Thu, 02 Jul 2015

Package gsscopu updated to version 0.9-3 with previous version 0.9-2 dated 2014-12-06

Title: Copula Density and 2-D Hazard Estimation using Smoothing Splines
Description: A collection of routines for the estimation of copula density and 2-D hazard function using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

Diff between gsscopu versions 0.9-2 dated 2014-12-06 and 0.9-3 dated 2015-07-02

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Package gss updated to version 2.1-5 with previous version 2.1-4 dated 2014-12-06

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

Diff between gss versions 2.1-4 dated 2014-12-06 and 2.1-5 dated 2015-07-02

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Package EpiContactTrace updated to version 0.9.0 with previous version 0.8.8 dated 2013-11-05

Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing and visualisation of network of contacts.
Author: Maria Noremark [aut], Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

Diff between EpiContactTrace versions 0.8.8 dated 2013-11-05 and 0.9.0 dated 2015-07-02

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Package AGSDest updated to version 2.3 with previous version 2.2 dated 2015-01-29

Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence intervals based on the stage-wise ordering in group sequential designs and adaptive group sequential designs. For adaptive group sequential designs the confidence intervals are based on the conditional rejection probability principle. Currently the procedures do not support the use of futility boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>

Diff between AGSDest versions 2.2 dated 2015-01-29 and 2.3 dated 2015-07-02

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Package scuba updated to version 1.8-0 with previous version 1.7-0 dated 2013-12-15

Title: Diving Calculations and Decompression Models
Description: Code for describing and manipulating scuba diving profiles (depth-time curves) and decompression models, for calculating the predictions of decompression models, for calculating maximum no-decompression time and decompression tables, and for performing mixed gas calculations.
Author: Adrian Baddeley [aut, cre], Vittorio Broglio [ctb, dtc], Pedro Antonio Neves [ctb, dtc], Andrew Bassom [ctb], Peter Buzzacott [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>

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Package RenextGUI updated to version 1.3-0 with previous version 1.0-2 dated 2013-10-08

Title: GUI for Renext
Description: Graphical User Interface for Renext.
Author: Yves Deville <deville.yves@alpestat.com> and IRSN <renext@irsn.fr>
Maintainer: Lise Bardet <lise.bardet@irsn.fr>

Diff between RenextGUI versions 1.0-2 dated 2013-10-08 and 1.3-0 dated 2015-07-02

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Package rEMM updated to version 1.0-10 with previous version 1.0-9 dated 2015-05-15

Title: Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Description: Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph], Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package recommenderlab updated to version 0.1-6 with previous version 0.1-5 dated 2014-08-18

Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package neuroim updated to version 0.0.4 with previous version 0.0.3 dated 2014-04-04

Title: Read, Write, and Process Brain Imaging Data
Description: A collection of data structures that represent volumetric brain imaging data. The focus is on basic data handling for 3D and 4D neuroimaging data. In addition, there are function to read and write NIFTI files and limited support for reading AFNI files.
Author: Bradley R. Buchsbaum
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>

Diff between neuroim versions 0.0.3 dated 2014-04-04 and 0.0.4 dated 2015-07-02

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Package meta updated to version 4.3-0 with previous version 4.2-0 dated 2015-05-08

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between meta versions 4.2-0 dated 2015-05-08 and 4.3-0 dated 2015-07-02

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Package foreign updated to version 0.8-65 with previous version 0.8-64 dated 2015-06-28

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

Diff between foreign versions 0.8-64 dated 2015-06-28 and 0.8-65 dated 2015-07-02

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Package binseqtest updated to version 1.0.1 with previous version 1.0 dated 2014-08-08

Title: Exact Binary Sequential Designs and Analysis
Description: For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.
Author: Jenn Kirk, Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>

Diff between binseqtest versions 1.0 dated 2014-08-08 and 1.0.1 dated 2015-07-02

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New package VTrack with initial version 1.10
Package: VTrack
Type: Package
Title: Software for Analysing and Visualising Animal Movement from Acoustic Telemetry Detections
Version: 1.10
Date: 2015-07-02
Author: Ross G. Dwyer, Mathew E. Watts, Hamish A. Campbell & Craig E. Franklin
Maintainer: Ross Dwyer <ross.dwyer@uq.edu.au>
Description: Designed to facilitate the assimilation, analysis and synthesis of animal location and movement data collected by the VEMCO suite of acoustic transmitters and receivers. As well as database and geographic information capabilities the principal feature of VTrack is the qualification and identification of ecologically relevant events from the acoustic detection and sensor data. This procedure condenses the acoustic detection database by orders of magnitude, greatly enhancing the synthesis of acoustic detection data.
Depends: R (>= 3.1.0), foreach(>= 1.2.0), parallel, doParallel
Imports: plotKML, sp, spacetime
License: GPL (>= 2)
URL: http://www.uq.edu.au/eco-lab/v-track
Encoding: latin1
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-07-02 07:24:56 UTC; rossd
Repository: CRAN
Date/Publication: 2015-07-02 13:42:37

