Thu, 18 Dec 2014

Package stream updated to version 1.1-0 with previous version 1.0-3 dated 2014-07-14

Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph], Matthew Bolanos [aut, cph], John Forrest [aut, cph]
Maintainer: Michael Hahsler

Diff between stream versions 1.0-3 dated 2014-07-14 and 1.1-0 dated 2014-12-18

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 96 files changed, 3841 insertions(+), 2835 deletions(-)

More information about stream at CRAN
Permanent link

New package srd with initial version 1.0
Package: srd
Type: Package
Title: Draws Scaled Rectangle Diagrams
Version: 1.0
Date: 2014-07-15
Author: Roger Marshall
Maintainer: Roger Marshall
Description: Draws scaled rectangle diagrams to represent a 2^k contingency table, for k<=6
License: GPL-2
Imports: plyr,animation,colorspace,stringr,survival
Packaged: 2014-12-18 22:35:36 UTC; rmar073
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-19 01:58:45

More information about srd at CRAN
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Package SemiParBIVProbit updated to version 3.2-13 with previous version 3.2-12.1 dated 2014-11-12

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-12.1 dated 2014-11-12 and 3.2-13 dated 2014-12-18

 ChangeLog                          |    9 +
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 NAMESPACE                          |    4 
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 44 files changed, 738 insertions(+), 609 deletions(-)

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New package spanr with initial version 1.0
Package: spanr
Type: Package
Title: Search Partition Analysis
Version: 1.0
Date: 2014-07-15
Author: Roger Marshall
Maintainer: Roger Marshall
Description: Carries out a search for an optimal partition in terms of a regular Boolean expression
License: GPL-2
Imports: plyr, stringr, survival
Packaged: 2014-12-18 22:25:39 UTC; rmar073
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-19 01:49:50

More information about spanr at CRAN
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Package hermite updated to version 1.0.1 with previous version 1.0 dated 2014-10-31

Title: Generalized Hermite Distribution
Description: Probability functions and utilities for the generalized Hermite distribution
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler

Diff between hermite versions 1.0 dated 2014-10-31 and 1.0.1 dated 2014-12-18

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 11 files changed, 81 insertions(+), 29 deletions(-)

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Permanent link

Package Luminescence updated to version 0.4.0 with previous version 0.3.4 dated 2014-06-08

Title: Package for Luminescence Dating data analysis
Description: Package provides a collection of various R functions for Luminescence Dating data analysis.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.3.4 dated 2014-06-08 and 0.4.0 dated 2014-12-18

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 132 files changed, 9405 insertions(+), 5962 deletions(-)

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New package GPC with initial version 0.1
Package: GPC
Type: Package
Title: Generalized Polynomial Chaos
Version: 0.1
Depends: R (>= 2.7.0), randtoolbox, orthopolynom, ks, lars
Date: 2013-02-01
Author: Miguel Munoz Zuniga and Jordan Ko
Maintainer: Miguel Munoz Zuniga
Description: A generalized polynomial chaos expansion of a model taking as input independent random variables is achieved. A statistical and a global sensitivity analysis of the model are also carried out.
License: GPL-3
Packaged: 2014-12-18 17:17:50 UTC; munozzum
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 21:08:58

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New package selfingTree with initial version 0.2
Package: selfingTree
Type: Package
Title: Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing
Version: 0.2
License: BSD_3_clause + file LICENSE
Copyright: (c) 2014, Pioneer Hi-Bred International, Inc.
Date: 2014-12-18
Authors@R: person(given = "Frank",family = "Technow", email = "Frank.Technow@pioneer.com", comment = "Pioneer Hi-Bred International, Inc., Johnston, Iowa", role = c("aut","cre"))
Author: Frank Technow [aut, cre] (Pioneer Hi-Bred International, Inc., Johnston, Iowa)
LazyData: TRUE
Maintainer: Frank Technow
Depends: R (>= 2.15.1),foreach
Description: A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.
Packaged: 2014-12-18 15:43:52 UTC; frank
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 17:31:18

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Package crs updated to version 0.15-24 with previous version 0.15-23 dated 2014-08-11

Title: Categorical Regression Splines
Description: Regression splines that handle a mix of continuous and categorical (discrete) data often encountered in applied settings. I would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).
Author: Jeffrey S. Racine [aut, cre], Zhenghua Nie [aut], Brian D. Ripley [ctb] (stepCV.R)
Maintainer: Jeffrey S. Racine

Diff between crs versions 0.15-23 dated 2014-08-11 and 0.15-24 dated 2014-12-18

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Package sprinter updated to version 1.1.0 with previous version 1.0.0 dated 2014-11-20

Title: Framework for Screening Prognostic Interactions
Description: The main function of this package builds prognostic models that consider interactions by combining available statistical components. Furthermore, it provides a function for evaluating the relevance of the selected interactions by resampling techniques.
Author: Isabell Hoffmann
Maintainer: Isabell Hoffmann

Diff between sprinter versions 1.0.0 dated 2014-11-20 and 1.1.0 dated 2014-12-18

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Package RnavGraph updated to version 0.1.8 with previous version 0.1.7 dated 2014-10-21

Title: Using Graphs as a Navigational Infrastructure
Description: GUI to explore high dimensional data (including image data) using graphs as navigational infrastructure.
Author: Adrian R. Waddell and R. Wayne Oldford
Maintainer: Adrian Waddell

Diff between RnavGraph versions 0.1.7 dated 2014-10-21 and 0.1.8 dated 2014-12-18

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Package party updated to version 1.0-19 with previous version 1.0-18 dated 2014-11-10

Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl [aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn

Diff between party versions 1.0-18 dated 2014-11-10 and 1.0-19 dated 2014-12-18

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Package mvtnorm updated to version 1.0-2 with previous version 1.0-1 dated 2014-11-13

Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates and densities.
Author: Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb], Martin Maechler [ctb], Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn

Diff between mvtnorm versions 1.0-1 dated 2014-11-13 and 1.0-2 dated 2014-12-18

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Package IsoGene updated to version 1.0-23 with previous version 1.0-22 dated 2013-11-05

Title: Order-Restricted Inference for Microarray Experiments
Description: The package offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
Author: Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Maintainer: Martin Otava

Diff between IsoGene versions 1.0-22 dated 2013-11-05 and 1.0-23 dated 2014-12-18

