Thu, 13 Aug 2015

New package walkr with initial version 0.3-2
Package: walkr
Version: 0.3-2
Date: 2015-08-04
Type: Package
Title: Random Walks the Intersection of the N-Simplex and Hyperplanes
Author: as.person(c( "David Kane <dave.kane@gmail.com> [aut]", "Andy Yao <andy.yao17@gmail.com> [aut]" ))
Maintainer: Andy Yao <andy.yao17@gmail.com>
Depends: R (>= 3.1), ggplot2
Suggests: testthat, knitr
Imports: hitandrun, limSolve, MASS, Rcpp (>= 0.11.6), shinystan
Description: Consider the intersection of two spaces: the complete solution space to Ax = b and the N-Simplex. The intersection of these two spaces is a convex polytope. The package walkr samples from this intersection using two Monte-Carlo Markov Chain (MCMC) methods: hit-and-run and Dikin walk. Walkr also provide tools to examine sample quality.
License: GPL-3
URL: https://github.com/andyyao95/walkr
BugReports: https://github.com/andyyao95/walkr/issues
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2015-08-13 20:12:23 UTC; AndyYao
Repository: CRAN
Date/Publication: 2015-08-14 02:06:37

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New package InterSIM with initial version 1.0
Package: InterSIM
Type: Package
Title: Simulation of Inter-Related Genomic Datasets
Version: 1.0
Date: 2015-07-23
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Rama Raghavan <rraghavan@kumc.edu>
Description: Generates three inter-related genomic datasets : methylation, gene expression and protein expression.
License: GPL
Depends: R (>= 2.14), MASS, NMF, tools
NeedsCompilation: no
Packaged: 2015-08-13 20:40:24 UTC; rama
Repository: CRAN
Date/Publication: 2015-08-14 02:06:53

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New package EGRETci with initial version 1.0.0
Package: EGRETci
Type: Package
Title: Exploration and Graphics for RivEr Trends (EGRET) Confidence Intervals
Version: 1.0.0
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov"), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"))
Description: Collection of functions to evaluate uncertainty of results from water quality analysis using the Weighted Regressions on Time Discharge and Season (WRTDS) method. This package is an add-on to the EGRET package that performs the WRTDS analysis.
License: CC0
Depends: R (>= 3.0)
Imports: EGRET (>= 2.1.1), binom, lubridate, stats, graphics
Suggests: knitr, testthat, foreach, doParallel, iterators, rmarkdown
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
URL: https://github.com/USGS-R/EGRETci
BugReports: https://github.com/USGS-R/EGRETci/issues
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright
NeedsCompilation: no
Packaged: 2015-08-13 19:46:18 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Repository: CRAN
Date/Publication: 2015-08-14 02:06:41

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Package dawai updated to version 1.2 with previous version 1.1 dated 2014-10-02

Title: Discriminant Analysis with Additional Information
Description: In applications it is usual that some additional information is available. This package dawai (an acronym for Discriminant Analysis With Additional Information) performs linear and quadratic discriminant analysis with additional information expressed as inequality restrictions among the populations means. It also computes several estimations of the true error rate.
Author: David Conde, Miguel A. Fernandez, Bonifacio Salvador
Maintainer: David Conde <dconde@eio.uva.es>

Diff between dawai versions 1.1 dated 2014-10-02 and 1.2 dated 2015-08-13

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Package diffIRT updated to version 1.5 with previous version 1.4 dated 2014-06-05

Title: Diffusion IRT Models for Response and Response Time Data
Description: Package to fit diffusion-based IRT models to response and response time data. Models are fit using marginal maximum likelihood. Parameter restrictions (fixed value and equality constraints) are possible. In addition, factor scores (person drift rate and person boundary separation) can be estimated. Model fit assessment tools are also available. The traditional diffusion model can be estimated as well.
Author: Dylan Molenaar
Maintainer: Dylan Molenaar <d.molenaar@uva.nl>

