Fri, 28 Nov 2014

Package MAVIS updated to version 1.0 with previous version 0.2 dated 2014-11-22

Title: Meta Analysis via Shiny
Description: Interactive shiny application for running a meta-analysis, provides support for both random effects and fixed effects models.
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton

Diff between MAVIS versions 0.2 dated 2014-11-22 and 1.0 dated 2014-11-28

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More information about MAVIS at CRAN
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New package EnsemblePenReg with initial version 0.6
Package: EnsemblePenReg
Type: Package
Title: Extensible Classes and Methods for Penalized-Regression-based Integration of Base Learners
Version: 0.6
Date: 2014-11-25
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: Extending the base classes and methods of EnsembleBase package for Penalized-Regression-based (Ridge and Lasso) integration of base learners. Default implementation uses cross-validation error to choose the optimal lambda (shrinkage parameter) for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods,glmnet
Packaged: 2014-11-28 06:57:09 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-28 09:31:26

More information about EnsemblePenReg at CRAN
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Package paleofire (with last version 1.1.4) was removed from CRAN

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

2014-11-18 1.1.4
2014-05-22 1.1.3
2014-03-15 1.1-2
2014-03-14 1.1
2014-01-08 1.0

Permanent link
Package RcppArmadillo updated to version 0.4.550.1.0 with previous version 0.4.500.0 dated 2014-10-30

Title: Rcpp Integration for the Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The RcppArmadillo package includes the header files from the templated Armadillo library. Thus users do not need to install Armadillo itself in order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.4.500.0 dated 2014-10-30 and 0.4.550.1.0 dated 2014-11-28

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Thu, 27 Nov 2014

Package superbiclust updated to version 1.1 with previous version 0.1 dated 2013-04-23

Title: Generating Robust Biclusters from a Bicluster Set (Ensemble Biclustering)
Description: Biclusters are submatrices in the data matrix which satisfy certain conditions of homogeneity. Package contains functions for generating robust biclusters with respect to the initialization parameters for a given bicluster solution contained in a bicluster set in data, the procedure is also known as ensemble biclustering. The set of biclusters is evaluated based on the similarity of its elements (the overlap), and afterwards the hierarchical tree is constructed to obtain cut-off points for the classes of robust biclusters. The result is a number of robust (or super) biclusters with none or low overlap.
Author: Tatsiana Khamiakova
Maintainer: Tatsiana Khamiakova

Diff between superbiclust versions 0.1 dated 2013-04-23 and 1.1 dated 2014-11-27

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New package NormPsy with initial version 1.0.2
Package: NormPsy
Type: Package
Title: Normalisation of psychometric tests
Version: 1.0.2
Date: 2014-05-28
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
Description: This package provides functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). The package also provides functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores.
License: GPL
Depends: R (>= 2.9.0)
Imports: lcmm (>= 1.6.4)
Packaged: 2014-11-27 20:56:50 UTC; cecile
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 23:19:56

More information about NormPsy at CRAN
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New package EnsemblePCReg with initial version 0.6
Package: EnsemblePCReg
Type: Package
Title: Extensible Package for Principal-Component-Regression-based Integration of Base Learners
Version: 0.6
Date: 2014-11-25
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: This package extends the base classes and methods of EnsembleBase package for Principal-Components-Regression-based (PCR) integration of base learners. Default implementation uses cross-validation error to choose the optimal number of PC components for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods
Packaged: 2014-11-26 22:37:10 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-28 00:21:18

More information about EnsemblePCReg at CRAN
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Package Ecfun updated to version 0.1-3 with previous version 0.1-2 dated 2014-10-28

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves

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Package genpathmox updated to version 0.2 with previous version 0.1 dated 2014-10-30

Title: Generalized PATHMOX Algorithm for PLS-PM, LS and LAD Regression
Description: genpathmox provides a very interesting solution for handling segmentation variables in complex statistical methodology. It contains en extended version of the PATHMOX algorithm in the context of partial least square path modeling (Sanchez, 2009) including the F-block test (to detect the responsible latent endogenous equations of the difference), the F-coefficient (to detect the path coefficients responsible of the difference) and the invariance test (to realize a comparison between the sub-models' latent variables). Furthermore, the package contains a generalized version of the PATHMOX algorithm to approach different methodologies: linear regression and least absolute regression models.
Author: "Giuseppe Lamberti" [aut, cre]
Maintainer: "Giuseppe Lamberti"

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Package erer updated to version 2.3 with previous version 2.2 dated 2014-08-11

Title: Empirical Research in Economics with R
Description: Functions, datasets, and sample codes related to the book of 'Empirical Research in Economics: Growing up with R' by Dr. Changyou Sun are included. The book is still under preparation as of 2014. Marginal effects for binary or ordered choice models can be calculated. Static and dynamic Almost Ideal Demand System (AIDS) models can be estimated. A typical event analysis in finance can be conducted with several functions included.
Author: Changyou Sun
Maintainer: Changyou Sun

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Package apt updated to version 2.3 with previous version 2.2 dated 2014-08-11

Title: Asymmetric Price Transmission (apt)
Description: This package focuses on asymmetric price transmission (APT) between two time series. It contains functions for linear and nonlinear threshold cointegration, and furthermore, symmetric and asymmetric error correction model. A graphical user interface is also included for major functions included in the package, so users can also use these functions in a more intuitive way.
Author: Changyou Sun
Maintainer: Changyou Sun

Diff between apt versions 2.2 dated 2014-08-11 and 2.3 dated 2014-11-27

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More information about apt at CRAN
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New package cmprskQR with initial version 0.9.0
Package: cmprskQR
Version: 0.9.0
Date: 2014-11-26
Title: Analysis of Competing Risks Using Quantile Regressions
Author: Stephan Dlugosz, based on code from Limin Peng and Ruosha Li
Maintainer: Stephan Dlugosz
Depends: R (>= 2.13.0)
Imports: survival, quantreg
Description: Estimation, testing and regression modeling of subdistribution functions in competing risks using quantile regressions, as described in Peng and Fine JP (2009), Competing risks quantile regression, JASA, 104:1440-1453
License: GPL (>= 2)
URL: http://www.r-project.org
NeedsCompilation: yes
Repository: CRAN
Packaged: 2014-11-27 15:09:46 UTC; sdl
Date/Publication: 2014-11-27 18:38:56

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Package visreg updated to version 2.1-0 with previous version 2.0-6 dated 2014-08-26

Title: Visualization of regression models
Description: Provides convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

Diff between visreg versions 2.0-6 dated 2014-08-26 and 2.1-0 dated 2014-11-27

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New package SSrat with initial version 1.0
Package: SSrat
Type: Package
Title: Two-dimensional sociometric status determination with rating scales
Version: 1.0
Date: 2014-09-09
Author: Hans Landsheer
Maintainer: Hans Landsheer
Description: SSRAT is a computer program for two-dimensional sociometric status determination with rating scales. For each person assessed, SSRAT computes probability distributions of the total scores for `sympathy' (S), `antipathy' (A), `social preference' (P) and `social impact' (I), and applies the criteria for sociometric status categorization.
License: GPL-2
Depends: plyr, sna
LazyData: yes
Packaged: 2014-11-27 14:18:47 UTC; lands101
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-27 16:04:43

