Wed, 23 Jul 2014

Package pdfetch updated to version 0.1.4 with previous version 0.1.3 dated 2014-04-19

Title: Fetch economic and financial time series data from public sources
Description: A package for downloading economic and financial time series from public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart

Diff between pdfetch versions 0.1.3 dated 2014-04-19 and 0.1.4 dated 2014-07-23

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Package IBDhaploRtools updated to version 1.7 with previous version 1.5 dated 2013-03-21

Title: Functions for the Analysis of IBD Haplo output
Description: IBDhaploRtools consists of several functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson

Diff between IBDhaploRtools versions 1.5 dated 2013-03-21 and 1.7 dated 2014-07-23

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Package hts updated to version 4.4 with previous version 4.3 dated 2014-06-10

Title: Hierarchical and grouped time series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Roman A Ahmed and Han Lin Shang to earlier versions of the package
Maintainer: Rob J Hyndman

Diff between hts versions 4.3 dated 2014-06-10 and 4.4 dated 2014-07-23

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More information about hts at CRAN
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Tue, 22 Jul 2014

Package sweSCB updated to version 0.3.5 with previous version 0.3.4 dated 2014-04-15

Title: An R interface to the web API of Statistics Sweden
Description: Interface for the REST API of Statistics Sweden. The package offers methods to fetch information about the data hierarchy stored behind the API; extract metadata; fetch actual data; and clean up the results.
Author: Love Hansson, Thomas Reinholdsson, Mans Magnusson
Maintainer: Mans Magnusson

Diff between sweSCB versions 0.3.4 dated 2014-04-15 and 0.3.5 dated 2014-07-22

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Package spartan updated to version 2.0 with previous version 1.3 dated 2014-03-19

Title: Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk.Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

Diff between spartan versions 1.3 dated 2014-03-19 and 2.0 dated 2014-07-22

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More information about spartan at CRAN
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Package SIS updated to version 0.7-3 with previous version 0.7-2 dated 2014-05-06

Title: Sure Independence Screening
Description: (Iterative) Sure Independence Screening for Generalized Linear Models and Cox's Proportional Hazards Models
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana

Diff between SIS versions 0.7-2 dated 2014-05-06 and 0.7-3 dated 2014-07-22

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Package deltaPlotR updated to version 1.4 with previous version 1.3 dated 2013-07-22

Title: Identification of dichotomous differential item functioning (DIF) using Angoff's Delta Plot method
Description: The deltaPlotR package proposes an implementation of Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported.
Author: David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
Maintainer: David Magis

Diff between deltaPlotR versions 1.3 dated 2013-07-22 and 1.4 dated 2014-07-22

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Package SPACECAP updated to version 1.1.0 with previous version 1.0.6 dated 2012-06-14

Title: A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models
Description: SPACECAP is a user-friendly software package for estimating animal densities using closed model capture-recapture sampling based on photographic captures using Bayesian spatially-explicit capture-recapture models. This approach offers advantage such as: substantially dealing with problems posed by individual heterogeneity in capture probabilities in conventional capture-recapture analyses. It also offers non-asymptotic inferences which are more appropriate for small samples of capture data typical of photo-capture studies.
Author: Arjun M. Gopalaswamy, Andrew J. Royle, Michael E. Meredith, Pallavi Singh, Devcharan Jathanna, N. Samba Kumar and K. Ullas Karanth
Maintainer: Arjun M. Gopalaswamy

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Package Rcpp11 updated to version 3.1.1 with previous version 3.1.0.1 dated 2014-04-16

Title: R and C++11
Description: Rcpp11 includes a header only C++11 library that facilitates integration between R and modern C++.
Author: Romain Francois [aut, cre], Kevin Ushey [aut], John Chambers [ctb]
Maintainer: Romain Francois

Diff between Rcpp11 versions 3.1.0.1 dated 2014-04-16 and 3.1.1 dated 2014-07-22

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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/diff.h                                 |  176 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/duplicated.h                           |   19 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/head.h                                 |   46 -
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/ifelse.h                               |  394 --------
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/import.h                               |  105 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/mean.h                                 |  131 ++
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/rep_len.h                              |  147 ++-
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/replicate.h                            |   76 +
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sapply.h                               |  267 +++---
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/seq_along.h                            |   64 +
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/setdiff.h                              |  247 ++---
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/sum.h                                  |  152 +--
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/table.h                                |  102 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/tail.h                                 |   46 -
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/var.h                                  |   34 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/which_max.h                            |   99 --
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/functions/which_min.h                            |   99 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/lower_tri.h                               |   21 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/outer.h                                   |   37 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/row.h                                     |   14 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/sugar/matrix/upper_tri.h                               |   18 
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/vector/impl/CharacterVector.h                          |  118 --
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 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/SexpConvertibleWrapper.h                          |    2 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/Wrapper.h                                         |    3 
 Rcpp11-3.1.1/Rcpp11/inst/include/Rcpp/wrap/forward.h                                         |   11 
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 262 files changed, 4387 insertions(+), 5963 deletions(-)

More information about Rcpp11 at CRAN
Permanent link

Package kinship2 updated to version 1.6.0 with previous version 1.5.7 dated 2014-03-20

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

Diff between kinship2 versions 1.5.7 dated 2014-03-20 and 1.6.0 dated 2014-07-22

 DESCRIPTION        |    8 ++++----
 MD5                |   22 ++++++++++++----------
 NAMESPACE          |    3 ++-
 R/align.pedigree.R |    8 ++++++--
 R/ped2df.R         |    3 ---
 R/pedigree.R       |    1 +
 inst/NEWS.Rd       |   13 +++++++++++++
 man/familycheck.Rd |   51 ++++++++++++++++++---------------------------------
 noweb/align.Rnw    |    8 ++++++--
 noweb/all.nw       |   23 +++++++++++++++++------
 noweb/pedigree.Rnw |   15 +++++++++++----
 tests/ped1.pdf     |only
 tests/ped2.pdf     |only
 13 files changed, 90 insertions(+), 65 deletions(-)

