Mon, 14 Dec 2015

Package simsalapar updated to version 1.0-6 with previous version 1.0-5 dated 2015-01-24

Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating large-scale simulation studies with graphics and tables, including parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between simsalapar versions 1.0-5 dated 2015-01-24 and 1.0-6 dated 2015-12-14

 DESCRIPTION        |   19 +++----
 MD5                |   21 ++++----
 NAMESPACE          |    4 +
 R/graphics.R       |  135 +++++------------------------------------------------
 R/grid-stuff.R     |    2 
 R/subjob.R         |   44 ++++++++++++++---
 R/tables.R         |  103 +---------------------------------------
 demo/VaRsuperadd.R |   39 ++++++++-------
 demo/robcovMCD.R   |   79 +++++++++++++++++++++----------
 man/device.Rd      |   15 +++--
 man/mayplot.Rd     |   16 ++----
 tests/tst-wrongs.R |only
 12 files changed, 173 insertions(+), 304 deletions(-)

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Permanent link

Package openssl updated to version 0.8 with previous version 0.6 dated 2015-11-18

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut], Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between openssl versions 0.6 dated 2015-11-18 and 0.8 dated 2015-12-14

 openssl-0.6/openssl/src/apple.h                             |only
 openssl-0.8/openssl/DESCRIPTION                             |   28 +-
 openssl-0.8/openssl/MD5                                     |  112 +++++----
 openssl-0.8/openssl/NAMESPACE                               |    7 
 openssl-0.8/openssl/NEWS                                    |   11 
 openssl-0.8/openssl/R/bignum.R                              |   14 -
 openssl-0.8/openssl/R/cert.R                                |   16 -
 openssl-0.8/openssl/R/hash.R                                |  142 ++++++------
 openssl-0.8/openssl/R/mykey.R                               |   29 ++
 openssl-0.8/openssl/R/stream.R                              |   19 +
 openssl-0.8/openssl/R/write.R                               |   16 +
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 openssl-0.8/openssl/man/aes_cbc.Rd                          |    2 
 openssl-0.8/openssl/man/base64_encode.Rd                    |    2 
 openssl-0.8/openssl/man/bignum.Rd                           |   16 +
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 openssl-0.8/openssl/man/encrypt_envelope.Rd                 |    2 
 openssl-0.8/openssl/man/hash.Rd                             |   56 ++--
 openssl-0.8/openssl/man/keygen.Rd                           |    2 
 openssl-0.8/openssl/man/my_key.Rd                           |   25 +-
 openssl-0.8/openssl/man/openssl.Rd                          |    2 
 openssl-0.8/openssl/man/rand_bytes.Rd                       |    2 
 openssl-0.8/openssl/man/read_key.Rd                         |    2 
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 openssl-0.8/openssl/man/signatures.Rd                       |    2 
 openssl-0.8/openssl/man/write_pem.Rd                        |    8 
 openssl-0.8/openssl/src/aes.c                               |    6 
 openssl-0.8/openssl/src/base64.c                            |    6 
 openssl-0.8/openssl/src/bignum.c                            |    6 
 openssl-0.8/openssl/src/cert.c                              |   25 +-
 openssl-0.8/openssl/src/envelope.c                          |    6 
 openssl-0.8/openssl/src/error.c                             |    1 
 openssl-0.8/openssl/src/hash.c                              |   29 +-
 openssl-0.8/openssl/src/keygen.c                            |    3 
 openssl-0.8/openssl/src/onload.c                            |    3 
 openssl-0.8/openssl/src/openssh.c                           |    3 
 openssl-0.8/openssl/src/rand.c                              |    6 
 openssl-0.8/openssl/src/read.c                              |    6 
 openssl-0.8/openssl/src/rsa.c                               |    6 
 openssl-0.8/openssl/src/signing.c                           |    7 
 openssl-0.8/openssl/src/ssl.c                               |   26 +-
 openssl-0.8/openssl/src/stream.c                            |   52 ++++
 openssl-0.8/openssl/src/utils.h                             |    1 
 openssl-0.8/openssl/src/write.c                             |   27 +-
 openssl-0.8/openssl/tests/testthat/test_cert.R              |only
 openssl-0.8/openssl/tests/testthat/test_hash_output_value.R |   59 ++--
 openssl-0.8/openssl/tests/testthat/test_keys_dsa.R          |   14 +
 openssl-0.8/openssl/tests/testthat/test_keys_ecdsa.R        |   14 +
 openssl-0.8/openssl/tests/testthat/test_keys_ecdsa384.R     |   14 +
 openssl-0.8/openssl/tests/testthat/test_keys_ecdsa521.R     |   14 +
 openssl-0.8/openssl/tests/testthat/test_keys_rsa.R          |   14 +
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 62 files changed, 603 insertions(+), 306 deletions(-)

