Fri, 23 Jan 2015

Package PBSmodelling updated to version 2.67.266 with previous version 2.66.264 dated 2014-04-07

Title: GUI Tools Made Easy: Interact with Models and Explore Data
Description: Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface (GUI). Although our simplified GUI language depends heavily on the R interface to the Tcl/Tk package, a user does not need to know Tcl/Tk. Examples illustrate models built with other R packages, including PBSmapping, PBSddesolve, and BRugs. A complete user's guide `PBSmodelling-UG.pdf' shows how to use this package effectively.
Author: Jon T. Schnute , Alex Couture-Beil , Rowan Haigh , A.R. (Rob) Kronlund , and Nicholas Boers
Maintainer: Rowan Haigh

Diff between PBSmodelling versions 2.66.264 dated 2014-04-07 and 2.67.266 dated 2015-01-23

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Package pipeR updated to version 0.6 with previous version 0.5 dated 2014-09-30

Title: Multi-paradigm Pipeline Implementation
Description: Provides various styles of function chaining methods: Pipe operator, Pipe object, and pipeline function, each representing a distinct pipeline model yet sharing almost a common set of features: A value can be piped to the first unnamed argument of a function and to dot symbol in an enclosed expression. The syntax is designed to make the pipeline more readable and friendly to a wide range of operations.
Author: Kun Ren
Maintainer: Kun Ren

Diff between pipeR versions 0.5 dated 2014-09-30 and 0.6 dated 2015-01-23

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Package ONETr updated to version 1.0.2 with previous version 1.0.1 dated 2014-11-04

Title: Efficient authenticated interaction with the O*NET API
Description: Provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API . The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Author: Eric Knudsen
Maintainer: Eric Knudsen

Diff between ONETr versions 1.0.1 dated 2014-11-04 and 1.0.2 dated 2015-01-23

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New package LDAvis with initial version 0.2
Package: LDAvis
Title: Interactive Visualization of Topic Models
Version: 0.2
Authors@R: c(person("Carson", "Sievert", role = c("aut", "cre"), email = "cpsievert1@gmail.com"), person("Kenny", "Shirley", role = "aut", email = "kshirley@research.att.com"))
Description: Tools to create an interactive web-based visualization of a topic model that has been fit to a corpus of text data using Latent Dirichlet Allocation (LDA). Given the estimated parameters of the topic model, it computes various summary statistics as input to an interactive visualization built with D3.js that is accessed via a browser. The goal is to help users interpret the topics in their LDA topic model.
Depends: R (>= 2.10)
Imports: proxy, RJSONIO, parallel
License: MIT + file LICENSE
Suggests: mallet, lda, topicmodels, gistr (>= 0.0.8.99), servr, shiny, knitr, rmarkdown
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/cpsievert/LDAvis
BugReports: https://github.com/cpsievert/LDAvis/issues
Packaged: 2015-01-23 16:58:48 UTC; cpsievert
Author: Carson Sievert [aut, cre], Kenny Shirley [aut]
Maintainer: Carson Sievert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-23 21:07:17

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Package ExomeDepth updated to version 1.1.4 with previous version 1.1.1 dated 2015-01-13

Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol

Diff between ExomeDepth versions 1.1.1 dated 2015-01-13 and 1.1.4 dated 2015-01-23

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Package unmarked updated to version 0.10-5 with previous version 0.10-4 dated 2014-04-28

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler

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Package rplos updated to version 0.4.6 with previous version 0.4.1 dated 2014-07-22

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

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Package repmis updated to version 0.4 with previous version 0.3.3 dated 2014-12-10

Title: Miscellaneous Tools for Reproducible Research with R.
Description: The package includes tools to load R packages and automatically generate BibTeX files citing them as well as load plain-text and Excel formatted data stored on Dropbox, GitHub, and from other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud

Diff between repmis versions 0.3.3 dated 2014-12-10 and 0.4 dated 2015-01-23

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Package rcicr updated to version 0.3.0 with previous version 0.2.6 dated 2014-12-19

Title: Reverse correlation image classification toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch

Diff between rcicr versions 0.2.6 dated 2014-12-19 and 0.3.0 dated 2015-01-23

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Package PowerTOST updated to version 1.2-06 with previous version 1.2-05 dated 2015-01-06

Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. ----- Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval). ----- Contains further functions for power and sample size calculations based on non-inferiority t-test. This is not a TOST procedure but eventually useful if the question of 'non-superiority' must be evaluated. The power and sample size calculations based on non-inferiority test may also performed via 'expected' power in case of uncertain (estimated) variability. ----- Contains functions power.scABEL() and sampleN.scABEL() to calculate power and sample size for the BE decision via scaled (widened) BE acceptance limits based on simulations. Contains further functions power.RSABE() and sampleN.RSABE() to calculate power and sample size for the BE decision via reference scaled ABE criterion according to the FDA procedure based on simulations. Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate power and sample size for the BE decision via the FDA procedure for NTID's based on simulations. ----- Contains functions for power analysis of a sample size plan for ABE (pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA()) analysing power if deviating from assumptions of the plan. ----- Contains further functions for power calculations / samplesize estimation for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre], Helmut Schuetz [aut], Benjamin Lang [ctb]
Maintainer: Detlew Labes