More information about kinship2 at CRAN
Permanent link

Package heatmapFit updated to version 2.0 with previous version 1.0 dated 2012-11-20

Title: Fit statistic for binary dependent variable models
Description: Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic (Esarey and Pierce, 2012).
Author: Justin Esarey [aut, cre], Andrew Pierce [aut], Jericho Du [aut]
Maintainer: Justin Esarey

Diff between heatmapFit versions 1.0 dated 2012-11-20 and 2.0 dated 2014-07-22

 heatmapFit-1.0/heatmapFit/R/Package.R             |only
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 12 files changed, 28 insertions(+), 22 deletions(-)

More information about heatmapFit at CRAN
Permanent link

Package clinfun updated to version 1.0.6 with previous version 1.0.5 dated 2013-04-16

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

Diff between clinfun versions 1.0.5 dated 2013-04-16 and 1.0.6 dated 2014-07-22

 CHANGES                  |    6 ++++++
 DESCRIPTION              |    9 ++++-----
 MD5                      |    8 ++++----
 R/jonkheere.R            |    6 +++---
 man/gsdesign-internal.Rd |   13 ++++++++-----
 5 files changed, 25 insertions(+), 17 deletions(-)

More information about clinfun at CRAN
Permanent link

Package llama updated to version 0.7 with previous version 0.6 dated 2014-04-29

Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb]
Maintainer: Lars Kotthoff

Diff between llama versions 0.6 dated 2014-04-29 and 0.7 dated 2014-07-22

 llama-0.6/llama/inst/tests                        |only
 llama-0.7/llama/DESCRIPTION                       |   17 ++---
 llama-0.7/llama/MD5                               |   73 +++++++++++-----------
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 llama-0.7/llama/R/classify.R                      |   70 ++++++++++++++-------
 llama-0.7/llama/R/classifyPairs.R                 |   72 ++++++++++++++-------
 llama-0.7/llama/R/cluster.R                       |   48 +++++++-------
 llama-0.7/llama/R/imputeCensored.R                |   12 ++-
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 llama-0.7/llama/man/classify.Rd                   |   35 ++++++----
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 llama-0.7/llama/man/cluster.Rd                    |   44 ++++++-------
 llama-0.7/llama/man/imputeCensored.Rd             |    8 --
 llama-0.7/llama/man/llama-package.Rd              |   38 +++--------
 llama-0.7/llama/man/misclassificationPenalties.Rd |    8 --
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More information about llama at CRAN
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Package Bergm updated to version 2.9 with previous version 2.8 dated 2014-07-02

Title: Bayesian analysis for exponential random graph models
Description: Set of tools to analyse Bayesian exponential random graph models
Author: Alberto Caimo and Nial Friel
Maintainer: Alberto Caimo

Diff between Bergm versions 2.8 dated 2014-07-02 and 2.9 dated 2014-07-22

 DESCRIPTION          |   10 +++++-----
 MD5                  |   23 ++++++++++++++---------
 R/abergm.R           |   22 ++++++++--------------
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 15 files changed, 61 insertions(+), 55 deletions(-)

More information about Bergm at CRAN
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Package AdaptFitOS updated to version 0.54 with previous version 0.50 dated 2014-03-19

Title: Adaptive Semiparametric Regression with Simultaneous Confidence Bands
Description: Based on the function "asp" of the AdaptFit package fits semiparametric regression models with spatially adaptive penalized splines and computes simultaneous confidence bands.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth

Diff between AdaptFitOS versions 0.50 dated 2014-03-19 and 0.54 dated 2014-07-22

 DESCRIPTION               |   10 
 MD5                       |   62 ++--
 R/almeAux.R               |  126 ++++-----
 R/arg.searchOS.r          |  117 ++++----
 R/asp-internal.r          |    6 
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 R/aspHetero.r             |   25 -
 R/aspOS.r                 |    4 
 R/aspmFormReadOS.r        |    5 
 R/firstlib.r              |    2 
 R/fitted.asp.r            |   14 -
 R/plot.scbTest.r          |    4 
 R/plot.scbm.r             |    3 
 R/predict.asp.r           |  591 ++++++++++++++++++++++---------------------
 R/print.asp.r             |   55 +---
 R/residuals.asp.r         |   32 --
 R/scbM.r                  |   15 -
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Package rplos updated to version 0.4.1 with previous version 0.4.0 dated 2014-05-13

Title: Interface to PLoS Journals search API.
Description: A programmatic interface to the Web Service methods provided by the Public Library of Science journals for search.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain

Diff between rplos versions 0.4.0 dated 2014-05-13 and 0.4.1 dated 2014-07-22

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Package mewAvg updated to version 0.3.0 with previous version 0.2.0 dated 2014-01-24

Title: A Fixed Memeory Moving Expanding Window Average
Description: Computes the average of a sequence of random vectors in a moving expanding window using a fixed amount of storage
Author: Adam L. Pintar and Zachary H. Levine
Maintainer: Adam L. Pintar

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Package leapp updated to version 1.2 with previous version 1.1 dated 2014-01-06

Title: latent effect adjustment after primary projection
Description: These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
Author: Yunting Sun , Nancy R.Zhang , Art B.Owen
Maintainer: Yunting Sun

Diff between leapp versions 1.1 dated 2014-01-06 and 1.2 dated 2014-07-22

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Package jsonlite updated to version 0.9.9 with previous version 0.9.8 dated 2014-06-02

Title: A smarter JSON encoder/decoder for R
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the same libjson c++ parser, but implements a smarter mapping between JSON data and R classes. The vignette describes the behavior in great detail. In addition to drop-in replacements for toJSON and fromJSON, the package contains funtions to validate, prettify and minify JSON, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Jonathan Wallace
Maintainer: Jeroen Ooms

