Thu, 04 Sep 2014

Package preseqR updated to version 1.0.1 with previous version 1.0 dated 2014-08-23

Title: Predicting Species Accumulation
Description: Estimating species accumulation curves by rational function approximations to the non-parametric empirical Bayes estimator and by the zero-truncated Negative Binomial distribution.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng

Diff between preseqR versions 1.0 dated 2014-08-23 and 1.0.1 dated 2014-09-04

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 5 files changed, 17 insertions(+), 17 deletions(-)

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Package kmi updated to version 0.5.1 with previous version 0.5 dated 2013-12-18

Title: Kaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting
Description: The package performs a Kaplan-Meier multiple imputation to recover the missing potential censoring information from competing risks events, so that standard right-censored methods could be applied to the imputed data sets to perform analyses of the cumulative incidence functions.
Author: Arthur Allignol
Maintainer: Arthur Allignol

Diff between kmi versions 0.5 dated 2013-12-18 and 0.5.1 dated 2014-09-04

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Package jsonlite updated to version 0.9.11 with previous version 0.9.10 dated 2014-08-02

Title: A smarter JSON encoder/decoder for R
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the same libjson c++ parser, but implements a smarter mapping between JSON data and R classes. This is particularly useful when working with JSON data from pipelines and web APIs. The vignettes describe the behavior in great detail. In addition to drop-in replacements for toJSON and fromJSON, the package contains functions to validate, prettify and minify JSON, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Jonathan Wallace
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.10 dated 2014-08-02 and 0.9.11 dated 2014-09-04

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New package GUILDS with initial version 1.0
Package: GUILDS
Type: Package
Title: Implementation of sampling formulas for the unified neutral model of biodiversity and biogeography, with or without guild structure.
Version: 1.0
Date: 2014-08-22
Author: Thijs Janzen
Maintainer: Thijs Janzen
Description: The GUILDS package combines a range of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen 2014), and the guilds sampling formula conditioned on guild size (Janzen 2014).
License: GPL-2
Depends: R (>= 3.0.2)
Imports: Rcpp (>= 0.11.0), pracma, subplex
LinkingTo: Rcpp
Packaged: 2014-09-04 14:21:25 UTC; p251362
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-05 00:53:26

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Package Cprob updated to version 1.2.3 with previous version 1.2.2 dated 2014-01-08

Title: Conditional probability function of a competing event
Description: Estimates the conditional probability function of a competing event, and fits, using the temporal process regression or the pseudo-value approach, a proportional-odds model to the conditional probability function
Author: Arthur Allignol
Maintainer: Arthur Allignol

Diff between Cprob versions 1.2.2 dated 2014-01-08 and 1.2.3 dated 2014-09-04

 ChangeLog                   |    4 ++++
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New package classyfire with initial version 0.1-0
Package: classyfire
Type: Package
Title: Robust multivariate classification using highly optimised SVM ensembles
Version: 0.1-0
Date: 2014-09-03
Author: Eleni Chatzimichali and Conrad Bessant
Maintainer: Eleni Chatzimichali
Description: A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing.
License: GPL (>= 2)
Depends: R (>= 3.0.0), snowfall (>= 1.84-6), e1071 (>= 1.6-3), boot (>= 1.3-11), neldermead (>= 1.0-9)
Imports: ggplot2 (>= 1.0-0), optimbase (>= 1.0-9)
Packaged: 2014-09-04 19:01:20 UTC; elenachatzimichali
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-05 00:49:30

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New package subrank with initial version 0.8.5
Package: subrank
Type: Package
Title: Computes copula using ranks and subsampling
Version: 0.8.5
Date: 2014-05-09
Author: Jerome Collet
Maintainer: Jerome Collet
Description: essentially a discussion tool about estimation of copula using ranks and subsampling.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2014-09-04 20:25:46 UTC; collet
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-04 23:01:43

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Package RcmdrMisc updated to version 1.0-2 with previous version 1.0-1 dated 2014-08-14

Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre], Robert Muenchen [ctb], Dan Putler [ctb]
Maintainer: John Fox

Diff between RcmdrMisc versions 1.0-1 dated 2014-08-14 and 1.0-2 dated 2014-09-04

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Package Rcmdr updated to version 2.1-1 with previous version 2.1-0 dated 2014-08-24

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Milan Bouchet-Valat [aut], Liviu Andronic [ctb], Michael Ash [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb], Kevin Wright [ctb]
Maintainer: John Fox

Diff between Rcmdr versions 2.1-0 dated 2014-08-24 and 2.1-1 dated 2014-09-04

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Package haplo.stats updated to version 1.6.11 with previous version 1.6.8 dated 2013-12-06

