Tue, 04 Aug 2015

Package yakmoR updated to version 0.1.1 with previous version 0.1.0 dated 2015-08-03

Title: A Simple Wrapper for the k-Means Library Yakmo
Description: This is a simple wrapper for the yakmo K-Means library (developed by Naoki Yoshinaga, see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/). It performs fast and robust (orthogonal) K-Means.
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>

Diff between yakmoR versions 0.1.0 dated 2015-08-03 and 0.1.1 dated 2015-08-04

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 src/yakmo.h |   10 +++++++++-
 3 files changed, 15 insertions(+), 7 deletions(-)

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Package RcppArmadillo updated to version 0.5.300.4 with previous version 0.5.200.1.0 dated 2015-06-05

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.5.200.1.0 dated 2015-06-05 and 0.5.300.4 dated 2015-08-04

 ChangeLog                                                |   33 +
 DESCRIPTION                                              |   10 
 MD5                                                      |  187 +++---
 NAMESPACE                                                |    2 
 R/RcppArmadillo.package.skeleton.R                       |    2 
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 inst/examples/kalman/benchmark.R                         |    2 
 inst/include/armadillo                                   |    1 
 inst/include/armadillo_bits/Cube_bones.hpp               |   15 
 inst/include/armadillo_bits/Cube_meat.hpp                |  159 +++--
 inst/include/armadillo_bits/Mat_bones.hpp                |    3 
 inst/include/armadillo_bits/Mat_meat.hpp                 |  102 ++-
 inst/include/armadillo_bits/SpMat_bones.hpp              |   45 -
 inst/include/armadillo_bits/SpMat_meat.hpp               |  423 ++++++++++-----
 inst/include/armadillo_bits/SpSubview_bones.hpp          |   38 -
 inst/include/armadillo_bits/SpSubview_iterators_meat.hpp |    6 
 inst/include/armadillo_bits/arma_boost.hpp               |   12 
 inst/include/armadillo_bits/arma_cmath.hpp               |    4 
 inst/include/armadillo_bits/arma_ostream_meat.hpp        |   13 
 inst/include/armadillo_bits/arma_version.hpp             |    6 
 inst/include/armadillo_bits/arpack_wrapper.hpp           |   24 
 inst/include/armadillo_bits/arrayops_bones.hpp           |   14 
 inst/include/armadillo_bits/arrayops_meat.hpp            |   54 +
 inst/include/armadillo_bits/atlas_wrapper.hpp            |   56 -
 inst/include/armadillo_bits/auxlib_bones.hpp             |   12 
 inst/include/armadillo_bits/auxlib_meat.hpp              |  241 ++++++++
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 inst/include/armadillo_bits/constants.hpp                |   54 -
 inst/include/armadillo_bits/constants_compat.hpp         |   46 -
 inst/include/armadillo_bits/debug.hpp                    |   27 
 inst/include/armadillo_bits/diagview_meat.hpp            |   10 
 inst/include/armadillo_bits/diskio_meat.hpp              |  182 +++---
 inst/include/armadillo_bits/fn_as_scalar.hpp             |   58 +-
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 inst/include/armadillo_bits/fn_cov.hpp                   |    4 
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 inst/include/armadillo_bits/fn_elem.hpp                  |   84 ++
 inst/include/armadillo_bits/fn_histc.hpp                 |   22 
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 inst/include/armadillo_bits/fn_sort_index.hpp            |    4 
 inst/include/armadillo_bits/fn_vectorise.hpp             |    2 
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 inst/include/armadillo_bits/glue_mixed_meat.hpp          |   52 -
 inst/include/armadillo_bits/lapack_bones.hpp             |   18 
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 inst/include/armadillo_bits/op_all_meat.hpp              |    4 
 inst/include/armadillo_bits/op_any_meat.hpp              |    4 
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 inst/include/armadillo_bits/op_max_bones.hpp             |   12 
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 inst/include/armadillo_bits/op_mean_bones.hpp            |   10 
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 inst/include/armadillo_bits/op_median_meat.hpp           |  214 ++++---
 inst/include/armadillo_bits/op_min_bones.hpp             |   11 
 inst/include/armadillo_bits/op_min_meat.hpp              |  169 ++++-
 inst/include/armadillo_bits/op_normalise_meat.hpp        |    8 
 inst/include/armadillo_bits/op_prod_meat.hpp             |    2 
 inst/include/armadillo_bits/op_shuffle_meat.hpp          |    2 
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 inst/include/armadillo_bits/op_stddev_meat.hpp           |   50 -
 inst/include/armadillo_bits/op_sum_bones.hpp             |   15 
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 inst/include/armadillo_bits/op_var_meat.hpp              |   56 +
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 inst/include/armadillo_bits/spglue_minus_meat.hpp        |    2 
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 inst/include/armadillo_bits/spglue_times_meat.hpp        |   11 
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 inst/include/armadillo_bits/spop_max_bones.hpp           |    6 
 inst/include/armadillo_bits/spop_max_meat.hpp            |  380 ++++---------
 inst/include/armadillo_bits/spop_mean_bones.hpp          |    7 
 inst/include/armadillo_bits/spop_mean_meat.hpp           |  199 ++++---
 inst/include/armadillo_bits/spop_min_bones.hpp           |    6 
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 inst/include/armadillo_bits/spop_misc_bones.hpp          |   64 ++
 inst/include/armadillo_bits/spop_misc_meat.hpp           |  247 +++++++-
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 inst/include/armadillo_bits/subview_bones.hpp            |    3 
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 inst/include/armadillo_bits/subview_cube_meat.hpp        |   88 ++-
 inst/include/armadillo_bits/subview_meat.hpp             |   52 +
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 vignettes/RcppArmadillo-intro.Rnw                        |    2 
 95 files changed, 3503 insertions(+), 1966 deletions(-)

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Mon, 03 Aug 2015

Package RObsDat updated to version 15.08 with previous version 15.02 dated 2015-02-27

Title: Data Management for Hydrology and Beyond Using the Observations Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>

Diff between RObsDat versions 15.02 dated 2015-02-27 and 15.08 dated 2015-08-03

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More information about RObsDat at CRAN
Permanent link

Package randNames updated to version 0.2.1 with previous version 0.2 dated 2015-04-28

Title: Package Provides Access to Fake User Data
Description: Generates random names with additional information including fake SSNs, gender, location, zip, age, address, and nationality.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between randNames versions 0.2 dated 2015-04-28 and 0.2.1 dated 2015-08-03

 DESCRIPTION       |    6 +++---
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More information about randNames at CRAN
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Package markovchain updated to version 0.4 with previous version 0.3.1 dated 2015-07-07

Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

Diff between markovchain versions 0.3.1 dated 2015-07-07 and 0.4 dated 2015-08-03

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More information about markovchain at CRAN
Permanent link

Package httpuv updated to version 1.3.3 with previous version 1.3.2 dated 2014-10-23

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>

Diff between httpuv versions 1.3.2 dated 2014-10-23 and 1.3.3 dated 2015-08-03

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More information about httpuv at CRAN
Permanent link

Package evolqg updated to version 0.1-6 with previous version 0.1-5 dated 2015-05-22

Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Maintainer: Diogo Melo <diogro@usp.br>

Diff between evolqg versions 0.1-5 dated 2015-05-22 and 0.1-6 dated 2015-08-03

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More information about evolqg at CRAN
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Package dr updated to version 3.0.10 with previous version 3.0.9 dated 2014-11-30