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Package glasso updated to version 1.8 with previous version 1.7 dated 2011-09-14

Title: Graphical lasso- estimation of Gaussian graphical models
Description: Graphical lasso
Author: Jerome Friedman, Trevor Hastie and Rob Tibshirani
Maintainer: Rob Tibshirani

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Package COUNT updated to version 1.3.1 with previous version 1.3.0 dated 2014-07-16

Title: Functions, data and code for count data.
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2-nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe
Maintainer: Andrew Robinson

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Mon, 21 Jul 2014

Package splusTimeDate updated to version 2.5.0-135 with previous version 2.0.0-117 dated 2014-02-02

Title: Times and Dates from S-PLUS
Description: Classes and methods for times and dates (ported from S-PLUS)
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny

Diff between splusTimeDate versions 2.0.0-117 dated 2014-02-02 and 2.5.0-135 dated 2014-07-21

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Package rnoaa updated to version 0.2.0 with previous version 0.1.0 dated 2014-03-03

Title: NOAA climate data from R.
Description: This is an R wrapper to many NOAA APIs including the NCDC climate API at http://www.ncdc.noaa.gov/cdo-web/webservices/v2. There are functions for each of the API endpoints: data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for NOAA sea ice data that is not part of the climate data API, the NOAA severe weather inventory, and ERDDAP data. NOAA buoy data is only on the buoy branch in the Github repository for this package (see url below).
Author: Hart Edmund [aut, cre], Scott Chamberlain [aut], Karthik Ram [aut]
Maintainer: Hart Edmund

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Package logitchoice updated to version 0.9.1 with previous version 0.9.0 dated 2014-07-21

Title: Fitting l2-regularized logit choice models via generalized gradient descent
Description: Fits linear discrete logit choice models with l2 regularization. To handle reasonably sized datasets, we employ an accelerated version of generalized gradient descent.
Author: Michael Lim
Maintainer: Michael Lim

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Package MDPtoolbox updated to version 4.0.2 with previous version 4.0.1 dated 2012-12-31

Title: Markov Decision Processes toolbox
Description: The Markov Decision Processes (MDP) toolbox proposes functions related to the resolution of discrete-time Markov Decision Processes: finite horizon, value iteration, policy iteration, linear programming algorithms with some variants and also proposes some functions related to Reinforcement Learning.
Author: Iadine Chades, Guillaume Chapron, Marie-Josee Cros, Frederick Garcia, Regis Sabbadin
Maintainer: Guillaume Chapron

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Package SuperLearner updated to version 2.0-15 with previous version 2.0-10 dated 2013-09-03

Title: Super Learner Prediction
Description: This package implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.
Author: Eric Polley, Mark van der Laan
Maintainer: Eric Polley

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Package texreg updated to version 1.33 with previous version 1.32 dated 2014-05-02

Title: Conversion of R regression output to LaTeX or HTML tables.
Description: texreg converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

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Package RANN updated to version 2.4.1 with previous version 2.3.0 dated 2013-07-24

Title: Fast Nearest Neighbour Search (wraps Arya and Mount's ANN library)
Description: Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis

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Package mvSLOUCH updated to version 1.1.2 with previous version 1.1.1 dated 2014-05-30

Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for phylogenetic Comparative hypotHeses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek

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Package mlr updated to version 2.1 with previous version 2.0 dated 2014-07-03

Title: mlr: Machine Learning in R.
Description: Interface to a large number of classification and regression techniques, including machine-readable parameter descriptions. There is also an experimental extension for survival analysis, clustering and general, example-specific cost-sensitive learning. Generic resampling, including cross-validation, bootstrapping and subsampling. Hyperparameter tuning with modern optimization techniques, for single- and multi-objective problems. Filter and wrapper methods for feature selection. Extension of basic learners with additional operations common in machine learning, also allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre], Michel Lang [aut], Jakob Bossek [aut], Leonard Judt [aut], Jakob Richter [aut], Tobias Kuehn [aut], Erich Studerus [aut]
Maintainer: Bernd Bischl

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Package ineq updated to version 0.2-13 with previous version 0.2-12 dated 2014-05-18

Title: Measuring Inequality, Concentration, and Poverty
Description: Inequality, concentration, and poverty measures. Lorenz curves (empirical and theoretical).
Author: Achim Zeileis [aut, cre], Christian Kleiber [ctb]
Maintainer: Achim Zeileis

Diff between ineq versions 0.2-12 dated 2014-05-18 and 0.2-13 dated 2014-07-21

 DESCRIPTION |    8 ++++----
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Permanent link

Package icd9 updated to version 0.5 with previous version 0.3 dated 2014-07-07

Title: Tools for Working with ICD-9 Codes, and Finding Comorbidities
Description: This package allows accurate manipulation, conversion, validation and comparison of ICD-9-CM (clinical modification) codes. Although ICD-9 codes appear numeric, this is not the case, since trailing zeroes, and a mixture of decimal and non-decimal "short" format codes exist. Tools to map ICD-9 codes to co-morbidities are also provided, with mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre]
Maintainer: Jack O. Wasey

Diff between icd9 versions 0.3 dated 2014-07-07 and 0.5 dated 2014-07-21

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 icd9-0.5/icd9/tests/testthat/test-validation.R  |  237 ++++++++++-
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More information about icd9 at CRAN
Permanent link

Package BTYD updated to version 2.3 with previous version 1.0 dated 2012-08-22

Title: Implementing Buy 'Til You Die Models
Description: This package contains functions for data preparation, parameter estimation, scoring, and plotting for the BG/BB, BG/NBD and Pareto/NBD models.
Author: Lukasz Dziurzynski [aut], Edward Wadsworth [aut], Peter Fader [ctb], Elea McDonnell Feit [ctb], Daniel McCarthy [aut, cre, ctb], Bruce Hardie [ctb], Arun Gopalakrishnan [ctb], Eric Schwartz [ctb], Yao Zhang [ctb]
Maintainer: Daniel McCarthy

