Wed, 01 Jul 2015

Package switchr updated to version 0.9.10 with previous version 0.9.6 dated 2015-06-16

Title: Installing, Managing, and Switching Between Distinct Sets of Installed Packages
Description: Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a devel/release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

Diff between switchr versions 0.9.6 dated 2015-06-16 and 0.9.10 dated 2015-07-01

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 MD5                          |   70 ++++++++++++++-------------
 NAMESPACE                    |   21 ++++++++
 NEWS                         |   24 ++++++++-
 R/AllClasses.R               |   23 ++++++--
 R/Install.R                  |  111 ++++++++++++++++++++++++-------------------
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 39 files changed, 449 insertions(+), 186 deletions(-)

More information about switchr at CRAN
Permanent link

Package Rglpk updated to version 0.6-1 with previous version 0.6-0 dated 2014-06-16

Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programming Kit. GLPK is open source software for solving large-scale linear programming (LP), mixed integer linear programming (MILP) and other related problems.
Author: Stefan Theussl [aut, cre], Kurt Hornik [aut], Christian Buchta [ctb], Heinrich Schuchardt [ctb], Andrew Makhorin [cph], Timothy A. Davis [cph], Niklas Sorensson [cph], Mark Adler [cph], Jean-loup Gailly [cph]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>

Diff between Rglpk versions 0.6-0 dated 2014-06-16 and 0.6-1 dated 2015-07-01

 DESCRIPTION       |   11 +--
 MD5               |   11 +--
 NAMESPACE         |    2 
 inst/CHANGELOG    |    7 ++
 src/Rglpk.h       |    3 
 src/Rglpk_error.c |only
 src/Rglpk_solve.c |  171 ++++++++++++++++++++++++++++--------------------------
 7 files changed, 114 insertions(+), 91 deletions(-)

More information about Rglpk at CRAN
Permanent link

Package rbison updated to version 0.4.8 with previous version 0.4.5 dated 2014-12-10

Title: Interface to the 'USGS' 'BISON' 'API'
Description: Interface to the 'USGS' 'BISON' 'API', a 'database' for species occurrence data on the web. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rbison versions 0.4.5 dated 2014-12-10 and 0.4.8 dated 2015-07-01

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 rbison-0.4.8/rbison/R/bison.R                        |   71 ++--
 rbison-0.4.8/rbison/R/bison_providers.R              |    3 
 rbison-0.4.8/rbison/R/bison_solr.R                   |    6 
 rbison-0.4.8/rbison/R/bison_stats.R                  |    1 
 rbison-0.4.8/rbison/R/bison_tax.R                    |   29 +
 rbison-0.4.8/rbison/R/bisonmap.R                     |   85 ++---
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 rbison-0.4.8/rbison/tests/testthat/test-bisonmap.R   |   16 
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 46 files changed, 1108 insertions(+), 1028 deletions(-)

More information about rbison at CRAN
Permanent link

Package raster updated to version 2.4-15 with previous version 2.3-40 dated 2015-04-11

Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Joe Cheng [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between raster versions 2.3-40 dated 2015-04-11 and 2.4-15 dated 2015-07-01

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 raster-2.4-15/raster/R/AAAClasses.R           |    2 
 raster-2.4-15/raster/R/GDALtransient.R        |    8 
 raster-2.4-15/raster/R/Geary.R                |    2 
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 raster-2.4-15/raster/R/approxNA.R             |    4 
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More information about raster at CRAN
Permanent link

Package geosphere updated to version 1.4-3 with previous version 1.3-13 dated 2015-04-11

Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut], Ed Williams [ctb], Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between geosphere versions 1.3-13 dated 2015-04-11 and 1.4-3 dated 2015-07-01

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More information about geosphere at CRAN
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Package sjPlot updated to version 1.8.2 with previous version 1.8.1 dated 2015-05-29

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjPlot versions 1.8.1 dated 2015-05-29 and 1.8.2 dated 2015-07-01

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Package pca3d updated to version 0.8 with previous version 0.3 dated 2014-11-04

Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between pca3d versions 0.3 dated 2014-11-04 and 0.8 dated 2015-07-01

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More information about pca3d at CRAN
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Package nat.templatebrains updated to version 0.6 with previous version 0.4.1 dated 2014-09-16