Title: Methods for Dimension Reduction for Regression
Description: Functions, methods, and datasets for fitting dimension reduction regression, using slicing (methods SAVE and SIR), Principal Hessian Directions (phd, using residuals and the response), and an iterative IRE. Partial methods, that condition on categorical predictors are also available. A variety of tests, and stepwise deletion of predictors, is also included. Also included is code for computing permutation tests of dimension. Adding additional methods of estimating dimension is straightforward. For documentation, see the vignette in the package. With version 3.0.4, the arguments for dr.step have been modified.
Author: Sanford Weisberg <sandy@umn.edu>,
Maintainer: Sanford Weisberg <sandy@umn.edu>

Diff between dr versions 3.0.9 dated 2014-11-30 and 3.0.10 dated 2015-08-03

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More information about dr at CRAN
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Package taber updated to version 0.1.0 with previous version 0.0.1 dated 2015-07-04

Title: Split and Recombine Your Data
Description: Sometimes you need to split your data and work on the two chunks independently before bringing them back together. 'Taber' allows you to do that with its two functions.
Author: Seth Wenchel [aut, cre, cph]
Maintainer: Seth Wenchel <seth@wenchel.com>

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Package ReporteRs updated to version 0.8.2 with previous version 0.7.8 dated 2015-03-06

Title: Microsoft Word, Microsoft Powerpoint and HTML Documents Generation
Description: Create Microsoft Word document (>=2007), Microsoft Powerpoint document (>=2007) and HTML documents from R. There are several features to let you format and present R outputs ; e.g. Editable Vector Graphics, functions for complex tables reporting, reuse of corporate template document (*.docx and *.pptx). You can use the package as a tool for fast reporting and as a tool for reporting automation. The package does not require any installation of Microsoft product to be able to write Microsoft files (docx and pptx).
Author: David Gohel [aut, cre], Bootstrap [ctb, cph] (Bootstrap development team), jQuery [ctb, cph] (The jQuery Foundation), Dmitry Baranovskiy [ctb, cph] (raphael javascript libraries)
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>

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Package pedgene updated to version 2.7 with previous version 2.1 dated 2014-06-24

Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut], Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>

Diff between pedgene versions 2.1 dated 2014-06-24 and 2.7 dated 2015-08-03

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 10 files changed, 111 insertions(+), 33 deletions(-)

More information about pedgene at CRAN
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Package kinship2 updated to version 1.6.4 with previous version 1.6.0 dated 2014-07-22

Title: Pedigree Functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
Author: Terry M Therneau [aut], Schaid Daniel [ctb], Jason Sinnwell [aut, cre], Elizabeth Atkinson [ctb]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>

Diff between kinship2 versions 1.6.0 dated 2014-07-22 and 1.6.4 dated 2015-08-03

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Package D3M updated to version 0.41 with previous version 0.40 dated 2015-08-02

Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>

Diff between D3M versions 0.40 dated 2015-08-02 and 0.41 dated 2015-08-03

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More information about D3M at CRAN
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Package aSPU updated to version 1.37 with previous version 1.36 dated 2015-07-28

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.36 dated 2015-07-28 and 1.37 dated 2015-08-03

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More information about aSPU at CRAN
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Package rts updated to version 1.0-10 with previous version 1.0-9 dated 2015-08-02

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-9 dated 2015-08-02 and 1.0-10 dated 2015-08-03

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

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Package maps updated to version 2.3-11 with previous version 2.3-10 dated 2015-07-09

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>. Enhancements by Thomas P Minka <tpminka@media.mit.edu>
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between maps versions 2.3-10 dated 2015-07-09 and 2.3-11 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about maps at CRAN
Permanent link

Package mapproj updated to version 1.2-4 with previous version 1.2-3 dated 2015-07-09

Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between mapproj versions 1.2-3 dated 2015-07-09 and 1.2-4 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about mapproj at CRAN
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Package mapdata updated to version 2.2-5 with previous version 2.2-4 dated 2015-07-09

Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

Diff between mapdata versions 2.2-4 dated 2015-07-09 and 2.2-5 dated 2015-08-03

 DESCRIPTION |   10 +++++-----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

More information about mapdata at CRAN
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Package cwhmisc updated to version 6.0 with previous version 5.0 dated 2014-10-15

Title: Miscellaneous Functions for Math, Plotting, Printing, Statistics, Strings, and Tools
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
Author: Christian W. Hoffmann <christian@echoffmann.ch> <http://www.echoffmann.ch>
Maintainer: Christian W. Hoffmann <christian@echoffmann.ch>

Diff between cwhmisc versions 5.0 dated 2014-10-15 and 6.0 dated 2015-08-03

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Package ALS updated to version 0.0.6 with previous version 0.0.5 dated 2012-07-02

Title: Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)
Description: Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.
Author: Katharine M. Mullen
Maintainer: Katharine Mullen <mullenkate@gmail.com>

Diff between ALS versions 0.0.5 dated 2012-07-02 and 0.0.6 dated 2015-08-03

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Package ggtern updated to version 1.0.6.0 with previous version 1.0.5.0 dated 2015-04-15

Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>

Diff between ggtern versions 1.0.5.0 dated 2015-04-15 and 1.0.6.0 dated 2015-08-03

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Package causaleffect updated to version 1.2.0 with previous version 1.1.3 dated 2015-06-30

Title: Deriving Expressions of Joint Interventional Distributions and Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for z-identifiability, transportability, z-transportability and meta-transportability of causal effects by Elias Bareinboim and Judea Pearl. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>

Diff between causaleffect versions 1.1.3 dated 2015-06-30 and 1.2.0 dated 2015-08-03

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Sun, 02 Aug 2015

Package forestFloor updated to version 1.8.3 with previous version 1.5 dated 2015-06-30

Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>

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Package D3M updated to version 0.40 with previous version 0.31 dated 2015-07-29

Title: Two Sample Test with Wasserstein Metric
Description: Two sample test based on Wasserstein metric. This is motivated from detection of differential DNA-methylation sites based on underlying distributions.
Author: Yusuke Matsui & Teppei Shimamura
Maintainer: Yusuke Matsui <ymatsui@med.nagoya-u.ac.jp>

Diff between D3M versions 0.31 dated 2015-07-29 and 0.40 dated 2015-08-02

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Package brms updated to version 0.4.1 with previous version 0.4.0 dated 2015-07-23

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 0.4.0 dated 2015-07-23 and 0.4.1 dated 2015-08-02

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Package GeneNet updated to version 1.2.13 with previous version 1.2.12 dated 2015-01-20

Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>

Diff between GeneNet versions 1.2.12 dated 2015-01-20 and 1.2.13 dated 2015-08-02

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Package Ecfun updated to version 0.1-6 with previous version 0.1-4 dated 2015-01-27

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>

Diff between Ecfun versions 0.1-4 dated 2015-01-27 and 0.1-6 dated 2015-08-02

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Package fast updated to version 0.64 with previous version 0.63 dated 2013-07-08

Title: Implementation of the Fourier Amplitude Sensitivity Test (FAST)
Description: The Fourier Amplitude Sensitivity Test (FAST) is a method to determine global sensitivities of a model on parameter changes with relatively few model runs. This package implements this sensitivity analysis method.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>