Diff between PowerTOST versions 1.2-05 dated 2015-01-06 and 1.2-06 dated 2015-01-23

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Package Power2Stage updated to version 0.3-1 with previous version 0.2-2 dated 2014-12-08

Title: Power and Sample-size Distribution of 2-stage Bioequivalence Studies
Description: - Contains a function to calculate power and sample-size distribution of 2-stage bioequivalence (BE) studies with a 2x2 crossover design according to Potvin et al. / Montague et al. modified to include a futility Nmax and modified to do the sample size estimation step with PE and mse of stage 1. - Contains further a function with the modifications according to Karalis & Macheras which use PE and mse from stage 1 also for the power monitoring steps. - The third function power.2stage.fC() calculates power and sample size distribution of 2-stage BE studies with a futility criterion for the point estimator or CI of T/R from stage 1. - The fourth function power.2stage.GS() calculates power of non-adaptive group sequential (2-stage) BE studies. - The fifth function power.2stage.p() calculates power and sample size distribution of 2-stage BE studies with 2 parallel groups. - Another function power.2stage.ssr() allows the power calculation for 2-stage studies with (blinded) interim sample size re-estimation. All the functions use simulations to obtain their results.
Author: Detlew Labes [aut, cre], Helmut Schuetz [ctb]
Maintainer: Detlew Labes

Diff between Power2Stage versions 0.2-2 dated 2014-12-08 and 0.3-1 dated 2015-01-23

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 20 files changed, 398 insertions(+), 404 deletions(-)

More information about Power2Stage at CRAN
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Package pbivnorm updated to version 0.6.0 with previous version 0.5-1 dated 2012-10-31

Title: Vectorized Bivariate Normal CDF
Description: Provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF.
Author: Fortran code by Alan Genz. R code by Brenton Kenkel, based on Adelchi Azzalini's 'mnormt' package.
Maintainer: Brenton Kenkel

Diff between pbivnorm versions 0.5-1 dated 2012-10-31 and 0.6.0 dated 2015-01-23

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 MD5             |    9 +++---
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Permanent link

Package grplasso updated to version 0.4-5 with previous version 0.4-4 dated 2014-08-18

Title: Fitting user specified models with Group Lasso penalty
Description: Fits user specified (GLM-) models with Group Lasso penalty
Author: Lukas Meier
Maintainer: Lukas Meier

Diff between grplasso versions 0.4-4 dated 2014-08-18 and 0.4-5 dated 2015-01-23

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Package geostatsp updated to version 1.1.9 with previous version 1.1.8 dated 2015-01-05

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown [aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown

Diff between geostatsp versions 1.1.8 dated 2015-01-05 and 1.1.9 dated 2015-01-23

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 50 files changed, 1246 insertions(+), 1130 deletions(-)

More information about geostatsp at CRAN
Permanent link

Package BDgraph updated to version 2.15 with previous version 2.14 dated 2014-12-19

Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: This package provides a general framework to perform Bayesian structure learning in undirected graphical models. The package provides recent improvements in the Bayesian literature. The package consists of two main MCMC sampling algorithm efficiently implemented in C++ to maximize computational speed. The main target of the package is high-dimensional data analysis wherein either continuous or discrete variables and usually number of variables are less than number of observations. Acknowledgements: The help of the CRAN team to integrate C++ code with R is gratefully acknowledged.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

Diff between BDgraph versions 2.14 dated 2014-12-19 and 2.15 dated 2015-01-23

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Package timeSeries updated to version 3012.99 with previous version 3011.98 dated 2014-10-28

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

Diff between timeSeries versions 3011.98 dated 2014-10-28 and 3012.99 dated 2015-01-23

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More information about timeSeries at CRAN
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Package timeDate updated to version 3012.100 with previous version 3011.99 dated 2014-10-27

Title: Rmetrics - Chronological and Calendar Objects
Description: Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre], Yohan Chalabi [ctb], Martin Maechler [ctb], Joe W. Byers [ctb]
Maintainer: Tobias Setz

Diff between timeDate versions 3011.99 dated 2014-10-27 and 3012.100 dated 2015-01-23

 DESCRIPTION  |    9 +++++----
 MD5          |    4 ++--
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New package SpatPCA with initial version 1.0
Package: SpatPCA
Type: Package
Title: Regularized Principal Component Analysis for Spatial Data
Version: 1.0
Date: 2015-01-11
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang
Description: This package provides regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using alternating direction method of multipliers (ADMM) algorithm.
License: GPL-2
Depends: fields
Imports: Rcpp (>= 0.11.2)
Suggests: foreach
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-01-23 02:59:16 UTC; Joseph
Repository: CRAN
Date/Publication: 2015-01-23 09:06:28