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Package streamMOA updated to version 1.1-1 with previous version 1.1-0 dated 2015-05-22

Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between streamMOA versions 1.1-0 dated 2015-05-22 and 1.1-1 dated 2015-07-02

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Package stream updated to version 1.1-5 with previous version 1.1-4 dated 2015-05-24

Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between stream versions 1.1-4 dated 2015-05-24 and 1.1-5 dated 2015-07-02

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Package RRTCS updated to version 0.0.2 with previous version 0.0.1 dated 2015-04-24

Title: Randomized Response Techniques for Complex Surveys
Description: Point and interval estimation of linear parameters with data obtained from complex surveys (including stratified and clustered samples) when randomization techniques are used. The randomized response technique was developed to obtain estimates that are more valid when studying sensitive topics. Estimators and variances for 14 randomized response methods for qualitative variables and 7 randomized response methods for quantitative variables are also implemented. In addition, some data sets from surveys with these randomization methods are included in the package.
Author: Beatriz Cobo Rodríguez, María del Mar Rueda García, Antonio Arcos Cebrián
Maintainer: Beatriz Cobo Rodríguez <beacr@ugr.es>

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Package pheatmap updated to version 1.0.7 with previous version 1.0.2 dated 2015-03-10

Title: Pretty Heatmaps
Description: Implementation of heatmaps that offers more control over dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde <rkolde@gmail.com>

Diff between pheatmap versions 1.0.2 dated 2015-03-10 and 1.0.7 dated 2015-07-02

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New package NCA with initial version 1.0
Package: NCA
Type: Package
Title: Necessary Condition Analysis
Version: 1.0
Date: 2015-07-01
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2015. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods) NCA identifies necessary (but not sufficient) conditions in datasets. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations. (Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or input) is necessary but not sufficient for a (desired) level of y (e.g. good performance or output).
License: GPL (>= 3)
Imports: yaml, gplots, quantreg, Benchmarking, sfa
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-07-02 10:43:20 UTC; govert
Date/Publication: 2015-07-02 13:42:32

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Package multipleNCC updated to version 1.1 with previous version 1.0 dated 2014-09-19

Title: Weighted Cox-Regression for Nested Case-Control Data
Description: Fits Cox proportional hazard models with a weighted partial likelihood. It handles one and multiple endpoints, additional matching and makes it possible to reuse controls for other endpoints.
Author: Nathalie C. Stoer, Sven Ove Samuelsen
Maintainer: Nathalie C. Stoer <nathalcs@math.uio.no>

Diff between multipleNCC versions 1.0 dated 2014-09-19 and 1.1 dated 2015-07-02

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Package itsadug updated to version 1.0.1 with previous version 0.8 dated 2015-02-27

Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package mgcv (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).
Author: Jacolien van Rij [aut, cre], Martijn Wieling [aut], R. Harald Baayen [aut], Hedderik van Rijn [aut]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>

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New package ComplexAnalysis with initial version 1.0
Package: ComplexAnalysis
Type: Package
Title: Numerically Evaluate Integrals and Derivatives (also Higher Order) of Vector- And Complex-Valued Functions
Version: 1.0
Date: 2015-06-25
Author: Char Leung
Maintainer: Char Leung <charleung@hotmail.fr>
Description: Evaluate complex integrals along a disc or a straight line. Evaluate higher-order derivatives by employing the Cauchy integral formula. Evaluate residues. Search for simple poles given a function. Evaluate limits.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-07-02 09:19:17 UTC; Char
Repository: CRAN
Date/Publication: 2015-07-02 13:42:31

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Package arulesNBMiner updated to version 0.1-5 with previous version 0.1-4 dated 2014-07-30

Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets presented in "Michael Hahsler. A model-based frequency constraint for mining associations from transaction data. Data Mining and Knowledge Discovery, 13(2):137-166, September 2006." In addition an extension for NB-precise rules is implemented.
Author: Michael Hahsler
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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

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

2013-10-10 1.0

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Package survival updated to version 2.38-3 with previous version 2.38-2 dated 2015-06-12

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

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Package autoencoder updated to version 1.1 with previous version 1.0 dated 2014-05-21