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New package RoughSetKnowledgeReduction with initial version 0.1
Package: RoughSetKnowledgeReduction
Type: Package
Title: Simplification of Decision Tables using Rough Sets
Version: 0.1
Date: 2012-03-13
Author: Alber Sanchez
Maintainer: Alber Sanchez
Description: Rough Sets were introduced by Zdzislaw Pawlak on his book "Rough Sets: Theoretical Aspects of Reasoning About Data". Rough Sets provide a formal method to approximate crisp sets when the set-element belonging relationship is either known or undetermined. This enables the use of Rough Sets for reasoning about incomplete or contradictory knowledge. A decision table is a prescription of the decisions to make given some conditions. Such decision tables can be reduced without losing prescription ability. This package provides the classes and methods for knowledge reduction from decision tables as presented in the chapter 7 of the aforementioned book. This package provides functions for calculating the both the discernibility matrix and the essential parts of decision tables.
License: MIT + file LICENSE
Depends: methods
Collate: DecisionTable.R ConditionReduct.R DiscernibilityMatrix.R ValueReduct.R
Packaged: 2014-12-07 14:02:21 UTC; alber
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 09:11:32

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Package REDCapR updated to version 0.7-1 with previous version 0.4-28 dated 2014-09-20

Title: Interaction between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.
Author: Will Beasley [aut, cre], David Bard [ctb], Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb], Benjamin Nutter [ctb], Andrew Peters [ctb]
Maintainer: Will Beasley

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New package multiband with initial version 0.1.0
Package: multiband
Title: Period Estimation for Multiple Bands
Description: Algorithms for performing joint parameter estimation in astronomical survey data acquired in multiple bands.
Version: 0.1.0
Maintainer: Eric C. Chi
Author: Eric C. Chi, James P. Long
Depends: R (>= 3.0.2)
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-12-18 05:28:46 UTC; ericchi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-18 07:12:06

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Package ggthemes updated to version 2.1.0 with previous version 1.7.0 dated 2014-04-22

Title: Extra themes, scales and geoms for ggplot
Description: Some extra themes, geoms, and scales for ggplot2.
Author: Jeffrey B. Arnold [aut, cre], Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb]
Maintainer: Jeffrey B. Arnold

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Package EGRET updated to version 2.1.0 with previous version 2.0.2 dated 2014-12-03

Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco

Diff between EGRET versions 2.0.2 dated 2014-12-03 and 2.1.0 dated 2014-12-18

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More information about EGRET at CRAN
Permanent link

Package DCGL updated to version 2.1.2 with previous version 2.1.1 dated 2013-12-31

Title: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
Description: Functions for 1) gene filtration; 2) link filtration; 3) differential co-expression analysis: DCG (Differential Coexpressed Gene) identification and DCL (Differentially Coexpressed Link) identification; and 4) differential regulation analysis: DRG (Differential Regulated Gene) identification, DRL (Differential Regulated Link) identification, DRL visualization and regulator ranking.
Author: Jing Yang, Hui Yu, Bao-Hong Liu, Zhongming Zhao, Lei Liu, Liang-Xiao Ma, Yi-Xue Li, Yuan-Yuan Li
Maintainer: Bao-Hong Liu

Diff between DCGL versions 2.1.1 dated 2013-12-31 and 2.1.2 dated 2014-12-18

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Package DDD updated to version 2.6 with previous version 2.5 dated 2014-05-26

Title: Diversity-Dependent Diversification
Description: implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439. DDD also implements a maximum likelihood method to detect key innovations defined as decoupling of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574. Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne

Diff between DDD versions 2.5 dated 2014-05-26 and 2.6 dated 2014-12-18

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Wed, 17 Dec 2014

Package Rlabkey updated to version 2.1.126 with previous version 2.1.125 dated 2014-08-28

Title: Data Exchange between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe

Diff between Rlabkey versions 2.1.125 dated 2014-08-28 and 2.1.126 dated 2014-12-17

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Package RcppDL updated to version 0.0.5 with previous version 0.0.3 dated 2014-12-15

Title: Deep Learning Methods via Rcpp
Description: This package is based on the C++ code from Yusuke Sugomori, which implements basic machine learning methods with many layers (deep learning), including dA (Denoising Autoencoder), SdA (Stacked Denoising Autoencoder), RBM (Restricted Boltzmann machine) and DBN (Deep Belief Nets).
Author: Qiang Kou, Yusuke Sugomori
Maintainer: Qiang Kou

Diff between RcppDL versions 0.0.3 dated 2014-12-15 and 0.0.5 dated 2014-12-17

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Permanent link

New package RcmdrPlugin.RMTCJags with initial version 1.0
Package: RcmdrPlugin.RMTCJags
Type: Package
Title: R MTC Jags Rcmdr Plugin
Version: 1.0
Date: 2014-12-16
Author: Marcelo Goulart Correia
Maintainer: Marcelo Goulart Correia
Depends: R (>= 3.0.0)
Imports: Rcmdr, runjags, rmeta, igraph, coda, rjags
SystemRequirements: jags (>= 3.0.0)
Description: This package provides an Rcmdr "plug-in" for perform Mixed Treatment Comparison for binary outcome using BUGS code from Bristol University (Lu and Ades)
License: GPL (>= 2)
Packaged: 2014-12-05 16:45:08 UTC; instituto
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 23:13:09

More information about RcmdrPlugin.RMTCJags at CRAN
Permanent link

Package Rchoice updated to version 0.2 with previous version 0.1 dated 2014-04-02

Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random Parameters
Description: Estimate Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters using Simulated Maximum Likelihood. Rchoice handles cross-sectional and panel databases.
Author: Mauricio Sarrias
Maintainer: Mauricio Sarrias

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Package plotpc updated to version 1.0.3 with previous version 1.0-2 dated 2009-03-23

Title: Plot principal component histograms around a scatter plot.
Description: Plot principal component histograms around a bivariate scatter plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

Diff between plotpc versions 1.0-2 dated 2009-03-23 and 1.0.3 dated 2014-12-17

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New package MenuCollection with initial version 1.0
Package: MenuCollection
Type: Package
Title: Collection of Configurable GTK+ Menus
Version: 1.0
Date: 2014-07-19
Author: Gianmarco Polotti
Maintainer: Gianmarco Polotti
Description: Set of configurable menus built with GTK+ to graphically interface new functions.
Depends: R (>= 3.0.0), RGtk2, RGtk2Extras
Imports: gplots, grDevices, graphics
Suggests:
License: GPL-2
Packaged: 2014-12-17 20:46:32 UTC; PolGia0
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 23:13:05