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Package matlib updated to version 0.6.0 with previous version 0.5.2 dated 2015-11-19

Title: Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. These functions are mainly for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb], Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

Diff between matlib versions 0.5.2 dated 2015-11-19 and 0.6.0 dated 2015-12-14

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 MD5                            |   46 ++++++++++++++++++++++++++++-------------
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 33 files changed, 145 insertions(+), 65 deletions(-)

More information about matlib at CRAN
Permanent link

Package dbscan updated to version 0.9-6 with previous version 0.9-5 dated 2015-10-05

Title: Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph], Sunil Arya [ctb, cph], David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between dbscan versions 0.9-5 dated 2015-10-05 and 0.9-6 dated 2015-12-14

 DESCRIPTION              |   13 ++--
 MD5                      |   60 ++++++++++-----------
 NAMESPACE                |   10 ++-
 R/LOF.R                  |   10 +--
 R/RcppExports.R          |    8 +-
 R/dbscan.R               |   41 ++++++++++----
 R/frNN.R                 |   37 ++++++++++++-
 R/kNN.R                  |   39 +++++++++++--
 R/kNNdist.R              |   12 ----
 R/optics.R               |   57 ++++++++++++++------
 README.md                |   47 +++++++++++-----
 inst/NEWS                |    7 ++
 inst/test_data           |only
 inst/tests/test-dbscan.R |    7 ++
 inst/tests/test-frNN.R   |   50 ++---------------
 inst/tests/test-kNN.R    |   34 ++++--------
 inst/tests/test-lof.R    |    5 +
 inst/tests/test-optics.R |   41 ++++++++++----
 man/dbscan.Rd            |   34 ++++++------
 man/frNN.Rd              |   16 +++--
 man/kNN.Rd               |   34 ++++++++----
 man/kNNdist.Rd           |   15 +----
 man/lof.Rd               |   10 ++-
 man/optics.Rd            |   67 ++++++++++++-----------
 src/R_dbscan.cpp         |   73 ++++++++++++++++---------
 src/R_frNN.cpp           |   16 ++---
 src/R_kNN.cpp            |    1 
 src/R_optics.cpp         |  133 ++++++++++++++++++++++++++++-------------------
 src/R_regionQuery.cpp    |    4 -
 src/R_regionQuery.h      |    2 
 src/RcppExports.cpp      |   14 ++--
 31 files changed, 538 insertions(+), 359 deletions(-)

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Package rTensor updated to version 1.3 with previous version 1.2 dated 2014-11-11

Title: Tools for Tensor Analysis and Decomposition
Description: A set of tools for creation, manipulation, and modeling of tensors with arbitrary number of modes. A tensor in the context of data analysis is a multidimensional array. rTensor does this by providing a S4 class 'Tensor' that wraps around the base 'array' class. rTensor provides common tensor operations as methods, including matrix unfolding, summing/averaging across modes, calculating the Frobenius norm, and taking the inner product between two tensors. Familiar array operations are overloaded, such as index subsetting via '[' and element-wise operations. rTensor also implements various tensor decomposition, including CP, GLRAM, MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements transpose, t-product, and t-SVD, as defined in Kilmer et al. (2013). Some auxiliary functions include the Khatri-Rao product, Kronecker product, and the Hamadard product for a list of matrices.
Author: James Li and Jacob Bien and Martin Wells
Maintainer: James Li <jamesyili@gmail.com>

Diff between rTensor versions 1.2 dated 2014-11-11 and 1.3 dated 2015-12-14

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Package rcbalance updated to version 1.8.0 with previous version 1.7.5 dated 2015-11-22

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

Diff between rcbalance versions 1.7.5 dated 2015-11-22 and 1.8.0 dated 2015-12-14

 DESCRIPTION              |    9 +++---
 MD5                      |   21 ++++++++++-----
 R/build.dist.struct.R    |   30 +++++++++++----------
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 10 files changed, 105 insertions(+), 66 deletions(-)

More information about rcbalance at CRAN
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Package plm updated to version 1.5-12 with previous version 1.4-0 dated 2013-12-28

Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data.
Author: Yves Croissant [aut, cre], Giovanni Millo [aut], Ott Toomet [ctb], Christian Kleiber [ctb], Achim Zeileis [ctb], Arne Henningsen [ctb], Liviu Andronic [ctb], Nina Schoenfelder [ctb], Kevin Tappe [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>

Diff between plm versions 1.4-0 dated 2013-12-28 and 1.5-12 dated 2015-12-14

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Package phangorn updated to version 2.0.1 with previous version 2.0.0 dated 2015-12-10

Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

Diff between phangorn versions 2.0.0 dated 2015-12-10 and 2.0.1 dated 2015-12-14

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Package gaston updated to version 1.3.1 with previous version 1.2 dated 2015-11-10

Title: Genetic Data Manipulation (Quality Control, GRM and LD Computations, PCA), Linear Mixed Models (AIREML Algorithm), Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>

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New package vita with initial version 1.0.0
Package: vita
Type: Package
Title: Variable Importance Testing Approaches
Version: 1.0.0
Date: 2015-12-12
Authors@R: person("Ender", "Celik", email = "celik.p.ender@gmail.com", role = c("aut", "cre"))
Author: Ender Celik [aut, cre]
Maintainer: Ender Celik <celik.p.ender@gmail.com>
Description: Implements the novel testing approach by Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> for the permutation variable importance measure in a random forest and the PIMP-algorithm by Altmann et al.(2010) <doi:10.1093/bioinformatics/btq134>. Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4> do not use the "standard" permutation variable importance but the cross-validated permutation variable importance for the novel test approach. The cross-validated permutation variable importance is not based on the out-of-bag observations but uses a similar strategy which is inspired by the cross-validation procedure. The novel test approach can be applied for classification trees as well as for regression trees. However, the use of the novel testing approach has not been tested for regression trees so far, so this routine is meant for the expert user only and its current state is rather experimental.
Depends: R (>= 3.1.0)
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.11.6),parallel,randomForest,stats
LinkingTo: Rcpp
Suggests: mnormt
NeedsCompilation: yes
Packaged: 2015-12-14 17:52:38 UTC; ender
Repository: CRAN
Date/Publication: 2015-12-14 19:05:44

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Package tnam updated to version 1.6 with previous version 1.5.3 dated 2015-09-22

Title: Temporal Network Autocorrelation Models (TNAM)
Description: Temporal and cross-sectional network autocorrelation models (TNAM).
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>

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Package SimCorMultRes updated to version 1.4.0 with previous version 1.3.1 dated 2015-09-08

Title: Simulates Correlated Multinomial Responses
Description: Simulates correlated multinomial responses by utilizing threshold approaches under a marginal model specification.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>

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Package RCircos updated to version 1.1.3 with previous version 1.1.2 dated 2013-10-30

Title: Circos 2D Track Plot
Description: A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
Author: Hongen Zhang
Maintainer: Hongen Zhang <hzhang@mail.nih.gov>

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Package morse updated to version 2.1.0 with previous version 2.0.0 dated 2015-09-01

Title: MOdelling Tools for Reproduction and Survival Data in Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of bioassay data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon- Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>

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Package InterSIM updated to version 2.0 with previous version 1.0 dated 2015-08-13

Title: Simulation of Inter-Related Genomic Datasets
Description: Generates three inter-related genomic datasets : methylation, gene expression and protein expression.
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Rama Raghavan <rraghavan@kumc.edu>

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New package hellno with initial version 0.0.1
Package: hellno
Type: Package
Title: Providing 'stringsAsFactors=FALSE' Variants of 'data.frame()' and 'as.data.frame()'
Version: 0.0.1
Date: 2015-12-14
Author: Peter Meissner
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Description: Base R's default setting for 'stringsAsFactors' within 'data.frame()' and 'as.data.frame()' is supposedly the most often complained about piece of code in the R infrastructure. The 'hellno' package provides an explicit solution without changing R itself or having to mess around with options. It tries to solve this problem by providing alternative 'data.frame()' and 'as.data.frame()' functions that are in fact simple wrappers around base R's 'data.frame()' and 'as.data.frame()' with 'stringsAsFactors' option set to 'HELLNO' ( which in turn equals FALSE ) by default.
License: MIT + file LICENSE
URL: https://github.com/petermeissner/hellno
BugReports: https://github.com/petermeissner/hellno/issues
LazyData: TRUE
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-14 17:06:22 UTC; peter
Repository: CRAN
Date/Publication: 2015-12-14 18:34:03

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Package ERP updated to version 1.1 with previous version 1.0.1 dated 2014-04-04