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Package DECIDE updated to version 1.2 with previous version 1.1 dated 2011-12-16

Title: DEComposition of Indirect and Direct Effects
Description: Calculates various estimates for measures of educational differentials, the relative importance of primary and secondary effects in the creation of such differentials and compares the estimates obtained from two datasets.
Author: Christiana Kartsonaki
Maintainer: Christiana Kartsonaki

Diff between DECIDE versions 1.1 dated 2011-12-16 and 1.2 dated 2014-11-27

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Package Taxonstand updated to version 1.6 with previous version 1.5 dated 2014-10-29

Title: Taxonomic Standardization of Plant Species Names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using the The Plant List (TPL) website (www.theplantlist.org)
Author: Luis Cayuela and Jari Oksanen
Maintainer: Luis Cayuela

Diff between Taxonstand versions 1.5 dated 2014-10-29 and 1.6 dated 2014-11-27

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Package mgcv updated to version 1.8-4 with previous version 1.8-3 dated 2014-08-29

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

Diff between mgcv versions 1.8-3 dated 2014-08-29 and 1.8-4 dated 2014-11-27

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Package rags2ridges updated to version 1.4 with previous version 1.3 dated 2014-08-06

Title: Ridge Estimation of Precision Matrices from High-Dimensional Data
Description: Package contains proper L2-penalized ML estimators for the precision matrix as well as supporting functions to employ these estimators in a graphical modeling setting.
Author: Carel F.W. Peeters, Wessel N. van Wieringen
Maintainer: Carel F.W. Peeters

Diff between rags2ridges versions 1.3 dated 2014-08-06 and 1.4 dated 2014-11-27

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Package fcros updated to version 1.3 with previous version 1.2 dated 2014-09-09

Title: FCROS to search for differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
Description: A fold change rank ordering statistics method is presented to search for differentially expressed genes and to detect recurrent chromosomal copy number aberrations. This method may be useful for high-throughput biological data (microarray, sequencing, ...). Probabilities are associated with genes in the dataset and there is no problem of multiple tests when using this method.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele

Diff between fcros versions 1.2 dated 2014-09-09 and 1.3 dated 2014-11-27

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Package deldir updated to version 0.1-7 with previous version 0.1-6 dated 2014-08-02

Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations.
Author: Rolf Turner
Maintainer: Rolf Turner

Diff between deldir versions 0.1-6 dated 2014-08-02 and 0.1-7 dated 2014-11-27

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Package DetR (with last version 0.0.1) was removed from CRAN

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

2014-11-13 0.0.1

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Package Rmpfr updated to version 0.5-7 with previous version 0.5-6 dated 2014-09-05

Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Rmpfr provides (S4 classes and methods for) arithmetic including transcendental ("special") functions for arbitrary precision floating point numbers. To this end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library.
Author: Martin Maechler
Maintainer: Martin Maechler

Diff between Rmpfr versions 0.5-6 dated 2014-09-05 and 0.5-7 dated 2014-11-27

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Package CINOEDV updated to version 2.0 with previous version 1.1 dated 2014-10-17

Title: Co-Information based N-Order Epistasis Detector and Visualizer
Description: Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms or epistatic interactions, especially high-order epistatic interactions, are important topics in bioinformatics because of their significant mathematical and computational challenges. We present CINOEDV (Co-Information based N-Order Epistasis Detector and Visualizer) for detecting, visualizing, and analyzing high-order epistatic interactions by introducing virtual vertices into the construction of a hypergraph. CINOEDV was developed as an alternative to existing software to build a global picture of epistatic interactions and unexpected high-order epistatic interactions, which might provide useful clues for understanding the underlying genetic architecture of complex diseases.
Author: Junliang Shang
Maintainer: Junliang Shang

Diff between CINOEDV versions 1.1 dated 2014-10-17 and 2.0 dated 2014-11-27

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New package orderedLasso with initial version 1.7
Package: orderedLasso
Title: Ordered Lasso and Time-lag Sparse Regression
Version: 1.7
Author: Jerome Friedman, Xiaotong Suo and Robert Tibshirani
Description: Ordered lasso and time-lag sparse regression. Ordered Lasso fits a linear model and imposes an order constraint on the coefficients. It writes the coefficients as positive and negative parts, and requires positive parts and negative parts are non-increasing and positive. Time-Lag Lasso generalizes the ordered Lasso to a general data matrix with multiple predictors. For more details, see Suo, X.,Tibshirani, R., (2014) 'An Ordered Lasso and Sparse Time-lagged Regression'.
Maintainer: Xiaotong Suo
Depends: R (>= 3.0.0), Matrix
Imports: Iso,quadprog,ggplot2,reshape2
License: GPL-2
Packaged: 2014-11-27 07:18:25 UTC; xiaotong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 08:32:37

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New package cqrReg with initial version 1.0
Package: cqrReg
Type: Package
Title: Quantile, Composite Quantile Regression and Regularized Versions
Version: 1.0
Date: 2014-11-07
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
License: GPL (>= 2)
Depends: Matrix,Rmosek
Imports: Rcpp (>= 0.10.0)
LinkingTo: Rcpp,RcppArmadillo
Packaged: 2014-11-27 00:30:38 UTC; billy
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 07:39:36

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Wed, 26 Nov 2014

Package secrdesign updated to version 2.2.1 with previous version 2.1.3 dated 2014-06-04

Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture--recapture studies of animal populations (primarily a simulation manager for package secr)
Author: Murray Efford
Maintainer: Murray Efford

Diff between secrdesign versions 2.1.3 dated 2014-06-04 and 2.2.1 dated 2014-11-26

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Package miRtest updated to version 1.8 with previous version 1.7 dated 2014-06-29

Title: combined miRNA- and mRNA-testing
Description: combined miRNA- and mRNA-testing
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann

Diff between miRtest versions 1.7 dated 2014-06-29 and 1.8 dated 2014-11-26

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Package MiClip updated to version 1.3 with previous version 1.2 dated 2013-11-16

Title: A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
Description: Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.
Author: Tao Wang
Maintainer: Tao Wang

Diff between MiClip versions 1.2 dated 2013-11-16 and 1.3 dated 2014-11-26

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Package secr updated to version 2.9.2 with previous version 2.9.1 dated 2014-11-18

Title: Spatially explicit capture-recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford

Diff between secr versions 2.9.1 dated 2014-11-18 and 2.9.2 dated 2014-11-26

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Package rowr updated to version 1.1.1 with previous version 1.0.1 dated 2014-08-15