Diff between BTYD versions 1.0 dated 2012-08-22 and 2.3 dated 2014-07-21

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Permanent link

Package SASxport updated to version 1.5.0 with previous version 1.3.6 dated 2013-10-09

Title: Read and Write SAS XPORT Files
Description: This package provides functions for reading, listing the contents of, and writing SAS xport format files. The functions support reading and writing of either individual data frames or sets of data frames. Further, a mechanism has been provided for customizing how variables of different data types are stored.
Author: Unless otherwise noted, the contents of this package were written by Gregory R. Warnes and are provided under the terms of the GNU General Public License, version 2.0 or later. -- The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John Muuss, Copyright (c) 2004-2007 United States Government as represented by the U.S. Army Research Laboratory, and is utilized and redistributed under the terms of the GNU Lesser General Public License, version 2.1. -- The files 'R/AFirst.lib.s', 'R/all.is.numeric.R', 'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R', 'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the 'Hmisc' package created by Frank E. Harrell, Jr. , and are utilized and redistributed under the terms of the GNU General Public License, version 2.0 or later. -- The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and 'src/foreign.h' are copied or adapted from the R 'foreign' package created by Douglas M. Bates and Saikat DebRoy , and are utilized and redistributed under the terms of the GNU General Public License, version 2.0 or later. -- The creation of this package was partially funded by Metrum Institute .
Maintainer: Gregory R. Warnes

Diff between SASxport versions 1.3.6 dated 2013-10-09 and 1.5.0 dated 2014-07-21

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More information about SASxport at CRAN
Permanent link

Package PottsUtils updated to version 0.3-1 with previous version 0.3-0 dated 2014-06-16

Title: Utility Functions of the Potts Models
Description: A package including several functions related to the Potts models.
Author: Dai Feng [aut, cre], Luke Tierney [ctb]
Maintainer: Dai Feng

Diff between PottsUtils versions 0.3-0 dated 2014-06-16 and 0.3-1 dated 2014-07-21

 ChangeLog          |    4 ++++
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Package BayesLogit updated to version 0.5.1 with previous version 0.4 dated 2014-04-25

Title: Logistic Regression
Description: The BayesLogit package does posterior simulation for binomial and multinomial logistic regression using the Polya-Gamma latent variable technique. This method is fully automatic, exact, and fast. A routine to efficiently sample from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle

Diff between BayesLogit versions 0.4 dated 2014-04-25 and 0.5.1 dated 2014-07-21

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Package BayesBridge updated to version 0.5 with previous version 0.4 dated 2014-04-23

Title: Bridge Regression
Description: This package implements Bayesian bridge regression.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle

Diff between BayesBridge versions 0.4 dated 2014-04-23 and 0.5 dated 2014-07-21

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Package dave updated to version 1.5 with previous version 1.4 dated 2013-05-08

Title: Functions for "Data Analysis in Vegetation Ecology"
Description: A collection of functions accompanying the book "Data Analysis in Vegetation Ecology", Second edition. 2013, Wiley-Blackwell, Chichester
Author: Otto Wildi
Maintainer: Otto Wildi

Diff between dave versions 1.4 dated 2013-05-08 and 1.5 dated 2014-07-21

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Package checkmate updated to version 1.2 with previous version 1.1 dated 2014-06-28

Title: Fast and versatile argument checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang , Bernd Bischl
Maintainer: Michel Lang

Diff between checkmate versions 1.1 dated 2014-06-28 and 1.2 dated 2014-07-21

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Package survsim updated to version 1.1.1 with previous version 1.1.0 dated 2014-04-25

Title: Simulation of simple and complex survival data
Description: Simulation of simple and complex survival data
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler

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Package mgcv updated to version 1.8-2 with previous version 1.8-1 dated 2014-07-05

Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood

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Package gamm4 updated to version 0.2-3 with previous version 0.2-2 dated 2013-09-25

Title: Generalized additive mixed models using mgcv and lme4
Description: Fit generalized additive mixed models via a version of mgcv's gamm function, using lme4 for estimation.
Author: Simon Wood, Fabian Scheipl
Maintainer: Simon Wood

Diff between gamm4 versions 0.2-2 dated 2013-09-25 and 0.2-3 dated 2014-07-21

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Package msme updated to version 0.5.1 with previous version 0.4.4 dated 2013-07-02

Title: Functions and Datasets for "Methods of Statistical Model Estimation".
Description: This package provides functions and datasets from the book "Methods of Statistical Model Estimation".
Author: Joseph Hilbe and Andrew Robinson
Maintainer: Andrew Robinson

Diff between msme versions 0.4.4 dated 2013-07-02 and 0.5.1 dated 2014-07-21

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Package Sunder updated to version 0.0.2 with previous version 0.0.1 dated 2014-06-30

Title: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Casper Eriksen, Gilles Guillot
Maintainer: ORPHANED

Diff between Sunder versions 0.0.1 dated 2014-06-30 and 0.0.2 dated 2014-07-21

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Package gss updated to version 2.1-3 with previous version 2.1-2 dated 2014-06-10

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu
Maintainer: Chong Gu

Diff between gss versions 2.1-2 dated 2014-06-10 and 2.1-3 dated 2014-07-21

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Package GeoGenetix updated to version 0.0.2 with previous version 0.0.1 dated 2014-06-27

Title: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Description: Quantification of the effect of geographic versus environmental isolation on genetic differentiation
Author: Filippo Botta, Gilles Guillot
Maintainer: ORPHANED

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Package class updated to version 7.3-11 with previous version 7.3-10 dated 2014-03-28