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Package extRemes updated to version 2.0-4 with previous version 2.0-3 dated 2014-08-26

Title: Extreme Value Analysis
Description: Functions for performing extreme value analysis.
Author: Eric Gilleland
Maintainer: Eric Gilleland

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Package eha updated to version 2.4-2 with previous version 2.4-1 dated 2014-02-17

Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in the Lexis diagram, bootstrapping. Parametric proportional hazards fitting with left truncation and right censoring for common families of distributions, piecewise constant hazards, and discrete models. AFT regression for left truncated and right censored data. Binary and Poisson regression for clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström [aut, cre]
Maintainer: Göran Broström

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Package earth updated to version 4.1.0 with previous version 4.0.0 dated 2014-12-12

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow

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Package dataRetrieval updated to version 2.1.0 with previous version 2.0.1 dated 2014-12-03

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from the National Water Information Services (NWIS) tools found here: http://waterservices.usgs.gov/ Both EPA and USGS water quality data are obtained from the Water Quality Portal found here: http://www.waterqualitydata.us/portal.jsp
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut]
Maintainer: Laura DeCicco

Diff between dataRetrieval versions 2.0.1 dated 2014-12-03 and 2.1.0 dated 2014-12-17

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Package CDM updated to version 4.1 with previous version 4.0 dated 2014-11-21

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous data. This package enables the estimation of the DINA and DINO model, the multiple group (polytomous) GDINA model, the multiple choice DINA model, the general diagnostic model (GDM), the multidimensional linear compensatory item response model and the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch

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Package amap updated to version 0.8-14 with previous version 0.8-12 dated 2014-03-01

Title: Another Multidimensional Analysis Package
Description: Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).
Author: Antoine Lucas
Maintainer: Antoine Lucas

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Package adehabitatLT updated to version 0.3.17 with previous version 0.3.16 dated 2014-06-02

Title: Analysis of animal movements
Description: A collection of tools for the analysis of animal movements
Author: Clement Calenge, contributions from Stephane Dray and Manuela Royer
Maintainer: Clement Calenge

Diff between adehabitatLT versions 0.3.16 dated 2014-06-02 and 0.3.17 dated 2014-12-17

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Package adehabitatHS updated to version 0.3.10 with previous version 0.3.9 dated 2014-03-08

Title: Analysis of habitat selection by animals
Description: A collection of tools for the analysis of habitat selection
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge

Diff between adehabitatHS versions 0.3.9 dated 2014-03-08 and 0.3.10 dated 2014-12-17

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Package adehabitatHR updated to version 0.4.12 with previous version 0.4.11 dated 2014-03-08

Title: Home range Estimation
Description: A collection of tools for the estimation of animals home range
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge

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Package adehabitat updated to version 1.8.15 with previous version 1.8.14 dated 2014-04-25

Title: Analysis of habitat selection by animals
Description: A collection of tools for the analysis of habitat selection by animals
Author: Clement Calenge, contributions from Mathieu Basille, Stephane Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge

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Package seqinr updated to version 3.1-3 with previous version 3.1-2 dated 2014-12-02

Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
Maintainer: Simon Penel

Diff between seqinr versions 3.1-2 dated 2014-12-02 and 3.1-3 dated 2014-12-17

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Package nullabor updated to version 0.3.1 with previous version 0.3.0 dated 2014-10-29

Title: Tools for Graphical Inference
Description: Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.
Author: Hadley Wickham , Niladri Roy Chowdhury , Di Cook
Maintainer: Di Cook

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Package BEQI2 (with last version 1.0-1) was removed from CRAN

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

2014-06-10 1.0-1
2014-04-16 1.0-0

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Package yhatr updated to version 0.13.2 with previous version 0.13.1 dated 2014-11-21

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

Diff between yhatr versions 0.13.1 dated 2014-11-21 and 0.13.2 dated 2014-12-17

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Package rioja updated to version 0.9-3 with previous version 0.8-7 dated 2014-06-30

Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: Steve Juggins

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Package plsRcox updated to version 1.7.2 with previous version 1.7.0 dated 2014-07-19

Title: Partial Least Squares Regression for Cox Models and Related Techniques
Description: Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings.
Author: Frederic Bertrand , Myriam Maumy-Bertrand , Nicolas Meyer .
Maintainer: Frederic Bertrand

Diff between plsRcox versions 1.7.0 dated 2014-07-19 and 1.7.2 dated 2014-12-17

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Package plsRbeta updated to version 0.2.0 with previous version 0.1.8 dated 2014-03-11

Title: Partial Least Squares Regression for Beta Regression Models
Description: Provides Partial least squares Regression for (weighted) beta regression models and k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand , Myriam Maumy-Bertrand , Nicolas Meyer .
Maintainer: Frederic Bertrand

Diff between plsRbeta versions 0.1.8 dated 2014-03-11 and 0.2.0 dated 2014-12-17

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Package mwa updated to version 0.4 with previous version 0.3.2 dated 2014-07-30

Title: MWA package for causal inference in spatiotemporal event data
Description: MWA grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.3.2 dated 2014-07-30 and 0.4 dated 2014-12-17

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Package influence.ME updated to version 0.9-5 with previous version 0.9-4 dated 2014-03-17

Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: influence.ME provides a collection of tools for detecting influential cases in generalized mixed effects models. It analyses models that were estimated using lme4. The basic rationale behind identifying influential data is that when iteratively single units are omitted from the data, models based on these data should not produce substantially different estimates. To standardize the assessment of how influential a (single group of) observation(s) is, several measures of influence are common practice, such as DFBETAS and Cook's Distance. In addition, we provide a measure of percentage change of the fixed point estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Maintainer: Rense Nieuwenhuis

Diff between influence.ME versions 0.9-4 dated 2014-03-17 and 0.9-5 dated 2014-12-17

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Package db.r updated to version 0.1.3 with previous version 0.1.1 dated 2014-12-04

Title: A Database Exploration Tool with Assisted Querying and Schema Exploration
Description: db.r uses OOP style objects (with an API akin to C++, Python, Ruby, Javascript, etc.) to help make visualizing the tables, columns, and available operations on your database easier. db.r dynamically loads database schemas, execute queries, and manage credentials.
Author: Greg Lamp
Maintainer: Greg Lamp

Diff between db.r versions 0.1.1 dated 2014-12-04 and 0.1.3 dated 2014-12-17

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Package daewr updated to version 1.1-4 with previous version 1.0-10 dated 2013-10-03