Title: Row-based functions for R objects.
Description: Rowr allows the manipulation of R objects as if they were organized rows in a way that is familiar to people used to working with databases. It allows more consistent and predictable output to common functions, and generalizes a number of utility functions to to be failsafe with any number and type of input objects.
Author: Craig Varrichio
Maintainer: Craig Varrichio

Diff between rowr versions 1.0.1 dated 2014-08-15 and 1.1.1 dated 2014-11-26

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Package gridGraphics updated to version 0.1-2 with previous version 0.1-1 dated 2014-11-25

Title: Redraw Base Graphics Using grid Graphics
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell

Diff between gridGraphics versions 0.1-1 dated 2014-11-25 and 0.1-2 dated 2014-11-26

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Package SunterSampling updated to version 1.0.1 with previous version 1.0 dated 2012-05-08

Title: Sunter's sampling design
Description: Functions for drawing samples according to Sunter's sampling design, and for computing first and second order inclusion probabilities
Author: Alessandro Barbiero, Giancarlo Manzi
Maintainer: alessandro.barbiero

Diff between SunterSampling versions 1.0 dated 2012-05-08 and 1.0.1 dated 2014-11-26

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Package rex updated to version 0.2.0 with previous version 0.1.2 dated 2014-10-31

Title: Friendly Regular Expressions
Description: A more friendly, human-readable interface for the construction of regular expressions.
Author: Kevin Ushey [aut], Jim Hester [cre, aut]
Maintainer: Jim Hester

Diff between rex versions 0.1.2 dated 2014-10-31 and 0.2.0 dated 2014-11-26

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More information about rex at CRAN
Permanent link

New package rclinicaltrials with initial version 1.4
Package: rclinicaltrials
Type: Package
Title: Download Aggregate Trial Information and Results from ClinicalTrials.gov
Description: ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. Users can search for information about and results from those trials. This provides a set of functions to interact with the search and download features. Results are downloaded to temporary directories and returned as R objects.
Version: 1.4
Date: 2014-11-25
Author: Michael C Sachs
Maintainer: Michael C Sachs
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
Imports: httr, XML, plyr
Suggests: devtools, knitr, roxygen2, testthat, ggplot2
VignetteBuilder: knitr
LazyData: true
Packaged: 2014-11-26 16:03:28 UTC; sachsmc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:37:28

More information about rclinicaltrials at CRAN
Permanent link

Package RaschSampler updated to version 0.8-7 with previous version 0.8-6 dated 2012-07-07

Title: Rasch Sampler
Description: Sampling binary matrices with fixed margins
Author: Patrick Mair [cre, aut], Reinhold Hatzinger [aut], Norman D. Verhelst [aut]
Maintainer: Patrick Mair

Diff between RaschSampler versions 0.8-6 dated 2012-07-07 and 0.8-7 dated 2014-11-26

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Permanent link

New package pointdensityP with initial version 0.1
Package: pointdensityP
Title: Point density for geospatial data
Version: 0.1
Author: "Paul Evangelista and Dave Beskow "
Maintainer: Paul Evangelista
Description: pointdensity returns a density count and the temporal average for every point in the original list. The dataframe returned includes four columns: lat, lon, count, and date_avg. The "lat" column is the original latitude data; the "lon" column is the original longitude data; the "count" is the density count of the number of points within a radius of radius*grid_size (the neighborhood); and the date_avg column includes the average date of each point in the neighborhood.
Depends: R (>= 3.1.1)
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-11-26 15:07:34 UTC; Paul.Evangelista
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:39:20

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Package mixPHM updated to version 0.7-1 with previous version 0.7.0 dated 2008-12-16

Title: Mixtures of proportional hazard models.
Description: This package fits multiple variable mixtures of various parametric proportional hazard models using the EM-Algorithm. Proportionality restrictions can be imposed on the latent groups and/or on the variables. Several survival distributions can be specified. Missing values and censored values are allowed. Independence is assumed over the single variables.
Author: Patrick Mair [cre, aut], Marcus Hudec [aut]
Maintainer: Patrick Mair

Diff between mixPHM versions 0.7.0 dated 2008-12-16 and 0.7-1 dated 2014-11-26

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Permanent link

New package kpodclustr with initial version 1.0
Package: kpodclustr
Title: Method for Clustering Partially Observed Data
Version: 1.0
Authors@R: as.person(c( "Jocelyn T. Chi [aut, cre]", "Eric C. Chi [ctb]" ))
Description: The kpodclustr package implements the k-POD method for clustering partially observed data.
URL: http://jocelynchi.com/kpodclustr
Depends: R (>= 3.1.0), clues
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-11-26 15:37:47 UTC; jocelyn
Author: Jocelyn T. Chi [aut, cre], Eric C. Chi [ctb]
Maintainer: Jocelyn T. Chi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:33:47

More information about kpodclustr at CRAN
Permanent link

Package jaatha updated to version 2.7.0 with previous version 2.6 dated 2014-09-03

Title: A Fast Parameter Estimation Method for Evolutionary Biology
Description: Jaatha is a composite likelihood method for inferring evolutionary parameters using genetic data. Given a model of the evolutionary history of two biological populations as well as SNP data from multiple individuals from each population, it estimates model parameters like the time of separation of both species.
Author: Paul Staab [aut, cre, cph], Lisha Mathew [aut, cph], Dirk Metzler [aut, cph, ths]
Maintainer: Paul Staab

Diff between jaatha versions 2.6 dated 2014-09-03 and 2.7.0 dated 2014-11-26

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Package irace updated to version 1.06 with previous version 1.05 dated 2014-07-09

Title: Iterated Racing Procedures
Description: Iterated racing for automatic algorithm configuration
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres, Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez

Diff between irace versions 1.05 dated 2014-07-09 and 1.06 dated 2014-11-26

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Permanent link

New package EstSimPDMP with initial version 1.2
Package: EstSimPDMP
Type: Package
Title: Estimation and Simulation for PDMPs
Version: 1.2
Date: 2014-11-25
Author: Romain Azais
Maintainer: Romain Azais
Description: This package deals with the estimation of the jump rate for piecewise-deterministic Markov processes (PDMPs), from only one observation of the process within a long time. The main functions provide an estimate of this function. The state space may be discrete or continuous. The associated paper has been published in Scandinavian Journal of Statistics and is given in references. Other functions provide a method to simulate random variables from their (conditional) hazard rate, and then to simulate PDMPs.
License: GPL (>= 2)
Packaged: 2014-11-26 14:50:50 UTC; azais
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:53:19

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Package catR updated to version 3.3 with previous version 3.2 dated 2014-09-10

Title: Procedures to Generate Patterns under Computerized Adaptive Testing
Description: Generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several item response theory (IRT) models, starting rules, next item selection routines, stopping rules and ability estimators.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis

