. Wong; M. Woringer; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>

Diff between spatstat versions 1.42-1 dated 2015-06-05 and 1.42-2 dated 2015-06-29

 DESCRIPTION                |   18 +--
 MD5                        |  237 ++++++++++++++++++++++-----------------------
 NAMESPACE                  |   10 +
 NEWS                       |  108 ++++++++++++++++++++
 R/First.R                  |   65 ++++++------
 R/affine.R                 |   13 --
 R/clusterinfo.R            |   11 ++
 R/formulae.R               |   26 ++++
 R/images.R                 |   51 +++++++--
 R/kppm.R                   |  149 +++++++++++++++++++++++-----
 R/lppm.R                   |    8 +
 R/mincontrast.R            |    4 
 R/objsurf.R                |    2 
 R/options.R                |    6 +
 R/pcf.R                    |   31 +++--
 R/pcfinhom.R               |   47 +++++---
 R/plot.fv.R                |    8 +
 R/plot.im.R                |   24 ++--
 R/ppmclass.R               |    7 -
 R/randomNS.R               |   38 ++++++-
 R/resolve.defaults.R       |    2 
 R/rose.R                   |   79 +++++++++++++--
 R/rotmean.R                |    9 +
 R/summary.im.R             |   16 +--
 R/tess.R                   |   52 ++++-----
 R/triangulate.R            |only
 R/update.ppm.R             |   14 --
 R/wingeom.R                |   63 ++++++++---
 README.md                  |   37 ++++---
 build/vignette.rds         |binary
 data/Kovesi.rda            |binary
 data/amacrine.rda          |binary
 data/anemones.rda          |binary
 data/ants.rda              |binary
 data/bdspots.rda           |binary
 data/bei.rda               |binary
 data/betacells.rda         |binary
 data/bramblecanes.rda      |binary
 data/bronzefilter.rda      |binary
 data/cells.rda             |binary
 data/chicago.rda           |binary
 data/chorley.rda           |binary
 data/clmfires.rda          |binary
 data/copper.rda            |binary
 data/demohyper.rda         |binary
 data/demopat.rda           |binary
 data/dendrite.rda          |binary
 data/finpines.rda          |binary
 data/flu.rda               |binary
 data/ganglia.rda           |binary
 data/gordon.rda            |binary
 data/gorillas.rda          |binary
 data/hamster.rda           |binary
 data/heather.rda           |binary
 data/humberside.rda        |binary
 data/hyytiala.rda          |binary
 data/japanesepines.rda     |binary
 data/lansing.rda           |binary
 data/letterR.rda           |binary
 data/longleaf.rda          |binary
 data/mucosa.rda            |binary
 data/murchison.rda         |binary
 data/nbfires.rda           |binary
 data/nztrees.rda           |binary
 data/osteo.rda             |binary
 data/paracou.rda           |binary
 data/ponderosa.rda         |binary
 data/pyramidal.rda         |binary
 data/redwood.rda           |binary
 data/redwoodfull.rda       |binary
 data/residualspaper.rda    |binary
 data/shapley.rda           |binary
 data/simba.rda             |binary
 data/simdat.rda            |binary
 data/simplenet.rda         |binary
 data/spiders.rda           |binary
 data/sporophores.rda       |binary
 data/spruces.rda           |binary
 data/swedishpines.rda      |binary
 data/urkiola.rda           |binary
 data/vesicles.rda          |binary
 data/waka.rda              |binary
 data/waterstriders.rda     |binary
 inst/CITATION              |    4 
 inst/doc/BEGINNER.txt      |   17 ++-
 inst/doc/datasets.Rnw      |    2 
 inst/doc/datasets.pdf      |binary
 inst/doc/getstart.R        |   42 +++----
 inst/doc/getstart.Rnw      |   32 +++---
 inst/doc/getstart.pdf      |binary
 inst/doc/replicated.pdf    |binary
 inst/doc/shapefiles.R      |   42 +++----
 inst/doc/shapefiles.Rnw    |    2 
 inst/doc/shapefiles.pdf    |binary
 inst/doc/updates.R         |    4 
 inst/doc/updates.Rnw       |   45 +++++++-
 inst/doc/updates.pdf       |binary
 man/clusterfit.Rd          |    7 +
 man/density.ppp.Rd         |   10 -
 man/fitted.lppm.Rd         |only
 man/fitted.ppm.Rd          |    2 
 man/kppm.Rd                |    9 +
 man/padimage.Rd            |   22 +++-
 man/quad.ppm.Rd            |    5 
 man/rCauchy.Rd             |   15 ++
 man/rMatClust.Rd           |   16 ++-
 man/rThomas.Rd             |   15 ++
 man/rVarGamma.Rd           |   15 ++
 man/rose.Rd                |   51 ++++++++-
 man/rotmean.Rd             |   23 +++-
 man/spatstat-internal.Rd   |   27 +++--
 man/spatstat-package.Rd    |   81 ++++++++++++---
 man/tess.Rd                |    7 +
 man/triangulate.owin.Rd    |only
 man/update.kppm.Rd         |   49 +++++----
 tests/alltests.R           |   10 +
 vignettes/datasets.Rnw     |    2 
 vignettes/getstart.Rnw     |   32 +++---
 vignettes/packagesizes.txt |    3 
 vignettes/shapefiles.Rnw   |    2 
 vignettes/updates.Rnw      |   45 +++++++-
 121 files changed, 1265 insertions(+), 508 deletions(-)

More information about spatstat at CRAN
Permanent link

Package seqminer updated to version 4.5 with previous version 4.2 dated 2015-06-10

Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu <dajiang.liu@gmail.com>, with contributions from Heng Li <lh3@live.co.uk> (Heng Li wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>

Diff between seqminer versions 4.2 dated 2015-06-10 and 4.5 dated 2015-06-29

 seqminer-4.2/seqminer/demo/workflow.R                            |only
 seqminer-4.5/seqminer/ChangeLog                                  |   14 
 seqminer-4.5/seqminer/DESCRIPTION                                |   13 
 seqminer-4.5/seqminer/MD5                                        |   97 +++---
 seqminer-4.5/seqminer/NAMESPACE                                  |    4 
 seqminer-4.5/seqminer/R/seqminer.R                               |  149 ++++++++--
 seqminer-4.5/seqminer/README.md                                  |    2 
 seqminer-4.5/seqminer/configure                                  |   42 +-
 seqminer-4.5/seqminer/configure.ac                               |   23 -
 seqminer-4.5/seqminer/configure.win                              |    2 
 seqminer-4.5/seqminer/demo/00Index                               |    4 
 seqminer-4.5/seqminer/demo/annotate.R                            |only
 seqminer-4.5/seqminer/demo/meta.workflow.R                       |only
 seqminer-4.5/seqminer/demo/vcf.workflow.R                        |only
 seqminer-4.5/seqminer/inst/rvtests/cfh.refFlat.txt               |only
 seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz     |only
 seqminer-4.5/seqminer/inst/rvtests/rvtest.MetaScore.assoc.gz.tbi |only
 seqminer-4.5/seqminer/man/SeqMiner.Rd                            |   16 -
 seqminer-4.5/seqminer/man/annotateGene.Rd                        |   13 
 seqminer-4.5/seqminer/man/annotatePlain.Rd                       |    8 
 seqminer-4.5/seqminer/man/annotateVcf.Rd                         |    8 
 seqminer-4.5/seqminer/man/download.annotation.resource.Rd        |only
 seqminer-4.5/seqminer/man/getCovPair.Rd                          |   21 -
 seqminer-4.5/seqminer/man/getRefBase.Rd                          |   11 
 seqminer-4.5/seqminer/man/hasIndex.Rd                            |    8 
 seqminer-4.5/seqminer/man/isDirWritable.Rd                       |only
 seqminer-4.5/seqminer/man/isInRange.Rd                           |    7 
 seqminer-4.5/seqminer/man/isURL.Rd                               |only
 seqminer-4.5/seqminer/man/makeAnnotationParameter.Rd             |    4 
 seqminer-4.5/seqminer/man/readVCFToListByGene.Rd                 |   32 --
 seqminer-4.5/seqminer/man/readVCFToListByRange.Rd                |   29 -
 seqminer-4.5/seqminer/man/readVCFToMatrixByGene.Rd               |   19 -
 seqminer-4.5/seqminer/man/readVCFToMatrixByRange.Rd              |   16 -
 seqminer-4.5/seqminer/man/rvmeta.readCovByRange.Rd               |    8 
 seqminer-4.5/seqminer/man/rvmeta.readDataByGene.Rd               |   22 -
 seqminer-4.5/seqminer/man/rvmeta.readDataByRange.Rd              |   19 -
 seqminer-4.5/seqminer/man/rvmeta.readNullModel.Rd                |    8 
 seqminer-4.5/seqminer/man/rvmeta.readScoreByRange.Rd             |   11 
 seqminer-4.5/seqminer/man/rvmeta.readSkewByRange.Rd              |    8 
 seqminer-4.5/seqminer/man/rvmeta.writeCovData.Rd                 |    8 
 seqminer-4.5/seqminer/man/rvmeta.writeScoreData.Rd               |   11 
 seqminer-4.5/seqminer/man/tabix.createIndex.Rd                   |   18 -
 seqminer-4.5/seqminer/man/tabix.createIndex.meta.Rd              |    4 
 seqminer-4.5/seqminer/man/tabix.createIndex.vcf.Rd               |    4 
 seqminer-4.5/seqminer/man/tabix.read.Rd                          |    7 
 seqminer-4.5/seqminer/man/tabix.read.header.Rd                   |    7 
 seqminer-4.5/seqminer/man/tabix.read.table.Rd                    |   13 
 seqminer-4.5/seqminer/man/validateAnnotationParameter.Rd         |    9 
 seqminer-4.5/seqminer/man/verifyFilename.Rd                      |only
 seqminer-4.5/seqminer/src/Makevars.in                            |    2 
 seqminer-4.5/seqminer/src/Makevars.win                           |    2 
 seqminer-4.5/seqminer/src/Profiler.cpp                           |   27 +
 seqminer-4.5/seqminer/src/Profiler.h                             |    6 
 seqminer-4.5/seqminer/src/SimpleTimer.h                          |  138 +++++++++
 seqminer-4.5/seqminer/src/rvMetaLoader.cpp                       |   44 ++
 55 files changed, 585 insertions(+), 333 deletions(-)

More information about seqminer at CRAN
Permanent link

Sun, 28 Jun 2015

Package sirt updated to version 1.8-9 with previous version 1.7-0 dated 2015-06-05

Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing functions in R, including multidimensional compensatory and noncompensatory IRT models, MCMC for hierarchical IRT models and testlet models, NOHARM, faceted and hierarchical rater models, ordinal IRT model (ISOP), latent regression models, DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between sirt versions 1.7-0 dated 2015-06-05 and 1.8-9 dated 2015-06-28

 sirt-1.7-0/sirt/R/plot.noharm.sirt.R           |only
 sirt-1.8-9/sirt/DESCRIPTION                    |   22 ++---
 sirt-1.8-9/sirt/MD5                            |   61 ++++++++-------
 sirt-1.8-9/sirt/NAMESPACE                      |   74 +++++++++++-------
 sirt-1.8-9/sirt/R/likelihood_adjustment.R      |only
 sirt-1.8-9/sirt/R/likelihood_adjustment_aux.R  |only
 sirt-1.8-9/sirt/R/likelihood_moments.R         |only
 sirt-1.8-9/sirt/R/mcmc.list.descriptives.R     |    5 -
 sirt-1.8-9/sirt/R/plot.mcmc.sirt.R             |   71 ++++++++++++++----
 sirt-1.8-9/sirt/R/rasch.mml2.R                 |   41 +++++-----
 sirt-1.8-9/sirt/R/rasch.mml2.missing1.R        |   36 ++++++---
 sirt-1.8-9/sirt/R/sia.sirt.R                   |   13 ---
 sirt-1.8-9/sirt/inst/NEWS                      |   21 +++++
 sirt-1.8-9/sirt/man/automatic.recode.Rd        |    2 
 sirt-1.8-9/sirt/man/data.big5.Rd               |   12 ---
 sirt-1.8-9/sirt/man/data.eid.Rd                |   14 +--
 sirt-1.8-9/sirt/man/data.read.Rd               |   12 ---
 sirt-1.8-9/sirt/man/data.wide2long.Rd          |    2 
 sirt-1.8-9/sirt/man/dif.logistic.regression.Rd |    2 
 sirt-1.8-9/sirt/man/dirichlet.mle.Rd           |    2 
 sirt-1.8-9/sirt/man/dirichlet.simul.Rd         |    2 
 sirt-1.8-9/sirt/man/greenyang.reliability.Rd   |    2 
 sirt-1.8-9/sirt/man/invariance.alignment.Rd    |    2 
 sirt-1.8-9/sirt/man/isop.scoring.Rd            |    2 
 sirt-1.8-9/sirt/man/likelihood.adjustment.Rd   |only
 sirt-1.8-9/sirt/man/lsem.estimate.Rd           |    2 
 sirt-1.8-9/sirt/man/mcmc.list.descriptives.Rd  |    5 -
 sirt-1.8-9/sirt/man/monoreg.rowwise.Rd         |    2 
 sirt-1.8-9/sirt/man/noharm.sirt.Rd             |   38 ++++-----
 sirt-1.8-9/sirt/man/plot.mcmc.sirt.Rd          |    5 -
 sirt-1.8-9/sirt/man/rasch.evm.pcm.Rd           |    4 -
 sirt-1.8-9/sirt/man/rasch.mirtlc.Rd            |    2 
 sirt-1.8-9/sirt/man/rasch.mml.Rd               |   98 ++++++++++++++++++++++---
 sirt-1.8-9/sirt/man/sirt-package.Rd            |   96 ++++++++++++------------
 34 files changed, 398 insertions(+), 252 deletions(-)

More information about sirt at CRAN
Permanent link

Package simsem updated to version 0.5-11 with previous version 0.5-8 dated 2014-10-03

Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut, cre], Patrick Miller [aut], Alexander Schoemann [aut], Corbin Quick [ctb], Terry Jorgensen [ctb]
Maintainer: Sunthud Pornprasertmanit <sunthud.pornprasertmanit@ttu.edu>

Diff between simsem versions 0.5-8 dated 2014-10-03 and 0.5-11 dated 2015-06-28

 DESCRIPTION               |   16 -
 MD5                       |   76 ++++-----
 NAMESPACE                 |    8 
 R/AllClass.R              |    4 
 R/analyze.R               |   12 -
 R/bindDist.R              |    1 
 R/clean.R                 |    7 
 R/combineSim.R            |   11 -
 R/createData.R            |    4 
 R/drawParam.R             |   16 +
 R/exportData.R            |    2 
 R/generate.R              |   10 -
 R/getCutoff.R             |    6 
 R/getKeywords.R           |    2 
 R/getPowerCoverage.R      |    3 
 R/imposeMissing.R         |    7 
 R/likRatioFit.R           |    1 
 R/miss.R                  |    2 
 R/model.R                 |  385 ++++++++++++++++++++++++++++++++++++++--------
 R/openMx.R                |   59 +++----
 R/pValue.R                |   12 -
 R/plotCutoff.R            |   14 -
 R/plotDist.R              |    9 -
 R/plotPowerCoverage.R     |    3 
 R/sim.R                   |  316 +++++++++++++++++++++++++++++--------
 R/summary-methods.R       |    5 
 R/summarySimResult.R      |  144 +++++++++++------
 R/validate.R              |    3 
 man/SimResult-class.Rd    |    2 
 man/bindDist.Rd           |    9 -
 man/getPopulation.Rd      |    5 
 man/inspect.Rd            |    3 
 man/miss.Rd               |    2 
 man/plotDist.Rd           |    7 
 man/plotPowerFitNested.Rd |    8 
 man/sim.Rd                |    7 
 man/summaryConverge.Rd    |    5 
 man/summaryParam.Rd       |    7 
 man/summaryPopulation.Rd  |    5 
 39 files changed, 856 insertions(+), 342 deletions(-)

More information about simsem at CRAN
Permanent link

Package semTools updated to version 0.4-9 with previous version 0.4-6 dated 2014-10-03

Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Sunthud Pornprasertmanit [aut, cre], Patrick Miller [aut], Alexander Schoemann [aut], Yves Rosseel [aut], Corbin Quick [ctb], Mauricio Garnier-Villarreal [ctb], James Selig [ctb], Aaron Boulton [ctb], Kristopher Preacher [ctb], Donna Coffman [ctb], Mijke Rhemtulla [ctb], Alexander Robitzsch [ctb], Craig Enders [ctb], Ruber Arslan [ctb], Bell Clinton [ctb], Pavel Panko [ctb], Edgar Merkle [ctb], Terry Jorgensen [ctb], Steven Chesnut [ctb], Jarrett Byrnes [ctb]
Maintainer: Sunthud Pornprasertmanit <sunthud.pornprasertmanit@ttu.edu>

Diff between semTools versions 0.4-6 dated 2014-10-03 and 0.4-9 dated 2015-06-28

 DESCRIPTION                     |   64 +++----
 MD5                             |   86 +++++-----
 NAMESPACE                       |   14 +
 R/NET.R                         |    4 
 R/auxiliary.R                   |   11 -
 R/clipboard.R                   |   14 -
 R/dataDiagnosis.R               |    2 
 R/efa.R                         |   11 -
 R/fitIndices.R                  |  142 +++++++++--------
 R/fitOpenMx.R                   |  309 +++++++++++++++++++------------------
 R/fmi.R                         |   14 -
 R/lavSpatialCorrect.R           |only
 R/longInvariance.R              |  326 +++++++++++++++++++++++++++++-----------
 R/measurementInvariance.R       |  144 +++++------------
 R/measurementInvarianceCat.R    |   89 +---------
 R/miPowerFit.R                  |   37 ++++
 R/monteCarloMed.R               |    1 
 R/partialInvariance.R           |   47 +++--
 R/partialInvarianceCat.R        |   51 +++---
 R/permuteMeasEq.R               |only
 R/powerAnalysisSS.R             |    4 
 R/quark.R                       |    4 
 R/reliability.R                 |    7 
 R/runMI.R                       |   22 +-
 R/singleParamTest.R             |  115 ++++++++------
 build/vignette.rds              |binary
 data/boreal.rda                 |only
 inst/CITATION                   |only
 man/BootMiss-class.Rd           |   82 +++++-----
 man/Net-class.Rd                |   68 ++++----
 man/boreal.Rd                   |only
 man/bsBootMiss.Rd               |    2 
 man/longInvariance.Rd           |    4 
 man/measurementInvariance.Rd    |    5 
 man/measurementInvarianceCat.Rd |    5 
 man/miPowerFit.Rd               |   19 +-
 man/moreFitIndices.Rd           |   12 -
 man/net.Rd                      |    2 
 man/partialInvariance.Rd        |    7 
 man/permuteMeasEq-class.Rd      |only
 man/permuteMeasEq.Rd            |only
 man/probe2WayMC.Rd              |    2 
 man/probe3WayMC.Rd              |    2 
 man/reliability.Rd              |    4 
 man/runMI.Rd                    |   19 ++
 man/singleParamTest.Rd          |    9 -
 man/spatialCorrect.Rd           |only
 man/standardizeMx.Rd            |    2 
 48 files changed, 968 insertions(+), 794 deletions(-)

More information about semTools at CRAN
Permanent link

Package hts updated to version 4.5 with previous version 4.4 dated 2014-07-23

Title: Hierarchical and Grouped Time Series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Shanika Wickramasuriya
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>