Title: Design and Analysis of Experiments with R
Description: Data frames and functions used in the book "Design and Analysis of Experiments with R"
Author: John Lawson
Maintainer: John Lawson

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Package epiR updated to version 0.9-61 with previous version 0.9-59 dated 2014-08-06

Title: An R package for the analysis of epidemiological data
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida and Simon Firestone
Maintainer: Mark Stevenson

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Package soil.spec updated to version 2.1.4 with previous version 2.1.3 dated 2013-08-27

Title: Soil Spectroscopy Tools and Reference Models
Description: Methods and classes for processing and analyzing soil and plant infrared (MIR, alpha-MIR and VISNIR) spectroscopy readings based on the Africa Soil Information Services (AfSIS) project data.
Author: Andrew Sila, Tomislav Hengl and Thomas Terhoeven-Urselmans
Maintainer: Andrew Sila

Diff between soil.spec versions 2.1.3 dated 2013-08-27 and 2.1.4 dated 2014-12-17

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Package rSFA updated to version 1.04 with previous version 1.03 dated 2014-02-15

Title: Slow Feature Analysis in R
Description: Slow Feature Analysis in R, ported to R based on the matlab versions SFA toolkit 1.0 by Pietro Berkes and SFA toolkit 2.8 by Wolfgang Konen for matlab.
Author: Wolfgang Konen , Martin Zaefferer, Patrick Koch; Bug hunting and testing by Ayodele Fasika, Ashwin Kumar, Prawyn Jebakumar
Maintainer: Martin Zaefferer

Diff between rSFA versions 1.03 dated 2014-02-15 and 1.04 dated 2014-12-17

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New package GPareto with initial version 1.0.0
Package: GPareto
Type: Package
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Version: 1.0.0
Date: 2014-12-17
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois
Description: Gaussian process regression models, a.k.a. kriging models, are applied to global multiobjective optimization of black-box functions. Multiobjective Expected Improvement and Stepwise Uncertainty Reduction sequential infill criteria are available. A quantification of uncertainty on Pareto fronts is provided using conditional simulations.
License: GPL-3
Depends: DiceKriging (>= 1.5.3), emoa, methods
Imports: Rcpp (>= 0.11.1), rgenoud, pbivnorm, pso, randtoolbox, KrigInv, MASS
Suggests: DiceDesign (>= 1.4)
LinkingTo: Rcpp
Packaged: 2014-12-17 09:42:42 UTC; a073501
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 13:08:28

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New package stpp with initial version 1.0-5
Package: stpp
Type: Package
Title: Space-Time Point Pattern simulation, visualisation and analysis
Version: 1.0-5
Date: 2014-12-11
Author: Edith Gabriel, Peter J Diggle, stan function by Barry Rowlingson
Maintainer: Edith Gabriel
Depends: R (>= 2.10), splancs, KernSmooth, spatstat
Suggests: rpanel, rgl
Description: A package for analysing, simulating and displaying space-time point patterns
License: GPL-3
LazyLoad: yes
Packaged: 2014-12-16 13:46:14 UTC; math
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 09:25:40

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Package recluster updated to version 2.7 with previous version 2.5 dated 2013-07-31

Title: Ordination Methods for the Analysis of Beta-Diversity Indices
Description: Beta-diversity indices provide dissimilarity matrices with particular distribution of data requiring specific treatment. For example the high frequency of ties and zero values in turnover indices produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, biogeographical regionalization can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to analyze pattern of similarity in species composition.
Author: Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger Vila, Gerard Talavera, Roger H.L. Dennis
Maintainer: Leonardo Dapporto

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Package hexView updated to version 0.3-3 with previous version 0.3-2 dated 2010-08-06

Title: Viewing Binary Files
Description: Functions to view files in raw binary form like in a hex editor. Additional functions to specify and read arbitrary binary formats.
Author: Paul Murrell
Maintainer: Paul Murrell

Diff between hexView versions 0.3-2 dated 2010-08-06 and 0.3-3 dated 2014-12-17

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Package EasyABC updated to version 1.4 with previous version 1.3.1 dated 2014-04-04

Title: Efficient Approximate Bayesian Computation Sampling Schemes
Description: Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot, Thierry Faure, Nicolas Dumoullin
Maintainer: Nicolas Dumoulin

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Package MuMIn updated to version 1.12.1 with previous version 1.10.5 dated 2014-08-12

Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria (AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń

Diff between MuMIn versions 1.10.5 dated 2014-08-12 and 1.12.1 dated 2014-12-17

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More information about MuMIn at CRAN
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Package forecast updated to version 5.7 with previous version 5.6 dated 2014-09-24

Title: Forecasting functions for time series and linear models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman with contributions from George Athanasopoulos, Slava Razbash, Drew Schmidt, Zhenyu Zhou, Yousaf Khan, Christoph Bergmeir, Earo Wang
Maintainer: Rob J Hyndman

Diff between forecast versions 5.6 dated 2014-09-24 and 5.7 dated 2014-12-17

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Permanent link

Tue, 16 Dec 2014

Package rmatio updated to version 0.11.0 with previous version 0.10.0 dated 2014-05-10

Title: Read and Write Matlab Files
Description: rmatio is a package for reading and writing Matlab MAT files from R. The rmatio package supports reading MAT version 4, MAT version 5 and MAT compressed version 5. The rmatio package can write version 5 MAT files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] (Author of the R interface to the C-library matio), Christopher Hulbert [aut] (Author of the C-library matio, http://sourceforge.net/projects/matio/)
Maintainer: Stefan Widgren

Diff between rmatio versions 0.10.0 dated 2014-05-10 and 0.11.0 dated 2014-12-16

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New package RSNPset with initial version 0.3
Package: RSNPset
Type: Package
Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Version: 0.3
Date: 2014-12-16
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
Description: RSNPset is an implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. The package provides three standard score statistics (Cox, Binomial, and Gaussian) but is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.
License: GPL-3
Imports: fastmatch (>= 1.0-4), foreach (>= 1.4.1), doRNG (>= 1.5.3), qvalue (>= 1.34), Rcpp (>= 0.10.4)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-16 19:06:52 UTC; abs33
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-17 01:59:36

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Package plsRglm updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-19