Title: Functions for Classification
Description: Various functions for classification.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley

Diff between class versions 7.3-10 dated 2014-03-28 and 7.3-11 dated 2014-07-21

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Sun, 20 Jul 2014

Package gWidgetstcltk updated to version 0.0-55 with previous version 0.0-54 dated 2013-01-31

Title: Toolkit implementation of gWidgets for tcltk package
Description: Port of the gWidgets API to the tcltk package. Requires Tk 8.5 or greater.
Author: John Verzani
Maintainer: John Verzani

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Package ProgGUIinR updated to version 0.0-4 with previous version 0.0-3 dated 2012-09-14

Title: support package for "Programming Graphical User Interfaces in R"
Description: sample code, appendices and functions for the text Programming GUIs in R
Author: Michael Lawrence and John Verzani
Maintainer: John Verzani

Diff between ProgGUIinR versions 0.0-3 dated 2012-09-14 and 0.0-4 dated 2014-07-20

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Package gWidgets updated to version 0.0-53 with previous version 0.0-52 dated 2012-10-09

Title: gWidgets API for building toolkit-independent, interactive GUIs
Description: gWidgets provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project http://scigraphica.sourceforge.net.
Author: John Verzani. Based on the iwidgets code of Simon Urbanek and suggestions by Simon Urbanek, Philippe Grosjean and Michael Lawrence
Maintainer: John Verzani

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Package googleVis updated to version 0.5.4 with previous version 0.5.3 dated 2014-06-28

Title: Interface between R and Google Charts
Description: The googleVis package provides an interface between R and the Google Charts API. It allows users to create web pages with interactive charts based on R data frames, using the Google Charts API and to display them either via the local R HTTP help server or within their own sites, without uploading the data to Google. A modern browser with Internet connection is required and for some charts Flash.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann

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Package sandwich updated to version 2.3-1 with previous version 2.3-0 dated 2013-10-05

Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.
Author: Thomas Lumley [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis

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Package HLSM updated to version 0.2 with previous version 0.1 dated 2014-06-19

Title: Hierarchical latent space network model (HLSM)
Description: Hierarchical latent space network model for ensemble of networks
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Samrachana Adhikari

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Package ExomeDepth updated to version 1.0.7 with previous version 1.0.5 dated 2014-06-26

Title: Calls CNV from exome sequence data
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol

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Sat, 19 Jul 2014

Package pcnetmeta updated to version 1.2 with previous version 1.1 dated 2014-03-09

Title: Methods for patient-centered network meta-analysis
Description: Provides functions to conduct network meta-analysis using arm-based method, which was proposed by Zhang et al (2014); contains functions to generate summary table for effect sizes (e.g., odds ratio, population-averaged event rate), plot network comparisons, and plot credible interval for population-averaged event rate.
Author: Lifeng Lin, Jing Zhang , and Haitao Chu
Maintainer: Lifeng Lin

Diff between pcnetmeta versions 1.1 dated 2014-03-09 and 1.2 dated 2014-07-19

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Package RGtk2 updated to version 2.20.31 with previous version 2.20.30 dated 2014-07-19

Title: R bindings for Gtk 2.8.0 and above
Description: Facilities in the R language for programming graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence and Duncan Temple Lang
Maintainer: Michael Lawrence

Diff between RGtk2 versions 2.20.30 dated 2014-07-19 and 2.20.31 dated 2014-07-19

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Package ergm updated to version 3.1.3 with previous version 3.1.2 dated 2014-01-31

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut], David R. Hunter [aut], Carter T. Butts [aut], Steven M. Goodreau [aut], Pavel N. Krivitsky [aut, cre], Martina Morris [aut]
Maintainer: Pavel N. Krivitsky

Diff between ergm versions 3.1.2 dated 2014-01-31 and 3.1.3 dated 2014-07-19

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Package RNeXML updated to version 1.1.2 with previous version 1.1-0 dated 2014-07-17

Title: Implement semantically rich I/O for NeXML format
Description: R package that allows access to phyloinformatic data in NeXML format. The package should add new functionality to R such as the possibility to manipulate NeXML objects in more various and refined way and compatibility with 'ape' objects. Note that the Sxslt package suggested can be installed from the Omegahat repository, though it can also be obtained from https://github.com/cboettig/Sxslt
Author: Carl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]
Maintainer: Carl Boettiger

Diff between RNeXML versions 1.1-0 dated 2014-07-17 and 1.1.2 dated 2014-07-19

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Package RGtk2 updated to version 2.20.30 with previous version 2.20.29 dated 2014-05-12

Title: R bindings for Gtk 2.8.0 and above
Description: Facilities in the R language for programming graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence and Duncan Temple Lang
Maintainer: Michael Lawrence

Diff between RGtk2 versions 2.20.29 dated 2014-05-12 and 2.20.30 dated 2014-07-19

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Package plsRglm updated to version 1.1.0 with previous version 1.0.1 dated 2014-06-28

Title: Partial least squares Regression for generalized linear models
Description: This package provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand , Nicolas Meyer , Myriam Maumy-Bertrand .
Maintainer: Frederic Bertrand

Diff between plsRglm versions 1.0.1 dated 2014-06-28 and 1.1.0 dated 2014-07-19

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Package plsRcox updated to version 1.7.0 with previous version 1.0 dated 2014-06-28

Title: Partial least squares Regression for Cox models and related techniques
Description: This packages provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings.
Author: Frederic Bertrand , Myriam Maumy-Bertrand , Nicolas Meyer .
Maintainer: Frederic Bertrand

Diff between plsRcox versions 1.0 dated 2014-06-28 and 1.7.0 dated 2014-07-19

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Package permGPU updated to version 0.14.6 with previous version 0.14.5 dated 2014-06-28

