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

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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

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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"

Diff between genpathmox versions 0.1 dated 2014-10-30 and 0.2 dated 2014-11-27

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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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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 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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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

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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

 DESCRIPTION                |    9 +++++----
 MD5                        |   20 ++++++++++----------
 R/compare.relimp.R         |   29 ++---------------------------
 R/relative.importance.R    |    2 +-
 man/DECIDE-package.Rd      |   12 ++++++------
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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

 DESCRIPTION  |   10 +++----
 MD5          |   10 +++----
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 man/TPL.Rd   |    7 ++++-
 man/TPLck.Rd |    8 ++++--
 6 files changed, 100 insertions(+), 33 deletions(-)

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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

 ChangeLog            |   63 +++
 DESCRIPTION          |    6 
 MD5                  |   48 +-
 NAMESPACE            |   19 -
 R/bam.r              |   85 ++--
 R/coxph.r            |    1 
 R/fast-REML.r        |   52 +-
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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

 DESCRIPTION             |   19 ++++----
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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

 ChangeLog          |   20 ++++++++++++++++++++
 DESCRIPTION        |    8 ++++----
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 6 files changed, 67 insertions(+), 27 deletions(-)

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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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 build/vignette.rds                    |binary
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 inst/doc/Rmpfr-pkg.pdf                |binary
 inst/doc/log1mexp-note.pdf            |binary
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 9 files changed, 19 insertions(+), 14 deletions(-)

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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

 DESCRIPTION              |   10 +-
 MD5                      |   20 +++--
 R/BatCINOEDV.R           |   49 ++++++++++++-
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 R/TestMaxOrder.R         |    8 +-
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 13 files changed, 171 insertions(+), 128 deletions(-)

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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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