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

Diff between plsRglm versions 1.1.0 dated 2014-07-19 and 1.1.1 dated 2014-12-16

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New package refset with initial version 0.1.0
Package: refset
Type: Package
Title: Subsets with Reference Semantics
Version: 0.1.0
Date: 2014-11-20
Author: David Hugh-Jones
Maintainer: David Hugh-Jones
Description: Provides subsets with reference semantics, i.e. subsets which automatically reflect changes in the original object, and which optionally update the original object when they are changed.
License: GPL-2
NeedsCompilation: no
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat
Packaged: 2014-12-16 21:42:46 UTC; david
Repository: CRAN
Date/Publication: 2014-12-17 01:57:34

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Package lqmm updated to version 1.5.1 with previous version 1.5 dated 2014-05-01

Title: Linear Quantile Mixed Models
Description: Fit quantile regression models for independent and hierarchical data
Author: Marco Geraci
Maintainer: Marco Geraci

Diff between lqmm versions 1.5 dated 2014-05-01 and 1.5.1 dated 2014-12-16

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Package lmmot updated to version 0.1.2 with previous version 0.1.1 dated 2014-08-18

Title: Multiple Ordinal Tobit (MOT) model
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright

Diff between lmmot versions 0.1.1 dated 2014-08-18 and 0.1.2 dated 2014-12-16

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Package HH updated to version 3.1-8 with previous version 3.1-5 dated 2014-09-13

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger

Diff between HH versions 3.1-5 dated 2014-09-13 and 3.1-8 dated 2014-12-16

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Package gridSVG updated to version 1.4-2 with previous version 1.4-0 dated 2013-09-18

Title: Export grid Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG format. Additional functions provide access to SVG features that are not available in standard R graphics, such as hyperlinks, animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut], Simon Potter [aut]
Maintainer: Paul Murrell

Diff between gridSVG versions 1.4-0 dated 2013-09-18 and 1.4-2 dated 2014-12-16

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Package EIAdata updated to version 0.0.2 with previous version 0.0.1 dated 2014-08-04

Title: R Wrapper for the Energy Information Administration (EIA) API
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API.
Author: Matthew Brigida
Maintainer: Matthew Brigida

Diff between EIAdata versions 0.0.1 dated 2014-08-04 and 0.0.2 dated 2014-12-16

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New package FPDclustering with initial version 1.0
Package: FPDclustering
Type: Package
Title: PD-Clustering and Factor PD-Clustering
Version: 1.0
Date: 2014-12-16
Author: Cristina Tortora and Paul D. McNicholas
Maintainer: Cristina Tortora
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. Facto PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It allows clustering of high dimensional data sets.
Depends: ThreeWay
License: GPL (>= 2)
Packaged: 2014-12-16 18:46:17 UTC; ctortora
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-17 01:54:43

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New package rSPACE with initial version 1.0
Package: rSPACE
Type: Package
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Version: 1.0
Date: 2014-12-15
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
License: GPL (>= 2)
Imports: raster, RMark, ggplot2, tcltk2, sp, grid, plyr, tcltk
Packaged: 2014-12-16 18:20:03 UTC; marthamellis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-16 22:38:08

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New package PRROC with initial version 1.0
Package: PRROC
Type: Package
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Version: 1.0
Date: 2014-12-16
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
License: GPL-3
Packaged: 2014-12-16 21:03:40 UTC; dev
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 22:34:59

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Package flexCWM updated to version 1.3 with previous version 1.1 dated 2013-11-09

Title: Flexible Cluster-Weighted Modeling
Description: This package implements a flexible version of the Cluster Weighted Model (CWM), which is an eminent member of the class of mixtures of regression models with random covariates.
Author: Mazza A., Punzo A., Ingrassia S.
Maintainer: Angelo Mazza

Diff between flexCWM versions 1.1 dated 2013-11-09 and 1.3 dated 2014-12-16

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Package compare updated to version 0.2-5 with previous version 0.2-4 dated 2014-02-24

Title: Comparing Objects for Differences
Description: Functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.
Author: Paul Murrell
Maintainer: Paul Murrell

Diff between compare versions 0.2-4 dated 2014-02-24 and 0.2-5 dated 2014-12-16

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Package sdnet updated to version 2.03.3 with previous version 2.01.3 dated 2014-02-27

Title: Soft Discretization-based Bayesian Network Inference
Description: Fitting discrete Bayesian networks using marginal mixture distributions
Author: Nikolay Balov
Maintainer: Nikolay Balov

Diff between sdnet versions 2.01.3 dated 2014-02-27 and 2.03.3 dated 2014-12-16

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Package packrat updated to version 0.4.2-1 with previous version 0.4.2 dated 2014-12-15

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: Packrat is a tool for managing the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey

Diff between packrat versions 0.4.2 dated 2014-12-15 and 0.4.2-1 dated 2014-12-16

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Package PHeval updated to version 0.5.2 with previous version 0.5.1 dated 2014-05-27

Title: Evaluation of the proportional hazards assumption with a standardized score process
Description: This package provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
Author: Cecile Chauvel
Maintainer: Cecile Chauvel

Diff between PHeval versions 0.5.1 dated 2014-05-27 and 0.5.2 dated 2014-12-16

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New package NeuralNetTools with initial version 1.0.0
Package: NeuralNetTools
Type: Package
Title: Visualization and Analysis Tools for Neural Networks
Version: 1.0.0
Date: 2014-12-10
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
BugReports: https://github.com/fawda123/NeuralNetTools/issues
License: CC0
LazyData: true
Imports: ggplot2, neuralnet, nnet, reshape2, RSNNS, scales
Depends: R (>= 3.1.1)
Authors@R: person(given = "Marcus W.", family = "Beck", role = c("aut","cre"), email = "mbafs2012@gmail.com")
Packaged: 2014-12-16 16:06:56 UTC; Marcus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 17:43:30

More information about NeuralNetTools at CRAN
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Package fda updated to version 2.4.4 with previous version 2.4.3 dated 2014-05-23

Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions of the code and sample analyses are no longer distributed through CRAN, as they were when the book was published. For those, ftp from http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There you find a set of .zip files containing the functions and sample analyses, as well as two .txt files giving instructions for installation and some additional information. The changes from Version 2.4.1 are fixes of bugs in density.fd and removal of functions create.polynomial.basis, polynompen, and polynomial. These were deleted because the monomial basis does the same thing and because there were errors in the code.
Author: J. O. Ramsay , Hadley Wickham , Spencer Graves , Giles Hooker
Maintainer: J. O. Ramsay

Diff between fda versions 2.4.3 dated 2014-05-23 and 2.4.4 dated 2014-12-16

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Package epinet updated to version 2.0.9 with previous version 2.0.8 dated 2014-10-14