Diff between catR versions 3.2 dated 2014-09-10 and 3.3 dated 2014-11-26

 DESCRIPTION             |   13 +++++++------
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 6 files changed, 40 insertions(+), 21 deletions(-)

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New package BayesianAnimalTracker with initial version 1.0
Package: BayesianAnimalTracker
Type: Package
Title: Bayesian Melding of GPS and DR Path for Animal Tracking
Version: 1.0
Date: 2014-11-07
Author: Yang (Seagle) Liu
Maintainer: Yang (Seagle) Liu
Suggests: TrackReconstruction
Description: Bayesian melding approach to combine the GPS observations and Dead-Reckoned path for an accurate animal's track, or equivalently, use the GPS observations to correct the Dead-Reckoned path. It can take the measurement errors in the GPS observations into account and provide uncertainty statement about the corrected path. The main calculation can be done by the BMAnimalTrack function.
License: GPL (>= 2)
Packaged: 2014-11-26 17:37:12 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:57:31

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Package aspect updated to version 1.0-3 with previous version 1.0-2 dated 2013-12-03

Title: Aspects of Multivariables
Description: This package consists of two main functions: The first function is corAspect() performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. The second function is lineals() performs optimal scaling by minimization a non-correlational aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as SEM. A platform including related PsychoR packages is provided on R-Forge.
Author: Patrick Mair [cre, aut], Jan De Leeuw [aut]
Maintainer: Patrick Mair

Diff between aspect versions 1.0-2 dated 2013-12-03 and 1.0-3 dated 2014-11-26

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Package agridat updated to version 1.10 with previous version 1.9 dated 2014-07-02

Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture. Example analyses are included. Includes functions for plotting field designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright

Diff between agridat versions 1.9 dated 2014-07-02 and 1.10 dated 2014-11-26

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New package timeseriesdb with initial version 0.1
Package: timeseriesdb
Title: Store and Organize Time Series in a Database
Description: An R package to store and organize time series and their multi-lingual meta information in a database. The timeseriesdb package suggests a simple yet powerful database structure to store a large amount of time series in a relational PostgreSQL database. The package provides an interface to the R user to create, update and delete time series.
Version: 0.1
Authors@R: 'Matthias Bannert [aut, cre]'
Depends: R (>= 3.0.0)
Suggests: RPostgreSQL
Imports: DBI
License: GPL-2
LazyData: true
Maintainer: 'Matthias Bannert'
Packaged: 2014-11-26 14:02:06 UTC; mbannert
Author: 'Matthias Bannert' [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 15:40:25

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Package sensitivity updated to version 1.10 with previous version 1.9 dated 2014-08-26

Title: Sensitivity Analysis
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis of model output.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Paul Lemaitre, Laurent Gilquin, Loic Le Gratiet, Taieb Touati, Bernardo Ramos, Jana Fruth and Sebastien Da Veiga
Maintainer: Bertrand Iooss

Diff between sensitivity versions 1.9 dated 2014-08-26 and 1.10 dated 2014-11-26

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Package icomp (with last version 0.1) was removed from CRAN

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

2008-07-07 0.1

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Package rspa updated to version 0.1-6 with previous version 0.1-5 dated 2014-05-16

Title: Adapt Numerical Records To Fit (In)Equality Restrictions
Description: Based on (optionally sparse) quadratic optimization with the main algorithms implemented in C. Includes features for easy processing of many (smaller) records. The algorithm has been tested on fairly large optimization problems with up to a few million variables and several hundred thousand restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo

Diff between rspa versions 0.1-5 dated 2014-05-16 and 0.1-6 dated 2014-11-26

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Package MCPMod updated to version 1.0-8 with previous version 1.0-7 dated 2010-07-24

Title: Design and Analysis of Dose-Finding Studies (see also DoseFinding package)
Description: This package implements a methodology for the design and analysis of dose-response studies that combines aspects of multiple comparison procedures and modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics 61, 738-748). The package provides tools for the analysis of dose finding trials as well as a variety of tools necessary to plan a trial to be conducted with the MCPMod methodology. ***NOTE*** The MCPMod package will not be further developed, all future development of the MCP-Mod methodology will be done in the DoseFinding R-package. ***NOTE***
Author: Bjoern Bornkamp, Jose Pinheiro and Frank Bretz
Maintainer: Bjoern Bornkamp

Diff between MCPMod versions 1.0-7 dated 2010-07-24 and 1.0-8 dated 2014-11-26

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Package knitcitations updated to version 1.0.5 with previous version 1.0.4 dated 2014-10-28

Title: Citations for knitr markdown files
Description: knitcitations provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as bibtex ahead of time. Knitcitations is primarily aimed at authoring in the R markdown format, and can provide outputs for web-based authoring such as linked text and tooltips over inline citations. Cite using a DOI, URL, or bibtex file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger

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New package SphericalK with initial version 1.0
Package: SphericalK
Type: Package
Title: Spherical K-function
Version: 1.0
Date: 2014-11-25
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li
Description: Spherical K-function for point-pattern analysis on the sphere
License: GPL (>= 2)
Packaged: 2014-11-26 02:06:14 UTC; Leon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 08:06:54

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Package RcmdrPlugin.EZR updated to version 1.27 with previous version 1.26 dated 2014-09-29

Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN-10: 4498109007), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda

Diff between RcmdrPlugin.EZR versions 1.26 dated 2014-09-29 and 1.27 dated 2014-11-26

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Package NHMM updated to version 3.5 with previous version 3.3 dated 2014-09-23

Title: Bayesian NHMM Modeling (Multiple Time Series)
Description: Bayesian NHMM modeling for multiple time series. The emission distribution can be mixtures of Gammas, Poissons, Normals and zero inflation is possible.
Author: Tracy Holsclaw
Maintainer: Tracy Holsclaw

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Package moduleColor updated to version 1.08-3 with previous version 1.08-1 dated 2009-10-11

Title: Basic Module Functions
Description: Methods for color labeling, calculation of eigengenes, merging of closely related modules.
Author: Peter Langfelder and Steve Horvath
Maintainer: Peter Langfelder

Diff between moduleColor versions 1.08-1 dated 2009-10-11 and 1.08-3 dated 2014-11-26

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Package hierarchicalDS updated to version 2.9 with previous version 2.01 dated 2012-09-28

Title: Functions For Performing Hierarchical Analysis of Distance Sampling Data
Description: Functions for performing hierarchical analysis of distance sampling data, with ability to use an areal spatial ICAR model on top of user supplied covariates to get at variation in abundance intensity. The detection model can be specified as a function of observer and individual covariates, where a parametric model is supposed for the population level distribution of covariate values. The model uses data augmentation and a reversible jump MCMC algorithm to sample animals that were never observed. Also included is the ability to include point independence (increasing correlation multiple observer's observations as a function of distance, with independence assumed for distance=0 or first distance bin), as well as the ability to model species misclassification rates using a multinomial logit formulation on data from double observers. New in version 2.1 is the ability to include zero inflation, but this is only recommended for cases where sample sizes and spatial coverage of the survey are high.
Author: P.B. Conn \email{paul.conn@@noaa.gov}
Maintainer: Paul B Conn