Diff between hts versions 4.4 dated 2014-07-23 and 4.5 dated 2015-06-28

 hts-4.4/hts/inst/tests          |only
 hts-4.4/hts/tests               |only
 hts-4.5/hts/ChangeLog           |   12 +
 hts-4.5/hts/DESCRIPTION         |   19 +-
 hts-4.5/hts/MD5                 |   56 ++---
 hts-4.5/hts/NAMESPACE           |    3 
 hts-4.5/hts/R/RcppExports.R     |only
 hts-4.5/hts/R/accuracy.gts.R    |   16 +
 hts-4.5/hts/R/aggts.R           |    2 
 hts-4.5/hts/R/combinef.R        |  380 ++++++++++------------------------------
 hts-4.5/hts/R/combineg.R        |   14 -
 hts-4.5/hts/R/forecast.gts.R    |   35 ++-
 hts-4.5/hts/R/gts.R             |   31 +--
 hts-4.5/hts/R/plot.gts.R        |   37 +++
 hts-4.5/hts/R/recursive.R       |only
 hts-4.5/hts/R/smatrix.R         |   64 +++---
 hts-4.5/hts/R/summary.gts.R     |    4 
 hts-4.5/hts/R/topdown.R         |   12 -
 hts-4.5/hts/R/tracemin.R        |only
 hts-4.5/hts/README.md           |    2 
 hts-4.5/hts/build/vignette.rds  |binary
 hts-4.5/hts/data/htseg2.rda     |binary
 hts-4.5/hts/inst/doc/hts.pdf    |binary
 hts-4.5/hts/man/combinef.Rd     |   10 -
 hts-4.5/hts/man/forecast.gts.Rd |    8 
 hts-4.5/hts/man/gts.Rd          |    2 
 hts-4.5/hts/man/hts.Rd          |    3 
 hts-4.5/hts/src                 |only
 28 files changed, 292 insertions(+), 418 deletions(-)

More information about hts at CRAN
Permanent link

Package GCPM updated to version 1.2 with previous version 1.1.1 dated 2014-12-01

Title: Generalized Credit Portfolio Model
Description: Analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
Author: Kevin Jakob
Maintainer: Kevin Jakob <Kevin.Jakob@Student.uni-augsburg.de>

Diff between GCPM versions 1.1.1 dated 2014-12-01 and 1.2 dated 2015-06-28

 DESCRIPTION            |   12 +-
 MD5                    |   24 ++---
 NAMESPACE              |    2 
 R/GCPM.R               |  228 ++++++++++++++++++++++++++++++++-----------------
 R/cpploss.R            |    4 
 R/other_functions.R    |   18 ++-
 data/portfolios.RData  |only
 man/GCPM-class.Rd      |    4 
 man/GCPM-package.Rd    |    8 -
 man/analyze-methods.Rd |   15 ++-
 man/init.Rd            |   12 +-
 man/portfolios.Rd      |only
 src/cpploss.cpp        |    4 
 src/cpploss.h          |    2 
 14 files changed, 210 insertions(+), 123 deletions(-)

More information about GCPM at CRAN
Permanent link

Package ddeploy updated to version 1.0.4 with previous version 1.0.2 dated 2015-05-08

Title: Wrapper for the Duke Deploy REST API
Description: A wrapper for the Duke Analytics model deployment API. See <http://www.dukeanalytics.com/products/dukedeployR.php> for more details.
Author: person("Niall", "McGearailt", role = c("aut", "cre"),email = "niall@dukeanalytics.com")
Maintainer: Niall McGearailt <niall@dukeanalytics.com>

Diff between ddeploy versions 1.0.2 dated 2015-05-08 and 1.0.4 dated 2015-06-28

 DESCRIPTION         |    8 ++++----
 MD5                 |   16 ++++++++--------
 R/duke_deploy.R     |    3 ++-
 R/duke_list.R       |   10 +++++-----
 R/duke_predict.R    |    5 +++--
 README.md           |   10 ++++++++++
 man/duke_deploy.Rd  |    5 ++++-
 man/duke_list.Rd    |    9 ++++++---
 man/duke_predict.Rd |    7 +++++--
 9 files changed, 47 insertions(+), 26 deletions(-)

More information about ddeploy at CRAN
Permanent link

Package ordinal updated to version 2015.6-28 with previous version 2015.1-21 dated 2015-01-21

Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit/... models. Estimation is via maximum likelihood and mixed models are fitted with the Laplace approximation and adaptive Gauss-Hermite quadrature. Multiple random effect terms are allowed and they may be nested, crossed or partially nested/crossed. Restrictions of symmetry and equidistance can be imposed on the thresholds (cut-points/intercepts). Standard model methods are available (summary, anova, drop-methods, step, confint, predict etc.) in addition to profile methods and slice methods for visualizing the likelihood function and checking convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>

Diff between ordinal versions 2015.1-21 dated 2015-01-21 and 2015.6-28 dated 2015-06-28

 DESCRIPTION                 |   12 ++++----
 MD5                         |   16 +++++-----
 NAMESPACE                   |   44 +++++++++++++++++++----------
 R/clmm.R                    |    6 ++--
 R/clmm.ssr.R                |    5 +++
 R/clmm2.R                   |   65 ++++++++++++++++++++++++++++++++++++++++++++
 inst/doc/clm_intro.pdf      |binary
 inst/doc/clm_tutorial.pdf   |binary
 inst/doc/clmm2_tutorial.pdf |binary
 9 files changed, 117 insertions(+), 31 deletions(-)

More information about ordinal at CRAN
Permanent link

Package dendextend updated to version 1.0.1 with previous version 0.18.3 dated 2015-01-31

Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a trees graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

Diff between dendextend versions 0.18.3 dated 2015-01-31 and 1.0.1 dated 2015-06-28

 ChangeLog                                  | 1240 ++++++++++++++++
 DESCRIPTION                                |   17 
 MD5                                        |  362 ++--
 NAMESPACE                                  |   17 
 NEWS                                       |  131 +
 R/all.equal.R                              |   36 
 R/ape.R                                    |    1 
 R/attr_access.R                            |  350 +++-
 R/bk_method.R                              |    4 
 R/branches_attr_by.R                       |   78 -
 R/color_branches.R                         |  176 +-
 R/colored_bars.R                           |    2 
 R/common_subtrees.R                        |only
 R/cor.dendlist.R                           |  128 +
 R/cor_bakers_gamma.R                       |   76 -
 R/cor_cophenetic.R                         |   48 
 R/cut_lower_fun.R                          |   24 
 R/cutree.dendrogram.R                      |   96 -
 R/data.R                                   |only
 R/dendextend-package.R                     |    2 
 R/dendextend_options.R                     |   46 
 R/dendlist.R                               |   20 
 R/distinct_edges.R                         |  116 -
 R/entanglement.R                           |   88 -
 R/get_nodes_xy.R                           |    6 
 R/ggdend.R                                 |   90 +
 R/ggdendro.R                               |    2 
 R/labels_colors.R                          |   28 
 R/magrittr.R                               |    4 
 R/nleaves.R                                |   13 
 R/prune.R                                  |  154 +-
 R/pvclust.R                                |   13 
 R/rect.dendrogram.R                        |   51 
 R/rotate.R                                 |   26 
 R/set.dendrogram.R                         |   85 -
 R/stats_imports.R                          |  605 ++++----
 R/tanglegram.R                             |  216 ++
 R/unbranch.R                               |   28 
 R/untangle.R                               |  662 ++++----
 R/zzz.R                                    |   35 
 README.md                                  |   53 
 TODO                                       |   18 
 build/vignette.rds                         |binary
 data                                       |only
 inst/doc/Cluster_Analysis.R                |only
 inst/doc/Cluster_Analysis.Rmd              |only
 inst/doc/Cluster_Analysis.html             |only
 inst/doc/FAQ.R                             |only
 inst/doc/FAQ.Rmd                           |only
 inst/doc/FAQ.html                          |only
 inst/doc/introduction.R                    |  234 ---
 inst/doc/introduction.Rmd                  |  379 +----
 inst/doc/introduction.html                 | 2154 ++++++++---------------------
 inst/tests/test-attr_access.R              |   19 
 inst/tests/test-branches_attr_by.R         |   33 
 inst/tests/test-common_subtrees.R          |only
 inst/tests/test-cut_lower_fun.R            |   14 
 inst/tests/test-cutree.dendrogram.R        |   30 
 inst/tests/test-dendlist.R                 |  158 +-
 inst/tests/test-distinct_edges.R           |    2 
 inst/tests/test-entanglement.R             |    2 
 inst/tests/test-ggdend.R                   |only
 inst/tests/test-rect.dendrogram.R          |only
 inst/tests/test-set.dendrogram.R           |   15 
 man/Bk.Rd                                  |    5 
 man/Bk_permutations.Rd                     |    3 
 man/Bk_plot.Rd                             |    3 
 man/DendSer.dendrogram.Rd                  |    3 
 man/FM_index.Rd                            |    3 
 man/FM_index_R.Rd                          |    3 
 man/FM_index_permutation.Rd                |    3 
 man/FM_index_profdpm.Rd                    |    3 
 man/all.equal.dendrogram.Rd                |    8 
 man/all_couple_rotations_at_k.Rd           |    3 
 man/all_unique.Rd                          |    3 
 man/as.dendlist.Rd                         |    3 
 man/as.phylo.dendrogram.Rd                 |    3 
 man/as_hclust_fixed.Rd                     |    3 
 man/assign_dendextend_options.Rd           |    3 
 man/assign_values_to_branches_edgePar.Rd   |   27 
 man/assign_values_to_leaves_edgePar.Rd     |   13 
 man/assign_values_to_leaves_nodePar.Rd     |    9 
 man/assign_values_to_nodes_nodePar.Rd      |    7 
 man/bakers_gamma_for_2_k_matrix.Rd         |    9 
 man/branches_attr_by_clusters.Rd           |   21 
 man/branches_attr_by_labels.Rd             |    3 
 man/click_rotate.Rd                        |    3 
 man/collapse_branch.Rd                     |    3 
 man/color_branches.Rd                      |   33 
 man/color_labels.Rd                        |    9 
 man/colored_bars.Rd                        |    5 
 man/common_subtrees_clusters.Rd            |only
 man/cor.dendlist.Rd                        |   26 
 man/cor_FM_index.Rd                        |only
 man/cor_bakers_gamma.Rd                    |   15 
 man/cor_common_nodes.Rd                    |only
 man/cor_cophenetic.Rd                      |   17 
 man/count_terminal_nodes.Rd                |    3 
 man/cut_lower_fun.Rd                       |   13 
 man/cutree-methods.Rd                      |    3 
 man/cutree_1h.dendrogram.Rd                |    9 
 man/cutree_1k.dendrogram.Rd                |    7 
 man/d3dendro_options.Rd                    |    3 
 man/d3dendrogram.Rd                        |    3 
 man/dend_diff.Rd                           |   15 
 man/dendextend-package.Rd                  |    3 
 man/dendextend_labels.dendrogram.Rd        |only
 man/dendextend_options.Rd                  |    3 
 man/dendlist.Rd                            |   14 
 man/dist.dendlist.Rd                       |    7 
 man/dist_long.Rd                           |    3 
 man/distinct_edges.Rd                      |   12 
 man/duplicate_leaf.Rd                      |    3 
 man/entanglement.Rd                        |   17 
 man/fac2num.Rd                             |    3 
 man/fix_members_attr.dendrogram.Rd         |    3 
 man/flatten.dendrogram.Rd                  |    3 
 man/flip_leaves.Rd                         |    3 
 man/get_branches_heights.Rd                |    7 
 man/get_childrens_heights.Rd               |    3 
 man/get_leaves_attr.Rd                     |    7 
 man/get_leaves_branches_attr.Rd            |only
 man/get_leaves_branches_col.Rd             |only
 man/get_leaves_edgePar.Rd                  |only
 man/get_leaves_nodePar.Rd                  |    8 
 man/get_nodes_attr.Rd                      |    7 
 man/get_nodes_xy.Rd                        |    7 
 man/get_root_branches_attr.Rd              |    3 
 man/ggdend.Rd                              |    8 
 man/hang.dendrogram.Rd                     |    3 
 man/heights_per_k.dendrogram.Rd            |    7 
 man/highlight_distinct_edges.Rd            |   17 
 man/identify.dendrogram.Rd                 |    9 
 man/intersect_trees.Rd                     |    9 
 man/is.dendlist.Rd                         |    3 
 man/is.dendrogram.Rd                       |    3 
 man/is.hclust.Rd                           |    3 
 man/is.natural.number.Rd                   |    3 
 man/is.phylo.Rd                            |    3 
 man/is_null_list.Rd                        |    3 
 man/khan.Rd                                |only
 man/labels-assign.Rd                       |    3 
 man/labels_colors.Rd                       |    9 
 man/ladderize.Rd                           |    9 
 man/leaf_Colors.Rd                         |    3 
 man/lowest_common_branch.Rd                |    3 
 man/match_order_by_labels.Rd               |    3 
 man/match_order_dendrogram_by_old_order.Rd |    3 
 man/na_locf.Rd                             |    3 
 man/nleaves.Rd                             |    8 
 man/nnodes.Rd                              |    3 
 man/noded_with_condition.Rd                |    3 
 man/order.dendrogram-assign.Rd             |    3 
 man/order.hclust.Rd                        |    3 
 man/partition_leaves.Rd                    |    7 
 man/pipe.Rd                                |    3 
 man/plot_horiz.dendrogram.Rd               |    3 
 man/prune.Rd                               |   16 
 man/prune_common_subtrees.dendlist.Rd      |only
 man/prune_leaf.Rd                          |    7 
 man/pvclust_show_signif.Rd                 |    3 
 man/pvclust_show_signif_gradient.Rd        |    3 
 man/raise.dendrogram.Rd                    |    3 
 man/rank_branches.Rd                       |    3 
 man/rank_order.dendrogram.Rd               |    5 
 man/rank_values_with_clusters.Rd           |only
 man/rect.dendrogram.Rd                     |   20 
 man/remove_branches_edgePar.Rd             |    7 
 man/remove_leaves_nodePar.Rd               |    7 
 man/remove_nodes_nodePar.Rd                |    7 
 man/rllply.Rd                              |    3 
 man/rotate.Rd                              |    6 
 man/rotate_DendSer.Rd                      |    3 
 man/sample.dendrogram.Rd                   |    3 
 man/set.Rd                                 |   22 
 man/shuffle.Rd                             |   15 
 man/sort_2_clusters_vectors.Rd             |    3 
 man/sort_dist_mat.Rd                       |    3 
 man/sort_levels_values.Rd                  |    3 
 man/tanglegram.Rd                          |   64 
 man/theme_dendro.Rd                        |    3 
 man/unbranch.Rd                            |   13 
 man/unclass_dend.Rd                        |    3 
 man/untangle.Rd                            |   10 
 man/untangle_DendSer.Rd                    |    3 
 man/untangle_random_search.Rd              |    9 
 man/untangle_step_rotate_1side.Rd          |    3 
 man/untangle_step_rotate_2side.Rd          |    3 
 man/which_leaf.Rd                          |    3 
 man/which_node.Rd                          |    3 
 tests/test-all.R                           |   17 
 vignettes/Cluster_Analysis.Rmd             |only
 vignettes/FAQ.Rmd                          |only
 vignettes/introduction.Rmd                 |  379 +----
 194 files changed, 5393 insertions(+), 4013 deletions(-)

More information about dendextend at CRAN
Permanent link

Package foreign updated to version 0.8-64 with previous version 0.8-63 dated 2015-02-20

Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...
Description: Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>

Diff between foreign versions 0.8-63 dated 2015-02-20 and 0.8-64 dated 2015-06-28

 DESCRIPTION |   12 ++++++------
 MD5         |    4 ++--
 NAMESPACE   |    3 ++-
 3 files changed, 10 insertions(+), 9 deletions(-)

More information about foreign at CRAN
Permanent link

Package stringi updated to version 0.5-4 with previous version 0.5-2 dated 2015-06-22

Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code); IBM and other contributors (ICU4C 55.1 source code); Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between stringi versions 0.5-2 dated 2015-06-22 and 0.5-4 dated 2015-06-28

 stringi-0.5-2/stringi/src/icu55_found.txt.in          |only
 stringi-0.5-2/stringi/src/install.libs.R              |only
 stringi-0.5-2/stringi/src/sys                         |only
 stringi-0.5-2/stringi/src/uconfig_local.h             |only
 stringi-0.5-4/stringi/DESCRIPTION                     |   11 
 stringi-0.5-4/stringi/INSTALL                         |  115 +
 stringi-0.5-4/stringi/MD5                             |   45 
 stringi-0.5-4/stringi/NAMESPACE                       |    5 
 stringi-0.5-4/stringi/NEWS                            |  102 -
 stringi-0.5-4/stringi/R/ICU_settings.R                |   15 
 stringi-0.5-4/stringi/R/install.R                     |   16 
 stringi-0.5-4/stringi/R/stringi-package.R             |   13 
 stringi-0.5-4/stringi/configure                       | 1199 ++++++++++--------
 stringi-0.5-4/stringi/configure.win                   |   22 
 stringi-0.5-4/stringi/inst/CITATION                   |    4 
 stringi-0.5-4/stringi/man/stri_info.Rd                |    4 
 stringi-0.5-4/stringi/man/stri_install.Rd             |    5 
 stringi-0.5-4/stringi/man/stringi-package.Rd          |    7 
 stringi-0.5-4/stringi/src/install.libs.R.in           |    9 
 stringi-0.5-4/stringi/src/stri_ICU_settings.cpp       |   12 
 stringi-0.5-4/stringi/src/stri_container_listutf8.cpp |    8 
 stringi-0.5-4/stringi/src/stri_container_listutf8.h   |    2 
 stringi-0.5-4/stringi/src/stri_exception.cpp          |    6 
 stringi-0.5-4/stringi/src/stri_messages.h             |    2 
 stringi-0.5-4/stringi/src/stri_stringi.cpp            |   19 
 stringi-0.5-4/stringi/src/uconfig_local.h.in          |only
 26 files changed, 965 insertions(+), 656 deletions(-)

More information about stringi at CRAN
Permanent link

New package cvxbiclustr with initial version 0.0.1
Package: cvxbiclustr
Title: Convex Biclustering Algorithm
Version: 0.0.1
Author: Eric C. Chi, Genevera I. Allen, Richard G. Baraniuk
Maintainer: Eric C. Chi <ecchi1105@gmail.com>
Description: An iterative algorithm for solving a convex formulation of the biclustering problem.
Depends: R (>= 3.1.3), Matrix, igraph,
License: MIT + file LICENSE
LazyData: true
Packaged: 2015-06-27 20:17:28 UTC; ericchi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-06-28 12:56:52

More information about cvxbiclustr at CRAN
Permanent link

Sat, 27 Jun 2015

New package LncMod with initial version 1.1
Package: LncMod
Type: Package
Title: Predicting Modulator and Functional/Survival Analysis
Version: 1.1
Author: Yongsheng Li,Zishan Wang,Juan Xu*,Xia Li*
Maintainer: Zishan Wang <azureskyeric@gmail.com>
Description: Predict modulators regulating the ability of effectors to regulate their targets and produce modulator-effector-target triplets followed by goterm functional enrichment and survival analysis.This is mainly applied to long non-coding RNAs (lncRNAs) as candidate modulators regulating the ability of transcription factors (TFs) to regulate their corresponding targets.
License: GPL-2
LazyData: TRUE
biocViews: long non-coding RNA,lncRNA,modulator,triplet,function,survival
Depends: R (>= 2.15.2),survival,pheatmap,parallel
Packaged: 2015-06-27 00:29:50 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-27 13:24:19

More information about LncMod at CRAN
Permanent link

Package ElemStatLearn updated to version 2015.6.26 with previous version 2012.04-0 dated 2012-04-10

Title: Data Sets, Functions and Examples from the Book: "The Elements of Statistical Learning, Data Mining, Inference, and Prediction" by Trevor Hastie, Robert Tibshirani and Jerome Friedman
Description: Useful when reading the book above mentioned, in the documentation referred to as `the book'.
Author: Material from the book's webpage, R port and packaging by Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>

Diff between ElemStatLearn versions 2012.04-0 dated 2012-04-10 and 2015.6.26 dated 2015-06-27

 DESCRIPTION      |   17 +++++++++--------
 MD5              |    8 ++++----
 NEWS             |    6 ++++++
 man/marketing.Rd |    4 ++--
 man/spam.Rd      |    2 ++
 5 files changed, 23 insertions(+), 14 deletions(-)

More information about ElemStatLearn at CRAN
Permanent link

Package dmm updated to version 1.6-2 with previous version 1.6-1 dated 2015-05-09

Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and pedigree-based partitioning of individual variation into a range of environmental and genetic variance components for individual and maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>

Diff between dmm versions 1.6-1 dated 2015-05-09 and 1.6-2 dated 2015-06-27

 DESCRIPTION                  |    8 
 MD5                          |   45 ++--
 NAMESPACE                    |    5 
 R/am.zandrel.R               |    4 
 R/gresponse.dmm.R            |  395 ++++++++++++++++++++++++++++++++++++-------
 R/make.dmmobj.R              |only
 R/part.add.R                 |only
 R/pedcheck.R                 |   37 +++-
 R/print.gresponse.dmm.R      |   26 --
 R/summary.gresponse.dmm.R    |only
 data/sheep.df.rda            |binary
 data/tstmo1.df.rda           |binary
 inst/doc/bugs.txt            |    6 
 inst/doc/dmmOverview.pdf     |binary
 inst/doc/mods.txt            |   12 +
 man/dmm-package.Rd           |   12 -
 man/dmm.Rd                   |   23 +-
 man/gprint.Rd                |    2 
 man/gprint.dmm.Rd            |    2 
 man/gresponse.dmm.Rd         |   75 +++++---
 man/make.dmmobj.Rd           |only
 man/pedcheck.Rd              |   20 +-
 man/print.dmm.Rd             |    2 
 man/print.gresponse.dmm.Rd   |   11 -
 man/sheep.df.Rd              |    4 
 man/summary.gresponse.dmm.Rd |only
 26 files changed, 527 insertions(+), 162 deletions(-)

More information about dmm at CRAN
Permanent link

Package crch updated to version 0.9-0 with previous version 0.1-0 dated 2013-10-22

Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with conditional heteroscedasticity are provided. First, continuous distributions can be used for the (right and/or left censored or truncated) response with separate linear predictors for the mean and variance. Second, cumulative link models for ordinal data (obtained by interval-censoring continuous data) can be employed for heteroscedastic extended logistic regression (HXLR). In the latter type of models, the intercepts depend on the thresholds that define the intervals.
Author: Jakob Messner [aut, cre], Achim Zeileis [aut]
Maintainer: Jakob Messner <Jakob.Messner@uibk.ac.at>

Diff between crch versions 0.1-0 dated 2013-10-22 and 0.9-0 dated 2015-06-27

 DESCRIPTION         |   27 +--
 MD5                 |   42 ++++-
 NAMESPACE           |   28 +++
 NEWS                |   29 +++
 R/clogis.R          |only
 R/cnorm.R           |only
 R/crch.R            |  383 ++++++++++++++++++++++++++++++++++++----------------
 R/ct.R              |only
 R/hxlr.R            |   40 ++---
 R/tlogis.R          |only
 R/tnorm.R           |only
 R/tt.R              |only
 build               |only
 data/RainIbk.rda    |binary
 inst/CITATION       |   13 +
 inst/doc            |only
 man/clogis.Rd       |only
 man/cnorm.Rd        |only
 man/coef.hxlr.Rd    |    3 
 man/crch.Rd         |   48 ++++--
 man/crch.control.Rd |   17 +-
 man/ct.Rd           |only
 man/hxlr.Rd         |   16 +-
 man/tlogis.Rd       |only
 man/tnorm.Rd        |only
 man/tt.Rd           |only
 tests               |only
 vignettes           |only
 28 files changed, 457 insertions(+), 189 deletions(-)

More information about crch at CRAN
Permanent link

Package qicharts updated to version 0.2.0 with previous version 0.1.3 dated 2015-05-01

Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control charts for measure and count data. The main function, qic(), creates run and control charts and has a simple interface with a rich set of options to control data analysis and plotting, including options for automatic data aggregation by subgroups, easy analysis of before-and-after data, exclusion of one or more data points from analysis, and splitting charts into sequential time periods. Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre], Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>

Diff between qicharts versions 0.1.3 dated 2015-05-01 and 0.2.0 dated 2015-06-27

 DESCRIPTION             |    8 
 MD5                     |   26 
 NEWS                    |   87 +
 R/paretochart.R         |  176 +--
 R/qic.R                 | 2209 ++++++++++++++++++++++++------------------------
 R/trc.R                 |  303 +++---
 build/vignette.rds      |binary
 inst/doc/runcharts.R    |  109 +-
 inst/doc/runcharts.Rmd  |   17 
 inst/doc/runcharts.html |  447 ++++-----
 man/paretochart.Rd      |    2 
 man/qic.Rd              |   50 -
 man/trc.Rd              |   28 
 vignettes/runcharts.Rmd |   17 
 14 files changed, 1779 insertions(+), 1700 deletions(-)

More information about qicharts at CRAN
Permanent link

New package knitLatex with initial version 0.9.0
Package: knitLatex
Title: 'Knitr' Helpers - Mostly Tables
Version: 0.9.0
Authors@R: person("John", "Shea", email = "coachshea@fastmail.com", role = c("aut", "cre"))
Description: Provides several helper functions for working with 'knitr' and 'LaTeX'. It includes 'xTab' for creating traditional 'LaTeX' tables, 'lTab' for generating 'longtable' environments, and 'sTab' for generating a 'supertabular' environment. Additionally, this package contains a knitr_setup() function which fixes a well-known bug in 'knitr', which distorts the 'results="asis"' command when used in conjunction with user-defined commands; and a com command (<<com=TRUE>>=) which renders the output from 'knitr' as a 'LaTeX' command.
Depends: R (>= 3.2.0)
License: GPL-3
LazyData: true
Imports: knitr (>= 1.10.5)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-06-26 21:38:25 UTC; coachshea
Author: John Shea [aut, cre]
Maintainer: John Shea <coachshea@fastmail.com>
Repository: CRAN
Date/Publication: 2015-06-27 11:56:19

More information about knitLatex at CRAN
Permanent link

Fri, 26 Jun 2015

Package TAM updated to version 1.8-0 with previous version 1.7-1 dated 2015-06-05

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

Diff between TAM versions 1.7-1 dated 2015-06-05 and 1.8-0 dated 2015-06-26

 DESCRIPTION                                    |   10 -
 MD5                                            |   55 +++++-----
 NAMESPACE                                      |   10 +
 R/IRT.informationCurve.R                       |only
 R/calc_exp_TK.R                                |   31 ++++-
 R/mml.3pl.calc_prob.v5.R                       |    4 
 R/plot.IRT.informationCurves.R                 |only
 R/plotDevianceTAM.R                            |    2 
 R/tam.latreg.R                                 |    3 
 R/tam.mml.2pl.R                                |    8 +
 R/tam.mml.3pl.R                                |   18 ++-
 R/tam.mml.3pl.est.guessing.R                   |   28 ++++-
 R/tam.mml.3pl.est.slopes.R                     |    3 
 R/tam.mml.3pl.preproc.R                        |   34 +++++-
 R/tam.mml.R                                    |   79 ++++++--------
 R/tam.mml.mfr.R                                |   10 +
 R/tamaan.3pl.trait.R                           |    3 
 R/tamaanify.R                                  |   15 +-
 R/tamaanify.modelconstraint.loadings.R         |    2 
 R/tamaanify.proc.items.R                       |   12 ++
 R/tamaanify.proc.loadings.B.fixed.R            |   10 +
 R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R |   22 +++-
 inst/NEWS                                      |   69 ++++++++----
 man/IRT.informationCurves.Rd                   |only
 man/TAM-package.Rd                             |    2 
 man/tam.mml.3pl.Rd                             |   33 +++++-
 man/tam.mml.Rd                                 |   17 ++-
 man/tamaanify.Rd                               |    1 
 src/tam_calcexp.cpp                            |  134 ++++++++++++++++++++++++-
 src/tam_mml_3pl_helper_functions.cpp           |   20 ++-
 30 files changed, 487 insertions(+), 148 deletions(-)

More information about TAM at CRAN
Permanent link

Package Rvcg updated to version 0.12.2 with previous version 0.12.1 dated 2015-06-23

Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package integrates nicely with the R-package 'rgl' to render the meshes processed by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager <zarquon42@gmail.com>

Diff between Rvcg versions 0.12.1 dated 2015-06-23 and 0.12.2 dated 2015-06-26

 DESCRIPTION         |    8 ++++----
 MD5                 |    8 ++++----
 R/Rvcg-package.R    |    4 ++--
 man/Rvcg-package.Rd |    4 ++--
 src/Rmarch.cpp      |    2 +-
 5 files changed, 13 insertions(+), 13 deletions(-)

More information about Rvcg at CRAN
Permanent link

Package lba updated to version 1.2 with previous version 1.0 dated 2015-01-22

Title: Latent Budget Analysis for Compositional Data
Description: Latent budget analysis is a method for the analysis of a two-way contingency table with an exploratory variable and a response variable. It is specially designed for compositional data.
Author: Enio G. Jelihovschi <eniojelihovs@gmail.com> and Ivan Bezerra Allaman <ivanalaman@gmail.com>
Maintainer: Enio G. Jelihovschi <eniojelihovs@gmail.com>

Diff between lba versions 1.0 dated 2015-01-22 and 1.2 dated 2015-06-26

 ChangeLog                 |only
 DESCRIPTION               |   10 +++++-----
 MD5                       |   30 ++++++++++++++++--------------
 NAMESPACE                 |   22 ++++++++++++++++++++++
 R/goodnessfit.R           |   12 ++++++------
 R/lba.ls.fe.R             |    9 +++++++++
 R/lba.ls.logit.R          |   29 ++++++++++++++++++++++++++++-
 R/lba.mle.R               |    2 +-
 R/lba.mle.fe.R            |   18 ++++++++++++++++++
 R/lba.mle.logit.R         |   27 +++++++++++++++++++++++++++
 R/plot.lba.R              |   12 ++++++++----
 R/summary.lba.ls.fe.R     |   14 ++++++++++----
 R/summary.lba.ls.logit.R  |   22 ++++++++++++++--------
 R/summary.lba.mle.fe.R    |   14 ++++++++++----
 R/summary.lba.mle.logit.R |   22 ++++++++++++++--------
 README.md                 |only
 man/lba.Rd                |    6 ++++--
 17 files changed, 192 insertions(+), 57 deletions(-)

More information about lba at CRAN
Permanent link

Package icenReg updated to version 1.2.5 with previous version 1.2.4 dated 2015-06-04

Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>

Diff between icenReg versions 1.2.4 dated 2015-06-04 and 1.2.5 dated 2015-06-26

 icenReg-1.2.4/icenReg/data/mice_data.RData                 |only
 icenReg-1.2.4/icenReg/man/mice_data.Rd                     |only
 icenReg-1.2.5/icenReg/DESCRIPTION                          |   10 
 icenReg-1.2.5/icenReg/MD5                                  |   35 +-
 icenReg-1.2.5/icenReg/NEWS                                 |only
 icenReg-1.2.5/icenReg/R/Utilities.R                        |  144 +++++++++--
 icenReg-1.2.5/icenReg/R/user_functions.R                   |   98 ++++---
 icenReg-1.2.5/icenReg/data/essIncData.RData                |only
 icenReg-1.2.5/icenReg/data/essIncData_small.RData          |only
 icenReg-1.2.5/icenReg/data/miceData.RData                  |only
 icenReg-1.2.5/icenReg/man/diag_baseline.Rd                 |   36 +-
 icenReg-1.2.5/icenReg/man/diag_covar.Rd                    |   40 +--
 icenReg-1.2.5/icenReg/man/essIncData.Rd                    |only
 icenReg-1.2.5/icenReg/man/essIncData_small.Rd              |only
 icenReg-1.2.5/icenReg/man/ic_par.Rd                        |   11 
 icenReg-1.2.5/icenReg/man/ic_sp.Rd                         |    8 
 icenReg-1.2.5/icenReg/man/miceData.Rd                      |only
 icenReg-1.2.5/icenReg/man/simIC_weib.Rd                    |    2 
 icenReg-1.2.5/icenReg/src/icenReg_files/basicUtilities.cpp |   15 -
 icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.cpp         |   66 +++--
 icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.h           |   11 
 icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.cpp       |  160 ++++++++++---
 icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.h         |   49 +++
 23 files changed, 489 insertions(+), 196 deletions(-)

More information about icenReg at CRAN
Permanent link

New package uniqueAtomMat with initial version 0.1-0
Package: uniqueAtomMat
Version: 0.1-0
Date: 2015-06-26
Title: Finding Unique or Duplicated Rows or Columns for Atomic Matrices
Authors@R: person("Long", "Qu", role=c("aut", "cre"), email="long.qu@wright.edu")
Depends: R (>= 3.1.2)
Enhances: base
Suggests: microbenchmark
Description: An alternative implementation and extension (grpDuplicated) of base::duplicated.matrix, base:anyDuplicated.matrix and base::unique.matrix for matrices of atomic mode, avoiding the time consuming collapse of the matrix into a character vector.
License: GPL (>= 2)
NeedsCompilation: yes
URL: https://github.com/gitlongor/uniqueAtomMat
BugReports: https://github.com/gitlongor/uniqueAtomMat/issues
Packaged: 2015-06-26 13:41:21 UTC; Long
Author: Long Qu [aut, cre]
Maintainer: Long Qu <long.qu@wright.edu>
Repository: CRAN
Date/Publication: 2015-06-26 20:09:52

More information about uniqueAtomMat at CRAN
Permanent link

Package amen updated to version 1.1 with previous version 1.0 dated 2015-02-26

Title: Additive and Multiplicative Effects Models for Networks and Relational Data
Description: Analysis of dyadic network and relational data using additive and multiplicative effects (AME) models. The basic model includes regression terms, the covariance structure of the social relations model (Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor models (Hoff(2009)). Four different link functions accommodate different relational data structures, including binary/network data (bin), normal relational data (nrm), ordinal relational data (ord) and data from fixed-rank nomination schemes (frn). Several of these link functions are discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff <pdhoff@uw.edu>

Diff between amen versions 1.0 dated 2015-02-26 and 1.1 dated 2015-06-26

 amen-1.0/amen/R/rs2_rep.R            |only
 amen-1.0/amen/data/YX_bin.rda        |only
 amen-1.0/amen/data/YX_bin_long.rda   |only
 amen-1.0/amen/data/YX_cbin.rda       |only
 amen-1.0/amen/data/YX_frn.rda        |only
 amen-1.0/amen/data/YX_nrm.rda        |only
 amen-1.0/amen/data/YX_ord.rda        |only
 amen-1.0/amen/data/YX_rrl.rda        |only
 amen-1.0/amen/data/conflict90s.RData |only
 amen-1.0/amen/man/conflict90s.Rd     |only
 amen-1.1/amen/DESCRIPTION            |   33 -
 amen-1.1/amen/MD5                    |  215 ++++++-----
 amen-1.1/amen/NAMESPACE              |   13 
 amen-1.1/amen/R/Xbeta.R              |   12 
 amen-1.1/amen/R/addlines.R           |only
 amen-1.1/amen/R/ame.R                |  324 +++++++++++-----
 amen-1.1/amen/R/ame_rep.R            |  674 ++++++++++++++++++++---------------
 amen-1.1/amen/R/amen-package.R       |   93 +++-
 amen-1.1/amen/R/circplot.R           |only
 amen-1.1/amen/R/design_array.R       |   11 
 amen-1.1/amen/R/el2sm.R              |only
 amen-1.1/amen/R/gofstats.R           |    7 
 amen-1.1/amen/R/mhalf.R              |    9 
 amen-1.1/amen/R/netplot.R            |only
 amen-1.1/amen/R/plot.ame.R           |   43 --
 amen-1.1/amen/R/rUV_fc.R             |   63 ---
 amen-1.1/amen/R/rUV_rep_fc.R         |   62 ---
 amen-1.1/amen/R/rUV_sym_fc.R         |only
 amen-1.1/amen/R/rZ_bin_fc.R          |   28 -
 amen-1.1/amen/R/rZ_cbin_fc.R         |   51 --
 amen-1.1/amen/R/rZ_frn_fc.R          |   59 ---
 amen-1.1/amen/R/rZ_nrm_fc.R          |   13 
 amen-1.1/amen/R/rZ_ord_fc.R          |   36 -
 amen-1.1/amen/R/rZ_rrl.R             |   52 --
 amen-1.1/amen/R/raSab_bin_fc.R       |   27 -
 amen-1.1/amen/R/raSab_cbin_fc.R      |   31 -
 amen-1.1/amen/R/raSab_frn_fc.R       |   24 -
 amen-1.1/amen/R/rbeta_ab_fc.R        |   84 ----
 amen-1.1/amen/R/rbeta_ab_rep_fc.R    |   94 ----
 amen-1.1/amen/R/rmvnorm.R            |    9 
 amen-1.1/amen/R/rrho_mh.R            |   22 -
 amen-1.1/amen/R/rrho_mh_rep.R        |   29 -
 amen-1.1/amen/R/rs2_fc.R             |   10 
 amen-1.1/amen/R/rs2_rep_fc.R         |only
 amen-1.1/amen/R/simY_bin.R           |   15 
 amen-1.1/amen/R/simY_frn.R           |   30 -
 amen-1.1/amen/R/simY_nrm.R           |   14 
 amen-1.1/amen/R/simY_ord.R           |   20 -
 amen-1.1/amen/R/simY_rrl.R           |   24 -
 amen-1.1/amen/R/simZ.R               |   12 
 amen-1.1/amen/R/sm2el.R              |only
 amen-1.1/amen/R/summary.ame.R        |   34 -
 amen-1.1/amen/R/xnet.R               |only
 amen-1.1/amen/R/zscores.R            |    9 
 amen-1.1/amen/build                  |only
 amen-1.1/amen/data/IR90s.RData       |only
 amen-1.1/amen/data/YX_bin.RData      |only
 amen-1.1/amen/data/YX_bin_long.RData |only
 amen-1.1/amen/data/YX_cbin.RData     |only
 amen-1.1/amen/data/YX_frn.RData      |only
 amen-1.1/amen/data/YX_nrm.RData      |only
 amen-1.1/amen/data/YX_ord.RData      |only
 amen-1.1/amen/data/YX_rrl.RData      |only
 amen-1.1/amen/data/coldwar.RData     |binary
 amen-1.1/amen/data/comtrade.RData    |binary
 amen-1.1/amen/data/datalist          |    3 
 amen-1.1/amen/data/sheep.RData       |only
 amen-1.1/amen/inst                   |only
 amen-1.1/amen/man/IR90s.Rd           |only
 amen-1.1/amen/man/Xbeta.Rd           |   14 
 amen-1.1/amen/man/YX_bin.Rd          |    3 
 amen-1.1/amen/man/YX_bin_long.Rd     |    3 
 amen-1.1/amen/man/YX_cbin.Rd         |    3 
 amen-1.1/amen/man/YX_frn.Rd          |    3 
 amen-1.1/amen/man/YX_nrm.Rd          |    3 
 amen-1.1/amen/man/YX_ord.Rd          |    3 
 amen-1.1/amen/man/YX_rrl.Rd          |    3 
 amen-1.1/amen/man/addhealthc3.Rd     |    5 
 amen-1.1/amen/man/addhealthc9.Rd     |    3 
 amen-1.1/amen/man/addlines.Rd        |only
 amen-1.1/amen/man/ame.Rd             |   28 -
 amen-1.1/amen/man/ame_rep.Rd         |   29 -
 amen-1.1/amen/man/amen-package.Rd    |    5 
 amen-1.1/amen/man/circplot.Rd        |only
 amen-1.1/amen/man/coldwar.Rd         |    7 
 amen-1.1/amen/man/comtrade.Rd        |   22 -
 amen-1.1/amen/man/design_array.Rd    |    7 
 amen-1.1/amen/man/dutchcollege.Rd    |    6 
 amen-1.1/amen/man/el2sm.Rd           |only
 amen-1.1/amen/man/gofstats.Rd        |    3 
 amen-1.1/amen/man/lazegalaw.Rd       |    3 
 amen-1.1/amen/man/mhalf.Rd           |   11 
 amen-1.1/amen/man/netplot.Rd         |only
 amen-1.1/amen/man/plot.ame.Rd        |   38 -
 amen-1.1/amen/man/rUV_fc.Rd          |   55 --
 amen-1.1/amen/man/rUV_rep_fc.Rd      |   63 ---
 amen-1.1/amen/man/rUV_sym_fc.Rd      |only
 amen-1.1/amen/man/rZ_bin_fc.Rd       |   30 -
 amen-1.1/amen/man/rZ_cbin_fc.Rd      |   51 --
 amen-1.1/amen/man/rZ_frn_fc.Rd       |   62 ---
 amen-1.1/amen/man/rZ_nrm_fc.Rd       |   13 
 amen-1.1/amen/man/rZ_ord_fc.Rd       |   34 -
 amen-1.1/amen/man/rZ_rrl_fc.Rd       |   48 --
 amen-1.1/amen/man/raSab_bin_fc.Rd    |   28 -
 amen-1.1/amen/man/raSab_cbin_fc.Rd   |   30 -
 amen-1.1/amen/man/raSab_frn_fc.Rd    |   24 -
 amen-1.1/amen/man/rbeta_ab_fc.Rd     |   86 ----
 amen-1.1/amen/man/rbeta_ab_rep_fc.Rd |   95 ----
 amen-1.1/amen/man/rmvnorm.Rd         |   11 
 amen-1.1/amen/man/rrho_mh.Rd         |   24 -
 amen-1.1/amen/man/rrho_mh_rep.Rd     |   30 -
 amen-1.1/amen/man/rs2_fc.Rd          |   12 
 amen-1.1/amen/man/rs2_rep_fc.Rd      |   17 
 amen-1.1/amen/man/rwish.Rd           |    3 
 amen-1.1/amen/man/sampsonmonks.Rd    |    3 
 amen-1.1/amen/man/sheep.Rd           |only
 amen-1.1/amen/man/simY_bin.Rd        |   17 
 amen-1.1/amen/man/simY_frn.Rd        |   30 -
 amen-1.1/amen/man/simY_nrm.Rd        |   16 
 amen-1.1/amen/man/simY_ord.Rd        |   21 -
 amen-1.1/amen/man/simY_rrl.Rd        |   26 -
 amen-1.1/amen/man/simZ.Rd            |   14 
 amen-1.1/amen/man/sm2el.Rd           |only
 amen-1.1/amen/man/summary.ame.Rd     |   24 -
 amen-1.1/amen/man/xnet.Rd            |only
 amen-1.1/amen/man/zscores.Rd         |   10 
 amen-1.1/amen/vignettes              |only
 127 files changed, 1033 insertions(+), 2335 deletions(-)