Title: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
Description: A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap; all of which have detailed examples in doc/manualHaploStats.pdf.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell

Diff between haplo.stats versions 1.6.8 dated 2013-12-06 and 1.6.11 dated 2014-09-04

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Package cluster updated to version 1.15.3 with previous version 1.15.2 dated 2014-03-31

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis Methods. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre], Peter Rousseeuw [aut] (Fortran original), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)), Matthias Studer [ctb], Pierre Roudier [ctb]
Maintainer: Martin Maechler

Diff between cluster versions 1.15.2 dated 2014-03-31 and 1.15.3 dated 2014-09-04

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Package PP updated to version 0.5.3 with previous version 0.5 dated 2014-08-30

Title: Person Parameter estimation
Description: The PP package includes estimation of (MLE, WLE, MAP, EAP, ROBUST) person parameters for the 1,2,3,4-PL model and the GPCM (generalized partial credit model). The parameters are estimated under the assumption that the item parameters are known and fixed. The package is useful e.g. in the case that items from an item pool / item bank with known item parameters are administered to a new population of test-takers and an ability estimation for every test-taker is needed.
Author: Manuel Reif
Maintainer: Manuel Reif

Diff between PP versions 0.5 dated 2014-08-30 and 0.5.3 dated 2014-09-04

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New package cooptrees with initial version 1.0
Package: cooptrees
Type: Package
Version: 1.0
Date: 2014-09-01
Title: Cooperative aspects of optimal trees in weighted graphs
Author: Manuel Fontenla
Maintainer: Manuel Fontenla
Depends: R (>= 2.7.0), igraph (>= 0.7.1), optrees (>= 1.0)
Imports: gtools
Description: Computes several cooperative games and allocation rules associated with minimum cost spanning tree problems and minimum cost arborescence problems.
License: GPL-3
Packaged: 2014-09-03 13:34:25 UTC; Manuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-04 19:13:22

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Package SDaA updated to version 0.1-3 with previous version 0.1-2 dated 2011-03-21

Title: Sampling: Design and Analysis
Description: Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, Duxbury.
Author: Tobias Verbeke
Maintainer: Tobias Verbeke

Diff between SDaA versions 0.1-2 dated 2011-03-21 and 0.1-3 dated 2014-09-04

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Package plsdof updated to version 0.2-7 with previous version 0.2-6 dated 2013-03-19

Title: Degrees of Freedom and Statistical Inference for Partial Least Squares Regression
Description: The plsdof package provides Degrees of Freedom estimates for Partial Least Squares (PLS) Regression. Model selection for PLS is based on various information criteria (aic, bic, gmdl) or on cross-validation. Estimates for the mean and covariance of the PLS regression coefficients are available. They allow the construction of approximate confidence intervals and the application of test procedures. Further, cross-validation procedures for Ridge Regression and Principal Components Regression are available.
Author: Nicole Kraemer, Mikio L. Braun
Maintainer: Nicole Kraemer

Diff between plsdof versions 0.2-6 dated 2013-03-19 and 0.2-7 dated 2014-09-04

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Package NPBayesImpute updated to version 0.2 with previous version 0.1 dated 2014-08-28

Title: Non-parametric Bayesian Multiple Imputation for Categorical Data
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang

Diff between NPBayesImpute versions 0.1 dated 2014-08-28 and 0.2 dated 2014-09-04

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Package MCDA updated to version 0.0.6 with previous version 0.0.3 dated 2013-12-11

Title: MCDA
Description: The MCDA package for the R statistical software allows you to use MCDA methods and functions in R.
Author: Patrick Meyer, Sébastien Bigaret.
Maintainer: Patrick Meyer

Diff between MCDA versions 0.0.3 dated 2013-12-11 and 0.0.6 dated 2014-09-04

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Package lmSupport updated to version 2.09 with previous version 1.07.1 dated 2013-10-22

Title: Support for Linear Models
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course graduate series in the General Linear Model (PSY 610/710).
Author: John Curtin
Maintainer: John Curtin

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Package helloJavaWorld updated to version 0.0-9 with previous version 0.0-7 dated 2010-02-23

Title: Hello Java World
Description: A dummy package to demonstrate how to interface to a jar file that resides inside an R package.
Author: Tobias Verbeke
Maintainer: Tobias Verbeke

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Package PepPrep updated to version 1.0.1 with previous version 1.0.0 dated 2014-07-09

Title: Insilico peptide mutation, digestion and homologous comparison.
Description: Amino acid exchange based on single nucleotide variant (SNV) information and tryptic digestion on peptide sequence. Searching for homologous by comparison of tryptic digested peptide sequences.
Author: Rafael Dellen
Maintainer: Rafael Dellen