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Package gWidgetsRGtk2 updated to version 0.0-83 with previous version 0.0-82 dated 2013-11-11

Title: Toolkit implementation of gWidgets for RGtk2
Description: Port of gWidgets API to RGtk2
Author: Michael Lawrence, John Verzani
Maintainer: John Verzani

Diff between gWidgetsRGtk2 versions 0.0-82 dated 2013-11-11 and 0.0-83 dated 2014-11-26

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Tue, 25 Nov 2014

New package lucid with initial version 1.0
Package: lucid
Version: 1.0
Date: 2014-11-24
Title: Lucid Printing of Floating Point Numbers
Author: Kevin Wright
Maintainer: Kevin Wright
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
LazyData: yes
License: GPL-2
URL: https://github.com/kwstat/lucid
BugReports: https://github.com/kwstat/lucid/issues
VignetteBuilder: knitr
Imports: nlme
Suggests: knitr, lattice, lme4
Packaged: 2014-11-25 22:00:33 UTC; wrightkevi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:52:34

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New package GMDH with initial version 1.0
Package: GMDH
Type: Package
Title: Predicting and Forecasting Time Series via GMDH-Type Neural Network Algorithms
Version: 1.0
Date: 2014-11-25
Depends: MASS, stats
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to predict and forecast a univariate time series.
License: GPL (>= 2)
Packaged: 2014-11-25 19:14:40 UTC; osmndg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:48:49

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New package EnsembleCV with initial version 0.7
Package: EnsembleCV
Type: Package
Title: Extensible Package for Cross-Validation-Based Integration of Base Learners
Version: 0.7
Date: 2014-11-17
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: This package extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods
Packaged: 2014-11-25 21:39:34 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:59:47

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Package SMR updated to version 2.0.1 with previous version 2.0 dated 2014-10-16

Title: Externally Studentized Midrange Distribution
Description: Computes the studentized midrange distribution (pdf, cdf and quantile) and generates random numbers
Author: Ben Deivide de Oliveira Batista, Daniel Furtado Ferreira
Maintainer: Daniel Furtado Ferreira

Diff between SMR versions 2.0 dated 2014-10-16 and 2.0.1 dated 2014-11-25

 DESCRIPTION |   10 +++----
 MD5         |    4 +-
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 3 files changed, 60 insertions(+), 35 deletions(-)

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New package gridGraphics with initial version 0.1-1
Package: gridGraphics
Title: Redraw Base Graphics Using grid Graphics
Version: 0.1-1
Authors@R: person("Paul", "Murrell", role = c("cre", "aut"), email = "paul@stat.auckland.ac.nz")
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Depends: grid, graphics
Suggests: KernSmooth
SystemRequirements: ImageMagick (for testing)
License: GPL (>= 2)
URL: https://github.com/pmur002/gridgraphics
Packaged: 2014-11-25 20:01:49 UTC; EC\pmur002
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 22:24:13

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New package KODAMA with initial version 0.0.1
Package: KODAMA
Version: 0.0.1
Date: 2013-11-20
Author: Stefano Cacciatore, Claudio Luchinat, Leonardo Tenori
Maintainer: Stefano Cacciatore
Title: Knowledge discovery by accuracy maximization
Description: KODAMA (KnOwledge Discovery by Accuracy MAximization) is an unsupervised and semisupervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Depends: R (>= 2.10.0),e1071,plsgenomics,class
Suggests: rgl,
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 15:41:39 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:05:43

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New package empiricalFDR.DESeq2 with initial version 1.0
Package: empiricalFDR.DESeq2
Type: Package
Title: Simulation-based False Discovery Rate in RNA-seq
Version: 1.0
Date: 2014-11-25
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
License: GPL-3
Depends: DESeq2,GenomicRanges
Packaged: 2014-11-25 15:48:11 UTC; c-monster
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:03:34

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Package synbreed updated to version 0.10-5 with previous version 0.10-4 dated 2014-11-11

Title: Framework for the analysis of genomic prediction data using R
Description: The package 'synbreed' was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer

Diff between synbreed versions 0.10-4 dated 2014-11-11 and 0.10-5 dated 2014-11-25

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Package redcapAPI updated to version 1.1 with previous version 1.0.1 dated 2014-10-20

Title: R interface to REDCap
Description: Access data stored in REDCap databases using the Application Programming Interface (API). REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The redcapAPI package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with contributions from Jeremy Stephens, and Will Beasley
Maintainer: Benjamin Nutter

Diff between redcapAPI versions 1.0.1 dated 2014-10-20 and 1.1 dated 2014-11-25

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Package mistral updated to version 1.1-1 with previous version 1.1-0 dated 2014-02-15

Title: Methods in Structural Reliability
Description: Various reliability analysis methods for: 1) computing failure probability (probability that the output of a numerical model exceeds a threshold); 2) computing the size of a sample to estimate a quantile with a confidence level.
Author: Nicolas BOUSQUET, Gilles DEFAUX, Bertrand IOOSS, Vincent MOUTOUSSAMY, Clement WALTER
Maintainer: Bertrand Iooss

Diff between mistral versions 1.1-0 dated 2014-02-15 and 1.1-1 dated 2014-11-25

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New package maboost with initial version 1.0-0
Package: maboost
Version: 1.0-0
Date: 2014-11-01
Title: Binary and Multiclass Boosting Algorithms
Author: Tofigh Naghibi
Depends: R(>= 2.10),rpart,C50
Description: Performs binary and multiclass boosting in maximum-margin, sparse, smooth and normal settings as described in "A Boosting Framework on Grounds of Online Learning" by T. Naghibi and B. Pfister, (2014). For further information regarding the algorithms, please refer to http://arxiv.org/abs/1409.7202
Maintainer: Tofigh Naghibi
License: GPL (>= 2)
Packaged: 2014-11-25 15:05:38 UTC; tofighn
Repository: CRAN
Date/Publication: 2014-11-25 17:03:41
Collate: 'maboost-package.r' 'maboost.R' 'maboost.default.R' 'maboost.formula.R' 'maboost.machine.bin.R' 'maboost.machine.multi.R' 'predict.maboost.R' 'print.maboost.R' 'projsplx.R' 'projsplx_k.R' 'summary.maboost.R' 'update.maboost.R' 'varplot.maboost.R'
NeedsCompilation: no

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Package effects updated to version 3.0-2 with previous version 3.0-1 dated 2014-08-14

Title: Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb]
Maintainer: John Fox

Diff between effects versions 3.0-1 dated 2014-08-14 and 3.0-2 dated 2014-11-25

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Package dslice updated to version 1.1.4 with previous version 1.1.3 dated 2014-11-24