More information about amen at CRAN
Permanent link

Package spcadjust updated to version 0.9 with previous version 0.1-3 dated 2014-08-26

Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy <jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>

Diff between spcadjust versions 0.1-3 dated 2014-08-26 and 0.9 dated 2015-06-26

 DESCRIPTION                            |   14 -
 MD5                                    |   35 ++
 R/main.R                               |   17 +
 build                                  |only
 inst/doc/CUSUM_LinearRegression.R      |only
 inst/doc/CUSUM_LinearRegression.Rmd    |only
 inst/doc/CUSUM_LinearRegression.html   |only
 inst/doc/CUSUM_LogisticRegression.R    |only
 inst/doc/CUSUM_LogisticRegression.Rmd  |only
 inst/doc/CUSUM_LogisticRegression.html |only
 inst/doc/CUSUM_NormalNormal.R          |only
 inst/doc/CUSUM_NormalNormal.Rmd        |only
 inst/doc/CUSUM_NormalNormal.html       |only
 inst/doc/Methods.pdf                   |only
 inst/doc/Shewhart_NormalNormal.R       |only
 inst/doc/Shewhart_NormalNormal.Rmd     |only
 inst/doc/Shewhart_NormalNormal.html    |only
 inst/doc/papers.bib                    |only
 inst/doc/spcadjust-intro.R             |  401 +++++++++++++++------------------
 inst/doc/spcadjust-intro.pdf           |binary
 man/SPCShew-class.Rd                   |    5 
 man/SPCShewNormalCenterScale-class.Rd  |   25 +-
 vignettes/CUSUM_LinearRegression.Rmd   |only
 vignettes/CUSUM_LogisticRegression.Rmd |only
 vignettes/CUSUM_NormalNormal.Rmd       |only
 vignettes/Shewhart_NormalNormal.Rmd    |only
 vignettes/spcadjust-intro.Rnw          |  131 +++++++---
 vignettes/spcadjustClasses.pdf         |binary
 28 files changed, 362 insertions(+), 266 deletions(-)

More information about spcadjust at CRAN
Permanent link

Package rentrez updated to version 0.4.2 with previous version 0.4.1 dated 2015-03-03

Title: Entrez in R
Description: Provides an R interact to the NCBI's EUtils API allowing users to search databases like genbank and pubmed, process the resulting files and pull data into their R sessions.
Author: David Winter [aut, cre], Scott Chamberlain [ctb]
Maintainer: David Winter <david.winter@gmail.com>

Diff between rentrez versions 0.4.1 dated 2015-03-03 and 0.4.2 dated 2015-06-26

 DESCRIPTION                    |   12 ++++----
 MD5                            |   42 ++++++++++++++--------------
 NAMESPACE                      |    2 -
 NEWS                           |    4 ++
 build/vignette.rds             |binary
 inst/doc/rentrez_tutorial.R    |   61 ++++++++++++++++-------------------------
 inst/doc/rentrez_tutorial.html |    8 ++---
 man/entrez_citmatch.Rd         |    2 -
 man/entrez_db_links.Rd         |    2 -
 man/entrez_db_searchable.Rd    |    2 -
 man/entrez_db_summary.Rd       |    2 -
 man/entrez_dbs.Rd              |    2 -
 man/entrez_fetch.Rd            |    2 -
 man/entrez_global_query.Rd     |    2 -
 man/entrez_info.Rd             |    2 -
 man/entrez_link.Rd             |    2 -
 man/entrez_post.Rd             |    2 -
 man/entrez_search.Rd           |    2 -
 man/entrez_summary.Rd          |    2 -
 man/parse_pubmed_xml.Rd        |    2 -
 man/rentrez.Rd                 |    2 -
 tests/testthat/test_webenv.r   |    4 +-
 22 files changed, 76 insertions(+), 85 deletions(-)

More information about rentrez at CRAN
Permanent link

Package netmeta updated to version 0.8-0 with previous version 0.7-0 dated 2015-02-04

Title: Network Meta-Analysis using Frequentist Methods
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013).
Author: Gerta Rücker [aut], Guido Schwarzer [aut, cre], Ulrike Krahn [aut], Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between netmeta versions 0.7-0 dated 2015-02-04 and 0.8-0 dated 2015-06-26

 DESCRIPTION       |   10 +++++-----
 MD5               |   17 ++++++++++-------
 NAMESPACE         |    4 +++-
 NEWS              |   26 ++++++++++++++++++++++++--
 R/netmeta.R       |    2 +-
 R/netrank.R       |only
 R/print.netmeta.R |    4 ++--
 R/print.netrank.R |only
 man/netgraph.Rd   |   46 +++++++++++++++++++++++++++-------------------
 man/netmeta.Rd    |   27 ++++++++++++++++++---------
 man/netrank.Rd    |only
 11 files changed, 90 insertions(+), 46 deletions(-)

More information about netmeta at CRAN
Permanent link

Package mkin updated to version 0.9-39 with previous version 0.9-38 dated 2015-06-23

Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the 'FME' package. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using compiled C functions. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

Diff between mkin versions 0.9-38 dated 2015-06-23 and 0.9-39 dated 2015-06-26

 mkin-0.9-38/mkin/NEWS                          |only
 mkin-0.9-38/mkin/inst/staticdocs               |only
 mkin-0.9-39/mkin/DESCRIPTION                   |   10 +--
 mkin-0.9-39/mkin/MD5                           |   42 +++++++-------
 mkin-0.9-39/mkin/NAMESPACE                     |    5 +
 mkin-0.9-39/mkin/NEWS.md                       |only
 mkin-0.9-39/mkin/R/mkinparplot.R               |    2 
 mkin-0.9-39/mkin/R/mmkin.R                     |only
 mkin-0.9-39/mkin/R/plot.mmkin.R                |only
 mkin-0.9-39/mkin/README.md                     |    3 -
 mkin-0.9-39/mkin/inst/doc/FOCUS_D.html         |   17 +++--
 mkin-0.9-39/mkin/inst/doc/FOCUS_L.html         |   74 ++++++++++++-------------
 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.R            |    2 
 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.Rnw          |    2 
 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.pdf          |binary
 mkin-0.9-39/mkin/inst/doc/compiled_models.html |   42 +++++++-------
 mkin-0.9-39/mkin/inst/doc/mkin.pdf             |binary
 mkin-0.9-39/mkin/man/DFOP.solution.Rd          |    2 
 mkin-0.9-39/mkin/man/Extract.mmkin.Rd          |only
 mkin-0.9-39/mkin/man/FOMC.solution.Rd          |    2 
 mkin-0.9-39/mkin/man/HS.solution.Rd            |    2 
 mkin-0.9-39/mkin/man/mkinresplot.Rd            |   13 +---
 mkin-0.9-39/mkin/man/mmkin.Rd                  |only
 mkin-0.9-39/mkin/man/plot.mkinfit.Rd           |   10 +--
 mkin-0.9-39/mkin/man/plot.mmkin.Rd             |only
 mkin-0.9-39/mkin/vignettes/FOCUS_Z.Rnw         |    2 
 26 files changed, 115 insertions(+), 115 deletions(-)

More information about mkin at CRAN
Permanent link

Package jomo updated to version 1.2-0 with previous version 1.1-0 dated 2015-06-12

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>

Diff between jomo versions 1.1-0 dated 2015-06-12 and 1.2-0 dated 2015-06-26

 DESCRIPTION                    |    8 +-
 MD5                            |  122 ++++++++++++++++++++---------------------
 R/jomo1.MCMCchain.R            |   10 +--
 R/jomo1.R                      |   10 +--
 R/jomo1cat.MCMCchain.R         |   34 ++++++++---
 R/jomo1cat.R                   |   37 +++++++++---
 R/jomo1con.MCMCchain.R         |   22 ++++---
 R/jomo1con.R                   |   25 +++++---
 R/jomo1mix.MCMCchain.R         |   34 ++++++++---
 R/jomo1mix.R                   |   37 +++++++++---
 R/jomo1ran.MCMCchain.R         |   22 +++----
 R/jomo1ran.R                   |   22 +++----
 R/jomo1rancat.MCMCchain.R      |   45 ++++++++++-----
 R/jomo1rancat.R                |   48 +++++++++++-----
 R/jomo1rancathr.MCMCchain.R    |   47 +++++++++++----
 R/jomo1rancathr.R              |   52 ++++++++++++-----
 R/jomo1rancon.MCMCchain.R      |   33 ++++++-----
 R/jomo1rancon.R                |   36 +++++++-----
 R/jomo1ranconhr.MCMCchain.R    |   35 +++++++----
 R/jomo1ranconhr.R              |   40 ++++++++-----
 R/jomo1ranmix.MCMCchain.R      |   45 ++++++++++-----
 R/jomo1ranmix.R                |   48 +++++++++++-----
 R/jomo1ranmixhr.MCMCchain.R    |   47 +++++++++++----
 R/jomo1ranmixhr.R              |   52 ++++++++++++-----
 man/jomo1.MCMCchain.Rd         |   12 +++-
 man/jomo1.Rd                   |    9 ++-
 man/jomo1cat.MCMCchain.Rd      |   11 ++-
 man/jomo1cat.Rd                |   10 +++
 man/jomo1con.MCMCchain.Rd      |   10 ++-
 man/jomo1con.Rd                |    9 ++-
 man/jomo1mix.MCMCchain.Rd      |   13 ++++
 man/jomo1mix.Rd                |    9 ++-
 man/jomo1ran.MCMCchain.Rd      |   12 +++-
 man/jomo1ran.Rd                |   11 +++
 man/jomo1rancat.MCMCchain.Rd   |   13 +++-
 man/jomo1rancat.Rd             |   10 ++-
 man/jomo1rancathr.MCMCchain.Rd |   11 +++
 man/jomo1rancathr.Rd           |   10 +++
 man/jomo1rancon.MCMCchain.Rd   |   11 ++-
 man/jomo1rancon.Rd             |    9 ++-
 man/jomo1ranconhr.MCMCchain.Rd |   12 ++--
 man/jomo1ranconhr.Rd           |   10 ++-
 man/jomo1ranmix.MCMCchain.Rd   |   12 +++-
 man/jomo1ranmix.Rd             |    9 ++-
 man/jomo1ranmixhr.MCMCchain.Rd |   12 +++-
 man/jomo1ranmixhr.Rd           |    9 ++-
 src/MCMCjomo1con.c             |   18 ++----
 src/MCMCjomo1mix.c             |   22 ++-----
 src/MCMCjomo1rancon.c          |   23 ++-----
 src/MCMCjomo1ranconhf.c        |   23 ++-----
 src/MCMCjomo1ranconhr.c        |   29 +++------
 src/MCMCjomo1ranmix.c          |   26 +++-----
 src/MCMCjomo1ranmixhf.c        |   27 +++------
 src/MCMCjomo1ranmixhr.c        |   32 ++++------
 src/jomo1con.c                 |    8 +-
 src/jomo1mix.c                 |   12 ++--
 src/jomo1rancon.c              |   12 ++--
 src/jomo1ranconhf.c            |   12 ++--
 src/jomo1ranconhr.c            |   18 +++---
 src/jomo1ranmix.c              |   16 ++---
 src/jomo1ranmixhf.c            |   16 ++---
 src/jomo1ranmixhr.c            |   22 +++----
 62 files changed, 906 insertions(+), 555 deletions(-)

More information about jomo at CRAN
Permanent link

New package interplot with initial version 0.1.0.0
Package: interplot
Title: Plot the Effects of Variables in Interaction Terms
Version: 0.1.0.0
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Depends: R (>= 3.1.1), ggplot2, abind, arm
License: MIT + file LICENSE
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-06-26 14:36:15 UTC; Sammo
Repository: CRAN
Date/Publication: 2015-06-26 18:23:27

More information about interplot at CRAN
Permanent link

Package unbalanced updated to version 2.0 with previous version 1.1 dated 2014-02-05

Title: Racing for Unbalanced Methods Selection
Description: A dataset is said to be unbalanced when the class of interest (minority class) is much rarer than normal behaviour (majority class). The cost of missing a minority class is typically much higher that missing a majority class. Most learning systems are not prepared to cope with unbalanced data and several techniques have been proposed. This package implements some of most well-known techniques and propose a racing algorithm to select adaptively the most appropriate strategy for a given unbalanced task.
Author: Andrea Dal Pozzolo, Olivier Caelen and Gianluca Bontempi
Maintainer: Andrea Dal Pozzolo <adalpozz@ulb.ac.be>

Diff between unbalanced versions 1.1 dated 2014-02-05 and 2.0 dated 2015-06-26

 DESCRIPTION               |   17 +++---
 MD5                       |   51 ++++++++++---------
 NAMESPACE                 |    4 -
 R/ubBalance.R             |  122 ++++++++++++++++++++++++----------------------
 R/ubCNN.R                 |    2 
 R/ubENN.R                 |   19 ++++---
 R/ubNCL.R                 |  102 ++++++++++++++++++--------------------
 R/ubOSS.R                 |   19 ++++---
 R/ubOver.R                |   60 +++++++++++-----------
 R/ubRacing.R              |only
 R/ubSMOTE.R               |    4 -
 R/ubSmoteExs.R            |   21 +++++--
 R/ubTomek.R               |    9 +--
 R/ubUnder.R               |   73 +++++++++++++--------------
 R/unbalanced-internal.R   |only
 data/ubIonosphere.rda     |binary
 man/ubBalance.Rd          |   30 ++++++-----
 man/ubCNN.Rd              |    2 
 man/ubENN.Rd              |    2 
 man/ubIonosphere.Rd       |    4 -
 man/ubNCL.Rd              |    2 
 man/ubOSS.Rd              |    4 -
 man/ubOver.Rd             |    5 +
 man/ubRacing.Rd           |only
 man/ubSMOTE.Rd            |    2 
 man/ubTomek.Rd            |    2 
 man/ubUnder.Rd            |   19 ++++---
 man/unbalanced-package.Rd |   42 +++++++++------
 28 files changed, 334 insertions(+), 283 deletions(-)

More information about unbalanced at CRAN
Permanent link

Package parallelSVM updated to version 0.1-9 with previous version 0.1-8 dated 2015-06-03

Title: A Parallel-Voting Version of the Support-Vector-Machine Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>

Diff between parallelSVM versions 0.1-8 dated 2015-06-03 and 0.1-9 dated 2015-06-26

 DESCRIPTION                |    8 ++++----
 MD5                        |    4 ++--
 man/parallelSVM-package.Rd |    1 +
 3 files changed, 7 insertions(+), 6 deletions(-)

More information about parallelSVM at CRAN
Permanent link

Package parallelML updated to version 1.2 with previous version 1.1 dated 2015-06-23

Title: A Parallel-Voting Algorithm for many Classifiers
Description: By sampling your data, running the provided classifier on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular machine learning algorithm and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>

Diff between parallelML versions 1.1 dated 2015-06-23 and 1.2 dated 2015-06-26

 DESCRIPTION               |    8 +++---
 MD5                       |   20 ++++++++-------
 NAMESPACE                 |    1 
 R/convertAverage.R        |only
 R/parallelML.R            |    8 +++---
 R/predictML.R             |   28 +++++++++++++++++++--
 R/trainSample.R           |   60 +++++++++++++++++++++++++++++-----------------
 man/convertAverage.Rd     |only
 man/parallelML-package.Rd |    1 
 man/parallelML.Rd         |   29 +++++++++++++++++++++-
 man/predictML.Rd          |   24 +++++++++++++++++-
 man/trainSample.Rd        |   15 +++++++++--
 12 files changed, 150 insertions(+), 44 deletions(-)

More information about parallelML at CRAN
Permanent link

Package KFAS updated to version 1.1.2 with previous version 1.1.1 dated 2015-04-29

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: Functions for Kalman filtering, smoothing, forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

Diff between KFAS versions 1.1.1 dated 2015-04-29 and 1.1.2 dated 2015-06-26

 ChangeLog            |    6 
 DESCRIPTION          |    8 
 MD5                  |   89 +++---
 NAMESPACE            |    1 
 R/KFAS-package.R     |    4 
 R/KFS.R              |  695 +++++++++++++++++++++++++--------------------------
 R/SSMarima.R         |  130 ++++-----
 R/SSMcustom.R        |  151 +++++------
 R/SSMcycle.R         |  173 ++++++------
 R/SSModel.R          |  433 ++++++++++++++++---------------
 R/SSMregression.R    |  344 ++++++++++++-------------
 R/SSMseasonal.R      |  235 ++++++++---------
 R/SSMtrend.R         |  183 ++++++-------
 R/approxSSM.R        |   32 +-
 R/checkModel.R       |   95 +++---
 R/coef.KFS.R         |   10 
 R/deviance.KFS.R     |    7 
 R/extract.SSModel.R  |  199 +++++++-------
 R/fitSSM.R           |    6 
 R/hatvalues.KFS.R    |    6 
 R/importanceSSM.R    |  146 +++++-----
 R/initTheta.R        |   51 +--
 R/internalResids.R   |   71 ++---
 R/interval.R         |  162 +++++------
 R/ldl.R              |   15 -
 R/logLik.SSModel.R   |  189 ++++++-------
 R/mvInnovations.R    |   12 
 R/predict.SSModel.R  |  128 ++++-----
 R/print.objects.R    |   59 ++--
 R/residuals.KFS.R    |  163 ++++++-----
 R/rstandard.KFS.R    |   32 +-
 R/signals.R          |  110 ++++----
 R/simHelper.R        |   11 
 R/simulateSSM.R      |  138 +++++-----
 R/subset.SSModel.R   |   11 
 R/transformSSM.R     |  250 +++++++++---------
 build/vignette.rds   |binary
 inst/CITATION        |    2 
 inst/doc/KFAS.pdf    |binary
 man/KFS.Rd           |    3 
 man/SSModel.Rd       |   44 ++-
 man/alcohol.Rd       |    4 
 man/mvInnovations.Rd |only
 src/approx.f95       |    6 
 src/gloglik.f95      |   12 
 src/ngloglik.f95     |    2 
 46 files changed, 2239 insertions(+), 2189 deletions(-)