Title: permPGU: Using GPUs in Statistical Genomics
Description: This R extension package can be used to carry out permutation resampling inference in the context of RNA microarray studies
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev

Diff between permGPU versions 0.14.5 dated 2014-06-28 and 0.14.6 dated 2014-07-19

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Package yhatr updated to version 0.12.1 with previous version 0.11.0 dated 2014-06-25

Title: R binder for the Yhat API
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat REST API.
Author: Greg Lamp , Eric Chiang
Maintainer: Greg Lamp

Diff between yhatr versions 0.11.0 dated 2014-06-25 and 0.12.1 dated 2014-07-19

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Package TEQR updated to version 5.0-0 with previous version 4.0-0 dated 2014-06-14

Title: Target Equivalence Range Design
Description: The target equivalence range (TEQR) design, previously named the toxicity equivalence range design is an up-down design patterned after the modified toxicity probability interval design.The TEQR design extends the well known 3+3 design to allow for: an explicit target range for the dose limiting toxicity (DLT) rate, more subjects at the maximum tolerated dose (MTD), and specification of a too-toxic rate, which closes a dose level, In addition, the TEQR design can be implemented to target a dose based either on toxicity rate or activity rate constrained for toxicity.
Author: M. Suzette Blanchard
Maintainer: M. Suzette Blanchard

Diff between TEQR versions 4.0-0 dated 2014-06-14 and 5.0-0 dated 2014-07-19

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Package NbClust updated to version 2.0.1 with previous version 2.0 dated 2014-05-30

Title: NbClust package for determining the best number of clusters
Description: NbClust package provides 30 indices for determining the optimal number of clusters in a dataset.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

Diff between NbClust versions 2.0 dated 2014-05-30 and 2.0.1 dated 2014-07-19

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Package geomorph updated to version 2.1.1 with previous version 2.1 dated 2014-05-30

Title: Geometric morphometric analyses of 2d/3d landmark data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams

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More information about geomorph at CRAN
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Fri, 18 Jul 2014

Package rfigshare updated to version 0.3.5 with previous version 0.3-1 dated 2014-04-29

Title: an R interface to figshare.com.
Description: an R interface to figshare.com.
Author: Carl Boettiger [aut, cre], Scott Chamberlain [aut], Karthik Ram [aut], Edmund Hart [aut]
Maintainer: Carl Boettiger

Diff between rfigshare versions 0.3-1 dated 2014-04-29 and 0.3.5 dated 2014-07-18

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 39 files changed, 505 insertions(+), 567 deletions(-)

More information about rfigshare at CRAN
Permanent link

Package mvmeta updated to version 0.4.4 with previous version 0.4.3 dated 2014-04-08

Title: Multivariate and univariate meta-analysis and meta-regression
Description: The package mvmeta consists of a collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression in R.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini

Diff between mvmeta versions 0.4.3 dated 2014-04-08 and 0.4.4 dated 2014-07-18

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Package sdcMicro updated to version 4.4.0 with previous version 4.3.0 dated 2014-03-03

Title: Statistical Disclosure Control methods for anonymization of microdata and risk estimation
Description: Data from statistical agencies and other institutions are mostly confidential. This package can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. In addition, various risk estimation methods are included. Note that the package sdcMicroGUI includes a graphical user interface for various methods in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ

Diff between sdcMicro versions 4.3.0 dated 2014-03-03 and 4.4.0 dated 2014-07-18

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More information about sdcMicro at CRAN
Permanent link

Package rattle updated to version 3.1.0 with previous version 3.0.2 dated 2014-02-06

Title: Graphical user interface for data mining in R
Description: Rattle (the R Analytic Tool To Learn Easily) provides a Gnome (RGtk2) based interface to R functionality for data mining. The aim is to provide a simple and intuitive interface that allows a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, build and evaluate models, and export models as PMML (predictive modelling markup language) or as scores. All of this with knowing little about R. All R commands are logged and commented through the log tab. Thus they are available to the user as a script file or as an aide for the user to learn R or to copy-and-paste directly into R itself. Rattle also exports a number of utility functions and the graphical user interface, invoked as rattle(), does not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre], Mark Vere Culp [cph], Ed Cox [ctb], Anthony Nolan [ctb], Denis White [cph], Daniele Medri [ctb], Akbar Waljee [ctb] (OOB AUC for Random Forest), Brian Ripley [cph] (Original author of print.summary.nnet)
Maintainer: Graham Williams

Diff between rattle versions 3.0.2 dated 2014-02-06 and 3.1.0 dated 2014-07-18

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Package MonetDB.R updated to version 0.9.4 with previous version 0.9.2 dated 2014-04-22

Title: Connect MonetDB to R
Description: Allows to pull data from MonetDB into R
Author: Hannes Muehleisen [aut, cre], Thomas Lumley [ctb], Anthony Damico [ctb]
Maintainer: Hannes Muehleisen

Diff between MonetDB.R versions 0.9.2 dated 2014-04-22 and 0.9.4 dated 2014-07-18

 DESCRIPTION |    8 +++----
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Package mem updated to version 1.4 with previous version 1.3 dated 2013-06-25

Title: Moving Epidemic Method R Package.
Description: Modelization of influenza epidemics in order to monitor future activity.
Author: Jose E. Lozano Alonso
Maintainer: Jose E. Lozano Alonso

Diff between mem versions 1.3 dated 2013-06-25 and 1.4 dated 2014-07-18

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More information about mem at CRAN
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Package cherry updated to version 0.5-10 with previous version 0.4-9 dated 2014-04-27

