Tue, 29 Jul 2014

Package pheno2geno updated to version 1.2.1 with previous version 1.2.0 dated 2014-06-10

Title: Pheno2Geno - Generating genetic markers and maps from molecular phenotypes
Description: Pheno2Geno is an R package for the computational generation genetic markers and maps from molecular phenotypes
Author: Konrad Zych and Danny Arends
Maintainer: Konrad Zych

Diff between pheno2geno versions 1.2.0 dated 2014-06-10 and 1.2.1 dated 2014-07-29

 DESCRIPTION              |    6 
 MD5                      |   14 -
 R/cross.saturate.R       |   14 -
 R/power.plot.R           |    3 
 data/yeastCross.rda      |binary
 data/yeastPopulation.rda |binary
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 tests/test_analysis.R    |   10 -
 8 files changed, 92 insertions(+), 333 deletions(-)

More information about pheno2geno at CRAN
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Package rorutadis updated to version 0.1.3 with previous version 0.1.1 dated 2014-04-11

Title: Robust Ordinal Regression UTADIS
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek

Diff between rorutadis versions 0.1.1 dated 2014-04-11 and 0.1.3 dated 2014-07-29

 rorutadis-0.1.1/rorutadis/README.md                                         |only
 rorutadis-0.1.3/rorutadis/DESCRIPTION                                       |    8 
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 rorutadis-0.1.3/rorutadis/NAMESPACE                                         |    2 
 rorutadis-0.1.3/rorutadis/R/main.R                                          |   58 ++++++-
 rorutadis-0.1.3/rorutadis/R/model.R                                         |    1 
 rorutadis-0.1.3/rorutadis/R/parameters.R                                    |    2 
 rorutadis-0.1.3/rorutadis/R/postFactumAnalysis.R                            |   76 +++++++--
 rorutadis-0.1.3/rorutadis/R/problem.R                                       |    2 
 rorutadis-0.1.3/rorutadis/inst/tests/test-main.R                            |   30 +++
 rorutadis-0.1.3/rorutadis/man/addAssignmentPairwiseAtLeastComparisons.Rd    |   23 +-
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 rorutadis-0.1.3/rorutadis/man/mergeAssignments.Rd                           |   53 +++---
 rorutadis-0.1.3/rorutadis/man/removeAssignmentPairwiseAtLeastComparisons.Rd |   23 +-
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 42 files changed, 510 insertions(+), 446 deletions(-)

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Package poppr updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-27

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

Diff between poppr versions 1.1.1 dated 2014-07-27 and 1.1.2 dated 2014-07-29

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 poppr-1.1.2/poppr/README.md                                  |    2 
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Package phreeqc updated to version 1.0-8877 with previous version 1.0-8847 dated 2014-07-16

Title: R interface to the phreeqc geochemical modeling program
Description: R interface to PHREEQC (Version 3). PHREEQC is a geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton

Diff between phreeqc versions 1.0-8847 dated 2014-07-16 and 1.0-8877 dated 2014-07-29

 DESCRIPTION                         |    6 -
 MD5                                 |  162 ++++++++++++++++++------------------
 NAMESPACE                           |    2 
 R/phreeqc.R                         |    2 
 man/Amm.dat.Rd                      |   18 ++--
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More information about phreeqc at CRAN
Permanent link

Package NeatMap updated to version 0.3.6.2 with previous version 0.3.6.1 dated 2013-11-01

Title: Non-clustered heatmap alternatives
Description: NeatMap is a package to create heatmap like plots in 2 and 3 dimensions, without the need for cluster analysis. Like the heatmap, the plots created by NeatMap display both a dimensionally reduced representation of the data as well as the data itself. They are intended to be used in conjunction with dimensional reduction techniques such as PCA.
Author: Satwik Rajaram and Yoshi Oono
Maintainer: Satwik Rajaram

Diff between NeatMap versions 0.3.6.1 dated 2013-11-01 and 0.3.6.2 dated 2014-07-29

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More information about NeatMap at CRAN
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Package meta updated to version 3.7-1 with previous version 3.7-0 dated 2014-07-11

Title: Meta-Analysis with R
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer

Diff between meta versions 3.7-0 dated 2014-07-11 and 3.7-1 dated 2014-07-29

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 5 files changed, 92 insertions(+), 22 deletions(-)