Title: Significance Analysis of Event-Related Potentials Data
Description: The functions provided in the package ERP are designed for the significance analysis of ERP data in a linear model framework. The possible procedures are either the collection of FDR or FWER controlling methods available in the generic function p.adjust, the same collection combined with a factor modeling of the time dependence among tests (see Sheu, Perthame, Lee and Causeur, 2016) and the Guthrie and Buchwald (1991) test.
Author: David Causeur (Agrocampus, Rennes, France) and Ching-Fan Sheu (National Cheng-Kung University, Tainan, Taiwan)
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>

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Package effects updated to version 3.0-5 with previous version 3.0-4 dated 2015-06-11

Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package crunch updated to version 1.7.3 with previous version 1.6.1 dated 2015-11-19

Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>

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Package ComICS updated to version 1.0.1 with previous version 1.0.0 dated 2015-12-09

Title: Computational Methods for Immune Cell-Type Subsets
Description: Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
Author: Yael Steuerman [aut, cre], Irit Gat-Viks [aut]
Maintainer: Yael Steuerman <yaelsteu@mail.tau.ac.il>

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Package car updated to version 2.1-1 with previous version 2.1-0 dated 2015-09-03

Title: Companion to Applied Regression
Description: Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Daniel Adler [ctb], Douglas Bates [ctb], Gabriel Baud-Bovy [ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Rafael Laboissiere [ctb], Georges Monette [ctb], Duncan Murdoch [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian Ripley [ctb], William Venables [ctb], David Winsemius [ctb], Achim Zeileis [ctb], R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package captr updated to version 0.1.3 with previous version 0.1.2 dated 2015-10-31

Title: Client for the Captricity API
Description: Get text from images of text using Captricity Optical Character Recognition (OCR) API. Captricity allows you to get text from handwritten forms --- think surveys --- and other structured paper documents. And it can output data in form a delimited file keeping field information intact. For more information, read https://shreddr.captricity.com/developer/overview/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>

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Package btergm updated to version 1.6 with previous version 1.5.9 dated 2015-09-24

Title: Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>

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Package AF updated to version 0.1.1 with previous version 0.1 dated 2015-08-26

Title: Model-Based Estimation of Confounder-Adjusted Attributable Fractions
Description: Estimates the attributable fraction in different sampling designs adjusted for measured confounders using logistic regression (cross-sectional and case-control designs), conditional logistic regression (matched case-control design) and Cox proportional hazard regression (cohort design with time-to-event outcome). The variance of the estimator is obtained by combining the delta method with the the sandwich formula.
Author: Elisabeth Dahlqwist and Arvid Sjolander
Maintainer: Elisabeth Dahlqwist <elisabeth.dahlqwist@ki.se>

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Package snht updated to version 1.0.3 with previous version 1.0.2 dated 2015-03-29

Title: Standard Normal Homogeneity Test
Description: Implementation of robust and non-robust Standard Normal Homogeneity Test (SNHT) for changepoint detection. This test statistic is equal sided, as proposed in "Homogenization of Radiosonde Temperature Time Series Using Innovation Statistics" by Haimberger, L., 2007. However, the statistic contains an estimate of sigma^2 in the denominator instead of sigma, which seems to be a more appropriate value (based on the paper "Homogenization of Swedish temperature data. Part I: Homogeneity test for linear trends." by Alexandersson, H., and A. Moberg, 1997).
Author: Josh Browning [aut, cre], Carina Schneider [aut]
Maintainer: Josh Browning <jbrownin@mines.edu>

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Package RRreg updated to version 0.6.0 with previous version 0.5.0 dated 2015-11-12

Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze randomized response (RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A survey technique for eliminating evasive answer bias. Journal of the American Statistical Association, 60, 63–69). Besides univariate estimates of true proportions, RR variables can be used for correlations, as dependent variable in a logistic regression (with or without random effects), as predictors in a linear regression, or as dependent variable in a beta-binomial ANOVA. For simulation and bootstrap purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>

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Package prepdat updated to version 1.0.5 with previous version 1.0.4 dated 2015-11-22

Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data collected in an experimental design for statistical analysis (e.g., analysis of variance ;ANOVA) by taking the individual data files and preparing one table that contains several possibilities for dependent variables. Most suitable when measuring reaction-times and/or accuracy, or any other variable in an interval or ratio scale. Functions included: file_merge(), read_data() and prep(). The file_merge() function vertically merges individual data files (in a long format) in which each line is a single trial within the experiment to one single dataset. The read_data() function reads a file in a txt or csv format that contains a single dataset in a long format table and creates a data frame from it. The prep() function aggregates the single dataset according to any combination of between and within grouping variables (i.e., between-subjects and within-subjects independent variables, respectively), and returns a data frame with a number of dependent measures for further analysis for each experimental cell according to the combination of provided grouping variables. Dependent measures for each experimental cell include among others means before and after rejecting all values according to a flexible standard deviation criterion/s, number of rejected values according to the flexible standard deviation criterion/s, proportions of rejected values according to the flexible standard deviation criterion/s, number of values before rejection, means after rejecting values according to procedures described in Van Selst & Jolicoeur (1994) (suitable when measuring reaction-times), standard deviations, medians, means according to any percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The data frame prep() returns can also be exported as a txt file to be used for statistical analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre], Roy Luria [aut], Jim Grange [ctb], Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>

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Package LightningR updated to version 1.0.2 with previous version 1.0.1 dated 2015-08-26

Title: Tools for Communication with Lightning-Viz Server
Description: The purpose of this package is to enable usage of lightningviz server to be accessible from R. The server itself can be found at http://lightning-viz.org/ and is required to work with this package. Package by itself cannot and will not create any visualizations.
Author: Ermlab
Maintainer: Kolodziejski Kamil <kolodziejski.kamil@hotmail.com>

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Package iClick updated to version 1.1 with previous version 1.0 dated 2015-12-09

Title: A Button-Based GUI for Financial and Economic Data Analysis
Description: A GUI designed to support the analysis of financial-economic time series data.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@mail.shu.edu.tw>

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Package gapmap updated to version 0.0.4 with previous version 0.0.3 dated 2015-11-16

Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Description: The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo@vda-lab.be>

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New package clusrank with initial version 0.1-0
Package: clusrank
Version: 0.1-0
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Imports: stats
Authors@R: c(person(given = "Yujing", family = "Jiang", email = "yujing.jiang@uconn.edu", role = c("aut","cre")), person(given = "Xin", family = "He", role = "ctb"), person(given = "Mei-Ling Ting", family = "Lee", role = "ctb"), person(given = "Jun", family = "Yan", role = "ctb"))
License: GPL (>= 3)
Depends: R (>= 3.1.0)
VignetteBuilder: knitr
Suggests: knitr
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-14 12:21:35 UTC; root
Author: Yujing Jiang [aut, cre], Xin He [ctb], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Repository: CRAN
Date/Publication: 2015-12-14 14:15:36

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Package scatterD3 updated to version 0.5.1 with previous version 0.5 dated 2015-11-27

Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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Package rTableICC updated to version 1.0.3 with previous version 1.0.2 dated 2015-03-23

Title: Random Generation of Contingency Tables
Description: Contains functions for random generation of R x C and 2 x 2 x K contingency tables. In addition to the generation of contingency tables over predetermined intraclass-correlated clusters, it is possible to generate contingency tables without intraclass correlations under product multinomial, multinomial, and Poisson sampling plans. It also consists of a function for generation of random data from a given discrete probability distribution function.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>

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Package hpoPlot updated to version 2.4 with previous version 2.2 dated 2015-08-26

Title: Functions for Plotting HPO Terms
Description: Collection of functions for manipulating sets of HPO terms and plotting them with a various options.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>