Diff between fast versions 0.63 dated 2013-07-08 and 0.64 dated 2015-08-02

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Package xgboost updated to version 0.4-2 with previous version 0.4-1 dated 2015-08-01

Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.
Author: Tianqi Chen <tianqi.tchen@gmail.com>, Tong He <hetong007@gmail.com>, Michael Benesty <michael@benesty.fr>
Maintainer: Tong He <hetong007@gmail.com>

Diff between xgboost versions 0.4-1 dated 2015-08-01 and 0.4-2 dated 2015-08-02

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Package squash updated to version 1.0.7 with previous version 1.0.6 dated 2014-08-04

Title: Color-Based Plots for Multivariate Visualization
Description: Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, display a matrix as an array of colors, and draw color keys. Higher-level plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.
Author: Aron C. Eklund
Maintainer: Aron C. Eklund <eklund@cbs.dtu.dk>

Diff between squash versions 1.0.6 dated 2014-08-04 and 1.0.7 dated 2015-08-02

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Package rts updated to version 1.0-9 with previous version 1.0-3 dated 2012-11-26

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between rts versions 1.0-3 dated 2012-11-26 and 1.0-9 dated 2015-08-02

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Package mixAK updated to version 4.2 with previous version 4.1-1 dated 2015-07-28

Title: Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between mixAK versions 4.1-1 dated 2015-07-28 and 4.2 dated 2015-08-02

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Package forecTheta updated to version 1.1 with previous version 1.0 dated 2015-04-15

Title: Forecasting Time Series by Theta Method
Description: Routines for forecasting univariate time series using Theta Method and Optimised Theta Method (Fioruci et al, 2015). Contains several cross-validation routines.
Author: Jose Augusto Fioruci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fioruci <jafioruci@gmail.com>

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Package descr updated to version 1.1.2 with previous version 1.1.1 dated 2015-05-06

Title: Descriptive Statistics
Description: Weighted frequency and contingency tables of categorical variables and of the comparison of the mean value of a numerical variable by the levels of a factor, and methods to produce xtable objects of the tables and to plot them. There are also functions to facilitate the character encoding conversion of objects, to quickly convert fixed width files into csv ones, and to export a data.frame to a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan Kraft
Maintainer: Jakson Aquino <jalvesaq@gmail.com>

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Sat, 01 Aug 2015

Package partools updated to version 1.1.3 with previous version 1.1.1 dated 2015-07-21

Title: Tools for the 'Parallel' Package
Description: Miscellaneous utilities for the 'parallel' package, cluster-oriented section; "Snowdoop" alternative to MapReduce; file splitting and distributed operations such as sort and aggregate. "Software Alchemy" method for parallelizing most statistical methods, presented in N. Matloff, Parallel Computation for Data Science, Chapman and Hall, 2015. Includes a debugging aid.
Author: Norm Matloff <normmatloff@gmail.com> [aut], Alex Rumbaugh <aprumbaugh@ucdavis.edu> [ctb]
Maintainer: Norm Matloff <normmatloff@gmail.com>

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Package nplr updated to version 0.1-4 with previous version 0.1-3 dated 2015-07-11

Title: N-Parameter Logistic Regression
Description: Performing drug response analyses and IC50 estimations using n-Parameter logistic regression. nplr can also be applied to proliferation analyses.
Author: Frederic Commo [aut, cre], Brian M. Bot [aut]
Maintainer: Frederic Commo <fredcommo@gmail.com>

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Package h5 updated to version 0.9.2 with previous version 0.9.1 dated 2015-05-10

Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The 'HDF5' format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>

Diff between h5 versions 0.9.1 dated 2015-05-10 and 0.9.2 dated 2015-08-01

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Package circlize updated to version 0.3.0 with previous version 0.2.5 dated 2015-07-08

Title: Circular Visualization in R
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between circlize versions 0.2.5 dated 2015-07-08 and 0.3.0 dated 2015-08-01

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Package rcbalance updated to version 1.7 with previous version 1.6 dated 2015-05-23

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>

Diff between rcbalance versions 1.6 dated 2015-05-23 and 1.7 dated 2015-08-01

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Package usdm updated to version 1.1-15 with previous version 1.1-12 dated 2013-07-23

Title: Uncertainty Analysis for Species Distribution Models
Description: This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between usdm versions 1.1-12 dated 2013-07-23 and 1.1-15 dated 2015-08-01

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Package phonenumber updated to version 0.2.0 with previous version 0.1.0 dated 2015-07-10

Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as on a telephone keypad. When converting letters to numbers, a character vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F" becoming 3, etc. When converting numbers to letters, a character vector is returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and "C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>

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Package distcomp updated to version 0.25.3 with previous version 0.25.2 dated 2015-07-14

Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre], Marina Bendersky [aut], Sam Gross [aut], Terry M. Therneau [ctb], Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>

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Package ConsRank updated to version 0.0.1 with previous version 0.0 dated 2015-07-22

Title: Compute the Median Ranking(s) According to the Kemeny's Axiomatic Approach
Description: Compute the median ranking according the Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete.
Author: Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio <sonia.amodio@unina.it>
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>

Diff between ConsRank versions 0.0 dated 2015-07-22 and 0.0.1 dated 2015-08-01

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Fri, 31 Jul 2015

Package ROracle updated to version 1.2-1 with previous version 1.1-12 dated 2014-11-20

Title: OCI Based Oracle Database Interface for R
Description: Oracle database interface (DBI) driver for R. This is a DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Rajendra S. Pingte <rajendra.pingte@oracle.com>

