Thu, 06 Jun 2013

Package metrumrg updated to version 5.50 with previous version 5.49 dated 2013-05-23

Title: Pharmacometric tools for data preparation, modeling, simulation, and reporting
Description: Pharmacometric tools for common data preparation tasks, stratified bootstrap resampling of data sets, NONMEM control stream creation/editing, NONMEM model execution, creation of standard and user-defined diagnostic plots, execution and summary of bootstrap and predictive check results, implementation of simulations from posterior parameter distributions, reporting of output tables and creation of detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma

Diff between metrumrg versions 5.49 dated 2013-05-23 and 5.50 dated 2013-06-06

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Package foreach updated to version 1.4.1 with previous version 1.4.0 dated 2012-04-16

Title: Foreach looping construct for R
Description: Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.
Author: Revolution Analytics, Steve Weston
Maintainer: Revolution Analytics

Diff between foreach versions 1.4.0 dated 2012-04-16 and 1.4.1 dated 2013-06-06

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Package abc updated to version 1.7 with previous version 1.6 dated 2012-08-14

Title: Tools for Approximate Bayesian Computation (ABC)
Description: The package implements several ABC algorithms for performing parameter estimation and model selection. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.
Author: Katalin Csillery, Michael Blum and Olivier Francois
Maintainer: Michael Blum

Diff between abc versions 1.6 dated 2012-08-14 and 1.7 dated 2013-06-06

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Package Reol updated to version 1.14 with previous version 1.8 dated 2013-04-23

Title: R interface to the Encyclopedia of Life
Description: An R interface to the EOL API. Includes functions for downloading and extracting information off the EOL pages.
Author: Barb Banbury , Brian O'Meara
Maintainer: Barb Banbury

Diff between Reol versions 1.8 dated 2013-04-23 and 1.14 dated 2013-06-06

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Package Rarity updated to version 1.2 with previous version 1.1 dated 2013-05-10

Title: Calculation of rarity indices for species and assemblages of species
Description: This package allows calculation of rarity weights for species and indices of rarity for assemblages of species according to different methods (Leroy et al. 2012, In Press).
Author: Boris Leroy
Maintainer: Boris Leroy

Diff between Rarity versions 1.1 dated 2013-05-10 and 1.2 dated 2013-06-06

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Package pegas updated to version 0.4-5 with previous version 0.4-4 dated 2013-01-23

Title: Population and Evolutionary Genetics Analysis System
Description: pegas provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences including coalescence analyses.
Author: Emmanuel Paradis, Alastair Potts
Maintainer: Emmanuel Paradis

Diff between pegas versions 0.4-4 dated 2013-01-23 and 0.4-5 dated 2013-06-06

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Package kinship2 updated to version 1.5.0 with previous version 1.3.7 dated 2012-10-31

Title: Pedigree functions
Description: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Martha Matsumoto, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell

Diff between kinship2 versions 1.3.7 dated 2012-10-31 and 1.5.0 dated 2013-06-06

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Package exams updated to version 1.9-6 with previous version 1.9-5 dated 2013-06-04

Title: Automatic Generation of Exams in R
Description: Sweave-based automatic generation of exams including multiple-choice questions and arithmetic problems. Exams can be produced in various formats, including PDF, HTML, Moodle XML, QTI 1.2 (for OLAT).
Author: Achim Zeileis [aut, cre], Bettina Gruen [aut], Friedrich Leisch [aut], Nikolaus Umlauf [aut]
Maintainer: Achim Zeileis

Diff between exams versions 1.9-5 dated 2013-06-04 and 1.9-6 dated 2013-06-06

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Package CLAG updated to version 2.16.1 with previous version 2.10 dated 2013-05-02