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Package parcor updated to version 0.2-6 with previous version 0.2-5 dated 2014-08-14

Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.
Author: Nicole Kraemer, Juliane Schaefer
Maintainer: Nicole Kraemer

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New package mpcv with initial version 1.0
Package: mpcv
Type: Package
Title: Multivariate Process Capability Vector
Version: 1.0
Date: 2014-07-07
Author: Krzysztof Ciupke
Maintainer: Krzysztof Ciupke
Depends: lpSolve
Description: Multivariate process capability analysis using the multivariate process capability vector. Allows to analyze a multivariate process with both normally and non-normally distributed and also with dependent and independent quality characteristics.
License: GPL (>= 2.0)
Packaged: 2014-09-04 11:31:13 UTC; kciupke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-04 14:39:33

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New package insuranceData with initial version 1.0
Package: insuranceData
Type: Package
Title: A Collection of Insurance Datasets Useful in Risk Classification in Non-life Insurance.
Version: 1.0
Date: 2014-09-04
Author: Alicja Wolny--Dominiak and Michal Trzesiok
Maintainer: Alicja Wolny--Dominiak
Description: Insurance datasets, which are often used in claims severity and claims frequency modelling. It helps testing new regression models in those problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data sets are applied in the project "Mixed models in ratemaking" supported by grant NN 111461540 from Polish National Science Center.
License: GPL-2
Packaged: 2014-09-04 10:38:28 UTC; Woali
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-04 13:46:39

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Package CopulaRegression updated to version 0.1-5 with previous version 0.1-4 dated 2014-04-23

Title: Bivariate Copula Based Regression Models
Description: This R-packages presents a bivariate, copula-based model for the joint distribution of a pair of continuous and discrete random variables. The two marginal random variables are modeled via generalized linear models, and their joint distribution (represented by a parametric copula family) is estimated using maximum-likelihood techniques.
Author: Nicole Kraemer, Daniel Silvestrini
Maintainer: Nicole Kraemer

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Package berryFunctions updated to version 1.5.1 with previous version 1.4 dated 2014-07-02

Title: function collection related to hydrology, zooming and shapefiles
Description: collection of functions to: zoom in X11 graphics and ESRI shapefile plots, use the unit hydrograph in a linear storage cascade, compare several extreme-value-distributions at return periods, draw horizontal histograms and scatterplots colored by 3rd dimension, convert lists to data.frames, fit multiple functions (power, reciprocal, exponential, logarithmic, polynomial, rational) by regression.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool

Diff between berryFunctions versions 1.4 dated 2014-07-02 and 1.5.1 dated 2014-09-04

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Package ppls updated to version 1.6-1 with previous version 1.6-0 dated 2013-08-20

Title: Penalized Partial Least Squares
Description: This package contains linear and nonlinear regression methods based on Partial Least Squares and Penalization Techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can be conducted via jackknifing.
Author: Nicole Kraemer Anne-Laure Boulesteix
Maintainer: Nicole Kraemer

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Package ClustVarLV updated to version 1.3.1 with previous version 1.3 dated 2014-07-25

Title: Clustering of variables around Latent Variables
Description: This package provides a set of functions that allows us to cluster a set of variables around Latent Variables. Each group is associated with a latent variable. External variables measured on the same observations or/and additional information on the variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau

Diff between ClustVarLV versions 1.3 dated 2014-07-25 and 1.3.1 dated 2014-09-04

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Package sparseSEM updated to version 2.5 with previous version 2.3 dated 2014-08-26

Title: Sparse-aware Maximum Likelihood for Structural Equation Models
Description: Sparse-aware maximum likelihood for structural equation models in inferring gene regulatory networks
Author: Anhui Huang
Maintainer: Anhui Huang

Diff between sparseSEM versions 2.3 dated 2014-08-26 and 2.5 dated 2014-09-04

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Package sanon updated to version 1.4 with previous version 1.3 dated 2013-12-07

Title: Stratified Analysis with Nonparametric covariable adjustment
Description: This package has several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi

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Package rdrobust updated to version 0.61 with previous version 0.6 dated 2014-06-17

Title: Robust data-driven statistical inference in Regression-Discontinuity designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform bandwidth selection for the different procedures implemented, and rdbinselect to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico , Matias D. Cattaneo , Rocio Titiunik
Maintainer: Sebastian Calonico

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Package RcmdrPlugin.BCA updated to version 0.9-8 with previous version 0.9-7 dated 2013-12-03

Title: Rcmdr Plug-In for Business and Customer Analytics
Description: An Rcmdr "plug-in" to accompany the book Customer and Business Analytics: Applied Data Mining for Business Decision Making Using R by Daniel S. Putler and Robert E. Krider.
Author: Dan Putler
Maintainer: Dan Putler