Title: NeuroAnatomy Toolbox (nat) Extension for Handling Template Brains
Description: Extends package nat (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
Author: James Manton and Gregory Jefferis
Maintainer: James Manton <ajd.manton@googlemail.com>

Diff between nat.templatebrains versions 0.4.1 dated 2014-09-16 and 0.6 dated 2015-07-01

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More information about nat.templatebrains at CRAN
Permanent link

New package iptools with initial version 0.2.0
Package: iptools
Type: Package
Title: Manipulate, Validate and Resolve IP Addresses
Version: 0.2.0
Date: 2015-07-01
Author: Bob Rudis <bob@rudis.net> [aut, cre], Oliver Keyes <ironholds@gmail.com> [aut]
Maintainer: Bob Rudis <bob@rudis.net>
Description: A toolkit for manipulating, validating and testing IP addresses and ranges, along with datasets relating to IP addresses. While it primarily has support for the IPv4 address space, more extensive IPv6 support is intended.
License: MIT + file LICENSE
SystemRequirements: Boost.Asio and Boost.Regex from http://www.boost.org/. See README.
NeedsCompilation: yes
Depends: R (>= 2.10)
Suggests: testthat, knitr
Imports: Rcpp (>= 0.11.2), utils, stats
LinkingTo: BH, Rcpp
VignetteBuilder: knitr
OS_type: unix
Packaged: 2015-07-01 20:04:38 UTC; bob
Repository: CRAN
Date/Publication: 2015-07-01 22:59:07

More information about iptools at CRAN
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Package interplot updated to version 0.1.0.1 with previous version 0.1.0.0 dated 2015-06-26

Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

Diff between interplot versions 0.1.0.0 dated 2015-06-26 and 0.1.0.1 dated 2015-07-01

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Package GRANBase updated to version 1.0.12 with previous version 1.0.8 dated 2015-06-19

Title: Creating Continuously Integrated Package Repositories from Manifests
Description: Repository based tools for department and analysis level reproducibility. 'GRANBase' allows creation of custom branched, continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

Diff between GRANBase versions 1.0.8 dated 2015-06-19 and 1.0.12 dated 2015-07-01

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Permanent link

New package FractalParameterEstimation with initial version 1.0
Package: FractalParameterEstimation
Type: Package
Title: Estimation of Parameters p and q for Randomized Sierpinski Carpet for [p-p-p-q]-Model
Version: 1.0
Date: 2015-06-30
Author: Philipp Hermann
Maintainer: Philipp Hermann <philipp.hermann@jku.at>
Description: The parameters p and q are estimated with the aid of randomized Sierpinski Carpet which is built on [p-p-p-q]-model. Thereby, for three times simulation with p-value and once with q-value is assumed. Hence these parameters are estimated and displayed.
License: GPL (>= 2)
LazyData: true
Packaged: 2015-07-01 14:16:58 UTC; Philipp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-01 22:50:01

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Package fitbitScraper updated to version 0.1.4 with previous version 0.1.3 dated 2015-05-14

Title: Scrapes Data from 'www.fitbit.com'
Description: Scrapes data from www.fitbit.com, the website that contains data for the popular fitness tracker. This does not use the official API, but instead uses the API that the web dashboard uses to generate the graphs displayed on the dashboard after login at www.fitbit.com.
Author: Cory Nissen <corynissen@gmail.com> [aut, cre]
Maintainer: Cory Nissen <corynissen@gmail.com>

Diff between fitbitScraper versions 0.1.3 dated 2015-05-14 and 0.1.4 dated 2015-07-01

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Package ddalpha updated to version 1.1.2.2 with previous version 1.1.1 dated 2015-05-19

Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut], Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>

Diff between ddalpha versions 1.1.1 dated 2015-05-19 and 1.1.2.2 dated 2015-07-01

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Package astrochron updated to version 0.4.3 with previous version 0.4.2 dated 2015-03-19

Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>

Diff between astrochron versions 0.4.2 dated 2015-03-19 and 0.4.3 dated 2015-07-01

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Package varSelectIP (with last version 0.2-1) was removed from CRAN

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

2013-10-31 0.2-1
2011-08-27 0.1-5
2011-01-24 0.1-4

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Package topicmodels updated to version 0.2-2 with previous version 0.2-1 dated 2014-06-11