More information about meta at CRAN
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Package lctools updated to version 0.1-3 with previous version 0.1-2 dated 2014-04-26

Title: Local Correlation, Spatial Inequalities and other tools
Description: Local Correlation Coefficients (Local Pearson and Geographically Weighted Pearson), Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics)
Author: Stamatis Kalogirou
Maintainer: Stamatis Kalogirou

Diff between lctools versions 0.1-2 dated 2014-04-26 and 0.1-3 dated 2014-07-29

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 14 files changed, 43 insertions(+), 36 deletions(-)

More information about lctools at CRAN
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Package hasseDiagram updated to version 0.1.1 with previous version 0.1 dated 2014-04-12

Title: Drawing Hasse diagram
Description: Drawing Hasse diagram - visualization of transitive reduction of a finite partially ordered set.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek

Diff between hasseDiagram versions 0.1 dated 2014-04-12 and 0.1.1 dated 2014-07-29

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More information about hasseDiagram at CRAN
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Package EpiModel updated to version 1.0.1 with previous version 1.0 dated 2014-06-09

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Li Wang [ctb]
Maintainer: Samuel Jenness

Diff between EpiModel versions 1.0 dated 2014-06-09 and 1.0.1 dated 2014-07-29

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Mon, 28 Jul 2014

Package TreeSim updated to version 2.0 with previous version 1.9.1 dated 2013-12-10

Title: Simulating trees under the birth-death model
Description: The package simulates phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and number of tips (sim.bd.taxa.age). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa). The function sim.bd.age (and sim.rateshift.taxa without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot, LTT.plot.gen and LTT.average.root. TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim). (ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa. The function sim.genespeciestree simulates coalescent gene trees within birth-death species trees, and sim.genetree simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreeSim versions 1.9.1 dated 2013-12-10 and 2.0 dated 2014-07-28

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More information about TreeSim at CRAN
Permanent link

Package TreePar updated to version 3.0 with previous version 2.5 dated 2013-06-09

Title: Estimating birth and death rates based on phylogenies
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. Both (1) and (2) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree).
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreePar versions 2.5 dated 2013-06-09 and 3.0 dated 2014-07-28

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More information about TreePar at CRAN
Permanent link

Package RCurl updated to version 1.95-4.2 with previous version 1.95-4.1 dated 2013-03-06

Title: General network (HTTP/FTP/...) client interface for R
Description: The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RCurl versions 1.95-4.1 dated 2013-03-06 and 1.95-4.2 dated 2014-07-28

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Package gmp updated to version 0.5-12 with previous version 0.5-11 dated 2013-12-04

Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme , Sylvain Jasson , Martin Maechler
Maintainer: Antoine Lucas

Diff between gmp versions 0.5-11 dated 2013-12-04 and 0.5-12 dated 2014-07-28

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Package cosinor updated to version 1.1 with previous version 1.0 dated 2014-07-25

Title: Tools for estimating and predicting the cosinor model
Description: cosinor is a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs
Maintainer: Michael Sachs

Diff between cosinor versions 1.0 dated 2014-07-25 and 1.1 dated 2014-07-28

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More information about cosinor at CRAN
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Package sda updated to version 1.3.4 with previous version 1.3.3 dated 2014-04-18

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using correlation-adjusted t-scores (CAT scores). Variable selection error is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer

Diff between sda versions 1.3.3 dated 2014-04-18 and 1.3.4 dated 2014-07-28

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Package Rtsne updated to version 0.8 with previous version 0.6 dated 2014-06-23

Title: T-distributed Stochastic Neighbor Embedding using Barnes-Hut implementation
Description: An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten
Author: Jesse Krijthe
Maintainer: Jesse Krijthe

Diff between Rtsne versions 0.6 dated 2014-06-23 and 0.8 dated 2014-07-28

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Permanent link

Package RJSONIO updated to version 1.3-0 with previous version 1.2-0.2 dated 2014-04-29

Title: Serialize R objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RJSONIO versions 1.2-0.2 dated 2014-04-29 and 1.3-0 dated 2014-07-28

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Package ltbayes updated to version 0.3 with previous version 0.2 dated 2014-05-15