Title: CLAG: an unsupervised non hierarchical clustering algorithm handling biological data
Description: CLAG (for CLusters AGgregation) is an unsupervised non hierarchical clustering algorithm designed to cluster a large variety of biological data and to provide a clustered matrix and numerical values indicating cluster strength. CLAG clusterizes correlation matrices for residues in protein families, gene-expression and miRNA data related to various cancer types, sets of species described by multidimensional vectors of characters, binary matrices. It does not ask to all data points to cluster and it converges yielding the same result at each run. Its simplicity and speed allows it to run on reasonably large datasets.
Author: Linda DIB, Raphael CHAMPEIMONT, Alessandra CARBONE
Maintainer: Raphael CHAMPEIMONT

Diff between CLAG versions 2.10 dated 2013-05-02 and 2.16.1 dated 2013-06-06

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Package ads updated to version 1.3-1 with previous version 1.2-13 dated 2013-05-16

Title: Spatial point patterns analysis
Description: Perform first- and second-order multi-scale analyses derived from Ripley's K-function, for univariate, multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with test of statistical significance based on Monte Carlo simulations.
Author: R. Pelissier and F. Goreaud
Maintainer: Raphael Pelissier

Diff between ads versions 1.2-13 dated 2013-05-16 and 1.3-1 dated 2013-06-06

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Package hydroPSO updated to version 0.3-3 with previous version 0.3-2 dated 2013-05-29

Title: Particle Swarm Optimisation, with focus on Environmental Models
Description: This package implements a state-of-the-art version of the Particle Swarm Optimisation (PSO) algorithm (SPSO-2011 and SPSO-2007 capable). hydroPSO can be used as a replacement of the 'optim' R function for (global) optimization of non-smooth and non-linear functions. However, the main focus of hydroPSO is the calibration of environmental and other real-world models that need to be executed from the system console. hydroPSO is model-independent, allowing the user to easily interface any computer simulation model with the calibration engine (PSO). hydroPSO communicates with the model through the model's own input and output files, without requiring access to the model's source code. Several PSO variants and controlling options are included to fine-tune the performance of the calibration engine to different calibration problems. An advanced sensitivity analysis function together with user-friendly plotting summaries facilitate the interpretation and assessment of the calibration results. hydroPSO is parallel-capable, to alleviate the computational burden of complex models with "long" execution time. Bugs reports/comments/questions are very welcomed (in English, Spanish or Italian).
Author: Mauricio Zambrano-Bigiarini [aut, cre], Rodrigo Rojas [ctb]
Maintainer: Mauricio Zambrano-Bigiarini

Diff between hydroPSO versions 0.3-2 dated 2013-05-29 and 0.3-3 dated 2013-06-06

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Package urca updated to version 1.2-8 with previous version 1.2-7 dated 2012-07-26

Title: Unit root and cointegration tests for time series data
Description: Unit root and cointegration tests encountered in applied econometric analysis are implemented.
Author: Bernhard Pfaff [aut, cre], Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff

Diff between urca versions 1.2-7 dated 2012-07-26 and 1.2-8 dated 2013-06-06

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Package StAMPP updated to version 1.1 with previous version 1.0 dated 2013-05-29

Title: Statistical Analysis of Mixed Ploidy Populations
Description: StAMPP allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton

Diff between StAMPP versions 1.0 dated 2013-05-29 and 1.1 dated 2013-06-06

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Package minPtest updated to version 1.6 with previous version 1.5 dated 2012-11-26

Title: Gene region-level testing procedure for SNP data, using the min P test resampling approach
Description: Package minPtest is designed for estimating a gene region-level summary for SNP data from case-control studies using a permutation-based resampling method, called min P test, allowing execution on a compute cluster or multicore computer.
Author: Stefanie Hieke
Maintainer: Stefanie Hieke

Diff between minPtest versions 1.5 dated 2012-11-26 and 1.6 dated 2013-06-06

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Package ConConPiWiFun updated to version 0.4.1 with previous version 0.3 dated 2013-02-13

Title: This package contains an implementation of continuous convex piecewise (linear and quadratic) functions
Description: Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.
Author: Robin Girard
Maintainer: Robin Girard

Diff between ConConPiWiFun versions 0.3 dated 2013-02-13 and 0.4.1 dated 2013-06-06