More information about KFAS at CRAN
Permanent link

Package igraphdata updated to version 1.0.0 with previous version 0.2.2 dated 2015-04-09

Title: A Collection of Network Data Sets for the 'igraph' Package
Description: A small collection of various network data sets, to use with the 'igraph' package: the Enron email network, various food webs, interactions in the immunoglobulin protein, the karate club network, Koenigsberg's bridges, visuotactile brain areas of the macaque monkey, UK faculty friendship network, domestic US flights network, etc.
Author: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between igraphdata versions 0.2.2 dated 2015-04-09 and 1.0.0 dated 2015-06-26

 DESCRIPTION          |   18 +--
 LICENSE              |   27 +++++
 MD5                  |   31 +++---
 README.md            |only
 data/Koenigsberg.rda |binary
 data/UKfaculty.rda   |binary
 data/USairports.rda  |binary
 data/enron.rda       |only
 data/foodwebs.rda    |binary
 data/immuno.rda      |binary
 data/karate.rda      |binary
 data/kite.rda        |only
 data/macaque.rda     |binary
 data/rfid.rda        |only
 data/yeast.rda       |binary
 inst/getdata.R       |  256 +++++++++++++++++++++++++++++++++++++++++++++++++--
 man/enron.Rd         |only
 man/karate.Rd        |    3 
 man/kite.Rd          |only
 man/rfid.Rd          |only
 20 files changed, 305 insertions(+), 30 deletions(-)

More information about igraphdata at CRAN
Permanent link

New package cusp with initial version 2.3.1
Package: cusp
Type: Package
Title: Cusp-Catastrophe Model Fitting Using Maximum Likelihood
Version: 2.3.1
Author: Raoul P. P. P. Grasman [aut, cre, cph]
Maintainer: Raoul Grasman <rgrasman@uva.nl>
LazyData: yes
NeedsCompilation: yes
Suggests: plot3D
Description: Cobb's maximum likelihood method for cusp-catastrophe modeling (Grasman, van der Maas, & Wagenmakers, 2009, JSS, 32:8; Cobb, L, 1981, Behavioral Science, 26:1, 75--78). Includes a cusp() function for model fitting, and several utility functions for plotting, and for comparing the model to linear regression and logistic curve models.
License: GPL-2
Repository: CRAN
Repository/R-Forge/Project: cusp
Repository/R-Forge/Revision: 18
Repository/R-Forge/DateTimeStamp: 2015-06-17 10:34:21
Date/Publication: 2015-06-26 13:34:32
Packaged: 2015-06-17 10:45:53 UTC; rforge

More information about cusp at CRAN
Permanent link

New package cmsaf with initial version 1.4
Package: cmsaf
Version: 1.4
Date: 2015-06-24
Title: Tools for CM SAF netcdf data
Author: Steffen Kothe
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable observing of the climate system by providing Essential Climate Variables related to the energy and water cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven National Meteorological and Hydrological Services, including the Deutscher Wetterdienst (DWD). The cmsaf R-package provides a small collection of R-functions, which are inspired by the Climate Data Operators (cdo). This gives the opportunity to analyse and manipulate CM SAF data without the need of installing cdo. The cmsaf R-package is tested for CM SAF netcdf data, which are structured in three-dimensional arrays (longitude, latitude, time) on a rectangular grid. Layered CM SAF data have to be converted with the provided `levbox_mergetime` function. The cmsaf R-package functions have only minor checks for deviations from the recommended data structure, and give only few specific error messages. Thus, there is no warranty of accurate results.
License: GPL (>= 3)
Depends: ncdf4, RNetCDF, sp, raster, stats, fields
Packaged: 2015-06-26 11:10:52 UTC; stkothe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-26 14:00:33

More information about cmsaf at CRAN
Permanent link

Package BrailleR updated to version 0.22.0 with previous version 0.20 dated 2015-05-30

Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>

Diff between BrailleR versions 0.20 dated 2015-05-30 and 0.22.0 dated 2015-06-26

 BrailleR-0.20/BrailleR/inst/PREFERENCES                |only
 BrailleR-0.22.0/BrailleR/DESCRIPTION                   |   13 +-
 BrailleR-0.22.0/BrailleR/MD5                           |   36 +++---
 BrailleR-0.22.0/BrailleR/NAMESPACE                     |    3 
 BrailleR-0.22.0/BrailleR/R/BRLThis.R                   |only
 BrailleR-0.22.0/BrailleR/R/MakeBatch.R                 |    2 
 BrailleR-0.22.0/BrailleR/R/MakeRprofile.R              |only
 BrailleR-0.22.0/BrailleR/R/Options.R                   |   79 +++++++++++++
 BrailleR-0.22.0/BrailleR/R/Premiere100.R               |only
 BrailleR-0.22.0/BrailleR/R/SVGThis.R                   |only
 BrailleR-0.22.0/BrailleR/R/VIMethod1_JG.R              |    4 
 BrailleR-0.22.0/BrailleR/R/zzz.R                       |   10 +
 BrailleR-0.22.0/BrailleR/inst/DEFAULTS                 |only
 BrailleR-0.22.0/BrailleR/inst/NEWS                     |   23 +++
 BrailleR-0.22.0/BrailleR/inst/doc/BrailleRHistory.html |   29 ++---
 BrailleR-0.22.0/BrailleR/inst/doc/Ex1histograms.html   |   98 ++++++++---------
 BrailleR-0.22.0/BrailleR/inst/fonts                    |only
 BrailleR-0.22.0/BrailleR/man/BRLThis.Rd                |only
 BrailleR-0.22.0/BrailleR/man/BrailleR-package.Rd       |   10 -
 BrailleR-0.22.0/BrailleR/man/Embossers.Rd              |only
 BrailleR-0.22.0/BrailleR/man/MakeRprofile.Rd           |only
 BrailleR-0.22.0/BrailleR/man/Options.Rd                |    4 
 BrailleR-0.22.0/BrailleR/man/SVGThis.Rd                |only
 BrailleR-0.22.0/BrailleR/man/SetOptions.Rd             |   33 +++++
 24 files changed, 244 insertions(+), 100 deletions(-)

More information about BrailleR at CRAN
Permanent link

Package AssocTests updated to version 0.0-2 with previous version 0.0-1 dated 2015-06-21

Title: Genetic Association Studies
Description: Some procedures including EIGENSTRAT (a procedure for detecting and correcting for population stratification through searching for the eigenvectors in genetic association studies), PCoC (a procedure for correcting for population stratification through calculating the principal coordinates and the clustering of the subjects), Tracy-Wisdom test (a procedure for detecting the significant eigenvalues of a matrix), distance regression (a procedure for detecting the association between a distance matrix and some independent variants of interest), single-marker test (a procedure for identifying the association between the genotype at a biallelic marker and a trait using the Wald test or the Fisher exact test), MAX3 (a procedure for testing for the association between a single nucleotide polymorphism and a binary phenotype using the maximum value of the three test statistics derived for the recessive, additive, and dominant models), nonparametric trend test (a procedure for testing for the association between a genetic variant and a non-normal distributed quantitative trait based on the nonparametric risk), and nonparametric MAX3 (a procedure for testing for the association between a biallelic single nucleotide polymorphism and a quantitative trait using the maximum value of the three nonparametric trend tests derived for the recessive, additive, and dominant models), which are commonly used in genetic association studies.
Author: Lin Wang [aut], Wei Zhang [aut], Qizhai Li [aut], Weicheng Zhu [ctb]
Maintainer: Lin Wang <wanglin2009@amss.ac.cn>

Diff between AssocTests versions 0.0-1 dated 2015-06-21 and 0.0-2 dated 2015-06-26

 DESCRIPTION |    8 ++++----
 MD5         |    2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

More information about AssocTests at CRAN
Permanent link

Package treemap updated to version 2.3 with previous version 2.2 dated 2014-03-31

Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

Diff between treemap versions 2.2 dated 2014-03-31 and 2.3 dated 2015-06-26

 DESCRIPTION                     |   12 -
 MD5                             |   54 ++---
 NAMESPACE                       |    2 
 NEWS                            |    8 
 R/comp2col.R                    |   13 -
 R/createRec.R                   |    4 
 R/dens2col.R                    |    6 
 R/itreemap.R                    |    2 
 R/pkg.R                         |    4 
 R/str2rect.R                    |   40 ++-
 R/tmColorsLegend.R              |   10 
 R/tmDrawRect.R                  |   20 +
 R/treecolors.R                  |    2 
 R/treefunctions.R               |    2 
 R/treegraph.R                   |   19 +
 R/treemap.R                     |   21 +-
 R/treepalette.R                 |    4 
 R/value2col.R                   |    6 
 man/GNI2010.Rd                  |    9 
 man/business.Rd                 |   16 -
 man/itreemap.Rd                 |   33 ---
 man/random.hierarchical.data.Rd |   87 ++------
 man/tmPlot.Rd                   |    4 
 man/treecolors.Rd               |   14 -
 man/treegraph.Rd                |  127 ++++--------
 man/treemap-package.Rd          |   24 +-
 man/treemap.Rd                  |  414 +++++++++++-----------------------------
 man/treepalette.Rd              |   85 ++------
 28 files changed, 395 insertions(+), 647 deletions(-)

More information about treemap at CRAN
Permanent link

Package bams (with last version 1.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-03-13 1.6
2012-06-28 1.2
2012-04-06 1.1

Permanent link
Package soilphysics updated to version 2.4 with previous version 2.3 dated 2015-05-09

Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

Diff between soilphysics versions 2.3 dated 2015-05-09 and 2.4 dated 2015-06-26

 DESCRIPTION                |   10 +-
 MD5                        |   14 +--
 NEWS                       |    7 +
 R/iwc.R                    |    9 +-
 R/llwr.R                   |  193 ++++++++++++++++++++++++++++-----------------
 man/iwc.Rd                 |   21 ++--
 man/llwr.Rd                |   74 +++++++++++------
 man/soilphysics-package.Rd |   78 ++++++------------
 8 files changed, 240 insertions(+), 166 deletions(-)

More information about soilphysics at CRAN
Permanent link

Package libamtrack updated to version 0.6.2 with previous version 0.6.1 dated 2015-05-22

Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>

Diff between libamtrack versions 0.6.1 dated 2015-05-22 and 0.6.2 dated 2015-06-26

 libamtrack-0.6.1/libamtrack/man/AT.Bethe.mean.energy.loss.MeV.Rd           |only
 libamtrack-0.6.1/libamtrack/man/AT.Vavilov.energy.loss.distribution.Rd     |only
 libamtrack-0.6.1/libamtrack/man/AT.energy.loss.FWHM.Rd                     |only
 libamtrack-0.6.1/libamtrack/man/AT.energy.loss.distribution.Rd             |only
 libamtrack-0.6.1/libamtrack/man/AT.energy.loss.mode.Rd                     |only
 libamtrack-0.6.1/libamtrack/man/AT.lambda.from.energy.loss.Rd              |only
 libamtrack-0.6.2/libamtrack/DESCRIPTION                                    |   13 
 libamtrack-0.6.2/libamtrack/MD5                                            |  173 -
 libamtrack-0.6.2/libamtrack/NAMESPACE                                      |   94 
 libamtrack-0.6.2/libamtrack/R/initial.R                                    |    2 
 libamtrack-0.6.2/libamtrack/R/libamtrack.R                                 |  385 ++-
 libamtrack-0.6.2/libamtrack/configure                                      |  922 ++-----
 libamtrack-0.6.2/libamtrack/configure.ac                                   |   36 
 libamtrack-0.6.2/libamtrack/man/AT.A.from.particle.no.Rd                   |    2 
 libamtrack-0.6.2/libamtrack/man/AT.CSDA.energy.after.slab.E.MeV.u.Rd       |    2 
 libamtrack-0.6.2/libamtrack/man/AT.CSDA.range.Bethe.g.cm2.Rd               |    2 
 libamtrack-0.6.2/libamtrack/man/AT.D.RDD.Gy.Rd                             |    2 
 libamtrack-0.6.2/libamtrack/man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd        |    2 
 libamtrack-0.6.2/libamtrack/man/AT.E.from.beta.Rd                          |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Gauss.IDF.Rd                            |only
 libamtrack-0.6.2/libamtrack/man/AT.Gauss.PDF.Rd                            |only
 libamtrack-0.6.2/libamtrack/man/AT.I.eV.from.composition.Rd                |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Landau.IDF.Rd                           |only
 libamtrack-0.6.2/libamtrack/man/AT.Landau.PDF.Rd                           |   11 
 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.Rd                  |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.with.no.Rd          |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Rutherford.SDCS.Rd                      |    4 
 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.Rd                       |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.with.no.Rd               |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Vavilov.IDF.Rd                          |only
 libamtrack-0.6.2/libamtrack/man/AT.Vavilov.PDF.Rd                          |   11 
 libamtrack-0.6.2/libamtrack/man/AT.WEPL.Bethe.Rd                           |    2 
 libamtrack-0.6.2/libamtrack/man/AT.Z.from.particle.no.Rd                   |    2 
 libamtrack-0.6.2/libamtrack/man/AT.atomic.weight.from.Z.Rd                 |    2 
 libamtrack-0.6.2/libamtrack/man/AT.average.A.from.composition.Rd           |    2 
 libamtrack-0.6.2/libamtrack/man/AT.average.Z.from.composition.Rd           |    2 
 libamtrack-0.6.2/libamtrack/man/AT.beam.par.physical.to.technical.Rd       |    4 
 libamtrack-0.6.2/libamtrack/man/AT.beam.par.technical.to.physical.Rd       |    4 
 libamtrack-0.6.2/libamtrack/man/AT.beta.from.E.Rd                          |    2 
 libamtrack-0.6.2/libamtrack/man/AT.dose.Gy.from.fluence.cm2.Rd             |    4 
 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.E.MeV.u.Rd                |    4 
 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.LET.MeV.cm2.g.Rd          |    4 
 libamtrack-0.6.2/libamtrack/man/AT.effective.Z.from.composition.Rd         |    2 
 libamtrack-0.6.2/libamtrack/man/AT.effective.charge.from.E.MeV.u.Rd        |    2 
 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.Rd                  |    2 
 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.composition.Rd |    2 
 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.material.no.Rd |    2 
 libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.gauss.Rd        |only
 libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.landau.Rd       |only
 libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.vavilov.Rd      |only
 libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.MeV2.cm2.g.Rd         |    4 
 libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.after.slab.E.MeV.u.Rd |    4 
 libamtrack-0.6.2/libamtrack/man/AT.fluence.cm2.from.dose.Gy.Rd             |    4 
 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.E.MeV.u.Rd             |    4 
 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.LET.MeV.cm2.g.Rd       |    4 
 libamtrack-0.6.2/libamtrack/man/AT.gamma.from.E.Rd                         |    2 
 libamtrack-0.6.2/libamtrack/man/AT.get.materials.data.Rd                   |    2 
 libamtrack-0.6.2/libamtrack/man/AT.kappa.Rd                                |   15 
 libamtrack-0.6.2/libamtrack/man/AT.lambda.landau.from.energy.loss.Rd       |only
 libamtrack-0.6.2/libamtrack/man/AT.lambda.max.Rd                           |only
 libamtrack-0.6.2/libamtrack/man/AT.lambda.mean.Rd                          |only
 libamtrack-0.6.2/libamtrack/man/AT.lambda.vavilov.from.energy.loss.Rd      |only
 libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.Rd                   |    2 
 libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.new.Rd               |only
 libamtrack-0.6.2/libamtrack/man/AT.max.electron.ranges.m.Rd                |    2 
 libamtrack-0.6.2/libamtrack/man/AT.mean.energy.loss.keV.Rd                 |only
 libamtrack-0.6.2/libamtrack/man/AT.mean.number.of.tracks.contrib.Rd        |    4 
 libamtrack-0.6.2/libamtrack/man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd        |    4 
 libamtrack-0.6.2/libamtrack/man/AT.nuclear.spin.from.particle.no.Rd        |    2 
 libamtrack-0.6.2/libamtrack/man/AT.particle.no.from.Z.and.A.Rd             |    2 
 libamtrack-0.6.2/libamtrack/man/AT.r.RDD.m.Rd                              |    2 
 libamtrack-0.6.2/libamtrack/man/AT.run.CPPSC.method.Rd                     |    2 
 libamtrack-0.6.2/libamtrack/man/AT.run.GSM.method.Rd                       |    2 
 libamtrack-0.6.2/libamtrack/man/AT.run.IGK.method.Rd                       |    2 
 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.Rd                    |    2 
 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.from.composition.Rd   |    2 
 libamtrack-0.6.2/libamtrack/man/AT.stopping.power.ratio.Rd                 |    4 
 libamtrack-0.6.2/libamtrack/man/AT.total.D.Gy.Rd                           |    4 
 libamtrack-0.6.2/libamtrack/man/AT.total.fluence.cm2.Rd                    |    4 
 libamtrack-0.6.2/libamtrack/man/AT.translate.dose.into.DSB.distribution.Rd |    2 
 libamtrack-0.6.2/libamtrack/man/AT.xi.keV.Rd                               |only
 libamtrack-0.6.2/libamtrack/man/libamtrack-package.Rd                      |    4 
 libamtrack-0.6.2/libamtrack/src/AT.c                                       |    4 
 libamtrack-0.6.2/libamtrack/src/AT.h                                       |    4 
 libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.c                           |only
 libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.h                           |only
 libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.c                            | 1240 ++++------
 libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.h                            |  517 ++--
 libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.c                       |  113 
 libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.h                       |   73 
 libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.c                             |  650 ++++-
 libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.h                             |  137 -
 libamtrack-0.6.2/libamtrack/src/AT_SPC.c                                   |   11 
 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.c                |  176 +
 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.h                |   75 
 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataFromFile.c             |    2 
 libamtrack-0.6.2/libamtrack/src/CERNLIBFUNS.f                              |only
 libamtrack-0.6.2/libamtrack/src/Makevars.in                                |    8 
 libamtrack-0.6.2/libamtrack/src/config.h                                   |   26 
 99 files changed, 2928 insertions(+), 1908 deletions(-)

More information about libamtrack at CRAN
Permanent link

Package igraph updated to version 1.0.1 with previous version 1.0.0 dated 2015-06-24

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between igraph versions 1.0.0 dated 2015-06-24 and 1.0.1 dated 2015-06-26

 DESCRIPTION                             |    6 ++--
 MD5                                     |   42 ++++++++++++++++----------------
 R/adjacency.R                           |   28 ++++++++++-----------
 R/attributes.R                          |   22 ++++++++--------
 R/centrality.R                          |   22 ++++++++--------
 R/conversion.R                          |   10 +++----
 R/make.R                                |   25 ++++++++++++++++++-
 R/structural.properties.R               |   14 +++++-----
 R/topology.R                            |   20 +++++++--------
 man/arpack.Rd                           |   22 ++++++++--------
 man/as.directed.Rd                      |   10 +++----
 man/canonical_permutation.Rd            |   20 +++++++--------
 man/graph_from_adjacency_matrix.Rd      |   28 ++++++++++-----------
 man/igraph-attribute-combination.Rd     |   22 ++++++++--------
 man/make_.Rd                            |   28 ++++++++++++++++++++-
 man/transitivity.Rd                     |   14 +++++-----
 src/Makevars.in                         |    2 -
 src/Makevars.win                        |    4 ---
 src/gengraph_graph_molloy_hash.cpp      |    4 +--
 src/gengraph_graph_molloy_optimized.cpp |   12 ++++-----
 src/prpack/prpack_solver.cpp            |    3 +-
 src/uuid/gen_uuid.c                     |   25 ++++++++++++++-----
 22 files changed, 221 insertions(+), 162 deletions(-)

More information about igraph at CRAN
Permanent link

Package wgaim updated to version 1.4-10 with previous version 1.4-8 dated 2015-05-06