Title: Dynamic slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye

Diff between dslice versions 1.1.3 dated 2014-11-24 and 1.1.4 dated 2014-11-25

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Package diptest updated to version 0.75-6 with previous version 0.75-5 dated 2013-07-23

Title: Hartigan's dip test statistic for unimodality - corrected code
Description: Compute Hartigan's dip test statistic for unimodality / multimodality and provide a test with simulation based p-values.
Author: Martin Maechler (originally from Fortran and S-plus by Dario Ringach, NYU.edu)
Maintainer: Martin Maechler

Diff between diptest versions 0.75-5 dated 2013-07-23 and 0.75-6 dated 2014-11-25

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Package audited (with last version 1.9) was removed from CRAN

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

2014-09-20 1.9

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Package metrumrg (with last version 5.55) was removed from CRAN

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

2014-02-18 5.55
2013-11-26 5.54
2013-06-06 5.50
2013-05-23 5.49
2013-05-01 5.45
2013-04-24 5.44
2013-03-28 5.36
2013-03-21 5.34
2012-11-27 5.27
2012-11-24 5.26
2012-11-05 5.25
2012-10-25 5.24
2012-10-01 5.23
2012-05-05 5.17
2012-02-09 5.13
2011-11-11 5.5
2011-10-24 5.3
2011-09-20 5.2
2011-09-08 5.1

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Package StressStrength updated to version 1.0.1 with previous version 1.0 dated 2012-01-16

Title: Computation and estimation of reliability of stress-strength models
Description: The package provide functions for computing the reliability of stress-strength models and for building two-sided or one-sided confidence intervals according to different approximate procedures
Author: Alessandro Barbiero , Riccardo Inchingolo
Maintainer: Alessandro Barbiero

Diff between StressStrength versions 1.0 dated 2012-01-16 and 1.0.1 dated 2014-11-25

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Package R0 updated to version 1.2-5 with previous version 1.2-4 dated 2013-12-13

Title: Estimation of R0 and real-time reproduction number from epidemics
Description: This package is designed to estimate reproduction numbers for disease outbreak, based on incidence data. It implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.
Author: Pierre-Yves Boelle, Thomas Obadia
Maintainer: Thomas Obadia

Diff between R0 versions 1.2-4 dated 2013-12-13 and 1.2-5 dated 2014-11-25

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Package questionr updated to version 0.4.2 with previous version 0.4.1 dated 2014-07-16

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 0.4.1 dated 2014-07-16 and 0.4.2 dated 2014-11-25

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Package PrevMap updated to version 1.1 with previous version 1.0 dated 2014-10-30

Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is also an extension of the 'geoR' package which should be installed first together with the 'maxLik', 'raster' and 'pdist' packages.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi

Diff between PrevMap versions 1.0 dated 2014-10-30 and 1.1 dated 2014-11-25

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Package kinfit updated to version 1.1.13 with previous version 1.1.12 dated 2013-11-27

Title: Routines for fitting kinetic models to chemical degradation data
Description: Simple calculation routines based on the FOCUS Kinetics Report (2006). Only kinetic models for parent only datasets are included (no metabolite formation/decline or multicompartment kinetics). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. This package is not actively developed at the moment. Please check the mkin package for an actively maintained package for kinetic evaluations of degradation data
Author: Johannes Ranke, with contributions from Katrin Lindenberger
Maintainer: Johannes Ranke

Diff between kinfit versions 1.1.12 dated 2013-11-27 and 1.1.13 dated 2014-11-25

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Package Julia updated to version 1.1 with previous version 1.0 dated 2011-02-12

Title: Fractal Image Data Generator
Description: Generates image data for fractals (Julia and Mandelbrot sets) on the complex plane in the given region and resolution.
Author: Mehmet Suzen [aut, main]
Maintainer: Mehmet Suzen

Diff between Julia versions 1.0 dated 2011-02-12 and 1.1 dated 2014-11-25

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New package IRTShiny with initial version 1.0
Package: IRTShiny
Type: Package
Title: Item Response Theory via Shiny
Version: 1.0
Date: 2014-11-24
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton
Description: Interactive shiny application for running Item Response Theory analysis.
License: GPL-3
Imports: shiny, shinyAce, beeswarm, CTT, ltm, parallel,
Suggests: psych
LazyData: true
Packaged: 2014-11-25 08:29:49 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 11:33:45

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Package distrMod updated to version 2.5.3 with previous version 2.5.2 dated 2013-09-12

Title: Object Oriented Implementation of Probability Models
Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx'
Author: Matthias Kohl, Peter Ruckdeschel
Maintainer: Peter Ruckdeschel

Diff between distrMod versions 2.5.2 dated 2013-09-12 and 2.5.3 dated 2014-11-25

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Package DiscreteInverseWeibull updated to version 1.0.1 with previous version 1.0 dated 2012-10-19

Title: Discrete inverse Weibull distribution
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the discrete inverse Weibull distribution
Author: Alessandro Barbiero, Riccardo Inchingolo, Mario Samigli
Maintainer: Alessandro Barbiero

Diff between DiscreteInverseWeibull versions 1.0 dated 2012-10-19 and 1.0.1 dated 2014-11-25

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Package GCPM (with last version 1.1) was removed from CRAN

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

2014-11-25 1.1

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Package vcrpart updated to version 0.2-3 with previous version 0.2-2 dated 2014-11-07

Title: Tree-Based Varying Coefficient Regression for Generalized Linear and Ordinal Mixed Models
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph], Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin

Diff between vcrpart versions 0.2-2 dated 2014-11-07 and 0.2-3 dated 2014-11-25

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New package USAboundaries with initial version 0.1
Package: USAboundaries
Type: Package
Title: Historical boundaries of the United States of America, 1629-2000
Date: 2014
Version: 0.1
Authors@R: c(person("Lincoln", "Mullen", email = "lincoln@lincolnmullen.com", role = c("aut", "cre")), person("Dr. William M. Scholl Center for American History and Culture, The Newberry Library", role = c("cph")))
Description: This package provides spatial objects with the boundaries of states or counties in the United States of America from 1629 to 2000. It provides data from the Atlas of Historical County Boundaries.
License: CC BY-NC-SA 4.0
LazyData: true
LazyDataCompression: xz
URL: https://github.com/ropensci/USAboundaries
BugReports: https://github.com/ropensci/USAboundaries/issues
Depends: R (>= 3.1.1),
Imports: assertthat (>= 0.1), dplyr (>= 0.3.0.1), ggplot2 (>= 1.0.0), lubridate (>= 1.3.3), maptools (>= 0.8-30), rgeos (>= 0.3-8), sp (>= 1.0.15)
Suggests: knitr, mapproj, testthat (>= 0.9.1)
VignetteBuilder: knitr
Packaged: 2014-11-24 18:25:13 UTC; lmullen
Author: Lincoln Mullen [aut, cre], Dr. William M. Scholl Center for American History and Culture, The Newberry Library [cph]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:42:09

