CRANberries

CRANberries aggregates information about new, updated and removed packages from the
CRAN network for R available as this html version and a corresponding RSS feed.
Created and provided by Dirk Eddelbuettel.

Sat, 28 Jan 2012

Package knitr updated to version 0.2 with previous version 0.1 dated 2012-01-17

Title: A general-purpose package for dynamic report generation in R
Description: This package provides a general-purpose tool for dynamic report generation in R, which can be used to deal with any type of (plain text) files, including Sweave and HTML. The patterns of code chunks and inline R expressions can be customized. R code is evaluated as if it were copied and pasted in an R terminal thanks to the evaluate package (e.g. we do not need to explicitly print() plots from ggplot2 or lattice). R code can be reformatted by the formatR package so that long lines are automatically wrapped, with indent and spaces being added, and comments being preserved. A simple caching mechanism is provided to cache results from computations for the first time and the computations will be skipped the next time. Almost all common graphics devices, including those in base R and add-on packages like Cairo, cairoDevice and tikzDevice, are built-in with this package and it is straightforward to switch between devices without writing any special functions. The width and height as well as alignment of plots in the output document can be specified in chunk options (the size of plots for graphics devices is still supported as usual). Multiple plots can be recorded in a single code chunk, and it is also allowed to rearrange plots to the end of a chunk or just keep the last plot. Warnings, messages and errors are written in the output document by default (can be turned off). Currently LaTeX, HTML and Markdown are supported, and other output formats can be supported by hook functions. The large collection of hooks in this package makes it possible for the user to control almost everything in the R code input and output. Hooks can be used either to format the output or to run a specified R code fragment before or after a code chunk. Most features are borrowed or inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between knitr versions 0.1 dated 2012-01-17 and 0.2 dated 2012-01-28

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 knitr-0.2/knitr/R/eclipse.R                            |    3 
 knitr-0.2/knitr/R/hooks.R                              |   48 +++--
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 knitr-0.2/knitr/R/package.R                            |   14 +
 knitr-0.2/knitr/R/parser.R                             |   30 ++-
 knitr-0.2/knitr/R/pattern.R                            |    2 
 knitr-0.2/knitr/R/plot.R                               |   19 ++
 knitr-0.2/knitr/R/themes.R                             |    5 
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More information about knitr at CRAN
Path: /cran/updated | permanent link

Package trapezoid updated to version 1.0-5 with previous version 1.0-4 dated 2012-01-02

Title: The Trapezoidal Distribution
Description: The trapezoid package provides dtrapezoid, ptrapezoid, qtrapezoid, and rtrapezoid functions for the trapezoidal distribution.
Author: Jeremy Thoms Hetzel [aut, cre]
Maintainer: Jeremy Thoms Hetzel

Diff between trapezoid versions 1.0-4 dated 2012-01-02 and 1.0-5 dated 2012-01-28

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 8 files changed, 29 insertions(+), 23 deletions(-)

More information about trapezoid at CRAN
Path: /cran/updated | permanent link

Package scam updated to version 1.1-1 with previous version 1.1 dated 2012-01-22

Title: Shape constrained additive models
Description: Routines for generalized additive modelling under shape constraints on the component functions of the linear predictor. Models can contain multiple shape constrained (univariate and/or bivariate) and unconstrained terms. The routines of mgcv(gam) package are used for setting up the model matrix, printing and plotting the results. Penalized likelihood maximization based on Newton-Raphson method is used to fit a model with multiple smoothing parameter selection by GCV or UBRE/AIC.
Author: Natalya Pya
Maintainer: Natalya Pya

Diff between scam versions 1.1 dated 2012-01-22 and 1.1-1 dated 2012-01-28

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More information about scam at CRAN
Path: /cran/updated | permanent link

Package tlmec updated to version 0.0-2 with previous version 0.0-1 dated 2011-12-02

Title: Linear Student-t Mixed-Effects Models with Censored Data
Description: Fit a linear mixed effects model for censored data with Student-t or normal distributions. The errors are assumed independent and identically distributed.
Author: Larissa Matos , Marcos Prates and Victor Lachos
Maintainer: Larissa Matos

Diff between tlmec versions 0.0-1 dated 2011-12-02 and 0.0-2 dated 2012-01-28

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More information about tlmec at CRAN
Path: /cran/updated | permanent link

New package ReCiPa with initial version 1.0
Package: ReCiPa
Type: Package
Title: Redundancy Control in Pathways databases
Version: 1.0
Date: 2012-01-26
Author: Juan C. Vivar
Maintainer: Juan C. Vivar
Description: Pathways in a database could have many redundancies among them. This package allows the user to set a maximum value for the proportion of these redundancies.
License: GPL-2
LazyLoad: yes
Packaged: 2012-01-27 14:47:33 UTC; jcvivar
Repository: CRAN
Date/Publication: 2012-01-28 17:00:22

More information about ReCiPa at CRAN
Path: /cran/new | permanent link

Package readMzXmlData updated to version 2.1.1 with previous version 2.1 dated 2012-01-26

