Fri, 05 Dec 2014

Package tourr updated to version 0.5.4 with previous version 0.5.3 dated 2014-04-23

Title: Implement Tour Methods in R Code
Description: Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Author: Dianne Cook , Hadley Wickham
Maintainer: Hadley Wickham

Diff between tourr versions 0.5.3 dated 2014-04-23 and 0.5.4 dated 2014-12-05

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Package Rcgmin updated to version 2013-2.21 with previous version 2013-02.20 dated 2013-02-27

Title: Conjugate Gradient Minimization of Nonlinear Functions
Description: Conjugate gradient minimization of nonlinear functions with box constraints incorporating the Dai/Yuan update. This implementation should be used in place of the "CG" algorithm of the optim() function.
Author: John C. Nash
Maintainer: John C. Nash

Diff between Rcgmin versions 2013-02.20 dated 2013-02-27 and 2013-2.21 dated 2014-12-05

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 8 files changed, 30 insertions(+), 21 deletions(-)

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Package performanceEstimation updated to version 1.0.0 with previous version 0.1.1 dated 2014-03-11

Title: An Infra-Structure for Performance Estimation of Predictive Models
Description: An infra-structure for estimating the predictive performance of predictive models. In this context, it can also be used to compare and/or select among different alternative ways of solving one or more predictive tasks. The main goal of the package is to provide a generic infra-structure to estimate the values of different metrics of predictive performance using different estimation procedures. These estimation tasks can be applied to any solutions (workflows) to the predictive tasks. The package provides easy to use standard workflows that allow the usage of any available R modeling algorithm together with some pre-defined data pre-processing steps and also prediction post-processing methods. It also provides means for addressing issues related with the statistical significance of the observed differences.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo

Diff between performanceEstimation versions 0.1.1 dated 2014-03-11 and 1.0.0 dated 2014-12-05

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Package optextras updated to version 2013-10.28 with previous version 2013-10.27 dated 2013-11-08

Title: Tools to Support Optimization Methods
Description: Tools to assist in safely applying user-generated objective and derivative functions to optimization programs. "Optimization" at the time of writing refers primarily to function minimization methods with at most bounds and masks on the parameters. Tools are provided to check the basic computation of objective functions that the user provides, along with proposed gradient and Hessian functions, as well as to wrap such functions to avoid failures when inadmissible parameters are provided. Checks on bounds and masks (fixed parameters) are available, as are a check on scaling or optimality conditions. An axial search to seek lower points on the objective function surface is included. Though numDeriv is used as the primary tool for numerical derivative approximations, forward, central and backward gradient approximation codes for convenience.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash

Diff between optextras versions 2013-10.27 dated 2013-11-08 and 2013-10.28 dated 2014-12-05

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 4 files changed, 26 insertions(+), 16 deletions(-)

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Package nlmrt updated to version 2013-9.25 with previous version 2013-9.24 dated 2014-05-05

Title: Functions for Nonlinear Least Squares Solutions
Description: nlmrt provides tools for working with nonlinear least squares problems using a calling structure similar to, but much simpler than, that of the nls() function. Moreover, where nls() specifically does NOT deal with small or zero residual problems, nlmrt is quite happy to solve them. It also attempts to be more robust in finding solutions, thereby avoiding 'singular gradient' messages that arise in the Gauss-Newton method within nls(). The Marquardt-Nash approach in nlmrt generally works more reliably to get a solution, though this solution may be one of a set of possibilities, and may also be statistically unsatisfactory. Because of the intended aggressive policy to find solutions, the approach may use additional and unnecessary function and Jacobian evaluations. Note that the Jacobian function is developed using analytic expressions rather than numerical approximations if this is possible. Added print and summary as of August 28, 2012.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash

Diff between nlmrt versions 2013-9.24 dated 2014-05-05 and 2013-9.25 dated 2014-12-05