Title: A Collection of Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre], David Welch [aut], David Hunter [ctb]
Maintainer: Chris Groendyke

Diff between epinet versions 2.0.8 dated 2014-10-14 and 2.0.9 dated 2014-12-16

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Package dti updated to version 1.2-0.1 with previous version 1.2-0 dated 2014-05-12

Title: Analysis of diffusion weighted imaging (DWI) data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data. The functionality includes diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), modeling for high angular resolution diffusion weighted imaging (HARDI) using Q-ball-reconstruction and tensor mixture models, several methods for structural adaptive smoothing including POAS and msPOAS, and a streamline fiber tracking for tensor and tensor mixture models. The package provides functionality to manipulate and visualize results in 2D and 3D.
Author: Karsten Tabelow [aut, cre], Joerg Polzehl [aut], Felix Anker [ctb]
Maintainer: Karsten Tabelow

Diff between dti versions 1.2-0 dated 2014-05-12 and 1.2-0.1 dated 2014-12-16

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Package CARBayes updated to version 4.0 with previous version 3.0 dated 2014-04-04

Title: Spatial Areal Unit Modelling
Description: Implements Bayesian hierarchical spatial areal unit models. In such models the spatial autocorrelation is modelled by a set of random effects, which are assigned a conditional autoregressive (CAR) prior distribution. Examples of the models included are the BYM model as well as a recently developed localised spatial smoothing model.The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development is supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1.
Author: Duncan Lee
Maintainer: Duncan Lee

Diff between CARBayes versions 3.0 dated 2014-04-04 and 4.0 dated 2014-12-16

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Package abctools updated to version 1.0 with previous version 0.3-2 dated 2014-06-25

Title: Tools for ABC analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage
Author: Matt Nunes [aut, cre], Dennis Prangle [aut]
Maintainer: Matt Nunes

Diff between abctools versions 0.3-2 dated 2014-06-25 and 1.0 dated 2014-12-16

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Package SCEPtER updated to version 0.2-0 with previous version 0.1-0 dated 2013-06-04

Title: Stellar CharactEristics Pisa Estimation gRid
Description: SCEPtER pipeline for estimating the stellar age, mass, and radius given observational effective temperature, [Fe/H], and astroseismic parameters. The results are obtained adopting a maximum likelihood technique over a grid of pre-computed stellar models.
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
Maintainer: Matteo Dell'Omodarme

Diff between SCEPtER versions 0.1-0 dated 2013-06-04 and 0.2-0 dated 2014-12-16

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Package jomo updated to version 0.1-1 with previous version 0.1-0 dated 2014-12-10

Title: A package for Multilevel Joint Modelling Multiple Imputation
Description: Building on Schafer's pan and on standalone program REALCOM, jomo is a package for multilevel joint modelling multiple imputation. Binary and categorical variables are handled through latent normal variables and algorithms for cluster specific covariance matrices are introduced.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno

Diff between jomo versions 0.1-0 dated 2014-12-10 and 0.1-1 dated 2014-12-16

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New package spca with initial version 0.6.0
Package: spca
Type: Package
Title: Sparse Principal Component Analysis
Version: 0.6.0
Date: 2014-12-14
Author: Giovanni Maria Merola
Maintainer: Giovanni Merola
URL: http://github.com/merolagio/spca
BugReports: http://github.com/merolagio/spca/issues
Description: Computes Least Squares Sparse Principal Components either by a Branch-and-Bound search or with an iterative Backward Elimination algorithm. Sparse solutions can be plotted, printed and compared using the methods included.
Depends: R (>= 3.1)
VignetteBuilder: knitr
Suggests: formatR, knitr (>= 1.8.0), ggplot2, reshape2
Imports: MASS
License: GPL-3
LazyData: true
Packaged: 2014-12-16 11:39:18 UTC; Glovani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 13:19:52

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Package Rvcg updated to version 0.10 with previous version 0.9 dated 2014-09-23

Title: Manipulations of triangular meshes (smoothing, quadric edge collapse decimation, im- and export of various mesh file-formats, cleaning, etc.) based on the VCGLIB API.
Description: Operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package "rgl" to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like metro and MeshLab. The vcglib source is pulled from trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager

Diff between Rvcg versions 0.9 dated 2014-09-23 and 0.10 dated 2014-12-16

 Rvcg-0.10/Rvcg/DESCRIPTION                                  |    8 
 Rvcg-0.10/Rvcg/MD5                                          |  108 ++++++------
 Rvcg-0.10/Rvcg/NAMESPACE                                    |    4 
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 Rvcg-0.10/Rvcg/R/vcgClean.r                                 |    8 
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 Rvcg-0.10/Rvcg/R/vcgClostKD.r                               |   18 +-
 Rvcg-0.10/Rvcg/R/vcgImport.r                                |    9 +
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 Rvcg-0.10/Rvcg/R/vcgIsosurface.r                            |    7 
 Rvcg-0.10/Rvcg/R/vcgPlyWrite.r                              |   25 ++
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 Rvcg-0.10/Rvcg/src/RallRead.cpp                             |   28 ++-
 Rvcg-0.10/Rvcg/src/Rclean.cpp                               |   35 ---
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 59 files changed, 396 insertions(+), 254 deletions(-)

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Package Morpho updated to version 2.2 with previous version 2.1 dated 2014-09-25

Title: Calculations and visualisations related to Geometric Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager
Maintainer: Stefan Schlager

Diff between Morpho versions 2.1 dated 2014-09-25 and 2.2 dated 2014-12-16

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Package marmap updated to version 0.9.1 with previous version 0.9 dated 2014-11-06

Title: Import, plot and analyze bathymetric and topographic data
Description: Import, plot and analyze bathymetric and topographic data
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante

Diff between marmap versions 0.9 dated 2014-11-06 and 0.9.1 dated 2014-12-16

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Package D2C updated to version 1.1 with previous version 1.0 dated 2014-11-10

Title: Predicting Causal Direction from Dependency Features
Description: The relationship between statistical dependency and causality lies at the heart of all statistical approaches to causal inference. The D2C package implements a supervised machine learning approach to infer the existence of a directed causal link between two variables in multivariate settings with n>2 variables. The approach relies on the asymmetry of some conditional (in)dependence relations between the members of the Markov blankets of two variables causally connected. The D2C algorithm predicts the existence of a direct causal link between two variables in a multivariate setting by (i) creating a set of of features of the relationship based on asymmetric descriptors of the multivariate dependency and (ii) using a classifier to learn a mapping between the features and the presence of a causal link
Author: Gianluca Bontempi, Catharina Olsen, Maxime Flauder
Maintainer: Catharina Olsen