Title: Sparse Autoencoder for Automatic Learning of Representative Features from Unlabeled Data
Description: Implementation of the sparse autoencoder in R environment, following the notes of Andrew Ng (http://www.stanford.edu/class/archive/cs/cs294a/cs294a.1104/sparseAutoencoder.pdf). The features learned by the hidden layer of the autoencoder (through unsupervised learning of unlabeled data) can be used in constructing deep belief neural networks.
Author: Eugene Dubossarsky (project leader, chief designer), Yuriy Tyshetskiy (design, implementation, testing)
Maintainer: Yuriy Tyshetskiy <yuriy.tyshetskiy@nicta.com.au>

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New package VIFCP with initial version 1.1
Package: VIFCP
Version: 1.1
Title: Detecting Change-Points via VIFCP Method
Author: Xiaoping Shi, Xiangsheng Wang, Dongwei Wei, Yuehua Wu
Maintainer: Dongwei Wei <weidw@mathstat.yorku.ca>
Depends: R (>= 3.1.3)
License: LGPL-3
Description: Contains a function to support the paper 'A sequential multiple change-point detection procedure via VIF regression' (Accepted by Computational Statistics).
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-07-01 21:12:30 UTC; weidw
Date/Publication: 2015-07-02 06:51:10

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Package translation.ko updated to version 0.0.1.5.2 with previous version 0.0.1.3 dated 2015-06-25

Title: R Manuals Literally Translated in Korean
Description: R version 2.1.0 and later support Korean translations of program messages. The continuous efforts have been made by <http://developer.r-project.org/TranslationTeams.html> The R Documentation files are licensed under the General Public License, version 2 or 3. This means that the pilot project to translate them into Korean has permission to reproduce them and translate them. This work is done with GNU 'gettext' utilities. The portable object template is updated a weekly basis or whenever changes are necessary. Comments and corrections via email to the maintainer is of course most welcome. In order to voluntarily participate in or offer your help with this translation, please contact the maintainer. To check the change and progress of Korean translation, please visit <http://www.openstatistics.net>.
Author: Chel Hee Lee [aut, cre], Edward Kang [ctb], Sunyoung Kim [ctb], Heather Kim [ctb]
Maintainer: Chel Hee Lee <chl948@mail.usask.ca>

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Package SRCS updated to version 1.1 with previous version 1.0 dated 2015-01-01

Title: Statistical Ranking Color Scheme for Multiple Pairwise Comparisons
Description: Implementation of the SRCS method for a color-based visualization of the results of multiple pairwise tests on a large number of problem configurations, proposed in: I.G. del Amo, D.A. Pelta. SRCS: a technique for comparing multiple algorithms under several factors in dynamic optimization problems. In: E. Alba, A. Nakib, P. Siarry (Eds.), Metaheuristics for Dynamic Optimization. Series: Studies in Computational Intelligence 433, Springer, Berlin/Heidelberg, 2012.
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>

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Package NHANES updated to version 2.1.0 with previous version 2.0 dated 2015-05-12

Title: Data from the US National Health and Nutrition Examination Study
Description: Body Shape and related measurements from the US National Health and Nutrition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/nchs/nhanes.htm for details.
Author: Randall Pruim <rpruim@calvin.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package memuse updated to version 2.5 with previous version 1.1 dated 2013-08-07

Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have? Learn the scintillating answer to these and many more such questions with the 'memuse' package.
Author: Drew Schmidt [aut, cre], Christian Heckendorf [ctb], Wei-Chen Chen [ctb]
Maintainer: Drew Schmidt <wrathematics@gmail.com>

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Package MASS updated to version 7.3-42 with previous version 7.3-41 dated 2015-06-18

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between MASS versions 7.3-41 dated 2015-06-18 and 7.3-42 dated 2015-07-02

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 MD5            |   10 +++++-----
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Permanent link

New package latex2exp with initial version 0.3.0
Package: latex2exp
Type: Package
Title: Use LaTeX Expressions in Plots
Version: 0.3.0
Date: 2015-06-30
Authors@R: person("Stefano", "Meschiari", email="stefano.meschiari@gmail.com", role=c("aut", "cre"))
Description: Parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.
License: MIT + file LICENSE
URL: http://github.com/stefano-meschiari/latex2exp
BugReports: https://github.com/stefano-meschiari/latex2exp/issues
Imports: stringr, magrittr
LazyData: TRUE
Suggests: testthat, knitr, ggplot2, plyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-07-01 21:42:19 UTC; sm52286
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Repository: CRAN
Date/Publication: 2015-07-02 06:47:22