Diff between ROracle versions 1.1-12 dated 2014-11-20 and 1.2-1 dated 2015-07-31

 DESCRIPTION                                     |   12 
 INSTALL                                         |  156 +++++----
 MD5                                             |  176 +++++------
 NAMESPACE                                       |    2 
 NEWS                                            |   26 +
 R/dbi.R                                         |   16 -
 R/oci.R                                         |  245 +++++++++++++--
 configure                                       |   18 -
 configure.ac                                    |    2 
 inst/Copyrights                                 |    2 
 inst/doc/man/de/OraConnection-class.Rd          |    4 
 inst/doc/man/de/Oracle.Rd                       |   50 ++-
 inst/doc/man/de/dbConnect-methods.Rd            |  102 +++---
 inst/doc/man/de/dbDriver-methods.Rd             |   50 +--
 inst/doc/man/de/dbGetInfo-methods.Rd            |  237 ++++++++++++++
 inst/doc/man/de/dbReadTable-methods.Rd          |  374 +++++++++++++++++++----
 inst/doc/man/de/dbSendQuery-methods.Rd          |   65 ++--
 inst/doc/man/en/Oracle.Rd                       |   47 ++
 inst/doc/man/en/dbDriver-methods.Rd             |   46 +-
 inst/doc/man/en/dbGetInfo-methods.Rd            |   26 +
 inst/doc/man/en/dbReadTable-methods.Rd          |  166 +++++++++-
 inst/doc/man/en/dbSendQuery-methods.Rd          |   64 ++--
 inst/doc/man/es/OraConnection-class.Rd          |    4 
 inst/doc/man/es/Oracle.Rd                       |   53 ++-
 inst/doc/man/es/dbConnect-methods.Rd            |   93 +++--
 inst/doc/man/es/dbDriver-methods.Rd             |   44 +-
 inst/doc/man/es/dbGetInfo-methods.Rd            |  237 ++++++++++++++
 inst/doc/man/es/dbReadTable-methods.Rd          |  342 ++++++++++++++++++---
 inst/doc/man/es/dbSendQuery-methods.Rd          |   68 ++--
 inst/doc/man/fr/OraConnection-class.Rd          |    4 
 inst/doc/man/fr/Oracle.Rd                       |   45 ++
 inst/doc/man/fr/dbConnect-methods.Rd            |  100 +++---
 inst/doc/man/fr/dbDriver-methods.Rd             |   46 +-
 inst/doc/man/fr/dbGetInfo-methods.Rd            |  239 ++++++++++++++-
 inst/doc/man/fr/dbReadTable-methods.Rd          |  344 ++++++++++++++++++---
 inst/doc/man/fr/dbSendQuery-methods.Rd          |   75 ++--
 inst/doc/man/it/OraConnection-class.Rd          |    4 
 inst/doc/man/it/Oracle.Rd                       |   43 ++
 inst/doc/man/it/dbConnect-methods.Rd            |   94 +++--
 inst/doc/man/it/dbDriver-methods.Rd             |   30 +
 inst/doc/man/it/dbGetInfo-methods.Rd            |  237 ++++++++++++++
 inst/doc/man/it/dbReadTable-methods.Rd          |  358 +++++++++++++++++++---
 inst/doc/man/it/dbSendQuery-methods.Rd          |   65 ++--
 inst/doc/man/ja/OraConnection-class.Rd          |    4 
 inst/doc/man/ja/Oracle.Rd                       |   61 ++-
 inst/doc/man/ja/dbConnect-methods.Rd            |  131 ++++----
 inst/doc/man/ja/dbDriver-methods.Rd             |   47 +-
 inst/doc/man/ja/dbGetInfo-methods.Rd            |  231 ++++++++++++++
 inst/doc/man/ja/dbReadTable-methods.Rd          |  359 +++++++++++++++++++---
 inst/doc/man/ja/dbSendQuery-methods.Rd          |   61 ++-
 inst/doc/man/ko/OraConnection-class.Rd          |    4 
 inst/doc/man/ko/Oracle.Rd                       |   52 ++-
 inst/doc/man/ko/dbConnect-methods.Rd            |  114 ++++---
 inst/doc/man/ko/dbDriver-methods.Rd             |   38 +-
 inst/doc/man/ko/dbGetInfo-methods.Rd            |  235 ++++++++++++++
 inst/doc/man/ko/dbReadTable-methods.Rd          |  380 +++++++++++++++++++-----
 inst/doc/man/ko/dbSendQuery-methods.Rd          |   55 ++-
 inst/doc/man/pt_BR/OraConnection-class.Rd       |    4 
 inst/doc/man/pt_BR/Oracle.Rd                    |   60 ++-
 inst/doc/man/pt_BR/dbConnect-methods.Rd         |  128 ++++----
 inst/doc/man/pt_BR/dbDriver-methods.Rd          |   50 +--
 inst/doc/man/pt_BR/dbGetInfo-methods.Rd         |  241 ++++++++++++++-
 inst/doc/man/pt_BR/dbReadTable-methods.Rd       |  376 +++++++++++++++++++----
 inst/doc/man/pt_BR/dbSendQuery-methods.Rd       |   85 +++--
 inst/doc/man/zh_CN/OraConnection-class.Rd       |    4 
 inst/doc/man/zh_CN/Oracle.Rd                    |   51 ++-
 inst/doc/man/zh_CN/dbConnect-methods.Rd         |  104 +++---
 inst/doc/man/zh_CN/dbDriver-methods.Rd          |   44 +-
 inst/doc/man/zh_CN/dbGetInfo-methods.Rd         |  231 ++++++++++++++
 inst/doc/man/zh_CN/dbReadTable-methods.Rd       |  340 ++++++++++++++++++---
 inst/doc/man/zh_CN/dbSendQuery-methods.Rd       |   57 ++-
 inst/doc/man/zh_TW/OraConnection-class.Rd       |    4 
 inst/doc/man/zh_TW/Oracle.Rd                    |   59 ++-
 inst/doc/man/zh_TW/dbConnect-methods.Rd         |  140 ++++----
 inst/doc/man/zh_TW/dbDriver-methods.Rd          |   46 +-
 inst/doc/man/zh_TW/dbGetInfo-methods.Rd         |  239 ++++++++++++++-
 inst/doc/man/zh_TW/dbListConnections-methods.Rd |    2 
 inst/doc/man/zh_TW/dbReadTable-methods.Rd       |  380 +++++++++++++++++++-----
 inst/doc/man/zh_TW/dbSendQuery-methods.Rd       |   87 +++--
 inst/doc/man/zh_TW/summary-methods.Rd           |    2 
 man/Oracle.Rd                                   |   47 ++
 man/dbDriver-methods.Rd                         |   46 +-
 man/dbGetInfo-methods.Rd                        |   26 +
 man/dbReadTable-methods.Rd                      |  166 +++++++++-
 man/dbSendQuery-methods.Rd                      |   64 ++--
 src/rodbi.c                                     |  285 +++++++++++++++---
 src/rodbi.h                                     |    7 
 src/rooci.c                                     |  159 ++++++----
 src/rooci.h                                     |    6 
 89 files changed, 7679 insertions(+), 2044 deletions(-)

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Package oglmx updated to version 1.0.3 with previous version 1.0.2 dated 2015-06-01

Title: Estimation of Ordered Generalized Linear Models
Description: Ordered models such as ordered probit and ordered logit presume that the error variance is constant across observations. In the case that this assumption does not hold estimates of marginal effects are typically biased. This package allows for generalization of ordered probit and ordered logit models by allowing the user to specify a model for the variance. Furthermore, the package includes functions to calculate the marginal effects.
Author: Nathan Carroll
Maintainer: Nathan Carroll <nathan.carroll@ur.de>

Diff between oglmx versions 1.0.2 dated 2015-06-01 and 1.0.3 dated 2015-07-31

 DESCRIPTION                 |   10 +-
 MD5                         |   20 ++--
 R/oglmx-functions.R         |  182 +++++++++++++++++++++++++++++++++-----------
 R/oglmx.margins-functions.R |    2 
 build/partial.rdb           |binary
 man/logit.reg.Rd            |   10 +-
 man/oglmx.Rd                |   19 +++-
 man/ologit.reg.Rd           |   10 +-
 man/oprobit.reg.Rd          |   11 ++
 man/probit.reg.Rd           |   10 +-
 man/summary.oglmx.Rd        |    2 
 11 files changed, 202 insertions(+), 74 deletions(-)

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Package multcompView updated to version 0.1-7 with previous version 0.1-5 dated 2012-05-26

Title: Visualizations of Paired Comparisons
Description: Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different. Designed for use in conjunction with the output of functions like TukeyHSD, dist{stats}, simint, simtest, csimint, csimtest{multcomp}, friedmanmc, kruskalmc{pgirmess}.
Author: Spencer Graves, Hans-Peter Piepho and Luciano Selzer with help from Sundar Dorai-Raj
Maintainer: Luciano Selzer <luciano.selzer@gmail.com>

Diff between multcompView versions 0.1-5 dated 2012-05-26 and 0.1-7 dated 2015-07-31