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New package NISTunits with initial version 1.0.0
Package: NISTunits
Type: Package
Title: Fundamental Physical Constants and Unit Conversions from NIST
Version: 1.0.0
Encoding: UTF-8
Authors@R: c(person(given = "Jose", family = "Gama", role = c("aut","cre"),email = "rxprtgama@gmail.com"))
Description: Fundamental physical constants (Quantity, Value, Uncertainty, Unit) for SI (International System of Units) and non-SI, plus unit conversions Based on the data from NIST (National Institute of Standards and Technology)
License: GPL (>= 3)
Depends: R (>= 2.7.0)
Packaged: 2014-12-05 22:45:28.711 UTC; poky
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-06 00:00:05

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Package ggRandomForests updated to version 1.1.0 with previous version 1.0.0 dated 2014-10-15

Title: Creating and Plotting Data Objects for Understanding Random Forests
Description: The ggRandomForests package contains tools for creating and plotting data structures to visually understand random forest models. The functions are designed for use with the randomForestSRC package. This package is structured to extract intermediate data objects from the random forest. S3 Plot functions, which use the ggplot2 package, are included for each data object.
Author: John Ehrlinger
Maintainer: John Ehrlinger

Diff between ggRandomForests versions 1.0.0 dated 2014-10-15 and 1.1.0 dated 2014-12-05

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Package chngpt updated to version 2014.12-2 with previous version 2014.5-29 dated 2014-05-29

Title: Change Point Logistic Regression
Description: Hypothesis testing in change point logistic regression with or without interaction terms. Several options are provided for testing in models with interaction, including a maximum of likelihood ratios test that determines p-value through Monte Carlo. Estimation under change point model is also included, but less developed at this point.
Author: Youyi Fong
Maintainer: Youyi Fong

Diff between chngpt versions 2014.5-29 dated 2014-05-29 and 2014.12-2 dated 2014-12-05

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Package tlm updated to version 0.1.3 with previous version 0.1.2 dated 2014-09-08

Title: Effects under Linear, Logistic and Poisson Regression Models with Transformed Variables
Description: Computation of effects under linear, logistic and Poisson regression models with transformed variables. Logarithm and power transformations are allowed. Effects can be displayed both numerically and graphically in both the original and the transformed space of the variables.
Author: Jose Barrera-Gomez and Xavier Basagana
Maintainer: Jose Barrera-Gomez

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Package tidyr updated to version 0.2.0 with previous version 0.1 dated 2014-07-21

Title: Easily Tidy Data with spread() and gather() Functions.
Description: An evolution of reshape2. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with dplyr data pipelines.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham

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Package rhosp updated to version 1.06 with previous version 1.05 dated 2013-12-11

Title: Side Effect Risks in Hospital : Simulation and Estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang

Diff between rhosp versions 1.05 dated 2013-12-11 and 1.06 dated 2014-12-05

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Package randtoolbox updated to version 1.16 with previous version 1.15 dated 2014-07-24

Title: Toolbox for Pseudo and Quasi Random Number Generation and RNG Tests.
Description: The package provides (1) pseudo random generators - general linear congruential generators (Park Miller) and multiple recursive generators (Knuth TAOCP), generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (thus include Van der Corput sequence) and (3) some additional tests such as the gap test, the serial test, the poker test... The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package, a number of RNGs and tests for RNGs are provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz (underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth).
Maintainer: Christophe Dutang

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Package outbreaker updated to version 1.1-4 with previous version 1.1-3 dated 2014-05-08

Title: Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data
Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.
Author: Thibaut Jombart , Anne Cori, Joel Hellewell
Maintainer: Thibaut Jombart

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Package gumbel updated to version 1.05 with previous version 1.04 dated 2012-07-31

Title: Gumbel Copula
Description: stand alone package providing R functions for the Gumbel-Hougaard copula. We provide probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Anne-Lise Caillat, Christophe Dutang, Veronique Larrieu and Triet Nguyen
Maintainer: Christophe Dutang

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Package crqa updated to version 1.0.5 with previous version 1.0.4 dated 2014-03-17

Title: Cross-Recurrence Quantification Analysis for Categorical and Continuous Time-Series
Description: CRQA is a package to perform cross-recurrence quantification analysis between two time-series, of either categorical or continuous values. It provides different methods for profiling cross-recurrence, i.e., only looking at the diagonal recurrent points, as well as more in-depth measures of the whole cross-recurrence plot, e.g., recurrence rate.
Author: Moreno I. Coco and Rick Dale
Maintainer: Moreno I. Coco