Title: Topic Models
Description: Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Grün [aut, cre], Kurt Hornik [aut]
Maintainer: Bettina Grün <Bettina.Gruen@jku.at>

Diff between topicmodels versions 0.2-1 dated 2014-06-11 and 0.2-2 dated 2015-07-01

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Package MXM updated to version 0.4 with previous version 0.3.1 dated 2015-05-25

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou <athineou@ics.forth.gr>

Diff between MXM versions 0.3.1 dated 2015-05-25 and 0.4 dated 2015-07-01

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Package maxstat updated to version 0.7-23 with previous version 0.7-22 dated 2015-02-20

Title: Maximally Selected Rank Statistics
Description: Maximally selected rank statistics with several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between maxstat versions 0.7-22 dated 2015-02-20 and 0.7-23 dated 2015-07-01

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New package GenCAT with initial version 1.0.1
Package: GenCAT
Type: Package
Title: Genetic Class Association Testing (GenCAT)
Version: 1.0.1
Date: 2015-06-12
Author: Eric Reed, Sara Nu<c3><b1>ez, Jing Qian, Andrea Foulkes
Maintainer: Eric Reed <reeder@bu.edu>
Description: Implementation of the genetic class level association testing (GenCAT) method from SNP level association data. Refer to: "Qian, J., Reed, E., Nunez, S., Qu, L., Reilly, M., Foulkes, A. (2015) Testing class-level genetic associations using single-element summary statistics. (Under review).".
License: GPL-2
Suggests: snpStats, knitr
Depends: R (>= 2.10), stats, dplyr, doParallel, ggplot2, foreach, parallel, methods
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-07-01 13:34:25 UTC; ericreed
Repository: CRAN
Date/Publication: 2015-07-01 16:06:25

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New package epiDisplay with initial version 3.2.0.6
Package: epiDisplay
Version: 3.2.0.6
Date: 2015-07-01
Title: Epidemiological Data Display Package
Author: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Maintainer: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Depends: R (>= 2.6.2), foreign, survival, MASS, nnet
Suggests:
Description: Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at the author's repository.
License: GPL (>= 2)
URL: http://CRAN.R-project.org/
Packaged: 2015-07-01 13:18:17 UTC; Virasakdi
Repository: CRAN
Date/Publication: 2015-07-01 16:06:29
NeedsCompilation: no

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New package CompR with initial version 1.0
Package: CompR
Version: 1.0
Date: 2015-07-01
Title: Paired Comparison Data Analysis
Author: Michel Semenou
Maintainer: Michel Semenou <michel.semenou@oniris-nantes.fr>
Depends: R (>= 3.1), methods, utils, MASS, graphics, stats
Description: Different tools for describing and analysing paired comparison data are presented. Main methods are estimation of products scores according Bradley Terry Luce model. A segmentation of the individual could be conducted on the basis of a mixture distribution approach. The number of classes can be tested by the use of Monte Carlo simulations. This package deals also with multi-criteria paired comparison data.
License: GPL-2
NeedsCompilation: no
Packaged: 2015-07-01 12:02:24 UTC; Utilisateur
Repository: CRAN
Date/Publication: 2015-07-01 16:06:23

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Package phom (with last version 1.0.3) was removed from CRAN

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

2014-02-09 1.0.3

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Package ringscale (with last version 0.1.2) was removed from CRAN

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

2009-10-21 0.1.2
2009-07-30 0.1.1

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Package reccsim (with last version 0.9-1) was removed from CRAN

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

2012-09-28 0.9-1

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Package phylosim (with last version 2.1.1) was removed from CRAN

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

2014-01-10 2.1.1
2014-01-07 2.1.0
2013-07-22 2.0.3
2013-06-12 2.0.2
2013-03-20 2.0.1
2013-01-15 2.0.0
2012-09-07 0.19
2012-03-01 0.17
2011-06-30 0.16
2011-06-28 0.15
2011-03-04 0.14
2011-02-15 0.13
2010-11-05 0.12
2010-10-27 0.11

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Package pcrcoal (with last version 1.1) was removed from CRAN

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

2014-02-24 1.1
2011-10-08 1.0

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Package merror (with last version 2.0.1) was removed from CRAN

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

2012-03-19 2.0.1
2011-08-04 2.0
2006-02-08 1.0

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Package qlspack (with last version 2.2) was removed from CRAN