Title: Multiple testing methods for exploratory research
Description: This package implements a class of multiple testing methods that does not prescribe the user what hypotheses to reject, but instead allows the user to select the set of selected hypotheses freely. The multiple testing procedure aids this selection by providing an upper confidence bound for the number of false rejections among the selected set. Because the confidence bounds are simultaneous for all possible rejected sets, the validity is not compromised by post hoc selection. Some of the functions in this package are optionally enhanced by the gurobi software and its accompanying R package. For installation of gurobi, follow the instructions at http://pages.gurobi.com/DownloadRegistration.html?/download/gurobi-optimizer and http://www.gurobi.com/documentation/5.6/quick-start-guide/r_installing_the_r_package.
Author: Jelle Goeman, Aldo Solari, Rosa Meijer
Maintainer: Jelle Goeman

Diff between cherry versions 0.4-9 dated 2014-04-27 and 0.5-10 dated 2014-07-18

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More information about cherry at CRAN
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Package StereoMorph updated to version 1.1 with previous version 1.0 dated 2014-04-15

Title: Stereo Camera Calibration and Reconstruction
Description: StereoMorph provides functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen

Diff between StereoMorph versions 1.0 dated 2014-04-15 and 1.1 dated 2014-07-18

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Package siRSM updated to version 1.1 with previous version 1.0 dated 2014-06-16

Title: Single-Index Response Surface Models
Description: This package fits single-index (quadratic) response surface models.
Author: Huan Cheng, Mu Zhu
Maintainer: Mu Zhu

Diff between siRSM versions 1.0 dated 2014-06-16 and 1.1 dated 2014-07-18

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More information about siRSM at CRAN
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Package rlist updated to version 0.2.3 with previous version 0.2.2 dated 2014-07-11

Title: A toolset for working with lists
Description: A toolset for working with lists as dataset, including filtering, mapping, grouping, sorting, updating, and many other functions, which allow functional programming style applied in list operations.
Author: Kun Ren
Maintainer: Kun Ren

Diff between rlist versions 0.2.2 dated 2014-07-11 and 0.2.3 dated 2014-07-18

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Package bezier updated to version 1.1 with previous version 1.0 dated 2014-03-26

Title: Bezier Curve and Spline Toolkit
Description: The bezier package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.
Author: Aaron Olsen
Maintainer: Aaron Olsen

Diff between bezier versions 1.0 dated 2014-03-26 and 1.1 dated 2014-07-18

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Thu, 17 Jul 2014

Package soilphysics updated to version 1.1 with previous version 1.0 dated 2014-01-25

Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva

Diff between soilphysics versions 1.0 dated 2014-01-25 and 1.1 dated 2014-07-17

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More information about soilphysics at CRAN
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Package SMNCensReg updated to version 2.4 with previous version 2.3 dated 2014-03-17

Title: Fitting univariate censored regression model under the scale mixture of normal distributions.
Description: Fit univariate right, left or interval censored regression model under the scale mixture of normal distributions.
Author: Aldo M. Garay , Victor Lachos , and Monique Bettio Massuia
Maintainer: Aldo M. Garay

Diff between SMNCensReg versions 2.3 dated 2014-03-17 and 2.4 dated 2014-07-17

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Package nsprcomp updated to version 0.5 with previous version 0.4.1 dated 2013-09-22

Title: Non-Negative and Sparse PCA
Description: This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function 'nsprcomp' computes one principal component (PC) after the other. Each PA is optimized such that the corresponding PC has maximum additional variance not explained by the previous components. In contrast, the function 'nscumcomp' jointly computes all PCs such that the cumulative variance is maximal. Both functions have the same interface as the 'prcomp' function from the 'stats' package (plus some extra parameters), and both return the result of the analysis as an object of class 'nsprcomp', which inherits from 'prcomp'.
Author: Christian Sigg [aut, cre], R Core team [aut]
Maintainer: Christian Sigg

Diff between nsprcomp versions 0.4.1 dated 2013-09-22 and 0.5 dated 2014-07-17

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Package flora updated to version 0.2.3 with previous version 0.2.2 dated 2014-07-03

Title: tools for interacting with the Brazilian Flora Checklist
Description: Tools to quickly compile taxonomic and distribution data from the Brazilian Flora Checklist. No internet connection needed.
Author: Gustavo Carvalho
Maintainer: Gustavo Carvalho

Diff between flora versions 0.2.2 dated 2014-07-03 and 0.2.3 dated 2014-07-17

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Package crrstep updated to version 2014-07.16 with previous version 2014-01.08 dated 2014-01-08

Title: Stepwise covariate selection for the Fine & Gray competing risks regression model
Description: Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events.
Author: Ravi Varadhan & Deborah Kuk
Maintainer: Ravi Varadhan

Diff between crrstep versions 2014-01.08 dated 2014-01-08 and 2014-07.16 dated 2014-07-17

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Package SCGLR updated to version 2.0 with previous version 1.2 dated 2014-03-18

Title: Supervised Component Generalized Linear Regression (SCGLR)
Description: SCGLR extends the Fisher Scoring Algorithm so as to combine PLS regression with GLM estimation in the multivariate context.
Author: Mortier F., Trottier C., Cornu G., Bry X.
Maintainer: "G. Cornu"

Diff between SCGLR versions 1.2 dated 2014-03-18 and 2.0 dated 2014-07-17

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Package randomForest updated to version 4.6-10 with previous version 4.6-7 dated 2012-10-16

Title: Breiman and Cutler's random forests for classification and regression
Description: Classification and regression based on a forest of trees using random inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw

Diff between randomForest versions 4.6-7 dated 2012-10-16 and 4.6-10 dated 2014-07-17

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Package numOSL updated to version 1.5 with previous version 1.4 dated 2014-06-08

Title: Numeric routines for optically stimulated luminescence dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation; decay curve decomposition and fast-component equivalent dose estimation; statistical age models analysis and radial plot drawing.
Author: Peng Jun
Maintainer: Peng Jun

Diff between numOSL versions 1.4 dated 2014-06-08 and 1.5 dated 2014-07-17

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Package BoolNet updated to version 2.0 with previous version 1.63 dated 2014-03-31