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Package soma updated to version 1.1.1 with previous version 1.1.0 dated 2011-07-28

Title: General-Purpose Optimisation With the Self-Organising Migrating Algorithm
Description: This package provides an R implementation of the Self-Organising Migrating Algorithm, a general-purpose, stochastic optimisation algorithm. The approach is similar to that of genetic algorithms, although it is based on the idea of a series of ``migrations'' by a fixed set of individuals, rather than the development of successive generations. It can be applied to any cost-minimisation problem with a bounded parameter space, and is robust to local minima.
Author: Jon Clayden; based on the work of Ivan Zelinka
Maintainer: Jon Clayden

Diff between soma versions 1.1.0 dated 2011-07-28 and 1.1.1 dated 2014-11-25

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Package ore updated to version 1.0.4 with previous version 1.0.1 dated 2014-10-21

Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden

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New package musicNMR with initial version 0.0.2
Package: musicNMR
Version: 0.0.2
Date: 2013-11-21
Author: Stefano Cacciatore, Edoardo Saccenti, Mario Piccioli
Maintainer: Stefano Cacciatore
Title: Conversion of Nuclear Magnetic Resonance spectrum in audio file
Description: This package is a collection of function for converting and modifying mono dimensional nuclear magnetic resonance spectra.
Depends: R (>= 2.10.0), seewave
Suggests: plsgenomics
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 06:58:47 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:50:06

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Package dataframes2xls updated to version 0.4.6 with previous version 0.4.5 dated 2011-05-03

Title: dataframes2xls writes data frames to xls files
Description: dataframes2xls writes data frames to xls files. It supports multiple sheets and basic formatting.
Author: Guido van Steen
Maintainer: Guido van Steen

Diff between dataframes2xls versions 0.4.5 dated 2011-05-03 and 0.4.6 dated 2014-11-25

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New package cjoint with initial version 1.0.2
Package: cjoint
Version: 1.0.2
Date: 2014-10-18
Title: AMCE Estimator for Conjoint Experiments
Author: Anton Strezhnev, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev
Depends: R (>= 2.0.0), sandwich, lmtest, ggplot2
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
License: GPL (>= 2)
Packaged: 2014-11-25 07:53:08 UTC; anton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:24:01

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Package bipartite updated to version 2.05 with previous version 2.04 dated 2014-03-25

Title: Visualising bipartite networks and calculating some (ecological) indices.
Description: Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focuses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones.
Maintainer: Carsten F. Dormann

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Package SweaveListingUtils updated to version 0.6.2 with previous version 0.6.1 dated 2013-02-09

Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most recent version (or another url) thereby avoiding inconsistencies between vignette and documented source code
Author: Peter Ruckdeschel
Maintainer: Peter Ruckdeschel

Diff between SweaveListingUtils versions 0.6.1 dated 2013-02-09 and 0.6.2 dated 2014-11-25

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Package summarytools updated to version 0.2 with previous version 0.1 dated 2014-08-10

Title: Dataframe Summaries, Frequency Tables and Numerical Summaries with Customizable Output
Description: Includes 3 summarizing functions; one for categorical data (freq), one for numerical (uni or multidimensional) data (desc), and one exclusively for dataframes. 'freq' generates frequency tables with valid and total proportions. 'desc' generates common central tendency statistics and measures of dispersion for numerical data. 'dfSummary' will generate a table containing as many rows as there are columns, each row giving variable information (class and type), labels if any, common statistics for numerical data and frequency tables for any type of data, along with number and proportion of valid (non-missing) values.
Author: Dominic Comtois
Maintainer: Dominic Comtois

Diff between summarytools versions 0.1 dated 2014-08-10 and 0.2 dated 2014-11-25

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Package setRNG updated to version 2013.9-1 with previous version 2011.11-2 dated 2012-03-27

Title: Set (Normal) Random Number Generator and Seed
Description: SetRNG provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.
Author: Paul Gilbert
Maintainer: Paul Gilbert

Diff between setRNG versions 2011.11-2 dated 2012-03-27 and 2013.9-1 dated 2014-11-25

 setRNG-2011.11-2/setRNG/S                  |only
 setRNG-2013.9-1/setRNG/DESCRIPTION         |   22 ++++++++++------------
 setRNG-2013.9-1/setRNG/MD5                 |   10 +++++-----
 setRNG-2013.9-1/setRNG/NEWS                |    4 ++++
 setRNG-2013.9-1/setRNG/build               |only
 setRNG-2013.9-1/setRNG/inst/doc/setRNG.pdf |binary
 setRNG-2013.9-1/setRNG/man/getRNG.Rd       |    2 +-
 7 files changed, 20 insertions(+), 18 deletions(-)

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Package rstiefel updated to version 0.10 with previous version 0.9 dated 2012-01-12

Title: Random orthonormal matrix generation on the Stiefel manifold
Description: This package simulates random orthonormal matrices from linear and quadratic exponential family distributions on the Stiefel manifold. The most general type of distribution covered is the matrix-variate Bingham-von Mises-Fisher distribution. Most of the simulation methods are presented in Hoff(2009) "Simulation of the Matrix Bingham-von Mises-Fisher Distribution, With Applications to Multivariate and Relational Data."
Author: Peter Hoff
Maintainer: Peter Hoff

Diff between rstiefel versions 0.9 dated 2012-01-12 and 0.10 dated 2014-11-25

 rstiefel-0.10/rstiefel/DESCRIPTION               |   18 ++----
 rstiefel-0.10/rstiefel/MD5                       |   17 +++---
 rstiefel-0.10/rstiefel/R/rbing.vector.gibbs.R    |    2 
 rstiefel-0.10/rstiefel/R/rmf.vector.R            |    2 
 rstiefel-0.10/rstiefel/build                     |only
 rstiefel-0.10/rstiefel/inst/doc/rstiefel.R       |only
 rstiefel-0.10/rstiefel/man/rbing.vector.gibbs.Rd |   24 +++++---
 rstiefel-0.10/rstiefel/man/rmf.vector.Rd         |    2 
 rstiefel-0.10/rstiefel/man/rstiefel-package.Rd   |    4 -
 rstiefel-0.10/rstiefel/vignettes/rstiefel.Rnw    |   62 ++++++++++++++++++++++-
 rstiefel-0.9/rstiefel/vignettes/rstiefel.bbl     |only
 11 files changed, 96 insertions(+), 35 deletions(-)

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Package multilevelPSA updated to version 1.2.2 with previous version 1.2 dated 2013-05-10

Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity score analysis for multilevel, or clustered, data.
Author: Jason Bryer
Maintainer: Jason Bryer

Diff between multilevelPSA versions 1.2 dated 2013-05-10 and 1.2.2 dated 2014-11-25