Title: Simulation-Based Bayesian Inference for Latent Traits of Item Response Models
Description: Functions for simulating realizations from the posterior distribution of a latent trait of an item response model. Distributions are conditional on one or a subset of response patterns (e.g., sum scores). Functions for computing likelihoods, Fisher and observed information, posterior modes, and profile likelihood confidence intervals are also included. These functions are designed to be easily amenable to user-specified models.
Author: Timothy R. Johnson
Maintainer: Timothy R. Johnson

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Package jaatha updated to version 2.5 with previous version 2.4 dated 2014-06-03

Title: A Fast Parameter Estimation Method for Evolutionary Biology
Description: Jaatha is a composite likelihood method for inferring evolutionary parameters using genetic data. Given a model of the evolutionary history of two biological populations as well as SNP data from multiple individuals from each population, it estimates model parameters like the time of separation of both species.
Author: Paul R. Staab, Lisha Mathew and Dirk Metzler
Maintainer: Paul R. Staab

Diff between jaatha versions 2.4 dated 2014-06-03 and 2.5 dated 2014-07-28

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Package httr updated to version 0.4 with previous version 0.3 dated 2014-03-19

Title: Tools for working with URLs and HTTP
Description: Provides useful tools for working with HTTP. The API is based around http verbs (GET(), POST(), etc) with pluggable components to control the request (authenticate(), add_headers() and so on).
Author: Hadley Wickham
Maintainer: Hadley Wickham

Diff between httr versions 0.3 dated 2014-03-19 and 0.4 dated 2014-07-28

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Package HTSDiff updated to version 1.0.2 with previous version 1.0.1 dated 2013-12-10

Title: Differential analysis of RNA-seq data with Poisson mixture models
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSDiff versions 1.0.1 dated 2013-12-10 and 1.0.2 dated 2014-07-28

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Package HTSCluster updated to version 2.0.3 with previous version 2.0.1 dated 2013-12-10

Title: Clustering high throughput sequencing (HTS) data
Description: This package implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the ICL criterion is used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSCluster versions 2.0.1 dated 2013-12-10 and 2.0.3 dated 2014-07-28

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Package HDPenReg updated to version 0.89.8 with previous version 0.89.7 dated 2014-07-17

Title: High-Dimensional Penalized Regression.
Description: This package contains algorithms for lasso and fused-lasso problems. It contains an implementation of the lars algorithm [1], for the lasso and fusion penalization and EM-based algorithms for (logistic) lasso and fused-lasso.
Author: Quentin Grimonprez [aut, cre], Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez

Diff between HDPenReg versions 0.89.7 dated 2014-07-17 and 0.89.8 dated 2014-07-28

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Package GeneNet updated to version 1.2.10 with previous version 1.2.9 dated 2014-04-15

Title: Modeling and Inferring Gene Networks
Description: GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between GeneNet versions 1.2.9 dated 2014-04-15 and 1.2.10 dated 2014-07-28

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Permanent link

Package cplexAPI updated to version 1.2.11 with previous version 1.2.9 dated 2013-05-23

Title: R Interface to C API of IBM ILOG CPLEX
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between cplexAPI versions 1.2.9 dated 2013-05-23 and 1.2.11 dated 2014-07-28

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Package care updated to version 1.1.5 with previous version 1.1.4 dated 2014-04-18

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.1.4 dated 2014-04-18 and 1.1.5 dated 2014-07-28

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More information about care at CRAN
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Package peptider updated to version 0.1.5 with previous version 0.1.4 dated 2014-05-19

Title: Evaluation of diversity in nucleotide libraries
Description: Functions for evaluating diversity in peptide libraries, including NNN, NNB, NNK/S, and trimer schemes. This includes expected coverage, relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare

Diff between peptider versions 0.1.4 dated 2014-05-19 and 0.1.5 dated 2014-07-28

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Package discreteRV updated to version 1.1.2 with previous version 1.1 dated 2014-04-01

Title: Functions to create and manipulate discrete random variables
Description: discreteRV implements a set of functions that allow computations involving discrete random variables. It uses a syntax which is familiar to that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare

Diff between discreteRV versions 1.1 dated 2014-04-01 and 1.1.2 dated 2014-07-28

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Package drfit updated to version 0.6.3 with previous version 0.6.1 dated 2014-03-20