Title: Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, and probabilistic Boolean networks, and to analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler

Diff between BoolNet versions 1.63 dated 2014-03-31 and 2.0 dated 2014-07-17

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Package mvcwt updated to version 1.3 with previous version 1.2 dated 2013-11-07

Title: Wavelet analysis of multiple time series
Description: This package computes the continuous wavelet transform of irregularly sampled time series.
Author: Timothy H. Keitt
Maintainer: Tim Keitt

Diff between mvcwt versions 1.2 dated 2013-11-07 and 1.3 dated 2014-07-17

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Wed, 16 Jul 2014

Package RMessenger updated to version 0.1.5 with previous version 0.1.4 dated 2014-03-27

Title: IM Client for R
Description: RMessenger contains 2 part of works: - A derivative work of libstrophe(http://strophe.im/libstrophe/) - A sole work of wrapping libstrophe into R For any suggestion or bug report, please visit https://github.com/wush978/RMessenger
Author: Wush Wu, Jack Moffitt and Patrick Powell
Maintainer: Wush Wu

Diff between RMessenger versions 0.1.4 dated 2014-03-27 and 0.1.5 dated 2014-07-16

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Package questionr updated to version 0.4.1 with previous version 0.4 dated 2014-03-28

Title: Functions to make surveys processing easier.
Description: This package provides some convenience functions to make the processing and analysis of surveys easier.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier

Diff between questionr versions 0.4 dated 2014-03-28 and 0.4.1 dated 2014-07-16

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Package tsintermittent updated to version 1.2 with previous version 1.1 dated 2014-07-03

Title: Intermittent Time Series Forecasting
Description: This package contains functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes

Diff between tsintermittent versions 1.1 dated 2014-07-03 and 1.2 dated 2014-07-16

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Package TSP updated to version 1.0-9 with previous version 1.0-8 dated 2013-09-06

Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling salesperson problem (also traveling salesman problem; TSP). The package provides some simple algorithms and an interface to Concorde, the currently fastest TSP solver. Concorde itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph], Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler

Diff between TSP versions 1.0-8 dated 2013-09-06 and 1.0-9 dated 2014-07-16

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Package phaseR updated to version 1.3 with previous version 1.2 dated 2013-10-09

Title: Phase Plane Analysis of One and Two Dimensional Autonomous ODE Systems
Description: phaseR is an R package for the qualitative analysis of one and two dimensional autonomous ODE systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one dimensional case, a program is also available to plot the phase portrait. Whilst in the two dimensional case, additionally a program is available to plot nullclines. Many example systems are provided for the user.
Author: Michael J. Grayling
Maintainer: Michael J. Grayling

Diff between phaseR versions 1.2 dated 2013-10-09 and 1.3 dated 2014-07-16

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Package NAPPA updated to version 2.0 with previous version 1.0 dated 2013-10-29

Title: Performs the processing and normalisation of Nanostring miRNA and mRNA data
Description: Enables the processing and normalisation of the standard mRNA data output from the Nanostring nCounter software
Author: Chris Harbron, Mark Wappett
Maintainer: Mark Wappett

Diff between NAPPA versions 1.0 dated 2013-10-29 and 2.0 dated 2014-07-16

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Package ORCME updated to version 2.0.1 with previous version 2.0 dated 2014-05-22

Title: Order Restricted Clustering for Microarray Experiments
Description: This package provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Martin Otava

Diff between ORCME versions 2.0 dated 2014-05-22 and 2.0.1 dated 2014-07-16

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Package Delaporte updated to version 2.2-0 with previous version 2.1-1 dated 2014-04-07

Title: Statistical functions for the Delaporte distribution
Description: Provides probability mass, distribution, quantile, random variate generation, and method of moments parameter estimation functions for the Delaporte distribution.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler

Diff between Delaporte versions 2.1-1 dated 2014-04-07 and 2.2-0 dated 2014-07-16

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Package PCovR updated to version 2.5 with previous version 2.4 dated 2014-02-28

Title: Principal Covariates Regression
Description: Analyzing regression data with many and/or highly collinear predictor variables, by simultaneously reducing the predictor variables to a limited number of components and regressing the criterion variables on these components. Several rotation options are provided in this package, as well as model selection options.
Author: Marlies Vervloet [aut, cre], Henk Kiers [aut], Eva Ceulemans [ctb]
Maintainer: Marlies Vervloet

Diff between PCovR versions 2.4 dated 2014-02-28 and 2.5 dated 2014-07-16

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Package magicaxis updated to version 1.9 with previous version 1.8 dated 2014-05-13

Title: Pretty scientific plotting with minor-tick and log minor-tick support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham

Diff between magicaxis versions 1.8 dated 2014-05-13 and 1.9 dated 2014-07-16

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Package COUNT updated to version 1.3.0 with previous version 1.2.3 dated 2012-08-01

Title: Functions, data and code for count data.
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2-nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe
Maintainer: Andrew Robinson

Diff between COUNT versions 1.2.3 dated 2012-08-01 and 1.3.0 dated 2014-07-16

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Package phreeqc updated to version 1.0-8847 with previous version 1.0-8809 dated 2014-06-30

Title: R interface to the phreeqc geochemical modeling program
Description: R interface to PHREEQC (Version 3). PHREEQC is a geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton

Diff between phreeqc versions 1.0-8809 dated 2014-06-30 and 1.0-8847 dated 2014-07-16

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Package functional updated to version 0.6 with previous version 0.4 dated 2013-04-04

Title: Curry, Compose, and other higher-order functions
Description: Curry, Compose, and other higher-order functions
Author: Peter Danenberg
Maintainer: Peter Danenberg

Diff between functional versions 0.4 dated 2013-04-04 and 0.6 dated 2014-07-16

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