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 multcompView-0.1-5/multcompView/man/multcompView.package.Rd  |only
 multcompView-0.1-5/multcompView/man/plot.multcomp.Rd         |only
 multcompView-0.1-5/multcompView/man/plotDisplay.Rd           |only
 multcompView-0.1-7/multcompView/DESCRIPTION                  |   30 
 multcompView-0.1-7/multcompView/MD5                          |   53 -
 multcompView-0.1-7/multcompView/NAMESPACE                    |   53 +
 multcompView-0.1-7/multcompView/R/extract_p.R                |   83 +-
 multcompView-0.1-7/multcompView/R/multcompBoxplot.R          |  378 +++++++----
 multcompView-0.1-7/multcompView/R/multcompLetters.R          |  243 +++++++
 multcompView-0.1-7/multcompView/R/multcompTs.R               |  117 +++
 multcompView-0.1-7/multcompView/R/multcompView-package.R     |only
 multcompView-0.1-7/multcompView/R/plot.multcompLetters.R     |  125 +++
 multcompView-0.1-7/multcompView/R/plot.multcompTs.R          |  133 +++
 multcompView-0.1-7/multcompView/R/plotBoxes.R                |   90 ++
 multcompView-0.1-7/multcompView/R/plotLetters.R              |  131 +++
 multcompView-0.1-7/multcompView/R/plotTs.R                   |   91 ++
 multcompView-0.1-7/multcompView/R/print.multcompLetters.R    |   28 
 multcompView-0.1-7/multcompView/R/vec2mat.R                  |   64 +
 multcompView-0.1-7/multcompView/R/vec2mat2.R                 |   36 +
 multcompView-0.1-7/multcompView/man/extract_p.Rd             |   54 -
 multcompView-0.1-7/multcompView/man/multcompBoxplot.Rd       |  196 ++---
 multcompView-0.1-7/multcompView/man/multcompLetters.Rd       |  231 ++----
 multcompView-0.1-7/multcompView/man/multcompTs.Rd            |  164 +---
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 multcompView-0.1-7/multcompView/man/vec2mat.Rd               |   75 --
 multcompView-0.1-7/multcompView/man/vec2mat2.Rd              |   60 -
 33 files changed, 1805 insertions(+), 689 deletions(-)

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Package mcmcse updated to version 1.1-1 with previous version 1.0-1 dated 2012-08-06

Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE computation for expectation and quantile estimators is supported as well as multivariate estimations. The package also provides functions for computing effective sample size and for plotting Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes <hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>

Diff between mcmcse versions 1.0-1 dated 2012-08-06 and 1.1-1 dated 2015-07-31

 DESCRIPTION           |   30 +++++++++++---------
 MD5                   |   36 +++++++++++++++++++-----
 NAMESPACE             |   16 ++++++++++
 R/RcppExports.R       |only
 R/confRegion.R        |only
 R/mcmcse.R            |   74 ++++++++++++++++++++++++++++++--------------------
 R/mcse_multi.R        |only
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 R/qq_test.R           |only
 R/zzz.R               |    7 ++--
 build                 |only
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 src                   |only
 tests                 |only
 vignettes             |only
 23 files changed, 143 insertions(+), 81 deletions(-)

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Package liftr updated to version 0.2 with previous version 0.1 dated 2015-07-15

Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb], Tengfei Yin [ctb], Nan Xiao [aut, cre]
Maintainer: Nan Xiao <nanx@uchicago.edu>

Diff between liftr versions 0.1 dated 2015-07-15 and 0.2 dated 2015-07-31

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 liftr-0.2/liftr/DESCRIPTION               |   20 +
 liftr-0.2/liftr/MD5                       |   25 -
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 liftr-0.2/liftr/R/lift.R                  |   26 +
 liftr-0.2/liftr/R/liftr-package.R         |    1 
 liftr-0.2/liftr/R/utils.R                 |   10 
 liftr-0.2/liftr/README.md                 |   21 -
 liftr-0.2/liftr/inst/Dockerfile.Rmd       |   11 
 liftr-0.2/liftr/inst/doc/liftr-intro.Rmd  |    2 
 liftr-0.2/liftr/inst/doc/liftr-intro.html |  405 ++++++++++--------------------
 liftr-0.2/liftr/inst/pandoc.Rmd           |only
 liftr-0.2/liftr/man/liftr-package.Rd      |    1 
 liftr-0.2/liftr/vignettes/liftr-intro.Rmd |    2 
 15 files changed, 218 insertions(+), 307 deletions(-)

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Package ORCME updated to version 2.0.2 with previous version 2.0.1 dated 2014-07-16

Title: Order Restricted Clustering for Microarray Experiments
Description: Provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>

Diff between ORCME versions 2.0.1 dated 2014-07-16 and 2.0.2 dated 2015-07-31

 DESCRIPTION       |   18 +++++++++---------
 MD5               |    8 ++++----
 NAMESPACE         |    4 +++-
 data/doseData.rda |binary
 data/geneData.rda |binary
 5 files changed, 16 insertions(+), 14 deletions(-)

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Package Kernelheaping updated to version 1.0 with previous version 0.9 dated 2015-06-13

Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymized data the user often encounters heaped data, i.e. data which are rounded (to a possibly different degree of coarseness). While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Varying rounding probabilities (depending on the true value) and asymmetric rounding is estimable as well. Additionally, bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>

Diff between Kernelheaping versions 0.9 dated 2015-06-13 and 1.0 dated 2015-07-31

 DESCRIPTION              |    8 +-
 MD5                      |   14 ++--
 NAMESPACE                |   19 +++++
 R/functions.R            |  154 ++++++++++++++++++++++++-----------------------
 data/students.rda        |binary
 man/dbivr.Rd             |    9 +-
 man/dheaping.Rd          |   17 +++--
 man/sim.Kernelheaping.Rd |    2 
 8 files changed, 126 insertions(+), 97 deletions(-)

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Package IsoGene updated to version 1.0-24 with previous version 1.0-23 dated 2014-12-18

Title: Order-Restricted Inference for Microarray Experiments
Description: Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
Author: Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>

Diff between IsoGene versions 1.0-23 dated 2014-12-18 and 1.0-24 dated 2015-07-31

 DESCRIPTION          |   16 ++++++++--------
 MD5                  |   10 +++++-----
 NAMESPACE            |    2 ++
 data/dopamine.rda    |binary
 data/exampleData.rda |binary
 inst/doc/IsoGene.pdf |binary
 6 files changed, 15 insertions(+), 13 deletions(-)

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Package FHtest updated to version 1.3 with previous version 1.2 dated 2015-05-27

Title: Tests for Right and Interval-Censored Survival Data Based on the Fleming-Harrington Class
Description: Functions to compare two or more survival curves with: a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes. b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>

Diff between FHtest versions 1.2 dated 2015-05-27 and 1.3 dated 2015-07-31

 FHtest-1.2/FHtest/R/FHtest-internal.R   |only
 FHtest-1.3/FHtest/DESCRIPTION           |    8 ++---
 FHtest-1.3/FHtest/MD5                   |   43 +++++++++++++++-----------------
 FHtest-1.3/FHtest/NAMESPACE             |    4 +-
 FHtest-1.3/FHtest/R/FHtesticp.R         |    2 -
 FHtest-1.3/FHtest/R/FHtesticp.formula.R |   22 ++++++++--------
 FHtest-1.3/FHtest/R/FHtestics.R         |    2 -
 FHtest-1.3/FHtest/R/FHtestics.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/FHtestrcc.R         |    5 +--
 FHtest-1.3/FHtest/R/FHtestrcc.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/FHtestrcp.R         |    5 +--
 FHtest-1.3/FHtest/R/FHtestrcp.formula.R |   30 +++++++++++-----------
 FHtest-1.3/FHtest/R/rcc.R               |   37 ++++++++++++++-------------
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 FHtest-1.3/FHtest/man/illust3.Rd        |   37 +++++++++++----------------
 FHtest-1.3/FHtest/man/rcc.Rd            |    2 -
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 23 files changed, 155 insertions(+), 171 deletions(-)