 DESCRIPTION                            |   23 +---
 MD5                                    |  120 ++++++++++++----------
 NAMESPACE                              |   14 ++
 NEWS                                   |   37 ++++++
 R/align.R                              |   35 +++++-
 R/covariate.balance.R                  |only
 R/covariateBalance.R                   |only
 R/cv.trans.psa.R                       |only
 R/mlpsa.R                              |  178 +++++++++++++++++++--------------
 R/mlpsa.ctree.R                        |    6 -
 R/mlpsa.logistic.R                     |   25 ++++
 R/mlpsa.print.R                        |    2 
 R/multilevelPSA-package.R              |    8 +
 R/plot.balance.R                       |only
 R/plot.loess.R                         |   37 +++++-
 R/plot.missing.R                       |    2 
 R/plot.mlpsa.R                         |   11 --
 R/plot.mlpsa.circ.R                    |    8 -
 R/plot.mlpsa.difference.R              |   57 +++++++++-
 R/plot.mlpsa.distribution.R            |   38 ++++---
 R/psrange.r                            |   49 ++++++---
 R/xtable.mlpsa.r                       |    2 
 data/pisa.colnames.rda                 |binary
 data/pisa.countries.rda                |binary
 data/pisana.rda                        |binary
 demo/00Index                           |    1 
 demo/pisa.R                            |   39 ++++---
 demo/pisa.loess.R                      |    3 
 demo/plotmissing.r                     |    8 -
 demo/psrange-trees.R                   |only
 man/align.plots.Rd                     |   14 +-
 man/as.data.frame.covariate.balance.Rd |only
 man/covariate.balance.Rd               |only
 man/covariateBalance.Rd                |only
 man/cv.trans.psa.Rd                    |only
 man/difftable.plot.Rd                  |   20 +--
 man/geom_rug_alt.Rd                    |   36 ++----
 man/getPropensityScores.Rd             |   17 +--
 man/getStrata.Rd                       |   19 +--
 man/is.mlpsa.Rd                        |    7 -
 man/loess.plot.Rd                      |   49 +++++----
 man/lsos.Rd                            |   14 +-
 man/missing.plot.Rd                    |   34 ++----
 man/mlpsa.Rd                           |   36 ++++--
 man/mlpsa.circ.plot.Rd                 |  103 +++++++------------
 man/mlpsa.ctree.Rd                     |   40 +++----
 man/mlpsa.difference.plot.Rd           |   70 ++++++------
 man/mlpsa.distribution.plot.Rd         |   37 ++----
 man/mlpsa.logistic.Rd                  |   27 ++---
 man/multilevelPSA-package.Rd           |   63 +++++------
 man/pisa.colnames.Rd                   |   11 --
 man/pisa.countries.Rd                  |    7 -
 man/pisa.psa.cols.Rd                   |    5 
 man/pisana.Rd                          |   27 ++---
 man/plot.covariate.balance.Rd          |only
 man/plot.mlpsa.Rd                      |   25 ++--
 man/plot.psrange.Rd                    |   53 ++++-----
 man/print.covariate.balance.Rd         |only
 man/print.mlpsa.Rd                     |    9 -
 man/print.psrange.Rd                   |    9 -
 man/print.xmlpsa.Rd                    |   18 +--
 man/psrange.Rd                         |   38 +++----
 man/summary.mlpsa.Rd                   |   13 +-
 man/summary.psrange.Rd                 |    9 -
 man/tree.plot.Rd                       |   56 ++++------
 man/xtable.mlpsa.Rd                    |   28 ++---
 man/zeroGrob.Rd                        |only
 67 files changed, 891 insertions(+), 706 deletions(-)

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New package mads with initial version 0.1.0
Package: mads
Depends: mrds
Suggests: testthat
Type: Package
Title: Multi-Analysis Distance Sampling.
Version: 0.1.0
Date: 2014-11-27
Author: Laura Marshall
Maintainer: Laura Marshall
Description: Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.
License: GPL (>= 2)
Packaged: 2014-11-25 02:50:52 UTC; laura
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:01:38

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Package GPArotation updated to version 2014.11-1 with previous version 2012.3-1 dated 2012-03-27

Title: GPA Factor Rotation
Description: Gradient Projection Algorithm Rotation for Factor Analysis. See ?GPArotation.Intro for more details.
Author: Coen Bernaards and Robert Jennrich
Maintainer: Paul Gilbert

Diff between GPArotation versions 2012.3-1 dated 2012-03-27 and 2014.11-1 dated 2014-11-25

 GPArotation-2012.3-1/GPArotation/Rbuildignore             |only
 GPArotation-2014.11-1/GPArotation/DESCRIPTION             |   14 ++++-----
 GPArotation-2014.11-1/GPArotation/MD5                     |   20 +++++++-------
 GPArotation-2014.11-1/GPArotation/NEWS                    |    4 ++
 GPArotation-2014.11-1/GPArotation/build                   |only
 GPArotation-2014.11-1/GPArotation/data/Harman.rda         |binary
 GPArotation-2014.11-1/GPArotation/data/Thurstone.rda      |binary
 GPArotation-2014.11-1/GPArotation/data/WansbeekMeijer.rda |binary
 GPArotation-2014.11-1/GPArotation/inst/doc/Guide.Stex     |    7 ----
 GPArotation-2014.11-1/GPArotation/inst/doc/Guide.pdf      |binary
 GPArotation-2014.11-1/GPArotation/man/rotations.Rd        |   15 +++++++---
 GPArotation-2014.11-1/GPArotation/vignettes/Guide.Stex    |    7 ----
 12 files changed, 32 insertions(+), 35 deletions(-)

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New package iccbeta with initial version 1.0
Package: iccbeta
Type: Package
Title: Multilevel model intraclass correlation for slope heterogeneity
Version: 1.0
Date: 2014-11-21
Authors@R: c(person("Steven Andrew", "Culpepper", role = c("aut", "cph","cre"), email = "sculpepp@illinois.edu"),person("Herman", "Aguinis", role = c("aut", "cph"), email = "haguinis@indiana.edu"))
Maintainer: Steven Andrew Culpepper
Description: A function and vignettes for computing an intraclass correlation described in Aguinis & Culpepper (in press). iccbeta quantifies the share of variance in a dependent variable that is attributed to group heterogeneity in slopes.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp (>= 0.11.1), RcppArmadillo
Depends: R (>= 3.0.2), lme4
Packaged: 2014-11-25 02:21:38 UTC; sculpepp
Author: Steven Andrew Culpepper [aut, cph, cre], Herman Aguinis [aut, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:52:58

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New package GCPM with initial version 1.1
Package: GCPM
Type: Package
Title: Generalized Credit Portfolio Model
Version: 1.1
Date: 2014-11-24
Author: Kevin Jakob
Maintainer: Kevin Jakob
Description: The package helps to analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
License: GPL-2
Imports: Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1)
LinkingTo: Rcpp, RcppProgress
Packaged: 2014-11-24 18:46:01 UTC; Kevin_Jakob
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:40:13

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