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Package doSNOW updated to version 1.0.7 with previous version 1.0.6 dated 2012-04-16

Title: Foreach parallel adaptor for the snow package
Description: Provides a parallel backend for the %dopar% function using Luke Tierney's snow package.
Author: Revolution Analytics
Maintainer: Revolution Analytics

Diff between doSNOW versions 1.0.6 dated 2012-04-16 and 1.0.7 dated 2013-06-06

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New package LVMMCOR with initial version 0.01.1
Package: LVMMCOR
Version: 0.01.1
Date: 2013-05-10
Title: A Latent Variable Model for Mixed Continuous and Ordinal Responses
Author: Ehsan Bahrami Samani and Nourallah Tazikeh Miyandarreh
Maintainer: Ehsan Bahrami Samani
Description: A model for mixed ordinal and continuous responses is presented where the heteroscedasticity of the variance of the continuous response is also modeled. In this model ordinal response can be dependent on the continuous response. The aim is to use an approach similar to that of Heckman (1978) for the joint modelling of the ordinal and continuous responses. With this model, the dependence between responses can be taken into account by the correlation between errors in the models for continuous and ordinal responses
Depends: R (>= 2.14.0),nlme,MASS
License: GPL (>= 2)
Contact: +982129902910
Packaged: 2013-06-05 19:35:59 UTC; StatisticS
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-06 07:49:30

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Package JMbayes updated to version 0.4-1 with previous version 0.4-0 dated 2013-05-15

Title: Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using JAGS, WinBUGS, or OpenBUGS.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos

Diff between JMbayes versions 0.4-0 dated 2013-05-15 and 0.4-1 dated 2013-06-06

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Package JM updated to version 1.2-0 with previous version 1.1-0 dated 2012-12-07

Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos

Diff between JM versions 1.1-0 dated 2012-12-07 and 1.2-0 dated 2013-06-06

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 JM-1.2-0/JM/R/ins.R                  |   10 -
 JM-1.2-0/JM/R/makepredictcall.dbs.R  |    4 
 JM-1.2-0/JM/R/makepredictcall.dns.R  |    4 
 JM-1.2-0/JM/R/makepredictcall.ibs.R  |    4 
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 JM-1.2-0/JM/R/survfitJM.R            |  252 -----------------------------------
 JM-1.2-0/JM/R/survfitJM.jointModel.R |only
 JM-1.2-0/JM/data/aids.id.rda         |binary
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 JM-1.2-0/JM/data/prothro.rda         |binary
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 JM-1.2-0/JM/man/survfitJM.Rd         |    8 -
 45 files changed, 118 insertions(+), 306 deletions(-)

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New package IUPS with initial version 1.0
Package: IUPS
Type: Package
Title: Incorporating Uncertainties in Propensity Scores
Version: 1.0
Date: 2013-6-5
Author: Weihua An, Huizi Xu, and Zhida Zheng, Indiana University Bloomington
Maintainer: Weihua An
Depends: R (>= 2.14), R2jags, Matching, boot
SystemRequirements: JAGS (>= 3.3.0)
Description: This package includes functions to incorporate uncertainties in estimated propensity scores and provide adjusted standard errors for making valid causal inference.
License: GPL-3
Packaged: 2013-06-06 05:10:06 UTC; weihuaan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-06 07:56:42

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Package FactoClass updated to version 1.0.9 with previous version 1.0.8 dated 2012-02-01

Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial analysis and cluster methods.
Author: Campo Elias Pardo , Pedro Cesar del Campo and Camilo Jose Torres , with the contributions from Ivan Diaz , Mauricio Sadinle .
Maintainer: Campo Elias Pardo

Diff between FactoClass versions 1.0.8 dated 2012-02-01 and 1.0.9 dated 2013-06-06

 DESCRIPTION           |   15 ++++++++-------
 MD5                   |    6 +++---
 R/plotFactoClass.R    |    2 +-
 man/plotFactoClass.Rd |   24 +++++++++++++-----------
 4 files changed, 25 insertions(+), 22 deletions(-)

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