More information about latex2exp at CRAN
Permanent link

Package dsample updated to version 0.91.1.5 with previous version 0.91.1 dated 2013-05-14

Title: Discretization-Based Direct Random Sample Generation
Description: Two discretization-based Monte Carlo algorithms, namely the Fu-Wang algorithm and the Wang-Lee algorithm, are provided for random sample generation from a high dimensional distribution of complex structure. The normalizing constant of the target distribution needs not to be known.
Author: Chel Hee Lee [aut, cre], Liqun Wang [aut]
Maintainer: Chel Hee Lee <gnustats@gmail.com>

Diff between dsample versions 0.91.1 dated 2013-05-14 and 0.91.1.5 dated 2015-07-02

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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>

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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

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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>

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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>

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More information about raster at CRAN
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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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 geosphere-1.4-3/geosphere/R/areaPolygon.R         |   59 +++++++++++--------
 geosphere-1.4-3/geosphere/R/bearing.R             |   31 +++++++---
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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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 sjPlot-1.8.2/sjPlot/R/sjPlotInteractions.R     | 2824 +++++++++--------
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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

 DESCRIPTION                          |   14 +-
 MD5                                  |   48 ++++--
 NAMESPACE                            |   17 ++
 NEWS                                 |   20 ++
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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

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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

 DESCRIPTION                      |    7 ++++---
 MD5                              |   21 +++++++++++----------
 NAMESPACE                        |    1 +
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 README.md                        |   16 ++++++++++++++--
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 vignettes/interplot-vignette.Rmd |    7 +++++++
 12 files changed, 62 insertions(+), 25 deletions(-)

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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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More information about GRANBase at CRAN
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 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 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 reccsim (with last version 0.9-1) was removed from CRAN

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2012-09-28 0.9-1

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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 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 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 phom (with last version 1.0.3) was removed from CRAN

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2014-02-09 1.0.3

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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 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 predfinitepop (with last version 1.0) was removed from CRAN

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2014-04-25 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/DESCRIPTION                                                      |   18 
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 nat-1.7.0/nat/NEWS                                                             |   29 
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 nat-1.7.0/nat/R/cmtk.R                                                         |    2 
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 nat-1.7.0/nat/R/neuron-plot.R                                                  |   30 
 nat-1.7.0/nat/R/neuron.R                                                       |   18 
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 nat-1.7.0/nat/R/neuronlistfh.R                                                 |   56 +
 nat-1.7.0/nat/R/ngraph.R                                                       |   24 
 nat-1.7.0/nat/R/nrrd-io.R                                                      |  305 +++++++---
 nat-1.7.0/nat/R/seglist.R                                                      |   22 
 nat-1.7.0/nat/R/xform.R                                                        |   55 +
 nat-1.7.0/nat/R/xformimage.R                                                   |   84 +-
 nat-1.7.0/nat/R/xformpoints.R                                                  |   65 +-
 nat-1.7.0/nat/R/zzz.R                                                          |    2 
 nat-1.7.0/nat/man/as.im3d.Rd                                                   |   14 
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 nat-1.7.0/nat/man/coord2ind.Rd                                                 |    2 
 nat-1.7.0/nat/man/dotprops.Rd                                                  |    3 
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 nat-1.7.0/nat/man/im3d-coords.Rd                                               |   12 
 nat-1.7.0/nat/man/im3d-io.Rd                                                   |   10 
 nat-1.7.0/nat/man/im3d.Rd                                                      |   10 
 nat-1.7.0/nat/man/imexpand.grid.Rd                                             |   10 
 nat-1.7.0/nat/man/imslice.Rd                                                   |   10 
 nat-1.7.0/nat/man/ind2coord.Rd                                                 |    8 
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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

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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>

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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 gbs (with last version 1.0) was removed from CRAN

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2008-05-06 1.0

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

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

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

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2014-07-04 1.0-1

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

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2013-09-24 2.0
2013-05-31 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 lazyWeave (with last version 2.2.5) was removed from CRAN

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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 branchLars (with last version 1.0) was removed from CRAN

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2013-05-29 1.0

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

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2014-06-30 1.0-1

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

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2014-11-27 0.9.0

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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 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>

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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>

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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

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

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

2014-02-03 1.0.0

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

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

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

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

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

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

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

2012-12-17 1.1-4

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

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

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 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 MGL (with last version 1.1) was removed from CRAN

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

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

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

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

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

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Package MADAM (with last version 1.2.2) was removed from CRAN

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

2013-07-05 1.2.2

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