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

2009-07-24 2.2
2009-06-09 2.1
2008-06-23 1.0-1
2008-06-23 1.0-1

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Package tslars (with last version 1.0) was removed from CRAN

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

2009-03-04 1.0

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Package predfinitepop (with last version 1.0) was removed from CRAN

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

2014-04-25 1.0

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Package lmmfit (with last version 1.0) was removed from CRAN

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

2011-08-08 1.0

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Package SSDforR updated to version 1.4.10 with previous version 1.4.9 dated 2015-04-18

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

Diff between SSDforR versions 1.4.9 dated 2015-04-18 and 1.4.10 dated 2015-07-01

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New package OneArmPhaseTwoStudy with initial version 0.1.3
Package: OneArmPhaseTwoStudy
Type: Package
Title: Planing, Monitoring and Evaluating Oncological Phase 2 Studies
Version: 0.1.3
Date: 2015-07-01
Author: Marius Wirths
Maintainer: Marius Wirths <wirths@imbi.uni-heidelberg.de>
Description: Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with this package a good starting point is to take a closer look at the functions getSolutions() and getSolutionsSub1().
License: GPL (>= 2)
Depends: methods, Rcpp (>= 0.9.11), R (>= 3.1.0)
LinkingTo: Rcpp
RcppModules: simon, sub1
Packaged: 2015-07-01 12:14:36 UTC; wirthsmarius
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-07-01 14:59:15

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Package nat updated to version 1.7.0 with previous version 1.6.6 dated 2015-05-27

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>

Diff between nat versions 1.6.6 dated 2015-05-27 and 1.7.0 dated 2015-07-01

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 nat-1.7.0/nat/R/zzz.R                                                          |    2 
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 nat-1.7.0/nat/man/ngraph.Rd                                                    |    4 
 nat-1.7.0/nat/man/nlapply.Rd                                                   |   12 
 nat-1.7.0/nat/man/nrrd.voxdims.Rd                                              |    5 
 nat-1.7.0/nat/man/origin.Rd                                                    |    8 
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 nat-1.7.0/nat/man/threshold.Rd                                                 |    7 
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 nat-1.7.0/nat/tests/testthat/test-dotprops.R                                   |   19 
 nat-1.7.0/nat/tests/testthat/test-graph-nodes.R                                |    5 
 nat-1.7.0/nat/tests/testthat/test-hxsurf.R                                     |    2 
 nat-1.7.0/nat/tests/testthat/test-im3d.R                                       |   27 
 nat-1.7.0/nat/tests/testthat/test-landmarks-io.R                               |    6 
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Package missMDA updated to version 1.8.2 with previous version 1.7.3 dated 2014-11-24

Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>

Diff between missMDA versions 1.7.3 dated 2014-11-24 and 1.8.2 dated 2015-07-01

 DESCRIPTION         |   17 ++++++-------
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Package medflex updated to version 0.5-1 with previous version 0.5-0 dated 2015-02-07

Title: Flexible Mediation Analysis Using Natural Effect Models
Description: Run flexible mediation analyses using natural effect models as described in Lange, Vansteelandt and Bekaert (2012), Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013).
Author: Johan Steen [aut, cre], Tom Loeys [aut], Beatrijs Moerkerke [aut], Stijn Vansteelandt [aut], Joris Meys [ctb] (technical support), Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen <johan.steen@gmail.com>

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Package HDclassif updated to version 1.3 with previous version 1.2.3 dated 2015-02-16

Title: High Dimensional Supervised Classification and Clustering
Description: Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.
Author: Laurent Berge, Charles Bouveyron and Stephane Girard
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>

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Package bayesmix updated to version 0.7-4 with previous version 0.7-3 dated 2014-03-11

Title: Bayesian Mixture Models with JAGS
Description: The fitting of finite mixture models of univariate Gaussian distributions using JAGS within a Bayesian framework is provided.
Author: Bettina Gruen [aut, cre], Martyn Plummer [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@jku.at>