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Package ape updated to version 3.2 with previous version 3.1-4 dated 2014-07-15

Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], Olivier Gascuel [aut, cph], Christoph Heibl [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis

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Package pvclust updated to version 1.3-1 with previous version 1.3-0 dated 2014-10-08

Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
Description: An implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-value as well as BP (bootstrap probability) value for each cluster in a dendrogram.
Author: Ryota Suzuki , Hidetoshi Shimodaira
Maintainer: Ryota Suzuki

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Package BBEST updated to version 0.1-1 with previous version 0.1-0 dated 2014-08-15

Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for subtraction of incoherent scattering from neutron total-scattering data. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin

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New package EpiResTest with initial version 1.0
Package: EpiResTest
Type: Package
Title: Latent Residuals Test for Epidemiology and Ecology Models
Version: 1.0
Date: 2014-07-07
Author: Max S. Y. Lau; Jeffrey Pollock
Maintainer: Max S. Y. Lau
Description: Latent residual tests recently developed (Lau et al. 2014) which are specifically designed to measure the goodness-of-fit of different model components of a general spatial S-E-I-R model commonly used in epidemiology and ecology studies. More restrictive model classes such as S-I-R can be accommodated. Note that although each test is specifically designed to be sensitive to one particular component of a spatio-temporal model, they are not theoretically restricted to only testing these specific aspects and can be used as a general model assessment tool like any other conventional model selection techniques. The underlying functions are coded in C++ so they should be generally quick.
Note: Under the null hypothesis that the model is correct, the residuals follow distribution U(0,1). The examples only compute a single set of residuals given actual values of most of the model components which are typically required to be imputed in data augmentation schemes such as MCMC in which multiple sets of residuals can be imputed. Only the raw residuals are outputted, a natural summary statistics of the residual samples is the p-value which may be computed using Kolmogorov-Smirnov or Anderson-Darling test.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.2)
LinkingTo: Rcpp, RcppArmadillo
Suggests: RUnit, ADGofTest
Packaged: 2014-12-05 14:12:57 UTC; sl451
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-05 15:29:39

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Package PKtools (with last version 1.5-0) was removed from CRAN

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

2009-10-08 1.5-0
2008-04-16 1.4-0
2007-03-27 1.3-0

Permanent link
Package AWS.tools (with last version 0.0.5) was removed from CRAN

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

2012-07-02 0.0.5

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Package robfilter updated to version 4.1 with previous version 4.0 dated 2012-09-13

Title: Robust Time Series Filters
Description: A set of functions to filter time series based on concepts from robust statistics.
Author: Roland Fried , Karen Schettlinger and Matthias Borowski
Maintainer: Roland Fried

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Package riskRegression updated to version 1.0.9 with previous version 0.0.8 dated 2013-01-08

Title: Risk regression models for survival analysis with competing risks
Description: Risk regression models for survival analysis with and without competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds

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Package pec updated to version 2.4.4 with previous version 2.3.7 dated 2014-09-05

Title: Prediction Error Curves for risk prediction models in survival analysis
Description: Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds

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Package PCAmixdata updated to version 2.2 with previous version 2.1 dated 2014-02-10

Title: Multivariate Analysis of Mixed Data
Description: Principal Component Analysis, orthogonal rotation and multiple factor analysis for a mixture of quantitative and qualitative variables.
Author: Marie Chavent and Vanessa Kuentz and Amaury Labenne and Benoit Liquet and Jerome Saracco.
Maintainer: Amaury Labenne

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Package prodlim updated to version 1.5.0 with previous version 1.4.5 dated 2014-09-02

Title: Product-limit estimation for censored event history analysis
Description: Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds

Diff between prodlim versions 1.4.5 dated 2014-09-02 and 1.5.0 dated 2014-12-05

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New package archiDART with initial version 1.0
Package: archiDART
Type: Package
Title: Plant Root System Architecture Analysis Using DART Output Files
Version: 1.0
Date: 2014-12-05
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory
Description: Analysis of complex plant root system architectures using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, 326, 261--273).
License: GPL-2
Imports: stats, utils, graphics, grDevices
Packaged: 2014-12-05 09:14:22 UTC; Benjamin Delory
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-05 11:00:19