Title: Whole Genome Average Interval Mapping for QTL Detection using Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

Diff between wgaim versions 1.4-8 dated 2015-05-06 and 1.4-10 dated 2015-06-26

 DESCRIPTION        |    8 +++---
 MD5                |   10 ++++----
 R/wgaim9.R         |   65 +++++------------------------------------------------
 R/zzz.R            |    4 +--
 inst/NEWS.Rd       |   11 +++++++-
 inst/doc/wgaim.pdf |binary
 6 files changed, 27 insertions(+), 71 deletions(-)

More information about wgaim at CRAN
Permanent link

Package TROM updated to version 1.1 with previous version 1.0 dated 2015-04-08

Title: Transcriptome Overlap Measure
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette.
Author: Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Maintainer: Jingyi Jessica Li <jli@stat.ucla.edu>

Diff between TROM versions 1.0 dated 2015-04-08 and 1.1 dated 2015-06-26

 TROM-1.0/TROM/inst/doc/Vignette.pdf              |only
 TROM-1.1/TROM/DESCRIPTION                        |   19 +
 TROM-1.1/TROM/MD5                                |   51 ++--
 TROM-1.1/TROM/NAMESPACE                          |    1 
 TROM-1.1/TROM/R/TROM-internal.R                  |  250 +++++++++++------------
 TROM-1.1/TROM/R/bs.trom.R                        |   16 +
 TROM-1.1/TROM/R/choose.z.R                       |only
 TROM-1.1/TROM/R/find.top.GO.slim.terms.R         |    2 
 TROM-1.1/TROM/R/find.top.GO.terms.R              |    1 
 TROM-1.1/TROM/R/select.associated.genes.R        |    6 
 TROM-1.1/TROM/R/select.associated.orthologs.R    |    9 
 TROM-1.1/TROM/R/sp.associated.idx.R              |    4 
 TROM-1.1/TROM/R/ws.trom.R                        |  133 ++++++------
 TROM-1.1/TROM/R/ws.trom.forZ.R                   |only
 TROM-1.1/TROM/R/ws.trom.orthologs.R              |  178 ++++++++--------
 TROM-1.1/TROM/R/ws.trom.three.R                  |only
 TROM-1.1/TROM/R/ws.trom.two.R                    |only
 TROM-1.1/TROM/data/GO_slim_id.rda                |binary
 TROM-1.1/TROM/inst/dm_associated_orthologs.xlsx  |binary
 TROM-1.1/TROM/inst/doc/TROM_Vignette.pdf         |only
 TROM-1.1/TROM/man/TROM-package.Rd                |    9 
 TROM-1.1/TROM/man/bs.trom.Rd                     |   17 -
 TROM-1.1/TROM/man/choose.z.Rd                    |only
 TROM-1.1/TROM/man/find.top.GO.slim.terms.Rd      |    2 
 TROM-1.1/TROM/man/find.top.GO.terms.Rd           |    2 
 TROM-1.1/TROM/man/heatmap.3.Rd                   |    4 
 TROM-1.1/TROM/man/select.associated.genes.Rd     |   18 -
 TROM-1.1/TROM/man/select.associated.orthologs.Rd |   16 -
 TROM-1.1/TROM/man/ws.trom.Rd                     |   52 +++-
 TROM-1.1/TROM/man/ws.trom.orthologs.Rd           |   66 +++---
 30 files changed, 465 insertions(+), 391 deletions(-)

More information about TROM at CRAN
Permanent link

Package SenSrivastava updated to version 2015.6.25 with previous version 2012-04-0 dated 2012-04-04

Title: Datasets from Sen & Srivastava
Description: Collection of datasets from Sen & Srivastava: "Regression Analysis, Theory, Methods and Applications", Springer. Sources for individual data files are more fully documented in the book.
Author: Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>

Diff between SenSrivastava versions 2012-04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26

 SenSrivastava-2012-04-0/SenSrivastava/SenSrivastava-Ex.R |only
 SenSrivastava-2015.6.25/SenSrivastava/DESCRIPTION        |   17 +++++++--------
 SenSrivastava-2015.6.25/SenSrivastava/MD5                |    5 +---
 SenSrivastava-2015.6.25/SenSrivastava/NEWS               |    3 ++
 4 files changed, 14 insertions(+), 11 deletions(-)

More information about SenSrivastava at CRAN
Permanent link

Package rvertnet updated to version 0.3.0 with previous version 0.2.2 dated 2015-01-21

Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives. Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rvertnet versions 0.2.2 dated 2015-01-21 and 0.3.0 dated 2015-06-26

 rvertnet-0.2.2/rvertnet/NEWS                                |only
 rvertnet-0.3.0/rvertnet/DESCRIPTION                         |   19 
 rvertnet-0.3.0/rvertnet/MD5                                 |   71 +-
 rvertnet-0.3.0/rvertnet/NAMESPACE                           |    5 
 rvertnet-0.3.0/rvertnet/R/bigsearch.R                       |   11 
 rvertnet-0.3.0/rvertnet/R/searchbyterm.R                    |   45 -
 rvertnet-0.3.0/rvertnet/R/vertmap.R                         |   25 
 rvertnet-0.3.0/rvertnet/R/vertsearch.R                      |   13 
 rvertnet-0.3.0/rvertnet/R/vertsummary.R                     |    2 
 rvertnet-0.3.0/rvertnet/R/yyy.R                             |    4 
 rvertnet-0.3.0/rvertnet/R/zzz.R                             |  163 +++--
 rvertnet-0.3.0/rvertnet/README.md                           |  196 ++++--
 rvertnet-0.3.0/rvertnet/build/vignette.rds                  |binary
 rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.Rmd      |  363 +++++++++---
 rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.html     |  346 ++++++++---
 rvertnet-0.3.0/rvertnet/inst/ignore                         |only
 rvertnet-0.3.0/rvertnet/inst/vign/figure                    |only
 rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.Rmd     |   79 ++
 rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.md      |  361 +++++++++--
 rvertnet-0.3.0/rvertnet/man/bigsearch.Rd                    |   11 
 rvertnet-0.3.0/rvertnet/man/rvertnet-defunct.Rd             |    2 
 rvertnet-0.3.0/rvertnet/man/rvertnet-package.Rd             |    2 
 rvertnet-0.3.0/rvertnet/man/searchbyterm.Rd                 |   34 -
 rvertnet-0.3.0/rvertnet/man/spatialsearch.Rd                |    2 
 rvertnet-0.3.0/rvertnet/man/vertavailablemaps-defunct.Rd    |    2 
 rvertnet-0.3.0/rvertnet/man/vertlocations-defunct.Rd        |    2 
 rvertnet-0.3.0/rvertnet/man/vertmap.Rd                      |   16 
 rvertnet-0.3.0/rvertnet/man/vertoccurrence-defunct.Rd       |    2 
 rvertnet-0.3.0/rvertnet/man/vertoccurrencecount-defunct.Rd  |    2 
 rvertnet-0.3.0/rvertnet/man/vertproviders-defunct.Rd        |    2 
 rvertnet-0.3.0/rvertnet/man/vertsearch.Rd                   |    8 
 rvertnet-0.3.0/rvertnet/man/vertsummary.Rd                  |    4 
 rvertnet-0.3.0/rvertnet/man/verttaxa-defunct.Rd             |    2 
 rvertnet-0.3.0/rvertnet/tests/testthat.R                    |only
 rvertnet-0.3.0/rvertnet/tests/testthat/test-bigsearch.R     |   10 
 rvertnet-0.3.0/rvertnet/tests/testthat/test-searchbyterm.R  |   65 +-
 rvertnet-0.3.0/rvertnet/tests/testthat/test-spatialsearch.R |   28 
 rvertnet-0.3.0/rvertnet/vignettes/rvertnet_vignette.Rmd     |  363 +++++++++---
 38 files changed, 1646 insertions(+), 614 deletions(-)

More information about rvertnet at CRAN
Permanent link

New package pmc with initial version 1.0.0
Package: pmc
Version: 1.0.0
Title: Phylogenetic Monte Carlo
Description: Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x.
Authors@R: person('Carl', 'Boettiger', email='cboettig@gmail.com', role =c('aut', 'cre'))
URL: https://github.com/cboettig/pmc
BugReports: https://github.com/cboettig/pmc/issues
License: CC0
LazyData: true
VignetteBuilder: knitr
Suggests: covr, gridExtra, knitr, testthat
Imports: dplyr, geiger, ggplot2, parallel, ouch, tidyr
NeedsCompilation: no
Packaged: 2015-06-26 05:57:42 UTC; rstudio
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Repository: CRAN
Date/Publication: 2015-06-26 10:57:51

More information about pmc at CRAN
Permanent link

Package Nippon updated to version 0.6.1 with previous version 0.5.3 dated 2013-07-26

Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com>
Maintainer: Susumu Tanimura <aruminat@gmail.com>

Diff between Nippon versions 0.5.3 dated 2013-07-26 and 0.6.1 dated 2015-06-26

 Nippon-0.5.3/Nippon/Nippon-Ex.R                |only
 Nippon-0.5.3/Nippon/configure.ac.orig          |only
 Nippon-0.5.3/Nippon/man/ja                     |only
 Nippon-0.5.3/Nippon/src/Makevars.in.orig       |only
 Nippon-0.5.3/Nippon/src/Makevars.orig          |only
 Nippon-0.6.1/Nippon/ChangeLog                  |   14 +
 Nippon-0.6.1/Nippon/DESCRIPTION                |   14 -
 Nippon-0.6.1/Nippon/MD5                        |   44 ++---
 Nippon-0.6.1/Nippon/NAMESPACE                  |    1 
 Nippon-0.6.1/Nippon/R/JapanPrefecturesMap.R    |    2 
 Nippon-0.6.1/Nippon/R/jholiday.R               |    7 
 Nippon-0.6.1/Nippon/R/kakasi.R                 |   32 ---
 Nippon-0.6.1/Nippon/R/zen2han.R                |   28 ++-
 Nippon-0.6.1/Nippon/TODO                       |    3 
 Nippon-0.6.1/Nippon/configure                  |  212 ++++++++++++-------------
 Nippon-0.6.1/Nippon/configure.ac               |    4 
 Nippon-0.6.1/Nippon/man/JapanPrefecturesMap.Rd |    4 
 Nippon-0.6.1/Nippon/man/Nippon-package.Rd      |   12 -
 Nippon-0.6.1/Nippon/man/jyear.Rd               |    1 
 Nippon-0.6.1/Nippon/man/kakasi.Rd              |   23 +-
 Nippon-0.6.1/Nippon/man/zen2han.Rd             |   15 -
 Nippon-0.6.1/Nippon/src/kakasi/config.h.in     |   10 -
 Nippon-0.6.1/Nippon/src/kakasi/libdict.c       |    4 
 Nippon-0.6.1/Nippon/src/kakasi/libhh2.c        |  132 ++++++++++-----
 Nippon-0.6.1/Nippon/src/kakasi/libhh2.c.new    |only
 Nippon-0.6.1/Nippon/src/kakasi/libkanjiio.c    |   10 -
 26 files changed, 308 insertions(+), 264 deletions(-)

More information about Nippon at CRAN
Permanent link

Package MIIVsem updated to version 0.3 with previous version 0.2 dated 2015-06-05

Title: Two Stage Least Squares with Model Implied Instrumental Variable Search
Description: Functions for estimating structural equation models using a model-implied instrumental variable (MIIV) search and two stage least squares (2SLS) estimator (MIIV-2SLS).
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>

Diff between MIIVsem versions 0.2 dated 2015-06-05 and 0.3 dated 2015-06-26

 DESCRIPTION     |    9 ++--
 MD5             |   12 ++---
 R/miive.R       |  117 +++++++++++++++++++++++++++++++++-----------------------
 R/miivs.R       |   82 +++++++++++++--------------------------
 R/print.miivs.R |   10 ++++
 man/miive.Rd    |    2 
 man/miivs.Rd    |    4 +
 7 files changed, 123 insertions(+), 113 deletions(-)

More information about MIIVsem at CRAN
Permanent link

New package loo with initial version 0.1.0
Package: loo
Type: Package
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
Version: 0.1.0
Date: 2015-06-24
Author: Aki Vehtari, Andrew Gelman, Jonah Gabry
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
URL: https://github.com/jgabry/loo
BugReports: https://github.com/jgabry/loo/issues
Description: We efficiently approximate leave-one-out cross-validation (LOO) using very good importance sampling (VGIS), a new procedure for regularizing importance weights. As a byproduct of our calculations, we also obtain approximate standard errors for estimated predictive errors, and for the comparison of predictive errors between two models. We also compute the widely applicable information criterion (WAIC).
License: GPL (>= 3)
LazyData: TRUE
Depends: R (>= 3.2.0)
Imports: matrixStats (>= 0.14.1), parallel
Suggests: knitr, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-06-26 01:00:17 UTC; jgabry
Repository: CRAN
Date/Publication: 2015-06-26 10:55:18

More information about loo at CRAN
Permanent link

Package Fahrmeir updated to version 2015.6.25 with previous version 2012.04-0 dated 2012-04-04

Title: Data from the Book "Multivariate Statistical Modelling Based on Generalized Linear Models", First Edition, by Ludwig Fahrmeir and Gerhard Tutz
Description: Data and functions for the book "Multivariate Statistical Modelling Based on Generalized Linear Models", first edition, by Ludwig Fahrmeir and Gerhard Tutz. Useful when using the book.
Author: compiled by Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>

Diff between Fahrmeir versions 2012.04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26

 DESCRIPTION |   23 ++++++++++++-----------
 MD5         |    4 ++--
 NEWS        |    5 +++++
 3 files changed, 19 insertions(+), 13 deletions(-)

More information about Fahrmeir at CRAN
Permanent link

Package EBEN updated to version 4.1 with previous version 1.1.1 dated 2014-06-09

Title: Empirical Bayesian Elastic Net
Description: Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet' package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>

Diff between EBEN versions 1.1.1 dated 2014-06-09 and 4.1 dated 2015-06-26

 DESCRIPTION                     |   13 
 MD5                             |   30 -
 R/EBelasticNet.Binomial.R       |only
 R/EBelasticNet.BinomialCV.R     |only
 R/EBelasticNet.Gaussian.R       |   41 +-
 R/EBelasticNet.GaussianCV.R     |   15 
 data/BASISbinomial.rda          |only
 data/yBinomial.rda              |only
 man/BASIS.Rd                    |    3 
 man/BASISbinomial.Rd            |only
 man/EBEN-package.Rd             |   34 +
 man/EBelasticNet.Binomial.Rd    |only
 man/EBelasticNet.BinomialCV.Rd  |only
 man/EBelasticNet.Gaussian.Rd    |   41 --
 man/EBelasticNet.GaussianCV.Rd  |   33 -
 man/y.Rd                        |    3 
 man/yBinomial.Rd                |only
 src/ElasticNetBinaryNEmainEff.c |only
 src/ElasticNetBinaryNeFull.c    |only
 src/elasticNetLinearNeFull2.c   |  629 +++++++++++++++++++------------
 src/elasticNetLinearNeMainEff.c |  809 +++++++++++++++++++++++++++-------------
 21 files changed, 1070 insertions(+), 581 deletions(-)

More information about EBEN at CRAN
Permanent link

Package BHH2 updated to version 2015.06.25 with previous version 2012.04-0 dated 2012-04-04

Title: Useful Functions for Box, Hunter and Hunter II
Description: Functions and data sets reproducing some examples in Box, Hunter and Hunter II. Useful for statistical design of experiments, especially factorial experiments.
Author: Ernesto Barrios
Maintainer: Kjetil B.Halvorsen <kjetil1001@gmail.com>

Diff between BHH2 versions 2012.04-0 dated 2012-04-04 and 2015.06.25 dated 2015-06-26

 DESCRIPTION              |   14 ++++++++------
 MD5                      |   26 ++++++++++++++------------
 NEWS                     |    2 ++
 build                    |only
 data/corrosion.data.rda  |binary
 data/heads.data.rda      |binary
 data/penicillin.data.rda |binary
 data/poison.data.rda     |binary
 data/shoes.data.rda      |binary
 data/tab03B1.rda         |binary
 data/tab03B2.rda         |binary
 data/tomato.data.rda     |binary
 data/woolen.data.rda     |binary
 inst/doc/BHH2.R          |only
 inst/doc/BHH2.pdf        |binary
 15 files changed, 24 insertions(+), 18 deletions(-)

More information about BHH2 at CRAN
Permanent link

Package asypow updated to version 2015.6.25 with previous version 2013.9-1 dated 2013-09-24

Title: Calculate Power Utilizing Asymptotic Likelihood Ratio Methods
Description: A set of routines written in the S language that calculate power and related quantities utilizing asymptotic likelihood ratio methods.
Author: S original by Barry W. Brown, James Lovato and Kathy Russel. R port by Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>

Diff between asypow versions 2013.9-1 dated 2013-09-24 and 2015.6.25 dated 2015-06-26

 asypow-2013.9-1/asypow/library.README               |only
 asypow-2015.6.25/asypow/DESCRIPTION                 |    8 ++++----
 asypow-2015.6.25/asypow/MD5                         |   10 +++++-----
 asypow-2015.6.25/asypow/NEWS                        |    5 +++++
 asypow-2015.6.25/asypow/README                      |only
 asypow-2015.6.25/asypow/inst/doc/asypow.pdf         |binary
 asypow-2015.6.25/asypow/inst/doc/asypow.statlib.pdf |binary
 7 files changed, 14 insertions(+), 9 deletions(-)

More information about asypow at CRAN
Permanent link

Package assertr updated to version 1.0.0 with previous version 0.4.1 dated 2015-03-24

Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>

Diff between assertr versions 0.4.1 dated 2015-03-24 and 1.0.0 dated 2015-06-26

 DESCRIPTION                      |   10 -
 MD5                              |   53 +++--
 NAMESPACE                        |   11 +
 NEWS                             |   29 ++
 R/assertions.R                   |  378 ++++++++++++++++++++++++++++++++++-----
 R/assertr.R                      |   27 ++
 R/predicates.R                   |  129 ++++++++++---
 R/row-redux.R                    |only
 R/utils.R                        |   56 +++++
 README.md                        |   87 +++++++-
 build/vignette.rds               |binary
 inst/doc/assertr.R               |    7 
 inst/doc/assertr.Rmd             |  295 +++++++++++++++++++++++++++---
 inst/doc/assertr.html            |  171 +++++++++++++++--
 man/assert.Rd                    |   38 +++
 man/assert_rows.Rd               |only
 man/assertr.Rd                   |   29 ++
 man/in_set.Rd                    |    2 
 man/insist.Rd                    |   28 ++
 man/insist_rows.Rd               |only
 man/maha_dist.Rd                 |only
 man/not_na.Rd                    |   16 -
 man/num_row_NAs.Rd               |only
 man/verify.Rd                    |    7 
 man/within_bounds.Rd             |   12 -
 man/within_n_mads.Rd             |only
 man/within_n_sds.Rd              |    7 
 tests/testthat/test-assertions.R |  367 +++++++++++++++++++++++++++++++++++++
 tests/testthat/test-predicates.R |  100 +++++++++-
 tests/testthat/test-row-redux.R  |only
 vignettes/assertr.Rmd            |  295 +++++++++++++++++++++++++++---
 31 files changed, 1908 insertions(+), 246 deletions(-)

More information about assertr at CRAN
Permanent link

Package ASMap updated to version 0.4-4 with previous version 0.4-1 dated 2015-05-04

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler <david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

Diff between ASMap versions 0.4-1 dated 2015-05-04 and 0.4-4 dated 2015-06-26

 DESCRIPTION                 |    8 +++---
 MD5                         |   12 ++++-----
 R/mstmap10.R                |   56 +++++++++++++++++++++++++-------------------
 build/vignette.rds          |binary
 inst/NEWS.Rd                |    7 +++++
 inst/doc/asmapvignette.Rnw  |    2 -
 vignettes/asmapvignette.Rnw |    2 -
 7 files changed, 52 insertions(+), 35 deletions(-)

More information about ASMap at CRAN
Permanent link

Package arulesViz updated to version 1.0-1 with previous version 1.0-0 dated 2014-12-08

Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between arulesViz versions 1.0-0 dated 2014-12-08 and 1.0-1 dated 2015-06-26

 DESCRIPTION             |   17 
 MD5                     |   29 
 NAMESPACE               |    7 
 R/graph.R               | 1405 ++++++++++++++++++++++++------------------------
 R/plot.R                |  152 ++---
 R/save.R                |    2 
 R/scatterplot.R         |    7 
 build/vignette.rds      |binary
 inst/NEWS               |    9 
 inst/doc/arulesViz.R    |    7 
 inst/doc/arulesViz.Rnw  |   22 
 inst/doc/arulesViz.pdf  |binary
 inst/n.html             |only
 man/plot.Rd             |   20 
 man/save.Rd             |    1 
 vignettes/arulesViz.Rnw |   22 
 16 files changed, 868 insertions(+), 832 deletions(-)

More information about arulesViz at CRAN
Permanent link

Thu, 25 Jun 2015

New package whoapi with initial version 0.1.0
Package: whoapi
Type: Package
Title: A 'Whoapi' API Client
Version: 0.1.0
Date: 2015-06-16
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Description: Retrieve data from the 'Whoapi' (https://whoapi.com) store of domain information, including a domain's geographic location, registration status and search prominence.
License: MIT + file LICENSE
LazyData: TRUE
Depends: httr
Suggests: testthat, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-06-25 17:44:21 UTC; ironholds
Repository: CRAN
Date/Publication: 2015-06-26 00:05:30

More information about whoapi at CRAN
Permanent link

New package TSMining with initial version 1.0
Package: TSMining
Type: Package
Title: Mining Univariate and Multivariate Motifs in Time-Series Data
Description: Implementations of a number of functions used to mine numeric time-series data. It covers the implementation of SAX transformation, univariate motif discovery (based on the random projection method), multivariate motif discovery (based on graph clustering), and several functions used for the ease of visualizing the motifs discovered. The details of SAX transformation can be found in J. Lin. E. Keogh, L. Wei, S. Lonardi, Experiencing SAX: A novel symbolic representation of time series, Data Mining and Knowledge Discovery 15 (2) (2007) 107-144. Details on univariate motif discovery method implemented can be found in B. Chiu, E. Keogh, S. Lonardi, Probabilistic discovery of time series motifs, ACM SIGKDD, Washington, DC, USA, 2003, pp. 493-498. Details on the multivariate motif discovery method implemented can be found in A. Vahdatpour, N. Amini, M. Sarrafzadeh, Towards unsupervised activity discovery using multi-dimensional motif detection in time series, IJCAI 2009 21st International Joint Conference on Artificial Intelligence.
Version: 1.0
Date: 2015-06-24
Author: Cheng Fan
Maintainer: Cheng Fan <raja8885@hotmail.com>
Depends: R (>= 3.0.1)
Imports: foreach, ggplot2, plyr, reshape2
Suggests: knitr
VignetteBuilder: knitr
LazyData: true
License: GPL-3
Packaged: 2015-06-25 13:09:35 UTC; Fan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-26 00:02:41

More information about TSMining at CRAN
Permanent link

Package sorvi updated to version 0.7.26 with previous version 0.7.20 dated 2015-02-17

Title: Finnish Open Government Data Toolkit
Description: Algorithms for Finnish open government data.
Author: Leo Lahti, Juuso Parkkinen, Joona Lehtomaki, Juuso Haapanen, Jussi Paananen, Einari Happonen
Maintainer: Leo Lahti <louhos@googlegroups.com>

Diff between sorvi versions 0.7.20 dated 2015-02-17 and 0.7.26 dated 2015-06-25

 sorvi-0.7.20/sorvi/R/postalcodes.R                         |only
 sorvi-0.7.20/sorvi/R/provinceinfo.R                        |only
 sorvi-0.7.20/sorvi/R/utilities.R                           |only
 sorvi-0.7.20/sorvi/R/visualization.R                       |only
 sorvi-0.7.20/sorvi/inst/NEWS                               |only
 sorvi-0.7.20/sorvi/man/get_postal_code_info.Rd             |only
 sorvi-0.7.20/sorvi/man/get_province_info_wikipedia.Rd      |only
 sorvi-0.7.20/sorvi/man/korvaa_skandit.Rd                   |only
 sorvi-0.7.20/sorvi/man/strip.Rd                            |only
 sorvi-0.7.20/sorvi/man/strstrip.Rd                         |only
 sorvi-0.7.20/sorvi/man/strstrip_single.Rd                  |only
 sorvi-0.7.20/sorvi/vignettes/TODO.Rmd                      |only
 sorvi-0.7.20/sorvi/vignettes/figure                        |only
 sorvi-0.7.26/sorvi/DESCRIPTION                             |   12 
 sorvi-0.7.26/sorvi/LICENSE                                 |    2 
 sorvi-0.7.26/sorvi/MD5                                     |   86 ++--
 sorvi-0.7.26/sorvi/NAMESPACE                               |   16 
 sorvi-0.7.26/sorvi/NEWS.md                                 |only
 sorvi-0.7.26/sorvi/R/convert_municipality_codes.R          |only
 sorvi-0.7.26/sorvi/R/convert_municipality_names.R          |only
 sorvi-0.7.26/sorvi/R/data.R                                |only
 sorvi-0.7.26/sorvi/R/firstlib.R                            |    4 
 sorvi-0.7.26/sorvi/R/get_municipality_info_mml.R           |only
 sorvi-0.7.26/sorvi/R/harmonize_names.R                     |only
 sorvi-0.7.26/sorvi/R/hetu.R                                |  115 ++++-
 sorvi-0.7.26/sorvi/R/is_url.R                              |only
 sorvi-0.7.26/sorvi/R/load_sorvi_data.R                     |only
 sorvi-0.7.26/sorvi/R/municipality_to_province.R            |only
 sorvi-0.7.26/sorvi/R/regression_plot.R                     |only
 sorvi-0.7.26/sorvi/R/ropengov_storage_path.R               |only
 sorvi-0.7.26/sorvi/R/sorvi-package.R                       |    6 
 sorvi-0.7.26/sorvi/R/synonymes.R                           |only
 sorvi-0.7.26/sorvi/README.md                               |   19 
 sorvi-0.7.26/sorvi/build/vignette.rds                      |binary
 sorvi-0.7.26/sorvi/inst/CITATION                           |    6 
 sorvi-0.7.26/sorvi/inst/doc/sorvi.pdf                      |binary
 sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.R               |   86 ++--
 sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.Rmd             |  118 +++--
 sorvi-0.7.26/sorvi/inst/doc/sorvi_tutorial.html            |  232 ++++-------
 sorvi-0.7.26/sorvi/inst/extdata/municipality_synonymes.csv |only
 sorvi-0.7.26/sorvi/man/check_synonymes.Rd                  |only
 sorvi-0.7.26/sorvi/man/convert_municipality_codes.Rd       |    4 
 sorvi-0.7.26/sorvi/man/convert_municipality_names.Rd       |    6 
 sorvi-0.7.26/sorvi/man/fi.en.maakunnat.Rd                  |    4 
 sorvi-0.7.26/sorvi/man/get_municipality_info_mml.Rd        |    9 
 sorvi-0.7.26/sorvi/man/harmonize_names.Rd                  |only
 sorvi-0.7.26/sorvi/man/hetu.Rd                             |   41 +
 sorvi-0.7.26/sorvi/man/is_url.Rd                           |    4 
 sorvi-0.7.26/sorvi/man/load_sorvi_data.Rd                  |    4 
 sorvi-0.7.26/sorvi/man/municipality_to_province.Rd         |    4 
 sorvi-0.7.26/sorvi/man/regression_plot.Rd                  |   16 
 sorvi-0.7.26/sorvi/man/ropengov_storage_path.Rd            |    4 
 sorvi-0.7.26/sorvi/man/sorvi-package.Rd                    |    8 
 sorvi-0.7.26/sorvi/man/valid_hetu.Rd                       |   15 
 sorvi-0.7.26/sorvi/tests                                   |only
 sorvi-0.7.26/sorvi/vignettes/TODO.md                       |only
 sorvi-0.7.26/sorvi/vignettes/sorvi_tutorial.Rmd            |  118 +++--
 sorvi-0.7.26/sorvi/vignettes/sorvi_tutorial.md             |  272 +++++--------
 58 files changed, 644 insertions(+), 567 deletions(-)

More information about sorvi at CRAN
Permanent link

Package seqMeta updated to version 1.6.0 with previous version 1.5 dated 2014-10-28

Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley
Maintainer: Brian Davis <Brian.Davis281@gmail.com>

Diff between seqMeta versions 1.5 dated 2014-10-28 and 1.6.0 dated 2015-06-25

 seqMeta-1.5/seqMeta/man/prepAdj.Rd            |only
 seqMeta-1.6.0/seqMeta/DESCRIPTION             |   20 
 seqMeta-1.6.0/seqMeta/MD5                     |   67 
 seqMeta-1.6.0/seqMeta/NAMESPACE               |   23 
 seqMeta-1.6.0/seqMeta/R/burdenMeta.R          |  313 ++--
 seqMeta-1.6.0/seqMeta/R/c.seqMeta.R           |   44 
 seqMeta-1.6.0/seqMeta/R/check_format_skat.R   |   37 
 seqMeta-1.6.0/seqMeta/R/coxlr.fit.R           |  170 +-
 seqMeta-1.6.0/seqMeta/R/pchisqsum2.R          |  140 -
 seqMeta-1.6.0/seqMeta/R/prepAdjust.R          |  154 +-
 seqMeta-1.6.0/seqMeta/R/prepCox.R             |  276 +--
 seqMeta-1.6.0/seqMeta/R/prepScores.R          |  882 ++++++-----
 seqMeta-1.6.0/seqMeta/R/prepScores2.R         |only
 seqMeta-1.6.0/seqMeta/R/seqMeta.R             |only
 seqMeta-1.6.0/seqMeta/R/singlesnpMeta.R       |  321 ++--
 seqMeta-1.6.0/seqMeta/R/skatMeta.R            |  358 +++-
 seqMeta-1.6.0/seqMeta/R/skatOMeta.R           |  698 +++++----
 seqMeta-1.6.0/seqMeta/R/utils.R               |only
 seqMeta-1.6.0/seqMeta/README.md               |only
 seqMeta-1.6.0/seqMeta/build/vignette.rds      |binary
 seqMeta-1.6.0/seqMeta/data/datalist           |    4 
 seqMeta-1.6.0/seqMeta/data/seqMetaExample.rda |binary
 seqMeta-1.6.0/seqMeta/inst/doc/seqMeta.R      |  390 ++---
 seqMeta-1.6.0/seqMeta/inst/doc/seqMeta.Rnw    | 1994 +++++++++++++-------------
 seqMeta-1.6.0/seqMeta/man/SNPInfo.Rd          |   70 
 seqMeta-1.6.0/seqMeta/man/burdenMeta.Rd       |  226 +-
 seqMeta-1.6.0/seqMeta/man/prepCondScores.Rd   |only
 seqMeta-1.6.0/seqMeta/man/prepScores.Rd       |  326 ++--
 seqMeta-1.6.0/seqMeta/man/prepScores2.Rd      |only
 seqMeta-1.6.0/seqMeta/man/seqMeta.Rd          |only
 seqMeta-1.6.0/seqMeta/man/seqMetaExample.Rd   |  136 -
 seqMeta-1.6.0/seqMeta/man/singlesnpMeta.Rd    |  208 +-
 seqMeta-1.6.0/seqMeta/man/skatMeta.Rd         |  312 +---
 seqMeta-1.6.0/seqMeta/man/skatOMeta.Rd        |  375 ++--
 seqMeta-1.6.0/seqMeta/tests                   |only
 seqMeta-1.6.0/seqMeta/vignettes/seqMeta.Rnw   | 1994 +++++++++++++-------------
 36 files changed, 5112 insertions(+), 4426 deletions(-)

More information about seqMeta at CRAN
Permanent link

Package PPtreeViz updated to version 1.1.0 with previous version 1.0.3 dated 2015-05-15

Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using various projection pursuit indices.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>

Diff between PPtreeViz versions 1.0.3 dated 2015-05-15 and 1.1.0 dated 2015-06-25

 DESCRIPTION                |   14 -
 MD5                        |   58 ++--
 NAMESPACE                  |    1 
 R/Huberplot.R              |   27 +-
 R/LDAopt.R                 |   13 -
 R/PDAopt.R                 |   17 -
 R/PPclassNodeViz.R         |   15 -
 R/PPclassify.R             |   23 +
 R/PPoptViz.R               |    4 
 R/PPtreeClass.R            |   31 +-
 R/RcppExports.R            |   27 +-
 R/plotPPtreeclass.R        |    8 
 R/predictPPtreeclass.R     |only
 R/printPPtreeclass.R       |    6 
 man/ENTROPYindex1D.Rd      |    5 
 man/GINIindex1D.Rd         |    5 
 man/Huber.plot.Rd          |   22 +
 man/LDAindex.Rd            |    2 
 man/LDAopt.Rd              |   15 -
 man/Lrindex.Rd             |    5 
 man/PDAindex.Rd            |    5 
 man/PDAopt.Rd              |   19 -
 man/PP.Tree.class.Rd       |   25 +-
 man/PP.classify.Rd         |   27 +-
 man/PPclassNode.Viz.Rd     |   13 -
 man/PPopt.Rd               |   15 -
 man/PPopt.Viz.Rd           |    7 
 man/plot.PPtreeclass.Rd    |   10 
 man/predict.PPtreeclass.Rd |only
 man/print.PPtreeclass.Rd   |    4 
 src/PPoptimize.cpp         |  528 +++++++++++++++++++++------------------------
 31 files changed, 503 insertions(+), 448 deletions(-)

More information about PPtreeViz at CRAN
Permanent link

Package MixGHD updated to version 1.7 with previous version 1.6 dated 2015-05-26

Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora <ctortora@math.mcmaster.ca>

Diff between MixGHD versions 1.6 dated 2015-05-26 and 1.7 dated 2015-06-25

 DESCRIPTION       |   12 +-
 MD5               |   45 +++++----
 NAMESPACE         |    4 
 R/ARI.R           |only
 R/DA.R            |   30 +++---
 R/GHD.R           |  258 ++++++++++++++++++++++++++++++++----------------------
 R/MCGHD.R         |   50 ++++------
 R/MGHD.R          |   47 +++++----
 R/MGHFA.R         |   57 +++++++----
 R/MSGHD.R         |   44 +++++----
 R/Selection.R     |   67 +++++++-------
 R/cMSGHD.R        |   50 +++++-----
 R/usedSelection.R |only
 data/banknote.rda |only
 data/datalist     |    1 
 man/ARI.Rd        |only
 man/DA.Rd         |    3 
 man/MCGHD.Rd      |   13 +-
 man/MGHD.Rd       |   17 ++-
 man/MGHFA.Rd      |   14 +-
 man/MSGHD.Rd      |    9 +
 man/Selection.Rd  |   11 +-
 man/banknote.Rd   |only
 man/bankruptcy.Rd |    2 
 man/cMSGHD.Rd     |   30 ++++--
 man/sonar.Rd      |    4 
 26 files changed, 440 insertions(+), 328 deletions(-)

More information about MixGHD at CRAN
Permanent link

Package GUTS updated to version 1.0.0 with previous version 0.9.3 dated 2015-05-15

Title: Fast Calculation of the Likelihood of a Stochastic Survival Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch> and Sören Vogel <soeren.vogel@posteo.ch>
Maintainer: Sören Vogel <soeren.vogel@posteo.ch>

Diff between GUTS versions 0.9.3 dated 2015-05-15 and 1.0.0 dated 2015-06-25

 GUTS-0.9.3/GUTS/R/RcppExports.R                 |only
 GUTS-0.9.3/GUTS/src/guts_calc_loglikelihood.cpp |only
 GUTS-1.0.0/GUTS/DESCRIPTION                     |   13 -
 GUTS-1.0.0/GUTS/MD5                             |   17 --
 GUTS-1.0.0/GUTS/R/GUTS.R                        |  198 +++++++-----------------
 GUTS-1.0.0/GUTS/data/diazinon.rda               |binary
 GUTS-1.0.0/GUTS/man/GUTS-package.Rd             |   15 -
 GUTS-1.0.0/GUTS/man/GUTS.Rd                     |  114 +++++--------
 GUTS-1.0.0/GUTS/man/diazinon.Rd                 |    6 
 GUTS-1.0.0/GUTS/src/RcppExports.cpp             |   21 +-
 GUTS-1.0.0/GUTS/src/guts_engine.cpp             |only
 11 files changed, 141 insertions(+), 243 deletions(-)

More information about GUTS at CRAN
Permanent link

New package Bagidis with initial version 1.0
Package: Bagidis
Type: Package
Title: BAses GIving DIStances
Version: 1.0
Date: 2015-06-24
Author: Catherine Timmermans
Maintainer: Catherine Timmermans <catherine.timmermans@uclouvain.be>
Description: This is the companion package of a PhD thesis entitled "Bases Giving Distances. A new paradigm for investigating functional data with applications for spectroscopy" by Timmermans (2012). See references for details and related publications. The core of the BAGIDIS methodology is a functional wavelet based semi-distance that has been introduced by Timmermans and von Sachs (2010, 2015) and Timmermans, Delsol and von Sachs (2013). This semi-distance allows for comparing curves with sharp local patterns that might not be well aligned from one curve to another. It is data-driven and highly adaptive to the curves being studied. Its main originality is its ability to consider simultaneously horizontal and vertical variations of patterns, which proofs highly useful when used together with clustering algorithms or visualization method. BAGIDIS is an acronym for BAsis GIving DIStances. The extension of BAGIDIS to image data relies on the same principles and has been described in Timmermans and Fryzlewicz (2012), Fryzlewicz and Timmermans (2015).
License: GPL
Depends: abind
Packaged: 2015-06-25 10:47:43 UTC; Catherine
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-26 00:36:18

More information about Bagidis at CRAN
Permanent link

Package covr updated to version 1.2.0 with previous version 1.0.0 dated 2015-05-20

Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally) upload the results to a coverage service like Codecov (http://codecov.io) or Coveralls (http://coveralls.io). Code coverage is a measure of the amount of code being exercised by the tests. It is an indirect measure of test quality. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/Fortran code.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>

Diff between covr versions 1.0.0 dated 2015-05-20 and 1.2.0 dated 2015-06-25

 DESCRIPTION                     |   11 +-
 MD5                             |   36 +++----
 R/codecov.R                     |   74 +++++++++-----
 R/covr.R                        |   18 ++-
 R/exclusions.R                  |   48 ++++++++-
 R/shiny.R                       |   28 ++---
 R/subprocess.R                  |    2 
 R/summary_functions.R           |   14 +-
 R/trace_calls.R                 |    3 
 README.md                       |   45 ++++++++
 build/vignette.rds              |binary
 man/codecov.Rd                  |   11 +-
 man/exclusions.Rd               |only
 man/package_coverage.Rd         |    9 +
 tests/testthat/test-closures.R  |only
 tests/testthat/test-codecov.R   |  204 +++++++++++++++++-----------------------
 tests/testthat/test-coveralls.R |    8 -
 tests/testthat/test-print.R     |   10 -
 tests/testthat/test-summary.R   |    4 
 vignettes/how_it_works.Rmd      |    2 
 20 files changed, 318 insertions(+), 209 deletions(-)

More information about covr at CRAN
Permanent link

New package translation.ko with initial version 0.0.1.3
Package: translation.ko
Title: R Manuals Literally Translated in Korean
Version: 0.0.1.3
Authors@R: person("Chel Hee", "Lee", email = "chl948@mail.usask.ca", role = c("aut", "cre"))
Description: R version 2.1.0 and later support Korean translations of program messages. The continuous efforts have been made by <http://developer.r-project.org/TranslationTeams.html> The R Documentation files are licensed under the General Public License, version 2 or 3. This means that the pilot project to translate them into Korean has permission to reproduce them and translate them. This work is done with GNU 'gettext' utilities. The portable object template is updated a weekly basis or whenever changes are necessary. Comments and corrections via email to the maintainer is of course most welcome. In order to voluntarily participate in or offer your help with this translation, please contact the maintainer. To check the change and progress of Korean translation, please visit <http://www.openstatistics.net>.
Maintainer: Chel Hee Lee <chl948@mail.usask.ca>
Depends: R (>= 3.2.1)
License: GPL (>= 2)
LazyData: true
URL: http://www.openstatistics.net
BugReports: chl948@mail.usask.ca
NeedsCompilation: no
Packaged: 2015-06-25 01:40:23 UTC; chel
Author: Chel Hee Lee [aut, cre]
Repository: CRAN
Date/Publication: 2015-06-25 12:15:03