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Package sudokuAlt updated to version 0.1-6 with previous version 0.1-5 dated 2015-07-24

Title: Tools for Making and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods. Solved sudoku games are of some interest in Experimental Design as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>

Diff between sudokuAlt versions 0.1-5 dated 2015-07-24 and 0.1-6 dated 2015-07-31

 DESCRIPTION        |   10 +++++-----
 MD5                |    8 ++++----
 R/sudokuAlt.R      |   21 +++++++++++++--------
 man/fetchAUGame.Rd |   13 ++++++-------
 man/fetchUKGame.Rd |    5 +++++
 5 files changed, 33 insertions(+), 24 deletions(-)

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Package shinyjs updated to version 0.0.8.3 with previous version 0.0.7.0 dated 2015-06-24

Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Examples include hiding an element, disabling an input, resetting an input back to its original value, and many more useful functions. Even if you do know JavaScript, 'shinyjs' can be used as convenience functions to avoid dealing with message passing and writing JavaScript code. 'shinyjs' can also be used to easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between shinyjs versions 0.0.7.0 dated 2015-06-24 and 0.0.8.3 dated 2015-07-31

 DESCRIPTION                                           |    6 
 MD5                                                   |   90 ++++-----
 NEWS.md                                               |   24 ++
 R/colourInput.R                                       |   47 +++-
 R/extendShinyjs.R                                     |   20 +-
 R/hidden.R                                            |    2 
 R/inlineCSS.R                                         |    6 
 R/jsFunc-aaa.R                                        |    7 
 R/jsFunc-classFuncs.R                                 |    4 
 R/jsFunc-messageFuncs.R                               |    2 
 R/jsFunc-runjs.R                                      |    2 
 R/jsFunc-stateFuncs.R                                 |    4 
 R/jsFunc-text.R                                       |    2 
 R/jsFunc-visibilityFuncs.R                            |    4 
 R/onclick.R                                           |    6 
 R/reset.R                                             |    6 
 R/useShinyjs.R                                        |    9 
 R/utils.R                                             |   25 --
 README.md                                             |   23 +-
 inst/doc/overview.Rmd                                 |   21 --
 inst/doc/overview.html                                |   38 +--
 inst/examples/basic/app.R                             |    2 
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 inst/examples/demo/server.R                           |    2 
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 man/hidden.Rd                                         |    2 
 man/inlineCSS.Rd                                      |    6 
 man/js.Rd                                             |    2 
 man/messageFuncs.Rd                                   |    2 
 man/onclick.Rd                                        |    2 
 man/reset.Rd                                          |    2 
 man/runjs.Rd                                          |    2 
 man/stateFuncs.Rd                                     |    4 
 man/text.Rd                                           |    2 
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 man/visibilityFuncs.Rd                                |    4 
 vignettes/overview.Rmd                                |   21 --
 46 files changed, 489 insertions(+), 282 deletions(-)

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Package nlstools updated to version 1.0-2 with previous version 1.0-1 dated 2015-02-26

Title: Tools for Nonlinear Regression Analysis
Description: Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
Author: Florent Baty <florent.baty@gmail.com> and Marie-Laure Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>, with contributions from Sandrine Charles, Jean-Pierre Flandrois, and Christian Ritz
Maintainer: Florent Baty <florent.baty@gmail.com>

Diff between nlstools versions 1.0-1 dated 2015-02-26 and 1.0-2 dated 2015-07-31

 ChangeLog       |    3 +++
 DESCRIPTION     |    8 ++++----
 MD5             |   12 ++++++------
 NAMESPACE       |    4 +++-
 inst/CITATION   |   40 ++++++++++++++++++++++++----------------
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 7 files changed, 50 insertions(+), 28 deletions(-)

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Package mipfp updated to version 2.2 with previous version 2.0 dated 2015-03-30

Title: Multidimensional Iterative Proportional Fitting and Alternative Models
Description: An implementation of the iterative proportional fitting (IPFP), maximum likelihood, minimum chi-square and weighted least squares procedures for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional). The package also provides an application of the IPFP to simulate multivariate Bernoulli distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>

Diff between mipfp versions 2.0 dated 2015-03-30 and 2.2 dated 2015-07-31

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 NAMESPACE                   |    2 
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 23 files changed, 623 insertions(+), 336 deletions(-)

More information about mipfp at CRAN
Permanent link

Package spsann updated to version 1.0.1 with previous version 1.0.0 dated 2015-07-15

Title: Optimization of Sample Configurations using Spatial Simulated Annealing
Description: Methods to optimize sample configurations using spatial simulated annealing. Multiple objective functions are implemented for various purposes, such as variogram estimation, trend estimation, and spatial interpolation. A general purpose spatial simulated annealing function enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B M Heuvelink [ths], Edzer Pebesma [ctb], Jon Skoien [ctb], Joshua French [ctb], Pierre Roudier [ctb], Dick Brus [ctb], Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

Diff between spsann versions 1.0.0 dated 2015-07-15 and 1.0.1 dated 2015-07-31

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More information about spsann at CRAN
Permanent link

Package quanteda updated to version 0.8.2-0 with previous version 0.8.0-4 dated 2015-07-13

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Pablo Barberá [ctb], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

Diff between quanteda versions 0.8.0-4 dated 2015-07-13 and 0.8.2-0 dated 2015-07-31

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More information about quanteda at CRAN
Permanent link

Thu, 30 Jul 2015

Package rdrop2 updated to version 0.7.0 with previous version 0.6 dated 2015-04-15

Title: Programmatic Interface to the 'Dropbox' API
Description: Provides full programmatic access to the Dropbox file hosting platform (dropbox.com), including support for all standard file operations.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between rdrop2 versions 0.6 dated 2015-04-15 and 0.7.0 dated 2015-07-30

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More information about rdrop2 at CRAN
Permanent link

Package phonTools updated to version 0.2-2.1 with previous version 0.2-2.0 dated 2014-08-04

Title: Tools for Phonetic and Acoustic Analyses
Description: Contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.
Author: Santiago Barreda
Maintainer: Santiago Barreda <sbarreda@ucdavis.edu>

Diff between phonTools versions 0.2-2.0 dated 2014-08-04 and 0.2-2.1 dated 2015-07-30

 DESCRIPTION              |   12 +--
 LICENSE                  |    2 
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More information about phonTools at CRAN
Permanent link

Package optmatch updated to version 0.9-5 with previous version 0.9-3 dated 2014-08-12

Title: Functions for Optimal Matching
Description: Provides routines for distance based bipartite matching to reduce covariate imbalance between treatment and control groups in observational studies. Routines are provided to generate distances from GLM models (propensity score matching) and formulas (Euclidean and Mahalanobis matching), stratified matching (exact matching), and calipers. Results of the fullmatch routine are guaranteed to provide minimum average within matched set distance.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, and Peter Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas <dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>