Diff between bayesmix versions 0.7-3 dated 2014-03-11 and 0.7-4 dated 2015-07-01

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New package autovarCore with initial version 1.0-0
Package: autovarCore
Type: Package
Title: Automated Vector Autoregression Models and Networks
Version: 1.0-0
Date: 2015-06-29
Authors@R: c(person("Ando","Emerencia",role = c("aut","cre"), email = "ando.emerencia@gmail.com"))
BugReports: https://github.com/roqua/autovarcore/issues
Maintainer: Ando Emerencia <ando.emerencia@gmail.com>
Description: Automatically find the best vector autoregression models and networks for a given time series data set. 'AutovarCore' evaluates eight kinds of models: models with and without log transforming the data, lag 1 and lag 2 models, and models with and without day dummy variables. For each of these 8 model configurations, 'AutovarCore' evaluates all possible combinations for including outlier dummies (at 2.5x the standard deviation of the residuals) and retains the best model. Model evaluation includes the Eigenvalue stability test and a configurable set of residual tests. These eight models are further reduced to four models because 'AutovarCore' determines whether adding day dummies improves the model fit.
License: MIT + file LICENSE
Suggests: testthat, roxygen2
Imports: Rcpp (>= 0.11.4), Amelia, jsonlite, parallel, stats, urca, vars
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2015-07-01 11:54:26 UTC; ando
Author: Ando Emerencia [aut, cre]
Repository: CRAN
Date/Publication: 2015-07-01 14:41:42

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Package lazyWeave (with last version 2.2.5) was removed from CRAN

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

2014-05-23 2.2.5
2012-09-11 2.2.0
2012-06-07 2.1.4
2012-04-06 2.1.3
2011-11-04 2.1.0

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Package cmprskQR (with last version 0.9.0) was removed from CRAN

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

2014-11-27 0.9.0

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Package enRich (with last version 2.0) was removed from CRAN

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

2013-09-24 2.0
2013-05-31 1.0

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Package iBATCGH (with last version 1.2) was removed from CRAN

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

2015-02-24 1.2
2014-09-13 1.1
2014-09-02 1.0

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Package epi2loc (with last version 1.0-1) was removed from CRAN

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

2014-07-04 1.0-1

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Package gbs (with last version 1.0) was removed from CRAN

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

2008-05-06 1.0

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Package diskmemoiser (with last version 1.0-1) was removed from CRAN

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

2014-06-30 1.0-1

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Package glassomix (with last version 1.2) was removed from CRAN

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

2013-11-05 1.2
2013-05-30 1.1
2013-05-13 1.0

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Package extracat (with last version 1.7-1) was removed from CRAN

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

2014-10-21 1.7-1
2014-05-20 1.7-0
2013-12-12 1.6-4
2013-05-27 1.6-3
2013-05-03 1.6-2
2012-10-04 1.6-1
2012-05-15 1.5-0
2011-08-30 1.4-0
2011-08-28 1.3-0
2011-02-14 1.1-0
2010-03-02 1.0-1
2010-01-19 1.0-0

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Package branchLars (with last version 1.0) was removed from CRAN

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

2013-05-29 1.0

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Package rplos updated to version 0.5.0 with previous version 0.4.7 dated 2015-04-27

Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based search 'API' (http://api.plos.org/) provided by the Public Library of Science journals to search their articles. Functions are included for searching for articles, retrieving articles, making plots, doing 'faceted' searches, 'highlight' searches, and viewing results of 'highlighted' searches in a browser.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rplos versions 0.4.7 dated 2015-04-27 and 0.5.0 dated 2015-07-01

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Package ppiPre updated to version 1.8 with previous version 1.7 dated 2015-03-02

Title: Predict Protein-Protein Interactions Based on Functional and Topological Similarities
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng <anfdeng@163.com>

Diff between ppiPre versions 1.7 dated 2015-03-02 and 1.8 dated 2015-07-01

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Package MiRSEA updated to version 1.1 with previous version 1.0 dated 2015-05-31

Title: 'MicroRNA' Set Enrichment Analysis
Description: The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.
Author: Junwei Han, Siyao Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>

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New package gquad with initial version 1.0-0
Package: gquad
Type: Package
Title: G Quadruplex Motif Prediction Tool
Version: 1.0-0
Date: 2015-06-26
Author: Hannah O. Ajoge
Maintainer: Hannah O. Ajoge <ohuajo@gmail.com>
Description: Nucleic acid sequences that are rich in guanine are capable of forming highly stable four-stranded structures known as G quadruplex motifs. This package provide functions for predicting G quadruplex motif(s) in nucleotide sequences.
License: Artistic-2.0
Imports: ape, seqinr
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-07-01 04:37:01 UTC; Hannah.Polytomella
Repository: CRAN
Date/Publication: 2015-07-01 11:30:11