More information about translation.ko at CRAN
Permanent link

Package Rhpc updated to version 0.15-176 with previous version 0.15-147 dated 2015-05-28

Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R. and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama<nakama@com-one.com>
Maintainer: Ei-ji Nakama <nakama@com-one.com>

Diff between Rhpc versions 0.15-147 dated 2015-05-28 and 0.15-176 dated 2015-06-25

 ChangeLog                 |   10 ++++++++++
 DESCRIPTION               |    8 ++++----
 MD5                       |   16 ++++++++--------
 README                    |    4 ++--
 configure                 |   22 +++++++++-------------
 configure.ac              |   25 +++++++++++--------------
 src/worker/Makefile.in    |    2 +-
 src/worker/Rhpc.cmd.in    |   18 +++++++++++-------
 src/worker/RhpcWin.cmd.in |   44 ++++++++++++++++++++++++++++----------------
 9 files changed, 84 insertions(+), 65 deletions(-)

More information about Rhpc at CRAN
Permanent link

Package httr updated to version 1.0.0 with previous version 0.6.1 dated 2015-01-01

Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between httr versions 0.6.1 dated 2015-01-01 and 1.0.0 dated 2015-06-25

 httr-0.6.1/httr/R/http--request.r                    |only
 httr-0.6.1/httr/R/perform.R                          |only
 httr-0.6.1/httr/man/brew_dr.Rd                       |only
 httr-0.6.1/httr/src                                  |only
 httr-0.6.1/httr/tests/testthat/test-oauth-listener.R |only
 httr-1.0.0/httr/DESCRIPTION                          |   21 -
 httr-1.0.0/httr/MD5                                  |  258 +++++++++----------
 httr-1.0.0/httr/NAMESPACE                            |   28 --
 httr-1.0.0/httr/R/authenticate.r                     |    8 
 httr-1.0.0/httr/R/body.R                             |   98 +++----
 httr-1.0.0/httr/R/cache.R                            |   17 -
 httr-1.0.0/httr/R/config.r                           |  106 +------
 httr-1.0.0/httr/R/content-parse.r                    |   48 +--
 httr-1.0.0/httr/R/content.r                          |   12 
 httr-1.0.0/httr/R/cookies.r                          |   12 
 httr-1.0.0/httr/R/doctor.R                           |    4 
 httr-1.0.0/httr/R/envvar.R                           |    2 
 httr-1.0.0/httr/R/handle.r                           |   22 -
 httr-1.0.0/httr/R/headers.r                          |   54 +++
 httr-1.0.0/httr/R/hmac.r                             |    2 
 httr-1.0.0/httr/R/http-delete.r                      |    5 
 httr-1.0.0/httr/R/http-get.r                         |    5 
 httr-1.0.0/httr/R/http-head.r                        |    7 
 httr-1.0.0/httr/R/http-patch.r                       |    5 
 httr-1.0.0/httr/R/http-post.r                        |   12 
 httr-1.0.0/httr/R/http-put.r                         |    6 
 httr-1.0.0/httr/R/http-verb.R                        |   15 -
 httr-1.0.0/httr/R/httr.r                             |    4 
 httr-1.0.0/httr/R/media-parse.r                      |    2 
 httr-1.0.0/httr/R/oauth-app.r                        |   11 
 httr-1.0.0/httr/R/oauth-endpoint.r                   |    2 
 httr-1.0.0/httr/R/oauth-init.R                       |    1 
 httr-1.0.0/httr/R/oauth-listener.r                   |   16 -
 httr-1.0.0/httr/R/oauth-signature.r                  |    4 
 httr-1.0.0/httr/R/oauth-token.r                      |   14 -
 httr-1.0.0/httr/R/progress.R                         |    7 
 httr-1.0.0/httr/R/proxy.r                            |   12 
 httr-1.0.0/httr/R/request.R                          |only
 httr-1.0.0/httr/R/safe-callback.R                    |   29 --
 httr-1.0.0/httr/R/timeout.r                          |    2 
 httr-1.0.0/httr/R/upload-file.r                      |   17 -
 httr-1.0.0/httr/R/url-query.r                        |   14 -
 httr-1.0.0/httr/R/url.r                              |    4 
 httr-1.0.0/httr/R/utils.r                            |   52 +++
 httr-1.0.0/httr/R/verbose.r                          |    9 
 httr-1.0.0/httr/R/write-function.R                   |  128 +--------
 httr-1.0.0/httr/README.md                            |    6 
 httr-1.0.0/httr/build/vignette.rds                   |binary
 httr-1.0.0/httr/demo/oauth1-twitter.r                |   10 
 httr-1.0.0/httr/demo/oauth1-vimeo.r                  |    7 
 httr-1.0.0/httr/demo/oauth1-withings.r               |   23 +
 httr-1.0.0/httr/demo/oauth1-yahoo.r                  |    7 
 httr-1.0.0/httr/demo/oauth2-github.r                 |   13 
 httr-1.0.0/httr/demo/oauth2-google.r                 |    7 
 httr-1.0.0/httr/demo/oauth2-linkedin.r               |   10 
 httr-1.0.0/httr/inst/doc/api-packages.R              |   10 
 httr-1.0.0/httr/inst/doc/api-packages.Rmd            |   12 
 httr-1.0.0/httr/inst/doc/api-packages.html           |   42 +--
 httr-1.0.0/httr/inst/doc/quickstart.R                |   10 
 httr-1.0.0/httr/inst/doc/quickstart.Rmd              |    2 
 httr-1.0.0/httr/inst/doc/quickstart.html             |  151 ++++-------
 httr-1.0.0/httr/man/BROWSE.Rd                        |    2 
 httr-1.0.0/httr/man/DELETE.Rd                        |    2 
 httr-1.0.0/httr/man/GET.Rd                           |    2 
 httr-1.0.0/httr/man/HEAD.Rd                          |    4 
 httr-1.0.0/httr/man/PATCH.Rd                         |    7 
 httr-1.0.0/httr/man/POST.Rd                          |    7 
 httr-1.0.0/httr/man/PUT.Rd                           |    7 
 httr-1.0.0/httr/man/Token-class.Rd                   |    2 
 httr-1.0.0/httr/man/VERB.Rd                          |   33 ++
 httr-1.0.0/httr/man/add_headers.Rd                   |    2 
 httr-1.0.0/httr/man/authenticate.Rd                  |    2 
 httr-1.0.0/httr/man/cache_info.Rd                    |    2 
 httr-1.0.0/httr/man/config.Rd                        |    6 
 httr-1.0.0/httr/man/content.Rd                       |   15 -
 httr-1.0.0/httr/man/content_type.Rd                  |    2 
 httr-1.0.0/httr/man/cookies.Rd                       |    2 
 httr-1.0.0/httr/man/guess_media.Rd                   |    2 
 httr-1.0.0/httr/man/handle.Rd                        |    5 
 httr-1.0.0/httr/man/handle_pool.Rd                   |    2 
 httr-1.0.0/httr/man/has_content.Rd                   |    2 
 httr-1.0.0/httr/man/headers.Rd                       |    2 
 httr-1.0.0/httr/man/hmac_sha1.Rd                     |    2 
 httr-1.0.0/httr/man/http_condition.Rd                |    2 
 httr-1.0.0/httr/man/http_error.Rd                    |    2 
 httr-1.0.0/httr/man/http_status.Rd                   |    2 
 httr-1.0.0/httr/man/httr.Rd                          |    6 
 httr-1.0.0/httr/man/httr_dr.Rd                       |only
 httr-1.0.0/httr/man/httr_options.Rd                  |    2 
 httr-1.0.0/httr/man/init_oauth1.0.Rd                 |    2 
 httr-1.0.0/httr/man/init_oauth2.0.Rd                 |    2 
 httr-1.0.0/httr/man/insensitive.Rd                   |    2 
 httr-1.0.0/httr/man/jwt_signature.Rd                 |    2 
 httr-1.0.0/httr/man/modify_url.Rd                    |    2 
 httr-1.0.0/httr/man/oauth1.0_token.Rd                |    2 
 httr-1.0.0/httr/man/oauth2.0_token.Rd                |    2 
 httr-1.0.0/httr/man/oauth_app.Rd                     |   13 
 httr-1.0.0/httr/man/oauth_callback.Rd                |    2 
 httr-1.0.0/httr/man/oauth_endpoint.Rd                |    4 
 httr-1.0.0/httr/man/oauth_endpoints.Rd               |    2 
 httr-1.0.0/httr/man/oauth_exchanger.Rd               |    2 
 httr-1.0.0/httr/man/oauth_listener.Rd                |    6 
 httr-1.0.0/httr/man/oauth_service_token.Rd           |    2 
 httr-1.0.0/httr/man/oauth_signature.Rd               |    2 
 httr-1.0.0/httr/man/parse_http_date.Rd               |    2 
 httr-1.0.0/httr/man/parse_media.Rd                   |    2 
 httr-1.0.0/httr/man/parse_url.Rd                     |    2 
 httr-1.0.0/httr/man/progress.Rd                      |    2 
 httr-1.0.0/httr/man/response.Rd                      |    2 
 httr-1.0.0/httr/man/revoke_all.Rd                    |    2 
 httr-1.0.0/httr/man/safe_callback.Rd                 |   15 -
 httr-1.0.0/httr/man/set_config.Rd                    |    2 
 httr-1.0.0/httr/man/set_cookies.Rd                   |    2 
 httr-1.0.0/httr/man/sign_oauth.Rd                    |    2 
 httr-1.0.0/httr/man/status_code.Rd                   |    2 
 httr-1.0.0/httr/man/timeout.Rd                       |    2 
 httr-1.0.0/httr/man/upload_file.Rd                   |    9 
 httr-1.0.0/httr/man/url_ok.Rd                        |    2 
 httr-1.0.0/httr/man/url_success.Rd                   |    2 
 httr-1.0.0/httr/man/use_proxy.Rd                     |    8 
 httr-1.0.0/httr/man/user_agent.Rd                    |    2 
 httr-1.0.0/httr/man/verbose.Rd                       |    2 
 httr-1.0.0/httr/man/with_config.Rd                   |    2 
 httr-1.0.0/httr/man/write_disk.Rd                    |    2 
 httr-1.0.0/httr/man/write_function.Rd                |   23 -
 httr-1.0.0/httr/man/write_stream.Rd                  |   10 
 httr-1.0.0/httr/tests/testthat/test-body.r           |   18 +
 httr-1.0.0/httr/tests/testthat/test-config.r         |   72 -----
 httr-1.0.0/httr/tests/testthat/test-header.r         |   27 -
 httr-1.0.0/httr/tests/testthat/test-oauth.R          |only
 httr-1.0.0/httr/tests/testthat/test-request.r        |   36 --
 httr-1.0.0/httr/tests/testthat/test-response.r       |   38 ++
 httr-1.0.0/httr/vignettes/api-packages.Rmd           |   12 
 httr-1.0.0/httr/vignettes/quickstart.Rmd             |    2 
 134 files changed, 876 insertions(+), 986 deletions(-)

More information about httr at CRAN
Permanent link

Package earth updated to version 4.4.2 with previous version 4.4.1 dated 2015-06-17

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>

Diff between earth versions 4.4.1 dated 2015-06-17 and 4.4.2 dated 2015-06-25

 DESCRIPTION                        |    6 +++---
 MD5                                |   18 +++++++++---------
 NEWS                               |    6 ++++++
 R/as.char.R                        |   13 +++++++++----
 R/lib.R                            |    3 +++
 R/model.matrix.earth.R             |   10 ++++++----
 R/stop.if.dots.R                   |    1 +
 inst/doc/earth-notes.pdf           |binary
 inst/doc/earth-varmod.pdf          |binary
 inst/slowtests/test.full.Rout.save |    4 ++--
 10 files changed, 39 insertions(+), 22 deletions(-)

More information about earth at CRAN
Permanent link

Package snowFT updated to version 1.4-0 with previous version 1.3-0 dated 2012-12-13

Title: Fault Tolerant Simple Network of Workstations
Description: Extension of the snow package supporting fault tolerant and reproducible applications, as well as supporting easy-to-use parallel programming - only one function is needed.
Author: Hana Sevcikova, A. J. Rossini
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between snowFT versions 1.3-0 dated 2012-12-13 and 1.4-0 dated 2015-06-25

 ChangeLog              |    4 ++
 DESCRIPTION            |   15 +++-----
 MD5                    |   14 +++----
 NAMESPACE              |    2 -
 R/snowFT.R             |   89 +++++++++++--------------------------------------
 man/snowFT-internal.Rd |   10 ++---
 man/snowFT-package.Rd  |    4 +-
 man/snowFT-rand.Rd     |   27 ++++----------
 8 files changed, 55 insertions(+), 110 deletions(-)

More information about snowFT at CRAN
Permanent link

Package learnstats updated to version 0.1.1 with previous version 0.1.0 dated 2015-05-02

Title: An Interactive Environment for Learning Statistics
Description: Allows students to use R as an interactive educational environment for statistical concepts, ranging from p-values to confidence intervals to stability in time series.
Author: Daniel Walter [aut, cre]
Maintainer: Daniel Walter <dswalter@gmail.com>

Diff between learnstats versions 0.1.0 dated 2015-05-02 and 0.1.1 dated 2015-06-25

 learnstats-0.1.0/learnstats/inst/uniform_two             |only
 learnstats-0.1.0/learnstats/man/s_uniform.Rd             |only
 learnstats-0.1.1/learnstats/DESCRIPTION                  |   17 
 learnstats-0.1.1/learnstats/MD5                          |   82 -
 learnstats-0.1.1/learnstats/NAMESPACE                    |   33 
 learnstats-0.1.1/learnstats/R/Rcmdr.R                    |   15 
 learnstats-0.1.1/learnstats/R/call_shinies.R             |  139 +-
 learnstats-0.1.1/learnstats/R/learnstats.R               |   24 
 learnstats-0.1.1/learnstats/R/prob.R                     |  530 +++++------
 learnstats-0.1.1/learnstats/R/pval.R                     |  722 +++++++--------
 learnstats-0.1.1/learnstats/R/qqsim.R                    |  562 +++++------
 learnstats-0.1.1/learnstats/R/timeseriessim.R            |  490 +++++-----
 learnstats-0.1.1/learnstats/inst/betabinomial/server.R   |  158 +--
 learnstats-0.1.1/learnstats/inst/betabinomial/ui.R       |  107 +-
 learnstats-0.1.1/learnstats/inst/fdist/server.R          |   44 
 learnstats-0.1.1/learnstats/inst/fdist/ui.R              |   44 
 learnstats-0.1.1/learnstats/inst/introbinomial/server.R  |  114 +-
 learnstats-0.1.1/learnstats/inst/introbinomial/ui.R      |   56 -
 learnstats-0.1.1/learnstats/inst/normapprox2bin/server.R |  102 +-
 learnstats-0.1.1/learnstats/inst/normapprox2bin/ui.R     |   60 -
 learnstats-0.1.1/learnstats/inst/propconfint/server.R    |  112 +-
 learnstats-0.1.1/learnstats/inst/propconfint/ui.R        |   92 -
 learnstats-0.1.1/learnstats/inst/tdist/server.R          |   88 -
 learnstats-0.1.1/learnstats/inst/tdist/ui.R              |   74 -
 learnstats-0.1.1/learnstats/inst/timeseries/server.R     |  190 +--
 learnstats-0.1.1/learnstats/inst/timeseries/ui.R         |   72 -
 learnstats-0.1.1/learnstats/inst/twonorm/server.R        |  114 +-
 learnstats-0.1.1/learnstats/inst/twonorm/ui.R            |   62 -
 learnstats-0.1.1/learnstats/inst/uniform/server.R        |   64 -
 learnstats-0.1.1/learnstats/inst/uniform/ui.R            |   42 
 learnstats-0.1.1/learnstats/man/Rcmdr.Rd                 |   34 
 learnstats-0.1.1/learnstats/man/prob.Rd                  |   30 
 learnstats-0.1.1/learnstats/man/pval.Rd                  |   30 
 learnstats-0.1.1/learnstats/man/qqsim.Rd                 |   30 
 learnstats-0.1.1/learnstats/man/s_fdist.Rd               |   30 
 learnstats-0.1.1/learnstats/man/s_introbinom.Rd          |   30 
 learnstats-0.1.1/learnstats/man/s_normbinom.Rd           |   30 
 learnstats-0.1.1/learnstats/man/s_propci.Rd              |   30 
 learnstats-0.1.1/learnstats/man/s_tdist.Rd               |   30 
 learnstats-0.1.1/learnstats/man/s_timeseries.Rd          |   30 
 learnstats-0.1.1/learnstats/man/s_twonorm.Rd             |   30 
 learnstats-0.1.1/learnstats/man/stats250.Rd              |   22 
 learnstats-0.1.1/learnstats/man/timeseressim.Rd          |   30 
 43 files changed, 2288 insertions(+), 2307 deletions(-)

More information about learnstats at CRAN
Permanent link

Package flam updated to version 2.0 with previous version 1.0 dated 2014-10-13

Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ajpete@uw.edu>

Diff between flam versions 1.0 dated 2014-10-13 and 2.0 dated 2015-06-25

 flam-1.0/flam/R/R_package_fcns_all_C.R |only
 flam-1.0/flam/man/flam-package.Rd      |only
 flam-1.0/flam/man/flam.Rd              |only
 flam-1.0/flam/man/flamCV.Rd            |only
 flam-1.0/flam/man/flamDOF.Rd           |only
 flam-1.0/flam/man/plot.flam.Rd         |only
 flam-1.0/flam/man/plot.flamCV.Rd       |only
 flam-1.0/flam/man/sim.data.Rd          |only
 flam-1.0/flam/man/summary.flamCV.Rd    |only
 flam-1.0/flam/src/Fit.cpp              |only
 flam-2.0/flam/DESCRIPTION              |   11 ++++++-----
 flam-2.0/flam/MD5                      |   26 ++++++++++++++------------
 flam-2.0/flam/NAMESPACE                |    1 +
 flam-2.0/flam/R/RcppExports.R          |only
 flam-2.0/flam/R/flam_fcns.R            |only
 flam-2.0/flam/man/flam-package.rd      |only
 flam-2.0/flam/man/flam.rd              |only
 flam-2.0/flam/man/flamcv.rd            |only
 flam-2.0/flam/man/flamdof.rd           |only
 flam-2.0/flam/man/plot.flam.rd         |only
 flam-2.0/flam/man/plot.flamcv.rd       |only
 flam-2.0/flam/man/sim.data.rd          |only
 flam-2.0/flam/man/summary.flamcv.rd    |only
 flam-2.0/flam/src/RcppExports.cpp      |only
 flam-2.0/flam/src/fit.cpp              |only
 25 files changed, 21 insertions(+), 17 deletions(-)

More information about flam at CRAN
Permanent link

New package XMRF with initial version 1.0
Package: XMRF
Type: Package
Title: Markov Random Fields for High-Throughput Genetics Data
Version: 1.0
Date: 2015-06-12
Author: Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Zhandong Liu
Maintainer: Ying-Wooi Wan <yingwoow@bcm.edu>
Depends: R (>= 3.0.2)
Imports: igraph, glmnet, MASS, snowfall, parallel, Matrix
Description: Fit Markov Networks to a wide range of high-throughput genomics data.
License: GPL-2
URL: http://www.liuzlab.org/XMRF/
LazyLoad: true
Packaged: 2015-06-24 19:28:43 UTC; wooi
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-06-25 07:07:40

More information about XMRF at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.