Diff between optmatch versions 0.9-3 dated 2014-08-12 and 0.9-5 dated 2015-07-30

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Package myTAI updated to version 0.3.0 with previous version 0.2.1 dated 2015-07-23

Title: Performing Phylotranscriptomics with R
Description: A statistical framework allowing users interested in the evolution of biological processes to capture evolutionary signals in transcriptomes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hajk-georg.drost@informatik.uni-halle.de>

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Package Harvest.Tree updated to version 1.1 with previous version 1.0 dated 2015-07-10

Title: Harvest the Classification Tree
Description: Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.
Author: Bingyuan Liu/Yan Yuan/Qian Shi
Maintainer: Bingyuan Liu <adler1016@gmail.com>

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Package dendextend updated to version 1.1.0 with previous version 1.0.1 dated 2015-06-28

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 tree's 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), Zuguang Gu [ctb] (circlize author), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package climwin updated to version 0.1.1 with previous version 0.1.0 dated 2015-07-19

Title: Climate Window Analysis
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@anu.edu.au>

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Package plotmo updated to version 3.1.4 with previous version 3.1.3 dated 2015-06-24

Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors while holding the other predictors constant. A poor man's partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package cmsaf updated to version 1.5 with previous version 1.4 dated 2015-06-26

Title: Tools for CM SAF Netcdf Data
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. A Windows binary file and scripts for an easy application of the functions are provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

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Package randtoolbox updated to version 1.17 with previous version 1.16 dated 2014-12-05

Title: Toolbox for Pseudo and Quasi Random Number Generation and RNG Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some RNG tests - the gap test, the serial test, the poker test. The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package. A number of RNGs and tests for RNGs are also provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

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Package CDVine updated to version 1.3 with previous version 1.2 dated 2014-03-27

Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine) and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate as well as vine copula selection are provided. Models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are also included. Data is assumed to lie in the unit hypercube (so-called copula data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>

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Package YuGene updated to version 1.1.4 with previous version 1.1.2 dated 2014-07-13

Title: A Simple Approach to Scale Gene Expression Data Derived from Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>

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Package mixOmics updated to version 5.1.1 with previous version 5.0-4 dated 2015-04-28

Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and variants to analyse highly dimensional data sets: regularized Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS') to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>

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Package wq updated to version 0.4.4 with previous version 0.4.3 dated 2015-04-03

Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from environmental monitoring programs. The package name stands for "water quality" and reflects the original focus on time series data for physical and chemical properties of water, as well as the plankton. Intended for programs that sample approximately monthly at discrete stations, a feature of many legacy data sets. Most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>

Diff between wq versions 0.4.3 dated 2015-04-03 and 0.4.4 dated 2015-07-30

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Package robustreg updated to version 0.1-8 with previous version 0.1-7 dated 2014-10-28

Title: Robust Regression Functions
Description: Linear regression functions using Huber and bisquare psi functions. Optimal weights are calculated using IRLS algorithm.
Author: Ian M. Johnson <ian@alpha-analysis.com>
Maintainer: Ian M. Johnson <ian@alpha-analysis.com>

Diff between robustreg versions 0.1-7 dated 2014-10-28 and 0.1-8 dated 2015-07-30

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Package RJafroc updated to version 0.1.0 with previous version 0.0.1 dated 2015-04-24

Title: Analysis of Data Acquired Using the Receiver Operating Characteristic Paradigm and Its Extensions
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software.
Author: Xuetong Zhai [aut, cre], Dev Chakraborty [aut, ths]
Maintainer: Xuetong Zhai <xuetong.zhai@gmail.com>

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Package RESS updated to version 1.2 with previous version 1.1 dated 2015-06-09

Title: Integrates R and Essentia
Description: Contains two functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.udb' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>

Diff between RESS versions 1.1 dated 2015-06-09 and 1.2 dated 2015-07-30

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Package ivmodel updated to version 1.1 with previous version 1.0 dated 2015-05-03

Title: Statistical Inference and Sensitivity Analysis for Instrumental Variables Model
Description: Contains functions for carrying out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics.
Author: Yang Jiang, Hyunseung Kang, and Dylan Small
Maintainer: Hyunseung Kang <hskang@stanford.edu>

Diff between ivmodel versions 1.0 dated 2015-05-03 and 1.1 dated 2015-07-30

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Package Cairo updated to version 1.5-8 with previous version 1.5-7 dated 2015-07-28

Title: R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output
Description: Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>

Diff between Cairo versions 1.5-7 dated 2015-07-28 and 1.5-8 dated 2015-07-30

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Package bayesDccGarch updated to version 1.2 with previous version 1.1 dated 2015-06-03

Title: The Bayesian Dynamic Conditional Correlation GARCH Model
Description: Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635).
Author: Jose A Fioruci <jafioruci@gmail.com>, Ricardo S Ehlers <ehlers@icmc.usp.br>, Francisco Louzada <louzada@icmc.usp.br>
Maintainer: Jose A Fioruci <jafioruci@gmail.com>

Diff between bayesDccGarch versions 1.1 dated 2015-06-03 and 1.2 dated 2015-07-30

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Wed, 29 Jul 2015

Package signal updated to version 0.7-6 with previous version 0.7-5 dated 2015-05-31

Title: Signal Processing
Description: A set of signal processing functions originally written for 'Matlab' and 'Octave'. Includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.
Author: Uwe Ligges [aut, cre] (new maintainer), Tom Short [aut] (port to R), Paul Kienzle [aut] (majority of the original sources), Sarah Schnackenberg [ctb] (various test cases and bug fixes), David Billinghurst [ctb], Hans-Werner Borchers [ctb], Andre Carezia [ctb], Pascal Dupuis [ctb], John W. Eaton [ctb], E. Farhi [ctb], Kai Habel [ctb], Kurt Hornik [ctb], Sebastian Krey [ctb], Bill Lash [ctb], Friedrich Leisch [ctb], Olaf Mersmann [ctb], Paulo Neis [ctb], Jaakko Ruohio [ctb], Julius O. Smith III [ctb], Doug Stewart [ctb], Andreas Weingessel [ctb]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

Diff between signal versions 0.7-5 dated 2015-05-31 and 0.7-6 dated 2015-07-29

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Package scatterplot3d updated to version 0.3-36 with previous version 0.3-35 dated 2014-02-11

Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

Diff between scatterplot3d versions 0.3-35 dated 2014-02-11 and 0.3-36 dated 2015-07-29

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Package RWinEdt updated to version 2.0-5 with previous version 2.0-4 dated 2015-06-17

Title: R Interface to WinEdt
Description: A plug in for using WinEdt as an editor for R.
Author: Uwe Ligges <Uwe.Ligges@R-project.org> with contributions (the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller
Maintainer: Uwe Ligges <Uwe.Ligges@R-project.org>

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Package R2WinBUGS updated to version 2.1-21 with previous version 2.1-20 dated 2015-05-31

Title: Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
Description: Invoke a 'BUGS' model in 'OpenBUGS' or 'WinBUGS', a class "bugs" for 'BUGS' results and functions to work with that class. Function write.model() allows a 'BUGS' model file to be written. The class and auxiliary functions could be used with other MCMC programs, including 'JAGS'.
Author: originally written by Andrew Gelman <gelman@stat.columbia.edu>; changes and packaged by Sibylle Sturtz <sturtz@statistik.tu-dortmund.de> and Uwe Ligges <ligges@statistik.tu-dortmund.de>. With considerable contributions by Gregor Gorjanc <gregor.gorjanc@bfro.uni-lj.si> and Jouni Kerman <kerman@stat.columbia.edu>. Ported to S-PLUS by Insightful Corp.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