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Package fork (with last version 1.2.4) was removed from CRAN

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

2011-09-02 1.2.4
2009-05-10 1.2.2
2007-11-27 1.2.1
2007-02-11 1.1.0

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Package seqminer (with last version 3.1) was removed from CRAN

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

2014-05-07 3.1
2014-04-19 3.0
2014-04-14 2.7
2014-01-27 2.2
2013-11-20 2.0
2013-11-15 1.9.1
2013-11-11 1.9
2013-09-29 1.4
2013-09-26 1.3
2013-09-04 1.0
2013-07-29 0.7
2013-05-28 0.5
2013-04-13 0.3
2013-04-01 0.2
2013-03-20 0.1

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Package TAQMNGR (with last version 2014.01-2) was removed from CRAN

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

2014-01-28 2014.01-2
2014-01-15 2014.01-1

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Package spectralGP updated to version 1.3.2 with previous version 1.3.1 dated 2012-11-17

Title: Approximate Gaussian processes Using the Fourier Basis
Description: Routines for creating, manipulating, and performing Bayesian inference about Gaussian processes in one and two dimensions using the Fourier basis approximation: simulation and plotting of processes, calculation of coefficient variances, calculation of process density, coefficient proposals (for use in MCMC). It uses R environments to store GP objects as references/pointers.
Author: Chris Paciorek
Maintainer: Chris Paciorek

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Package popReconstruct updated to version 1.0-4 with previous version 1.0-3 dated 2013-09-24

Title: Reconstruct Human Populations of the Recent Past
Description: Implements the Bayesian hierarchical model described by Wheldon, Raftery, Clark and Gerland (see: http://www.csss.washington.edu/Papers/wp108.pdf) for simultaneously estimating age-specific population counts, fertility rates, mortality rates and net international migration flows, at the national level.
Author: Mark C. Wheldon
Maintainer: "Mark C. Wheldon"

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Package okmesonet updated to version 0.1.5 with previous version 0.1.4 dated 2012-09-14

Title: Retrieve Oklahoma Mesonet climatological data
Description: okmesonet retrieves and summarizes Oklahoma (USA) Mesonet climatological data provided by the Oklahoma Climatological Survey. Measurements are recorded every five minutes at approximately 120 stations throughout Oklahoma and are available in near real-time.
Author: Brady Allred, Torre Hovick, Samuel Fuhlendorf
Maintainer: Brady Allred

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Package CLME updated to version 2.0-1 with previous version 1.0-1 dated 2014-10-17

Title: Constrained Inference for Linear Mixed Effects Models
Description: Constrained inference for linear mixed effects models using residual bootstrap methodology
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema

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Package brnn updated to version 0.4 with previous version 0.3 dated 2013-03-15

Title: brnn (Bayesian regularization for feed-forward neural networks)
Description: Bayesian regularization for feed-forward neural networks
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez

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Package BLR updated to version 1.4 with previous version 1.3 dated 2012-03-20

Title: Bayesian Linear Regression
Description: Bayesian Linear Regression
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez

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 BLR-1.4/BLR/NAMESPACE   |    8 +-------
 BLR-1.4/BLR/R/BLRw_c.R  |    8 ++++----
 BLR-1.4/BLR/inst        |only
 6 files changed, 15 insertions(+), 20 deletions(-)

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Package ars updated to version 0.5 with previous version 0.4 dated 2009-03-24

Title: Adaptive Rejection Sampling
Description: Adaptive Rejection Sampling, Original version
Author: Paulino Perez Rodriguez original C++ code from Arnost Komarek based on ars.f written by P. Wild and W. R. Gilks
Maintainer: Paulino Perez Rodriguez

Diff between ars versions 0.4 dated 2009-03-24 and 0.5 dated 2014-12-05

 ars-0.4/ars/index       |only
 ars-0.5/ars/DESCRIPTION |   13 +++++++------
 ars-0.5/ars/MD5         |only
 ars-0.5/ars/R/ars.R     |   12 ++++++------
 ars-0.5/ars/src/ars.cpp |    4 ++--
 5 files changed, 15 insertions(+), 14 deletions(-)

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