More information about SpatPCA at CRAN
Permanent link

New package remMap with initial version 0.2-0
Package: remMap
Version: 0.2-0
Date: 2008-12-3
Title: Regularized Multivariate Regression for Identifying Master Predictors
Author: Jie Peng , Pei Wang , Ji Zhu .
Maintainer: Pei Wang
Description: remMap is developed for fitting multivariate response regression models under the high-dimension-low-sample-size setting
License: GPL (>= 2)
Packaged: 2015-01-22 19:04:20 UTC; xwan2
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-23 09:17:05

More information about remMap at CRAN
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Package RcmdrPlugin.temis updated to version 0.7.3 with previous version 0.7.2 dated 2014-09-06

Title: Graphical Integrated Text Mining Solution
Description: An R Commander plug-in providing an integrated solution to perform a series of text mining tasks such as importing and cleaning a corpus, and analyses like terms and documents counts, vocabulary tables, terms co-occurrences and documents similarity measures, time series analysis, correspondence analysis and hierarchical clustering. Corpora can be imported from spreadsheet-like files, directories of raw text files, Twitter queries, as well as from Dow Jones Factiva, LexisNexis, Europresse and Alceste files.
Author: Milan Bouchet-Valat [aut, cre], Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat

Diff between RcmdrPlugin.temis versions 0.7.2 dated 2014-09-06 and 0.7.3 dated 2015-01-23

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Package evmix updated to version 2.4 with previous version 2.3 dated 2014-09-07

Title: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models are provided. Kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the evd package is provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott

Diff between evmix versions 2.3 dated 2014-09-07 and 2.4 dated 2015-01-23

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More information about evmix at CRAN
Permanent link

Package compareGroups updated to version 3.0 with previous version 2.0.5 dated 2014-08-28

Title: Descriptive analysis by groups
Description: This package is designed to read, interpret, summarise, display and analyse epidemiological data. Can be used to create data summaries for quality control, extensive reports for exploring data, including publication-ready univariate or bivariate tables in plain text HTML and LaTeX, and a figures to quickly visualise the distribution of your data. Depending on the nature of the variable, various statistics are calculated (mean, median, frequencies, incidences) and appropriate tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...). The latest version includes functionality for summarising genetic data, and for performing low-level quality control of your database (see radiograph()) to help identify data-entry errors. This version has also been implemented in a web-interface to make this package accessible to non-R-users.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel and David Giménez
Maintainer: Isaac Subirana

Diff between compareGroups versions 2.0.5 dated 2014-08-28 and 3.0 dated 2015-01-23

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Package bnlearn updated to version 3.7.1 with previous version 3.7 dated 2015-01-13

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with the latest bugfixes are available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari

Diff between bnlearn versions 3.7 dated 2015-01-13 and 3.7.1 dated 2015-01-23

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Package blockcluster updated to version 3.0.2 with previous version 3.0.1 dated 2014-01-16

Title: Coclustering package for binary, contingency, continuous and categorical data-sets
Description: Simultaneous clustering of rows and columns, usually designated by biclustering, co-clustering or block clustering, is an important technique in two way data analysis. It consists of estimating a mixture model which takes into account the block clustering problem on both the individual and variables sets. The blockcluster package provides a bridge between the C++ core library and the R statistical computing environment. This package allows to co-cluster binary, contingency, continuous and categorical data-sets. It also provides utility functions to visualize the results. This package may be useful for various applications in fields of Data mining,Information retrieval, Biology, computer vision and many more. More information about the project and comprehensive tutorial can be found on the link mentioned in URL.
Author: Parmeet Singh Bhatia , Serge Iovleff, Gerard Goavert, Vincent Brault, with contributions from Christophe Biernacki and Gilles Celeux.
Maintainer: Vincent KUBICKI

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Package nlrwr (with last version 1.1-0) was removed from CRAN

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

2011-11-02 1.1-0
2009-03-25 1.0-6
2009-01-07 1.0-5
2008-03-21 1.0

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Package LogicReg updated to version 1.5.6 with previous version 1.5.5 dated 2013-12-03

Title: Logic Regression
Description: Routines for Logic Regression
Author: Charles Kooperberg and Ingo Ruczinski
Maintainer: Charles Kooperberg

Diff between LogicReg versions 1.5.5 dated 2013-12-03 and 1.5.6 dated 2015-01-23

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Package hysteresis updated to version 2.5 with previous version 2.0 dated 2013-11-19

Title: Tools for Modeling Rate-Dependent Hysteretic Processes and Ellipses
Description: Fit, summarize and plot sinusoidal hysteretic processes using: two-step simple harmonic least squares, ellipse-specific non-linear least squares, the direct method, geometric least squares or linear least squares.
Author: Spencer Maynes, Fan Yang, and Anne Parkhurst
Maintainer: Anne Parkhurst

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