Diff between diffIRT versions 1.4 dated 2014-06-05 and 1.5 dated 2015-08-13

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New package trib with initial version 1.2.0
Package: trib
Type: Package
Title: Analysing and Visualizing Tribology Measurements
Version: 1.2.0
Date: 2015-08-13
Authors@R: c(person("Gokce Mehmet", "AY", role = c("aut", "cre"), email = "gmehmetay@gmail.com"), person("Osman Nuri","CELIK", role="ths", email = "celikon@gmail.com"))
Author: Gokce Mehmet AY [aut, cre], Osman Nuri CELIK [ths]
Maintainer: Gokce Mehmet AY <gmehmetay@gmail.com>
Description: Tribology test devices such as pin-on-disk, ball-on-disk machines and profilometers give important data for tribological analysis. trib is built to analyze and visualize that data into human understandable form. It has functions for finding coefficient of friction, Friction Force vs Distance graphs and calculating Wear Track Volume and Wear Track plotting.
License: GPL-3
LazyData: TRUE
Imports: zoo
URL: https://github.com/gokcemay/trib
NeedsCompilation: no
Packaged: 2015-08-13 08:27:11 UTC; Gokce
Repository: CRAN
Date/Publication: 2015-08-13 19:24:51

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Package sdcTable updated to version 0.19.3 with previous version 0.19.1 dated 2015-07-21

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>

Diff between sdcTable versions 0.19.1 dated 2015-07-21 and 0.19.3 dated 2015-08-13

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New package SIBER with initial version 2.0
Package: SIBER
Type: Package
Title: Stable Isotope Bayesian Ellipses in R
Version: 2.0
Date: 2015-7-31
Depends: R (>= 2.10)
Imports: rjags, mnormt, hdrcde, graphics, stats, grDevices
Author: Andrew Jackson and Andrew Parnell
Maintainer: Andrew Jackson <a.jackson@tcd.ie>
Description: Fits bivariate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.
License: GPL (>= 2)
LazyLoad: yes
LazyData: true
Encoding: UTF-8
Packaged: 2015-08-13 13:14:06 UTC; andrewjackson
NeedsCompilation: yes
Suggests: knitr
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2015-08-13 20:15:49

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Package rebmix updated to version 2.7.2 with previous version 2.7.1 dated 2015-04-04

Title: Rough - Enhanced - Bayesian Finite Mixture Modeling
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

Diff between rebmix versions 2.7.1 dated 2015-04-04 and 2.7.2 dated 2015-08-13

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New package rase with initial version 0.2-2
Package: rase
Title: Range Ancestral State Estimation for Phylogeography and Comparative Analyses
Version: 0.2-2
Date: 2015-08-13
Authors@R: c(person("Ignacio", "Quintero", role = c("aut", "cre"), email = "ignacio.quintero@yale.edu"), person("Forrest W.", "Crawford", role = "aut", email = "forrest.crawford@yale.edu"), person("Petr", "Keil", role = "aut", email = "petrkeil@seznam.cz"))
Depends: R (>= 2.14.0), methods, grDevices, stats, ape (>= 3.1-0),
Imports: mvtnorm (>= 1.0-0), polyCub (>= 0.5-0), spatstat (>= 1.36-0), rgl, sm, phytools
Suggests: sp, ggmcmc, rpanel, tcltk
Description: The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-08-13 14:22:07 UTC; ignacioquintero
Author: Ignacio Quintero [aut, cre], Forrest W. Crawford [aut], Petr Keil [aut]
Maintainer: Ignacio Quintero <ignacio.quintero@yale.edu>
Repository: CRAN
Date/Publication: 2015-08-13 19:21:26

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Package QuantifQuantile updated to version 2.2 with previous version 2.1 dated 2015-04-27

Title: Estimation of Conditional Quantiles using Optimal Quantization
Description: Estimation of conditional quantiles using optimal quantization. Construction of an optimal grid of N quantizers, estimation of conditional quantiles and data driven selection of the size N of the grid. Graphical illustrations for the selection of N and of resulting estimated curves or surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier <ischarli@ulb.ac.be>

Diff between QuantifQuantile versions 2.1 dated 2015-04-27 and 2.2 dated 2015-08-13

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Package provenance updated to version 0.3 with previous version 0.2 dated 2015-06-05

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between provenance versions 0.2 dated 2015-06-05 and 0.3 dated 2015-08-13