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Package nortest updated to version 1.0-4 with previous version 1.0-3 dated 2015-02-26

Title: Tests for Normality
Description: Five omnibus tests for testing the composite hypothesis of normality.
Author: Juergen Gross [aut], Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

Diff between nortest versions 1.0-3 dated 2015-02-26 and 1.0-4 dated 2015-07-29

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Package BRugs updated to version 0.8-5 with previous version 0.8-4 dated 2015-05-31

Title: Interface to the 'OpenBUGS' MCMC Software
Description: Fully-interactive R interface to the 'OpenBUGS' software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

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Package tcR updated to version 2.1.1 with previous version 2.1 dated 2015-07-28

Title: Advanced Data Analysis of T Cell Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>

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Package rfPermute updated to version 1.9.2 with previous version 1.7 dated 2015-06-15

Title: Estimate Permutation p-Values for Random Forest Importance Metrics
Description: Estimate significance of importance metrics for a Random Forest model by permuting the response variable. Produces null distribution of importance metrics for each predictor variable and p-value of observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>

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Package pedometrics updated to version 0.6-3 with previous version 0.6-2 dated 2015-06-02

Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the field of pedometrics (see http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics). These functions were developed to fulfil the demands created by the PhD research project (2012-2016) entitled "Contribution to the Construction of Models for Predicting Soil Properties", developed by Alessandro Samuel-Rosa under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands). The project is supported by the CAPES, Ministério da Educação, Brasília - DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions simply extend the functionalities of other functions commonly used for the analysis of pedometric data. It should be noted that changes are likely to occur quite often and the use of this package as a dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre], Lúcia Anjos [ths], Gustavo Vasques [ths], Gerard Heuvelink [ths], Tony Olsen [ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo Garcia [ctb], Pablo Garcia Rodriguez [ctb], Joshua French [ctb], Ken Kleinman [ctb], Dick Brus [ctb], Frank Harrell Jr [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

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More information about pedometrics at CRAN
Permanent link

Package Pade updated to version 0.1-4 with previous version 0.1-3 dated 2015-07-01

Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Pade versions 0.1-3 dated 2015-07-01 and 0.1-4 dated 2015-07-29

 DESCRIPTION  |    8 ++++----
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 inst/NEWS.Rd |    8 ++++++++
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More information about Pade at CRAN
Permanent link

Package ggmcmc updated to version 0.7.1 with previous version 0.6 dated 2014-12-30

Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tool for assessing and diagnosing convergence of Markov Chain Monte Carlo simulations, as well as for graphically display results from full MCMC analysis. The package also facilitates the graphical interpretation of models by providing flexible functions to plot the results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>

Diff between ggmcmc versions 0.6 dated 2014-12-30 and 0.7.1 dated 2015-07-29

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 NAMESPACE                   |    4 +
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More information about ggmcmc at CRAN
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Package dsm updated to version 2.2.9 with previous version 2.2.5 dated 2014-09-15

Title: Density Surface Modelling of Distance Sampling Data
Description: Density surface modelling of line transect data. A Generalized Additive Model-based approach is used to calculate spatially-explicit estimates of animal abundance from distance sampling (also presence/absence and strip transect) data. Several utility functions are provided for model checking, plotting and variance estimation.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington, Sharon Hedley.
Maintainer: David Lawrence Miller <dave@ninepointeightone.net>

Diff between dsm versions 2.2.5 dated 2014-09-15 and 2.2.9 dated 2015-07-29

 DESCRIPTION                    |   29 ++---------
 MD5                            |  106 ++++++++++++++++++++---------------------
 NAMESPACE                      |   37 +++++++++++++-
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More information about dsm at CRAN
Permanent link

Package yhatr updated to version 0.13.7 with previous version 0.13.6 dated 2015-06-19

Title: R Binder for the Yhat API
Description: Deploy, maintain, and invoke models via the Yhat REST API.
Author: Greg Lamp <greg@yhathq.com>, Eric Chiang <eric@yhathq.com>
Maintainer: Greg Lamp <greg@yhathq.com>

Diff between yhatr versions 0.13.6 dated 2015-06-19 and 0.13.7 dated 2015-07-29

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More information about yhatr at CRAN
Permanent link

Package mrds updated to version 2.1.14 with previous version 2.1.12 dated 2015-02-04

Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers <dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: David Miller <dave@ninepointeightone.net>

Diff between mrds versions 2.1.12 dated 2015-02-04 and 2.1.14 dated 2015-07-29

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Package Distance updated to version 0.9.4 with previous version 0.9.3 dated 2015-02-04

Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated (via a Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: David Lawrence Miller <dave@ninepointeightone.net>

Diff between Distance versions 0.9.3 dated 2015-02-04 and 0.9.4 dated 2015-07-29

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Package bda updated to version 5.1.6 with previous version 5.1.3 dated 2015-04-04

Title: Density Estimation for Grouped Data
Description: Functions for density estimation based on grouped (or pre-binned) data.
Author: Bin Wang <bwang@southalabama.edu>.
Maintainer: Bin Wang <bwang@southalabama.edu>

Diff between bda versions 5.1.3 dated 2015-04-04 and 5.1.6 dated 2015-07-29

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Package webuse updated to version 0.1.2 with previous version 0.1.1 dated 2015-07-28

Title: Import Stata 'webuse' Datasets
Description: A Stata-style `webuse()` function for importing named datasets from Stata's online collection.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between webuse versions 0.1.1 dated 2015-07-28 and 0.1.2 dated 2015-07-29

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Package Crossover updated to version 0.1-15 with previous version 0.1-14 dated 2015-03-26

Title: Analysis and Search of Crossover Designs
Description: Package Crossover provides different crossover designs from combinatorial or search algorithms as well as from literature and a GUI to access them.
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>

Diff between Crossover versions 0.1-14 dated 2015-03-26 and 0.1-15 dated 2015-07-29

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Package biogas updated to version 1.1.0 with previous version 1.0.1 dated 2015-05-28

Title: Analyze Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated from individual biogas volume (or reactor mass) and biogas composition measurements for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>

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Package swfscMisc updated to version 1.0.6 with previous version 1.0.3 dated 2014-12-31

Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and plotting functions. Used to support packages and code written by researchers at the Southwest Fisheries Science Center of the National Oceanic and Atmospheric Administration.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>

Diff between swfscMisc versions 1.0.3 dated 2014-12-31 and 1.0.6 dated 2015-07-29

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Package sns updated to version 1.1.0 with previous version 1.0.0 dated 2015-02-07

Title: Stochastic Newton Sampler (SNS)
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability density functions (PDFs) where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A Boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the PDF (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle. Numerical differentiation is available when analytical expressions for gradient and Hessian are not available. Facilities for validation and numerical differentiation of log-density are provided.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani <alireza.mahani@sentrana.com>

Diff between sns versions 1.0.0 dated 2015-02-07 and 1.1.0 dated 2015-07-29

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Package ranger updated to version 0.2.7 with previous version 0.2.6 dated 2015-07-28

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package GenABEL) can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>

Diff between ranger versions 0.2.6 dated 2015-07-28 and 0.2.7 dated 2015-07-29

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