Diff between hpoPlot versions 2.2 dated 2015-08-26 and 2.4 dated 2015-12-14

 hpoPlot-2.2/hpoPlot/man/get.grey.borders.Rd                          |only
 hpoPlot-2.2/hpoPlot/man/get.hpo.terms.Rd                             |only
 hpoPlot-2.2/hpoPlot/man/get.no.borders.Rd                            |only
 hpoPlot-2.2/hpoPlot/man/get.standard.sizes.Rd                        |only
 hpoPlot-2.2/hpoPlot/man/get.white.nodes.Rd                           |only
 hpoPlot-2.4/hpoPlot/DESCRIPTION                                      |   12 
 hpoPlot-2.4/hpoPlot/MD5                                              |  123 ++++------
 hpoPlot-2.4/hpoPlot/NAMESPACE                                        |    7 
 hpoPlot-2.4/hpoPlot/R/data.R                                         |   92 +++----
 hpoPlot-2.4/hpoPlot/R/graphs.R                                       |   66 +----
 hpoPlot-2.4/hpoPlot/R/sets.R                                         |   10 
 hpoPlot-2.4/hpoPlot/build/vignette.rds                               |binary
 hpoPlot-2.4/hpoPlot/data/hpo.terms.RData                             |binary
 hpoPlot-2.4/hpoPlot/data/mpo.terms.RData                             |binary
 hpoPlot-2.4/hpoPlot/data/mpo.to.hpo.RData                            |binary
 hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.R                         |    2 
 hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.Rmd                       |    4 
 hpoPlot-2.4/hpoPlot/inst/doc/hpoPlot-guide.html                      |    6 
 hpoPlot-2.4/hpoPlot/man/apply.term.filters.Rd                        |    4 
 hpoPlot-2.4/hpoPlot/man/calibrate.sizes.Rd                           |    2 
 hpoPlot-2.4/hpoPlot/man/clean.terms.Rd                               |    2 
 hpoPlot-2.4/hpoPlot/man/exclude.branch.Rd                            |    2 
 hpoPlot-2.4/hpoPlot/man/get.ancestors.Rd                             |    2 
 hpoPlot-2.4/hpoPlot/man/get.case.based.colours.Rd                    |    2 
 hpoPlot-2.4/hpoPlot/man/get.case.based.labels.Rd                     |    2 
 hpoPlot-2.4/hpoPlot/man/get.case.term.matrix.Rd                      |    2 
 hpoPlot-2.4/hpoPlot/man/get.code.node.labels.Rd                      |    2 
 hpoPlot-2.4/hpoPlot/man/get.descendants.Rd                           |    2 
 hpoPlot-2.4/hpoPlot/man/get.frequency.based.colours.Rd               |    2 
 hpoPlot-2.4/hpoPlot/man/get.frequency.based.labels.Rd                |    2 
 hpoPlot-2.4/hpoPlot/man/get.frequency.based.sizes.Rd                 |    2 
 hpoPlot-2.4/hpoPlot/man/get.full.labels.Rd                           |    2 
 hpoPlot-2.4/hpoPlot/man/get.hpo.graph.Rd                             |   12 
 hpoPlot-2.4/hpoPlot/man/get.informative.node.labels.Rd               |    2 
 hpoPlot-2.4/hpoPlot/man/get.mpo.to.hpo.Rd                            |    2 
 hpoPlot-2.4/hpoPlot/man/get.node.friendly.long.names.Rd              |    2 
 hpoPlot-2.4/hpoPlot/man/get.ontology.Rd                              |    6 
 hpoPlot-2.4/hpoPlot/man/get.pop.frequency.based.colours.Rd           |    2 
 hpoPlot-2.4/hpoPlot/man/get.shortened.names.Rd                       |    2 
 hpoPlot-2.4/hpoPlot/man/get.significance.based.sizes.Rd              |    2 
 hpoPlot-2.4/hpoPlot/man/get.simple.node.labels.Rd                    |    2 
 hpoPlot-2.4/hpoPlot/man/get.term.adjacency.matrix.Rd                 |    2 
 hpoPlot-2.4/hpoPlot/man/get.term.descendancy.matrix.Rd               |    9 
 hpoPlot-2.4/hpoPlot/man/get.term.frequencies.Rd                      |    2 
 hpoPlot-2.4/hpoPlot/man/get.term.info.content.Rd                     |    2 
 hpoPlot-2.4/hpoPlot/man/get.term.pseudo.adjacency.matrix.Rd          |    2 
 hpoPlot-2.4/hpoPlot/man/hpo.plot.Rd                                  |   16 -
 hpoPlot-2.4/hpoPlot/man/hpo.terms.Rd                                 |    4 
 hpoPlot-2.4/hpoPlot/man/hpoPlot-package.Rd                           |    7 
 hpoPlot-2.4/hpoPlot/man/intersection.with.branches.Rd                |    2 
 hpoPlot-2.4/hpoPlot/man/mpo.terms.Rd                                 |    4 
 hpoPlot-2.4/hpoPlot/man/mpo.to.hpo.Rd                                |    4 
 hpoPlot-2.4/hpoPlot/man/n.most.frequent.terms.Rd                     |    6 
 hpoPlot-2.4/hpoPlot/man/p.values.for.occurrence.of.term.in.group.Rd  |    2 
 hpoPlot-2.4/hpoPlot/man/prune.branch.Rd                              |    2 
 hpoPlot-2.4/hpoPlot/man/remove.links.Rd                              |    2 
 hpoPlot-2.4/hpoPlot/man/remove.non.pa.terms.Rd                       |    2 
 hpoPlot-2.4/hpoPlot/man/remove.terms.with.less.than.n.occurrences.Rd |    6 
 hpoPlot-2.4/hpoPlot/man/remove.uninformative.for.plot.Rd             |    6 
 hpoPlot-2.4/hpoPlot/man/remove.uninformative.terms.Rd                |    2 
 hpoPlot-2.4/hpoPlot/man/setDimNames.Rd                               |    2 
 hpoPlot-2.4/hpoPlot/man/simpleCap.Rd                                 |    2 
 hpoPlot-2.4/hpoPlot/man/swap.out.alt.ids.Rd                          |    2 
 hpoPlot-2.4/hpoPlot/man/term.set.list.from.character.Rd              |    2 
 hpoPlot-2.4/hpoPlot/vignettes/hpoPlot-guide.Rmd                      |    4 
 65 files changed, 225 insertions(+), 253 deletions(-)