Diff between RcmdrPlugin.BCA versions 0.9-7 dated 2013-12-03 and 0.9-8 dated 2014-09-04

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New package pxweb with initial version 0.4
Package: pxweb
Type: Package
Title: R interface to the PX-Web/PC-Axis API
Version: 0.4
Date: 2014-09-03
Author: Mans Magnusson, Leo Lahti, Love Hansson
Maintainer: Mans Magnusson
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API is used by organizations such as Statistics Sweden and Statistics Finland to disseminate data. The R package can interact with all PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract metadata and extract and parse statistics to R data.frame format. PX-Web is a solution to disseminate PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains an API to disseminate PC-Axis files. PX-Web/PC-Axis API information can be found at: http://www.scb.se/Grupp/OmSCB/API/API-description.pdf
VignetteBuilder: knitr
URL: https://github.com/rOpenGov/pxweb/
BugReports: https://github.com/rOpenGov/pxweb/issues
Imports: data.table, plyr, stringr, RJSONIO, httr
License: BSD_2_clause + file LICENSE
Suggests: testthat, ggplot2, knitr
Packaged: 2014-09-03 18:47:58 UTC; manma97
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-04 07:27:20

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Package rpf updated to version 0.38 with previous version 0.36 dated 2014-07-26

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb]
Maintainer: Joshua Pritikin

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Package pqantimalarials updated to version 0.2 with previous version 0.1 dated 2014-03-18

Title: web tool for estimating under-five deaths caused by poor-quality antimalarials in sub-Saharan Africa
Description: This package allows users to calculate the number of under-five child deaths caused by consumption of poor quality antimalarials across 39 sub-Saharan nations. The package supports one function, that starts an interactive web tool created using the shiny R package. The web tool runs locally on the user's machine. The web tool allows users to set input parameters (prevalence of poor quality antimalarials, case fatality rate of children who take poor quality antimalarials, and sample size) which are then used to perform an uncertainty analysis following the Latin hypercube sampling scheme. Users can download the output figures as PDFs, and the output data as CSVs. Users can also download their input parameters for reference. This package was designed to accompany the analysis presented in: J. Patrick Renschler, Kelsey Walters, Paul Newton, Ramanan Laxminarayan "Estimated under-five deaths associated with poor-quality antimalarials in sub-Saharan Africa", 2014. Paper submitted.
Author: J. Patrick Renschler
Maintainer: J. Patrick Renschler

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Package multigroup updated to version 0.4.1 with previous version 0.4 dated 2014-05-27

Title: methods for multigroup data analysis
Description: This package includes several methods to study multigroup data, where the same set of variables are measured on different groups of individuals.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez Questions and comments go to Aida Eslami and Stephanie Bougeard
Maintainer: Aida Eslami

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Package MRCV updated to version 0.3-3 with previous version 0.3-2 dated 2014-07-25

Title: Methods for Analyzing Multiple Response Categorical Variables (MRCVs)
Description: The MRCV package provides functions for analyzing the association between one single response categorical variable (SRCV) and one multiple response categorical variable (MRCV), or between two or three MRCVs. A modified Pearson chi-square statistic can be used to test for marginal independence for the one or two MRCV case, or a more general loglinear modeling approach can be used to examine various other structures of association for the two or three MRCV case. Bootstrap- and asymptotic-based standardized residuals and model-predicted odds ratios are available, in addition to other descriptive information.
Author: Natalie Koziol and Chris Bilder
Maintainer: Natalie Koziol

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Package miscset updated to version 0.4 with previous version 0.3.1 dated 2014-07-11

Title: Miscellaneous Tools Set
Description: A set of miscellaneous R tools to simplify the work with several data types and formats.
Author: Sven E. Templer
Maintainer: Sven E. Templer

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Package idr updated to version 1.2 with previous version 1.1.1 dated 2012-10-27

Title: Irreproducible discovery rate
Description: This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel
Author: Qunhua Li
Maintainer: Qunhua Li

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Package Ecdat updated to version 0.2-7 with previous version 0.2-6 dated 2014-06-27

Title: Data sets for econometrics
Description: Data sets for econometrics
Author: Yves Croissant
Maintainer: Spencer Graves

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Package BCA updated to version 0.9-3 with previous version 0.9-2 dated 2013-02-28

Title: Business and Customer Analytics
Description: Underlying support functions for RcmdrPlugin.BCA and a companion to the book Customer and Business Analytics: Applied Data Mining for Business Decision Making Using R by Daniel S. Putler and Robert E. Krider
Author: Dan Putler
Maintainer: Dan Putler

Diff between BCA versions 0.9-2 dated 2013-02-28 and 0.9-3 dated 2014-09-04

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