More information about gquad at CRAN
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Package ggthemes updated to version 2.2.1 with previous version 2.1.2 dated 2015-03-01

Title: Extra Themes, Scales and Geoms for `ggplot2`
Description: Some extra themes, geoms, and scales for `ggplot2`.
Author: Jeffrey B. Arnold [aut, cre], Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb], Baptise Auguie [ctb], Bob Rudis [ctb], Justin Talbot [ctb] (Some code from the labeling package)
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

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Package CDM updated to version 4.4-1 with previous version 4.3-0 dated 2015-06-05

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>

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Package BEST updated to version 0.3.0 with previous version 0.2.2 dated 2014-06-06

Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates for group means and standard deviations and their differences and effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>

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Package alphaOutlier updated to version 1.1.0 with previous version 1.0.1 dated 2015-05-15

Title: Obtain Alpha-Outlier Regions for Well-Known Probability Distributions
Description: Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, doi: 10.1080/01621459.1993.10476339 for details.
Author: Andre Rehage, Sonja Kuhnt
Maintainer: Andre Rehage <rehage@statistik.tu-dortmund.de>

Diff between alphaOutlier versions 1.0.1 dated 2015-05-15 and 1.1.0 dated 2015-07-01

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Permanent link

Package VPdtw (with last version 2.1-10) was removed from CRAN

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

2012-08-22 2.1-10
2012-04-22 2.1-9
2010-10-12 2.1-8
2010-05-20 2.1-6
2009-11-19 2.1-4
2009-11-18 2.1-3

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Package PIGShift (with last version 1.0.0) was removed from CRAN

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2014-02-03 1.0.0

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Package Watersheds (with last version 1.0) was removed from CRAN

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2014-11-05 1.0

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Package SurvRegCensCov (with last version 1.3) was removed from CRAN

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2014-04-24 1.3
2014-04-07 1.2
2014-02-05 1.1
2014-01-15 1.0

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Package MGL (with last version 1.1) was removed from CRAN

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2014-11-05 1.1
2014-11-03 1.0

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Package SPMS (with last version 2.0) was removed from CRAN

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2013-08-08 2.0
2013-05-29 1.0

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Package Multiclasstesting (with last version 1.3.9) was removed from CRAN

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2014-03-17 1.3.9
2009-06-17 1.2.0
2009-04-23 1.0.0

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Package MFDA (with last version 1.1-4) was removed from CRAN

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2012-12-17 1.1-4

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2013-07-05 1.2.2

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Package RHive (with last version 2.0-0.2) was removed from CRAN

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2014-09-30 2.0-0.2
2014-08-27 2.0-0.1
2014-04-16 2.0-0.0

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Package BHMSMAfMRI (with last version 1.0) was removed from CRAN

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2014-08-04 1.0

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Package DBFTest (with last version 1.0) was removed from CRAN

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2014-03-19 1.0

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Package CALINE3 (with last version 1.0-2) was removed from CRAN

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2012-01-24 1.0
2012-01-24 1.0-2

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Package HistogramTools (with last version 0.3.1) was removed from CRAN

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2014-08-26 0.3.1
2013-12-11 0.3
2013-10-03 0.2

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Package BayesComm (with last version 0.1-0) was removed from CRAN

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2013-05-15 0.1-0

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Package CLAG (with last version 2.18.1) was removed from CRAN

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2013-09-13 2.18.1
2013-08-19 2.17.1
2013-06-06 2.16.1
2013-05-02 2.10
2013-04-30 2.7
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Package Brq (with last version 1.0) was removed from CRAN

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Package LVQTools (with last version 1.2) was removed from CRAN

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2013-04-08 1.2
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Package COP (with last version 1.0-2) was removed from CRAN

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2011-02-21 1.0-2
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Package ABCp2 (with last version 1.1) was removed from CRAN

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2013-07-23 1.1
2013-07-15 1.0

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Package spectralGP updated to version 1.3.3 with previous version 1.3.2 dated 2014-12-05