Diff between D2C versions 1.0 dated 2014-11-10 and 1.1 dated 2014-12-16

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 D2C-1.1/D2C/R/D2c.network.R                          |  254 ++++++++++-----
 D2C-1.1/D2C/R/d2c.R                                  |   93 ++---
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Permanent link

New package WaveletComp with initial version 1.0
Package: WaveletComp
Type: Package
Title: Computational Wavelet Analysis
Version: 1.0
Date: 2014-12-15
Author: Angi Roesch and Harald Schmidbauer
Maintainer: Angi Roesch
Description: Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.
Depends: R (>= 2.10)
License: GPL-2
URL: http://www.hs-stat.com/projects/WaveletComp/WaveletComp_guided_tour.pdf
Packaged: 2014-12-16 07:19:23 UTC; angi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 09:26:23

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Package season updated to version 0.3-5 with previous version 0.3-4 dated 2014-08-23

Title: Seasonal analysis of health data
Description: Routines for the seasonal analysis of health data, including regression models, time-stratified case-crossover, plotting functions and residual checks. Thanks to Yuming Guo for checking the case-crossover code.
Author: Adrian Barnett and Peter Baker
Maintainer: Adrian Barnett

Diff between season versions 0.3-4 dated 2014-08-23 and 0.3-5 dated 2014-12-16

 DESCRIPTION               |    8 ++++----
 MD5                       |   24 +++++++++++++-----------
 R/cosinor.R               |   30 ++++++++++++++++++++----------
 R/invyrfraction.R         |    5 +++++
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 14 files changed, 80 insertions(+), 38 deletions(-)

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Package rplexos updated to version 0.11 with previous version 0.10.0.1 dated 2014-10-20

Title: Read and Analyze PLEXOS Solutions from R
Description: Efficiently read and analyze PLEXOS solutions by converting them into SQLite databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.10.0.1 dated 2014-10-20 and 0.11 dated 2014-12-16

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 MD5                    |   45 +++----
 NAMESPACE              |   12 -
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Package rotations updated to version 1.3 with previous version 1.2 dated 2014-04-07

Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including simulation from the most commonly used distributions on SO(3), methods for different Bayes, mean and median type estimators for the central orientation of a sample, confidence/credible regions for the central orientation based on those estimators and a novel visualization technique for rotation data. Most recently, functions to identify potentially discordant (outlying) values have been added.
Author: Bryan Stanfill , Heike Hofmann , Ulrike Genschel
Maintainer: Bryan Stanfill

Diff between rotations versions 1.2 dated 2014-04-07 and 1.3 dated 2014-12-16

 DESCRIPTION                             |   28 
 LICENSE                                 |    2 
 MD5                                     |  161 +--
 NAMESPACE                               |  219 ++--
 NEWS                                    |  229 ++--
 R/RcppExports.R                         |  342 +++---
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 man/zhang.Rd                            |  122 +-
 src/CppBayesFunctions.cpp               |    1 
 src/Makevars.win                        |   12 
 src/RcppExports.cpp                     |  146 ++
 src/ZhangMethod.cpp                     |    1 
 src/estimators.cpp                      |    2 
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 tests/test-all.R                        |    2 
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 tests/testthat/test_basics.R            |   90 -
 tests/testthat/test_conversions.R       |   40 
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 tests/testthat/test_estimators.R        |   60 -
 tests/testthat/test_metrics.R           |   24 
 vignettes/RJournal_edited.sty           |  670 ++++++-------
 vignettes/rotations-intro.Rnw           |  728 +++++++-------
 vignettes/stanfill-hofmann-genschel.bib |  733 +++++++-------
 84 files changed, 9688 insertions(+), 9350 deletions(-)

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New package networkD3 with initial version 0.1.1
Package: networkD3
Type: Package
Title: Tools for Creating D3 JavaScript Network Graphs from R
Description: Creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
Version: 0.1.1
Date: 2014-12-16
Author: Christopher Gandrud, J.J. Allaire, and B.W. Lewis
Maintainer: Christopher Gandrud
URL: http://github.com/christophergandrud/networkD3/
License: GPL (>= 3)
Depends: R (>= 3.0.0)
Imports: htmlwidgets (>= 0.3.2), plyr, rjson
Suggests: htmltools (>= 0.2.6), RCurl
Enhances: knitr, shiny
Packaged: 2014-12-16 06:52:00 UTC; christophergandrud
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:22:39

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Package GrammR updated to version 1.0.1 with previous version 1.0.0 dated 2014-08-11

Title: Graphical Representation and Modeling of Metagenomic Reads
Description: Represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall's tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.
Author: Deepak N. Ayyala, Shili Lin, Department of Statistics, The Ohio State University, Columbus, Ohio, USA.
Maintainer: Deepak Nag Ayyala

Diff between GrammR versions 1.0.0 dated 2014-08-11 and 1.0.1 dated 2014-12-16

 DESCRIPTION          |    8 ++++----
 MD5                  |   24 ++++++++++++------------
 R/GrammRServ.R       |    4 +++-
 R/Make2DPlots.R      |    8 ++------
 R/Make3DPlots.R      |   15 ++-------------
 R/Make4DPlots.R      |   33 +++------------------------------
 R/MakePlots2D.R      |   11 ++---------
 R/MakePlots3D.R      |   17 ++---------------
 R/MakePlots4D.R      |   43 ++-----------------------------------------
 R/OptimClusts.R      |   19 +++++++++++++------
 man/MCError.Rd       |    6 +++++-
 man/MakeGUIPlots.Rd  |   18 +++++++++++++++++-
 man/MakeServPlots.Rd |   19 ++++++++++++++++++-
 13 files changed, 85 insertions(+), 140 deletions(-)

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New package BinNonNor with initial version 1.0
Package: BinNonNor
Type: Package
Title: Data Generation with Binary and Continuous Non-normal Components
Version: 1.0
Date: 2014-12-15
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
Description: Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012).
License: GPL (>= 2)
Depends: BB, corpcor, mvtnorm, Matrix
Packaged: 2014-12-15 19:20:02 UTC; arcelik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-16 08:17:47

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Mon, 15 Dec 2014

Package qtl updated to version 1.35-3 with previous version 1.35-1 dated 2014-12-12