More information about hpoPlot at CRAN
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New package gge with initial version 1.0
Package: gge
Title: Genotype Plus Genotype-by-Environment Biplots
Version: 1.0
Date: 2015-12-13
Authors@R: c( person("Kevin","Wright", email="kw.stat@gmail.com", role=c("aut","cre")), person("Jean-Louis","Laffont", role=c("aut")) )
Description: Create biplots for GGE (genotype plus genotype-by-environment) and GGB (genotype plus genotype-by-block-of-environments) models.
Type: Package
Imports: reshape2
Suggests: agridat, knitr
License: GPL-2
LazyData: yes
URL: https://github.com/kwstat/gge
BugReports: https://github.com/kwstat/gge/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-13 21:30:33 UTC; wrightkevi
Author: Kevin Wright [aut, cre], Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-14 11:53:30

More information about gge at CRAN
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Package dendsort updated to version 0.3.3 with previous version 0.3.2 dated 2014-09-29

Title: Modular Leaf Ordering Methods for Dendrogram Nodes
Description: An implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai <ryo@vda-lab.be>

Diff between dendsort versions 0.3.2 dated 2014-09-29 and 0.3.3 dated 2015-12-14

 DESCRIPTION             |   30 ++++++++++++++++--------------
 MD5                     |   32 ++++++++++++++++----------------
 NAMESPACE               |   14 +++++++++++++-
 R/dendsort-package.R    |    3 ++-
 R/dendsort.R            |   14 ++++----------
 R/sort_smallest.R       |    3 ---
 build/vignette.rds      |binary
 man/cal_length.Rd       |    4 +++-
 man/cal_node_limit.Rd   |    4 +++-
 man/cal_total_length.Rd |    4 +++-
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 man/dendsort.Rd         |   18 ++++++++++--------
 man/sample_tcga.Rd      |    3 ++-
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 man/sort_average_r.Rd   |   14 ++++++++------
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 man/sort_smallest_r.Rd  |   10 ++++++----
 17 files changed, 107 insertions(+), 83 deletions(-)

More information about dendsort at CRAN
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New package exif with initial version 0.1.0
Package: exif
Type: Package
Title: Read EXIF Metadata from JPEGs
Version: 0.1.0
Date: 2015-12-13
Author: Oliver Keyes [aut, cre], Penelope Hopkins [ctb], Robyn Temple-Wood [ctb], Mayank Lahiri [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Description: Extracts Exchangeable Image File Format (EXIF) metadata, such as camera make and model, ISO speed and the date-time the picture was taken on, from JPEG images. Incorporates the 'easyexif' (https://github.com/mayanklahiri/easyexif) library.
License: BSD_2_clause + file LICENSE
Copyright: Mayank Lahiri for 'easyexif', Oliver Keyes for the integration with R, and Penelope Hopkins and Robyn Temple-Wood for the included test images (which are licensed CC-BY 4.0).
Suggests: testthat
LinkingTo: Rcpp
Imports: Rcpp
URL: https://github.com/Ironholds/exif
BugReports: https://github.com/Ironholds/exif/issues
SystemRequirements: C++11
OS_type: unix
NeedsCompilation: yes
Packaged: 2015-12-13 20:04:13 UTC; ironholds
Repository: CRAN
Date/Publication: 2015-12-14 11:53:29

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Package timeSeries updated to version 3022.101.2 with previous version 3022.101.1 dated 2015-12-11

Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching "Financial Engineering and Computational Finance". Managing financial time series objects.
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb]
Maintainer: Tobias Setz <tobias.setz@rmetrics.org>

Diff between timeSeries versions 3022.101.1 dated 2015-12-11 and 3022.101.2 dated 2015-12-14