Title: Dose-response data evaluation
Description: drfit provides basic and easy-to-use functions for fitting dose-response curves to dose-response data, calculating some (eco)toxicological parameters and plotting the results. Functions that are fitted are the cumulative density function of the lognormal distribution (probit fit), of the logistic distribution (logit fit), of the weibull distribution (weibull fit) and a linear-logistic model ("linlogit" fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving dose-response data retrieved from a database accessed via RODBC are included. As an alternative to the original fitting methods, the algorithms from the drc package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke

Diff between drfit versions 0.6.1 dated 2014-03-20 and 0.6.3 dated 2014-07-28

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Package Gmisc updated to version 0.6.7 with previous version 0.6.4 dated 2014-06-16

Title: Collection of functions for plotting relations, generating tables, and more.
Description: This is a collection of functions for tables, plots, and more. For tables you'll find the convenient htmlTable() that I use for advanced markdown table layout. A major focus has been to have it compatible with LibreOffice and MS Word - you can now copy-paste most tables directly into your document from the viewer. The main plots in the package are the transitionPlot() and forestplot2(), see the examples for demo. Apart from those it is worth mentioning the getDescriptionStatsBy() and its associated function that help you generate a descriptive table (i.e. the Table 1 in most journals), the pvalueFormatter() that formats p-values, and mergeLists() that provides a complex recursive list merge.
Author: Max Gordon
Maintainer: Max Gordon

Diff between Gmisc versions 0.6.4 dated 2014-06-16 and 0.6.7 dated 2014-07-28

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Package cvxclustr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-26

Title: Splitting methods for convex clustering
Description: Alternating Minimization Algorithm (AMA) and Alternating Direction Method of Multipliers (ADMM) splitting methods for convex clustering.
Author: Eric C. Chi, Kenneth Lange
Maintainer: Eric C. Chi

Diff between cvxclustr versions 1.1.0 dated 2014-07-26 and 1.1.1 dated 2014-07-28

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Sun, 27 Jul 2014

Package stsm updated to version 1.4 with previous version 1.3 dated 2014-05-30

Title: Structural Time Series Models
Description: This package provides algorithms to fit structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between stsm versions 1.3 dated 2014-05-30 and 1.4 dated 2014-07-27

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Package migest updated to version 1.6 with previous version 1.5 dated 2014-03-27

Title: Useful R code for the Estimation of Migration
Description: The migest package contains a collection of R functions that are useful to estimate migration when there is missing data. Included is the ffs routine to estimate migration flows from stock data, as well as various other functions to indirectly estimate flows where marginal totals are known. Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel

Diff between migest versions 1.5 dated 2014-03-27 and 1.6 dated 2014-07-27

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Package GrapheR updated to version 1.9-84 with previous version 1.9-83 dated 2014-06-28

Title: A multi-platform GUI for drawing customizable graphs in R
Description: GrapheR is a multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Herv
Maintainer: Maxime Herv

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Package DatABEL updated to version 0.9-4.1 with previous version 0.9-4 dated 2013-03-12

Title: file-based access to large matrices stored on HDD in binary format
Description: a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar
Maintainer: Yurii Aulchenko

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Package poppr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-24

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

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Package openxlsx updated to version 2.0.15 with previous version 2.0.1 dated 2014-05-29

Title: .xlsx reading, writing and editing.
Description: This package simplifies the creation of .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre], Luca Braglia [ctb]
Maintainer: Alexander Walker

Diff between openxlsx versions 2.0.1 dated 2014-05-29 and 2.0.15 dated 2014-07-27

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Package KFKSDS updated to version 1.5 with previous version 1.4 dated 2014-06-15

Title: Kalman Filter, Smoother and Disturbance Smoother
Description: Naive implementation of the Kalman filter, smoother and disturbance smoother for state space models. An interface to other implementations of the filter that are available in other packages is also provided.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between KFKSDS versions 1.4 dated 2014-06-15 and 1.5 dated 2014-07-27

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More information about KFKSDS at CRAN
Permanent link