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman

Diff between qtl versions 1.35-1 dated 2014-12-12 and 1.35-3 dated 2014-12-15

 DESCRIPTION           |   10 +++++-----
 MD5                   |   24 ++++++++++++------------
 inst/INSTALL_ME.txt   |   16 ++++++++--------
 inst/STATUS.txt       |    4 +++-
 inst/doc/rqtltour.pdf |binary
 man/scanonevar.Rd     |    2 +-
 src/hmm_bcsft.c       |   20 ++++++++++----------
 src/hmm_main.c        |   16 ++++++++--------
 src/lapackutil.c      |    2 +-
 src/mqmdatatypes.cpp  |    2 +-
 src/mqmmixture.cpp    |    4 +---
 src/mqmprob.cpp       |   47 +++++++++++++++++++++++------------------------
 src/simulate.c        |    6 +++---
 13 files changed, 76 insertions(+), 77 deletions(-)

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Package hergm updated to version 2.0-0 with previous version 1.3-11 dated 2013-12-01

Title: Hierarchical Exponential-Family Random Graph Models with Local Dependence
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger [aut, cre], Mark S. Handcock [ctb], Pamela Luna [ctb]
Maintainer: Michael Schweinberger

Diff between hergm versions 1.3-11 dated 2013-12-01 and 2.0-0 dated 2014-12-15

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 hergm-2.0-0/hergm/src/MHproposal.h              |    9 
 hergm-2.0-0/hergm/src/MHproposals.c             |   20 
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 hergm-2.0-0/hergm/src/changestat.c              |    9 
 hergm-2.0-0/hergm/src/changestat.h              |    9 
 hergm-2.0-0/hergm/src/changestats.c             |  164 +++++
 hergm-2.0-0/hergm/src/changestats.h             |   13 
 hergm-2.0-0/hergm/src/edgelist.c                |   42 -
 hergm-2.0-0/hergm/src/edgelist.h                |    9 
 hergm-2.0-0/hergm/src/edgetree.c                |  108 +--
 hergm-2.0-0/hergm/src/edgetree.h                |   26 
 hergm-2.0-0/hergm/src/h_ergm.c                  |  678 +++++++++++++-----------
 hergm-2.0-0/hergm/src/h_ergm.h                  |   29 -
 hergm-2.0-0/hergm/src/h_ergm_basics.c           |   11 
 hergm-2.0-0/hergm/src/h_ergm_latent.c           |   25 
 hergm-2.0-0/hergm/src/h_ergm_latent.h           |    4 
 hergm-2.0-0/hergm/src/h_ergm_mcmc.c             |   27 
 hergm-2.0-0/hergm/src/h_ergm_mcmc.h             |    8 
 hergm-2.0-0/hergm/src/h_ergm_variational.c      |    2 
 hergm-2.0-0/hergm/src/model.c                   |    9 
 hergm-2.0-0/hergm/src/model.h                   |    9 
 hergm-2.0-0/hergm/src/netstats.c                |    9 
 hergm-2.0-0/hergm/src/netstats.h                |    9 
 57 files changed, 1280 insertions(+), 1004 deletions(-)

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Package DEoptim updated to version 2.2-3 with previous version 2.2-2 dated 2013-04-20

Title: Global Optimization by Differential Evolution
Description: Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.
Author: David Ardia [aut], Katharine Mullen [aut, cre], Brian Peterson [aut], Joshua Ulrich [aut], Kris Boudt [ctb]
Maintainer: Katharine Mullen

Diff between DEoptim versions 2.2-2 dated 2013-04-20 and 2.2-3 dated 2014-12-15

 DEoptim-2.2-2/DEoptim/COPYING                                    |only
 DEoptim-2.2-2/DEoptim/COPYRIGHTS                                 |only
 DEoptim-2.2-3/DEoptim/DESCRIPTION                                |   27 ++---
 DEoptim-2.2-3/DEoptim/MD5                                        |   19 ++-
 DEoptim-2.2-3/DEoptim/NEWS                                       |    7 +
 DEoptim-2.2-3/DEoptim/R/DEoptim.R                                |   49 +++++++---
 DEoptim-2.2-3/DEoptim/THANKS                                     |    5 -
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 DEoptim-2.2-3/DEoptim/man/DEoptim.Rd                             |    3 
 DEoptim-2.2-3/DEoptim/man/DEoptim.control.Rd                     |    4 
 DEoptim-2.2-3/DEoptim/src/de4_0.c                                |   21 ++--
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 13 files changed, 86 insertions(+), 49 deletions(-)

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Package actuar updated to version 1.1-8 with previous version 1.1-7 dated 2014-12-11

Title: Actuarial functions
Description: Additional actuarial science functionality, mostly in the fields of loss distributions, risk theory (including ruin theory), simulation of compound hierarchical models and credibility theory. The package also features 17 probability laws commonly used in insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet

Diff between actuar versions 1.1-7 dated 2014-12-11 and 1.1-8 dated 2014-12-15

 actuar-1.1-7/actuar/inst/po/en@quot          |only
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 actuar-1.1-8/actuar/build/vignette.rds       |binary
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 actuar-1.1-8/actuar/inst/doc/actuar.pdf      |binary
 actuar-1.1-8/actuar/inst/doc/coverage.pdf    |binary
 actuar-1.1-8/actuar/inst/doc/credibility.pdf |binary
 actuar-1.1-8/actuar/inst/doc/lossdist.pdf    |binary
 actuar-1.1-8/actuar/inst/doc/risk.pdf        |binary
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 actuar-1.1-8/actuar/man/UniformSupp.Rd       |    6 ++---
 actuar-1.1-8/actuar/src/hierarc.c            |   20 +++++++++----------
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 actuar-1.1-8/actuar/src/unif.c               |    4 +--
 15 files changed, 44 insertions(+), 35 deletions(-)

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Package gimme updated to version 0.1-1 with previous version 0.1 dated 2014-12-12

Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and individual-level relations in time series data from within a structural equation modeling framework.
Author: Stephanie Lane
Maintainer: Stephanie Lane

Diff between gimme versions 0.1 dated 2014-12-12 and 0.1-1 dated 2014-12-15

 gimme-0.1-1/gimme/DESCRIPTION          |    6 ++--
 gimme-0.1-1/gimme/MD5                  |   34 +++++++++++------------
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 28 files changed, 94 insertions(+), 51 deletions(-)

More information about gimme at CRAN
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