 DESCRIPTION    |    8 ++++----
 MD5            |    4 ++--
 R/methods-is.R |   18 ++++++++----------
 3 files changed, 14 insertions(+), 16 deletions(-)

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Package ThresholdROC updated to version 2.3 with previous version 2.2 dated 2015-11-12

Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>

Diff between ThresholdROC versions 2.2 dated 2015-11-12 and 2.3 dated 2015-12-14

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 man/thres3.Rd               |    6 +++---
 9 files changed, 26 insertions(+), 23 deletions(-)

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Permanent link

Package RcmdrPlugin.KMggplot2 updated to version 0.2-1 with previous version 0.2-0 dated 2013-01-23

Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram, Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart, bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>

Diff between RcmdrPlugin.KMggplot2 versions 0.2-0 dated 2013-01-23 and 0.2-1 dated 2015-12-14

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 RcmdrPlugin.KMggplot2-0.2-1/RcmdrPlugin.KMggplot2/man/util-gettextKmg2.Rd                           |   11 
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 179 files changed, 1894 insertions(+), 1438 deletions(-)

More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link

Package MicroDatosEs updated to version 0.7.1 with previous version 0.6.3.1 dated 2014-08-11

Title: Utilities for Official Spanish Microdata
Description: The MicroDatosEs package provides utilities for reading and processing microdata from Spanish official statistics with R.
Author: Carlos J. Gil Bellosta [aut, cre], Carlos Neira [ctb], Diego Paniagua Sánchez [ctb], José Luis Cañadas Reche [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>

Diff between MicroDatosEs versions 0.6.3.1 dated 2014-08-11 and 0.7.1 dated 2015-12-14

 MicroDatosEs-0.6.3.1/MicroDatosEs/inst/extdata/sampleCenso.txt            |only
 MicroDatosEs-0.7.1/MicroDatosEs/DESCRIPTION                               |   14 
 MicroDatosEs-0.7.1/MicroDatosEs/MD5                                       |   38 +
 MicroDatosEs-0.7.1/MicroDatosEs/NAMESPACE                                 |    7 
 MicroDatosEs-0.7.1/MicroDatosEs/R/ees2010.R                               |    2 
 MicroDatosEs-0.7.1/MicroDatosEs/R/epa2005.R                               |    2 
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 MicroDatosEs-0.7.1/MicroDatosEs/inst/metadata/censo_2010_mdat1.txt        |  240 +++++-----
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 30 files changed, 190 insertions(+), 145 deletions(-)

More information about MicroDatosEs at CRAN
Permanent link

New package desplot with initial version 1.0
Package: desplot
Title: Plotting Field Plans for Agricultural Experiments
Version: 1.0
Date: 2015-12-13
Authors@R: person("Kevin","Wright", email="kw.stat@gmail.com", role=c("aut","cre"))
Type: Package
Description: A function for plotting maps of agricultural field experiments that are laid out in grids.
Imports: grid, lattice, reshape2,
Suggests: agridat, knitr
License: GPL-2
LazyData: yes
URL: https://github.com/kwstat/desplot
BugReports: https://github.com/kwstat/desplot/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-13 20:54:35 UTC; wrightkevi
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-14 08:57:11

More information about desplot at CRAN
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Package arules updated to version 1.3-1 with previous version 1.3-0 dated 2015-11-14

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>

Diff between arules versions 1.3-0 dated 2015-11-14 and 1.3-1 dated 2015-12-14

 DESCRIPTION                        |   12 
 MD5                                |   48 +--
 NAMESPACE                          |    9 
 R/AllClasses.R                     |  565 ++++++++++++++++++-------------------
 R/AllGenerics.R                    |    6 
 R/aggregate.R                      |  143 +++++----
 R/associations.R                   |    3 
 R/is.maximal.R                     |   13 
 R/is.redundant.R                   |only
 R/is.significant.R                 |only
 R/itemMatrix.R                     |   17 -
 R/parameter.R                      |   92 +++---
 R/transactions.R                   |    2 
 inst/CITATION                      |   28 +
 inst/NEWS                          |    8 
 inst/doc/arules.pdf                |binary
 man/APappearance-class.Rd          |    7 
 man/ASparameter-class.Rd           |    3 
 man/affinity.Rd                    |    2 
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 man/is.redundant.Rd                |only
 man/is.significant.Rd              |only
 man/random.transactions.Rd         |    4 
 src/warm.c                         |    2 
 tests/testthat/test-transactions.R |    3 
 27 files changed, 630 insertions(+), 455 deletions(-)

More information about arules at CRAN
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