Title: Reads mass spectrometry data in mzXML format.
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb, Jarek Tuszynski
Maintainer: Sebastian Gibb

Diff between readMzXmlData versions 2.1 dated 2012-01-26 and 2.1.1 dated 2012-01-28

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More information about readMzXmlData at CRAN
Path: /cran/updated | permanent link

Package randomNames updated to version 0.0-5 with previous version 0.0-4 dated 2011-11-20

Title: Random name generating function and data set
Description: Function to generate random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner

Diff between randomNames versions 0.0-4 dated 2011-11-20 and 0.0-5 dated 2012-01-28

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More information about randomNames at CRAN
Path: /cran/updated | permanent link

Package R2jags updated to version 0.03-06 with previous version 0.03-05 dated 2012-01-27

Title: A Package for Running jags from R
Description: Using this package to call jags from R.
Author: Yu-Sung Su , Masanao Yajima ,
Maintainer: Yu-Sung Su

Diff between R2jags versions 0.03-05 dated 2012-01-27 and 0.03-06 dated 2012-01-28

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More information about R2jags at CRAN
Path: /cran/updated | permanent link

Package lestat updated to version 1.7 with previous version 1.6 dated 2011-12-21

Title: A package for LEarning STATistics
Description: This package contains some simple objects and functions to do statistics using linear models and a Bayesian framework.
Author: Petter Mostad
Maintainer: Petter Mostad

Diff between lestat versions 1.6 dated 2011-12-21 and 1.7 dated 2012-01-28

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More information about lestat at CRAN
Path: /cran/updated | permanent link

Package HLMdiag updated to version 0.1.4 with previous version 0.1.3 dated 2012-01-03

Title: Diagnostic tools for two-level normal hierarchical linear models
Description: A suite of diagnostic tools for two-level normal hierarchical linear models. The package offers not only traditional case-deletion diagnostics (Cook's distance, covratio, covtrace, and MDFFITS) but also provides graphics for residual analysis. Currently, case deletion is performed by iteratively refitting the model using lmer in the lme4 package, so for data sets with many groups, computation is currently slow.
Author: Adam Loy
Maintainer: Adam Loy

Diff between HLMdiag versions 0.1.3 dated 2012-01-03 and 0.1.4 dated 2012-01-28

 DESCRIPTION                        |   26 +++++++++++++-------------
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More information about HLMdiag at CRAN
Path: /cran/updated | permanent link

Package gRim updated to version 0.1.7 with previous version 0.1.6 dated 2012-01-19

Title: Graphical Interaction Models
Description: Implements graphical interaction models for contingency tables (i.e. log-linear models) and graphical Gaussian models for the multivariate normal data (i.e. covariance selection models) and mixed interaction models
Author: Søren Højsgaard
Maintainer: Søren Højsgaard

Diff between gRim versions 0.1.6 dated 2012-01-19 and 0.1.7 dated 2012-01-28

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More information about gRim at CRAN
Path: /cran/updated | permanent link

New package geotools with initial version 0.1
Package: geotools
Version: 0.1
Date: 2007-10-03
Suggests:
Title: Geo tools
Author: Antoine Lucas
Maintainer: Antoine Lucas
Description: Tools
License: GPL
Packaged: 2012-01-28 11:49:33 UTC; antoine
Repository: CRAN
Date/Publication: 2012-01-28 18:08:23

More information about geotools at CRAN
Path: /cran/new | permanent link

Package ensembleBMA updated to version 5.0.3 with previous version 5.0.2 dated 2011-11-09

Title: Probabilistic Forecasting using Ensembles and Bayesian Model Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann Gneiting, University of Washington.
Maintainer: Chris Fraley

Diff between ensembleBMA versions 5.0.2 dated 2011-11-09 and 5.0.3 dated 2012-01-28

 CHANGELOG        |    2 ++
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More information about ensembleBMA at CRAN
Path: /cran/updated | permanent link

Package emdbook updated to version 1.3.2 with previous version 1.3.1 dated 2011-04-28

Title: Ecological models and data (book support)
Description: Auxiliary functions and data sets for _Ecological Models and Data_, a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0)
Author: Ben Bolker
Maintainer: Ben Bolker

Diff between emdbook versions 1.3.1 dated 2011-04-28 and 1.3.2 dated 2012-01-28

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More information about emdbook at CRAN
Path: /cran/updated | permanent link

Package CommonJavaJars updated to version 1.0-1 with previous version 1.0-0 dated 2011-05-17

Title: Useful libraries for building a Java based GUI under R
Description: Useful libraries for building a Java based GUI under R
Author: Kornelius Rohmeyer
Maintainer: Kornelius Rohmeyer

Diff between CommonJavaJars versions 1.0-0 dated 2011-05-17 and 1.0-1 dated 2012-01-28

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More information about CommonJavaJars at CRAN
Path: /cran/updated | permanent link