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Package PrevMap updated to version 1.2.1 with previous version 1.2 dated 2015-08-05

Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Description: It provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data, and is also an extension of the 'geoR' package.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi <e.giorgi@lancaster.ac.uk>

Diff between PrevMap versions 1.2 dated 2015-08-05 and 1.2.1 dated 2015-08-13

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Package MfUSampler updated to version 1.0.0 with previous version 0.9.1 dated 2014-12-26

Title: Multivariate-from-Univariate (MfU) MCMC Sampler
Description: Convenience functions for multivariate MCMC using univariate samplers including: slice sampler with stepout and shrinkage (Neal, 2003), adaptive rejection sampler (Gilks and Wild, 1992), adaptive rejection Metropolis (Gilks et al 1995), and univariate Metropolis with Gaussian proposal.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>

Diff between MfUSampler versions 0.9.1 dated 2014-12-26 and 1.0.0 dated 2015-08-13

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Package backtestGraphics updated to version 0.1.5 with previous version 0.1.4 dated 2015-08-12

Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics interface to visualize backtest results of different financial instruments, such as equities, futures, and credit default swaps. The package does not run backtests on the given data set but displays a graphical explanation of the backtest results. Users can look at backtest graphics for different instruments, investment strategies, and portfolios. Summary statistics of different portfolio holdings are shown in the left panel, and interactive plots of profit and loss (P\&L), net market value (NMV) and gross market value (GMV) are displayed in the right panel.
Author: as.person(c( "David Kane <dave.kane@gmail.com> [aut]", "Ziqi Lu <ziqi.lu@williams.edu> [aut]", "Fan Zhang <fan.zhang@williams.edu> [aut]", "Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]" ))
Maintainer: Miller Zijie Zhu <zijie.miller.zhu@gmail.com>

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Package agricolae updated to version 1.2-2 with previous version 1.2-1 dated 2014-09-01

Title: Statistical Procedures for Agricultural Research
Description: Agricolae was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, mention Systems Engineering, Faculty of Industrial and Systems Engineering, National Engineering University (UNI), Lima-Peru. Original idea, support and data sets came from CIP (International Potato Center). Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>

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Package shinyjs updated to version 0.1.0 with previous version 0.0.8.3 dated 2015-07-31

Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Examples include hiding an element, disabling an input, resetting an input back to its original value, and many more useful functions. Even if you do know JavaScript, 'shinyjs' can be used as convenience functions to avoid dealing with message passing and writing JavaScript code. 'shinyjs' can also be used to easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package SciencesPo updated to version 1.3.7 with previous version 1.3.6 dated 2015-07-27

Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>

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New package lfda with initial version 1.0.0
Package: lfda
Type: Package
Title: Local Fisher Discriminant Analysis
Version: 1.0.0
Date: 2015-08-10
Author: Yuan Tang <terrytangyuan@gmail.com> with great contributions from Zachary Deane-Mayer.
URL: https://github.com/terrytangyuan/lfda
BugReports: https://github.com/terrytangyuan/lfda/issues
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
License: MIT + file LICENSE
Description: Functions for performing and visualizing Local Fisher Discriminant Analysis(LFDA) and Kernel Fisher Discriminant Analysis(KLFDA).
Depends: R (>= 3.1.0)
Imports: plyr, grDevices, rARPACK, rgl
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-08-13 02:02:54 UTC; Yuan
Repository: CRAN
Date/Publication: 2015-08-13 08:35:26

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Package geospt updated to version 1.0-2 with previous version 1.0-1 dated 2015-02-08

Title: Geostatistical Analysis and Design of Optimal Spatial Sampling Networks
Description: Estimation of the variogram through trimmed mean, radial basis functions (optimization, prediction and cross-validation), summary statistics from cross-validation, pocket plot, and design of optimal sampling networks through sequential and simultaneous points methods.
Author: Carlos Melo , Alí Santacruz, Oscar Melo
Maintainer: Alí Santacruz

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Package evaluate updated to version 0.7.2 with previous version 0.7 dated 2015-04-21

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Barret Schloerke [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package EGRET updated to version 2.3.1 with previous version 2.3.0 dated 2015-07-07

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 <ldecicco@usgs.gov>

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