Title: Approximate Gaussian Processes Using the Fourier Basis
Description: Routines for creating, manipulating, and performing Bayesian inference about Gaussian processes in one and two dimensions using the Fourier basis approximation: simulation and plotting of processes, calculation of coefficient variances, calculation of process density, coefficient proposals (for use in MCMC). It uses R environments to store GP objects as references/pointers.
Author: Chris Paciorek <paciorek@alumni.cmu.edu>
Maintainer: Chris Paciorek <paciorek@alumni.cmu.edu>

Diff between spectralGP versions 1.3.2 dated 2014-12-05 and 1.3.3 dated 2015-07-01

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New package samplesize with initial version 0.2-2
Package: samplesize
Type: Package
Title: Sample Size Calculation for Various t-Tests and Wilcoxon-Test
Version: 0.2-2
Date: 2015-06-30
Author: Ralph Scherer
Maintainer: Ralph Scherer <shearer.ra76@gmail.com>
Description: Computes sample size for Student's t-test and for the Wilcoxon-Mann-Whitney test for categorical data. The t-test function allows paired and unpaired (balanced / unbalanced) designs as well as homogeneous and heterogeneous variances. The Wilcoxon function allows for ties.
License: GPL (>= 2)
URL: https://github.com/shearer/samplesize
BugReports: https://github.com/shearer/samplesize/issues
NeedsCompilation: no
Packaged: 2015-06-30 18:05:13 UTC; ralph
Repository: CRAN
Date/Publication: 2015-07-01 06:11:47

More information about samplesize at CRAN
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Package rsunlight updated to version 0.4.0 with previous version 0.3.0 dated 2014-08-20

Title: Interface to 'Sunlight' Foundation 'APIs'
Description: Interface to four 'Sunlight' Foundation 'APIs' (http://sunlightfoundation.com/api/) for government data, including the Congress 'API' 'v3', the Capitol Words 'API', the Influence Explorer 'API', and the Open States 'API'. 'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that collects and provides data on government activities, and those that influence government. Functions are provided to interact with each of the four 'APIs'.
Author: Scott Chamberlain [aut, cre], Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rerddap updated to version 0.2.0 with previous version 0.1.0 dated 2015-05-11

Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes functions to search for 'datasets', get summary information on 'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format. 'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package ptw updated to version 1.9-10 with previous version 1.0-7 dated 2014-03-29

Title: Parametric Time Warping
Description: Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.
Author: Jan Gerretzen <j.gerretzen@science.ru.nl>, Paul Eilers <p.eilers@erasmusmc.nl>, Hans Wouters, Tom Bloemberg <t.bloemberg@science.ru.nl>, Ron Wehrens <ron.wehrens@gmail.com>
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

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Package pollstR updated to version 1.2.1 with previous version 1.2.0 dated 2015-03-09

Title: Client for the HuffPost Pollster API
Description: Client for the HuffPost Pollster API, which provides access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre], Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

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Package Pade updated to version 0.1-3 with previous version 0.1-2 dated 2015-06-10

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 0.1-2 dated 2015-06-10 and 0.1-3 dated 2015-07-01

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Package Delaporte updated to version 2.2-3 with previous version 2.2-2 dated 2014-12-04

Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Delaporte versions 2.2-2 dated 2014-12-04 and 2.2-3 dated 2015-07-01

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Package cowplot updated to version 0.5.0 with previous version 0.4.0 dated 2015-06-14

Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2' library. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre], Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>

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Package causalsens updated to version 0.1.1 with previous version 0.1 dated 2013-04-21

Title: Selection Bias Approach to Sensitivity Analysis for Causal Effects
Description: The causalsens package provides functions to perform sensitivity analyses and to study how various assumptions about selection bias affects estimates of causal effects.
Author: Matthew Blackwell <mblackwell@gov.harvard.edu.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>

Diff between causalsens versions 0.1 dated 2013-04-21 and 0.1.1 dated 2015-07-01

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Package arulesViz updated to version 1.0-2 with previous version 1.0-1 dated 2015-06-26

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

Diff between arulesViz versions 1.0-1 dated 2015-06-26 and 1.0-2 dated 2015-07-01

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Package arules updated to version 1.1-7 with previous version 1.1-6 dated 2014-12-08

Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides interfaces to C implementations of the association mining algorithms Apriori and Eclat by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Bettina Gruen [aut, cph], Kurt Hornik [aut, cph], Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package archivist updated to version 1.5 with previous version 1.3 dated 2015-03-01

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between archivist versions 1.3 dated 2015-03-01 and 1.5 dated 2015-07-01

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