New package bild with initial version 1.0-3
Package: bild
Type: Package
Title: bild: a package for BInary Longitudinal Data
Version: 1.0-3
Date: 2012-1-28
Author: M. Helena Gonçalves, M. Salomé Cabral and Adelchi Azzalini, apart from a set of Fortran-77 subroutines written by R. Piessens and E. de Doncker, belonging to the suite "Quadpack"
Maintainer: M. Helena Gonçalves
Description: bild performs logistic regression for binary longitudinal data, allowing for serial dependence among observations from a given individual and a random intercept term. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed, with some restrictions.
Encoding: latin1
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Depends: R (>= 2.10.0), methods, stats, graphics, utils
Packaged: 2012-01-28 13:46:17 UTC; Helena
Repository: CRAN
Date/Publication: 2012-01-28 16:55:03

More information about bild at CRAN
Path: /cran/new | permanent link

Package bbmle updated to version 1.0.4.1 with previous version 1.0.4 dated 2012-01-02

Title: Tools for general maximum likelihood estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the mle classes in the stats4 package.
Author: Ben Bolker , R Development Core Team
Maintainer: Ben Bolker

Diff between bbmle versions 1.0.4 dated 2012-01-02 and 1.0.4.1 dated 2012-01-28

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More information about bbmle at CRAN
Path: /cran/updated | permanent link

Package AICcmodavg updated to version 1.23 with previous version 1.22 dated 2012-01-20

Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). Tables are printed with delta AIC and Akaike weights. The package also features functions to conduct classic model averaging (multimodel inference) for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with linear models ('lm' class), generalized linear models ('glm' class), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' class), multinomial and ordinal logistic regressions ('multinom' and 'polr' classes), and nonlinear models ('nls' class). The package also supports various models incorporating detection probabilities such as single-season occupancy models ('unmarkedFitOccu' class), multiple-season occupancy models ('unmarkedFitColExt' class), single-season heterogeneity models ('unmarkedFitOccuRN' class), single-season and multiple-season N-mixture models for repeated counts ('unmarkedFitPCount' and 'unmarkedFitPCO' classes, respectively), and distance sampling models ('unmarkedFitDS' and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle . Special thanks to T. Ergon for the original idea of storing candidate models in a list.
Maintainer: Marc J. Mazerolle

Diff between AICcmodavg versions 1.22 dated 2012-01-20 and 1.23 dated 2012-01-28

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More information about AICcmodavg at CRAN
Path: /cran/updated | permanent link

Package RMark updated to version 2.1.0 with previous version 2.0.9 dated 2011-12-06

Title: R Code for MARK Analysis
Description: This package provides an interface to the software package MARK developed by Gary White. MARK is freely available at (http://www.phidot.org/software/mark/download/) but is not open source.
Author: Jeff Laake with contributions from Eldar Rakimberdiev, Bret Collier, Jay Rotella and Andrew Paul
Maintainer: Jeff Laake

Diff between RMark versions 2.0.9 dated 2011-12-06 and 2.1.0 dated 2012-01-28

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More information about RMark at CRAN
Path: /cran/updated | permanent link

Package sdcMicro updated to version 3.0.0 with previous version 2.6.7 dated 2011-11-10

Title: Statistical Disclosure Control methods for the generation of public- and scientific-use files.
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 generation of public- and scientific-use files. The package includes also a graphical user interface.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ

Diff between sdcMicro versions 2.6.7 dated 2011-11-10 and 3.0.0 dated 2012-01-28

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 60 files changed, 212 insertions(+), 212 deletions(-)

More information about sdcMicro at CRAN
Path: /cran/updated | permanent link

Package CORElearn updated to version 0.9.39 with previous version 0.9.37 dated 2012-01-17

Title: CORElearn - classification, regression, feature evaluation and ordinal evaluation
Description: CORElearn is machine learning suite ported to R from standalone C++ package. It contains several model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leafs, random forests, kNN, naive Bayes, and locally weighted regression. It is especially strong in feature evaluation algorithms where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM, ... Its additional strength is ordEval algorithm and its visualization used for ordinal features and class. Several algorithms support parallel multithreaded execution via OpenMP. Windows binary versions supporting multithreading are available on package website, as CRAN uses different toolchain. The top level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja , Petr Savicky
Maintainer: Marko Robnik-Sikonja

Diff between CORElearn versions 0.9.37 dated 2012-01-17 and 0.9.39 dated 2012-01-28

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 CORElearn-0.9.39/CORElearn/R/testCore.R     |  233 ++++++++++++++++------------
 CORElearn-0.9.39/CORElearn/man/testCore.Rd  |   29 +--
 CORElearn-0.9.39/CORElearn/src/Makevars     |    4 
 CORElearn-0.9.39/CORElearn/src/frontend.cpp |    2 
 CORElearn-0.9.39/CORElearn/src/relieff.cpp  |    2 
 9 files changed, 169 insertions(+), 126 deletions(-)

More information about CORElearn at CRAN
Path: /cran/updated | permanent link

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