Package HiClimR updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-14

Title: Hierarchical Climate Regionalization: An Improved Hierarchical Clustering in R for Climate Regionalization
Description: HiClimR package modifies and improves hierarchical clustering in R ('hclust' function in 'stats' library), for climate regionalization. It adds a new clustering method (called, regional linkage) to the set of available methods together with several features including regridding, coarsening spatial resolution, geographic masking, data thresholds, detrending and standardization preprocessing, faster correlation function, hybrid hierarchical clustering, and cluster validation. Badr et. al (2014) describes the regionalization algorithms and data processing tools included in the package and presents a demonstration application in which the package is used to regionalize Africa on the basis of interannual precipitation variability. It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr

Diff between HiClimR versions 1.1.1 dated 2014-07-14 and 1.1.2 dated 2014-07-27

 Changelog       |   23 +++++++++++++++++------
 DESCRIPTION     |    8 ++++----
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More information about HiClimR at CRAN
Permanent link

Sat, 26 Jul 2014

Package dendextend updated to version 0.16.1 with previous version 0.14.2 dated 2014-03-15

Title: Extending R's dendrogram functionality
Description: Functions and methods for extending dendrogram objects in R.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), Gregory [ctb], R core team [ctb] (Other than the Infastructure, some code came from their examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Yoav Benjamini [ths]
Maintainer: Tal Galili

Diff between dendextend versions 0.14.2 dated 2014-03-15 and 0.16.1 dated 2014-07-26

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More information about dendextend at CRAN
Permanent link

Package arules updated to version 1.1-4 with previous version 1.1-3 dated 2014-06-17

Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides interfaces to C implementations of the association mining algorithms Apriori and Eclat by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Bettina Gruen [aut, cph], Kurt Hornik [aut, cph], Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler

Diff between arules versions 1.1-3 dated 2014-06-17 and 1.1-4 dated 2014-07-26

 DESCRIPTION         |    8 ++++----
 MD5                 |   30 +++++++++++++++---------------
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 16 files changed, 62 insertions(+), 43 deletions(-)

More information about arules at CRAN
Permanent link

Package stsm.class updated to version 1.3 with previous version 1.2 dated 2014-05-29

Title: Class and Methods for Structural Time Series Models
Description: This package defines an S4 class for structural time series models and provides some basic methods to work with it.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between stsm.class versions 1.2 dated 2014-05-29 and 1.3 dated 2014-07-26

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Permanent link

Package influence.SEM updated to version 1.4 with previous version 1.3 dated 2014-05-26

Title: Case Influence in Structural Equation Models
Description: influence.SEM provides a set of tools for evaluating several measures of case influence for Structural Equation Models following the approach of Pek and MacCallum (2011).
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore

Diff between influence.SEM versions 1.3 dated 2014-05-26 and 1.4 dated 2014-07-26

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Permanent link

Package shiny updated to version 0.10.1 with previous version 0.10.0 dated 2014-06-14

Title: Web Application Framework for R
Description: Shiny makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Author: RStudio, Inc.
Maintainer: Winston Chang

Diff between shiny versions 0.10.0 dated 2014-06-14 and 0.10.1 dated 2014-07-26

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 shiny-0.10.1/shiny/R/app.R                                       |   55 +-
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 shiny-0.10.1/shiny/R/react.R                                     |    4 
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Package rpf updated to version 0.36 with previous version 0.35 dated 2014-06-30

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 rlist updated to version 0.2.4 with previous version 0.2.3 dated 2014-07-18

Title: A set of tools for working with list objects
Description: A set of tools for working with lists as dataset, including filtering, mapping, grouping, sorting, updating, and many other functions. It recommends functional programming in list operations.
Author: Kun Ren
Maintainer: Kun Ren

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Package pipeR updated to version 0.3-2 with previous version 0.3-1 dated 2014-06-28

Title: Specialized, high-performance pipeline operators
Description: Provides specialized, high-performance operators for chaining commands with three forward-piping operations: first-argument piping, free piping, and lambda piping, making command chaining clear, fast, readable and flexible.
Author: Kun Ren
Maintainer: Kun Ren

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Package OUwie updated to version 1.43 with previous version 1.42 dated 2014-04-01

Title: Analysis of evolutionary rates in an OU framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu , Brian O'Meara
Maintainer: Jeremy Beaulieu

Diff between OUwie versions 1.42 dated 2014-04-01 and 1.43 dated 2014-07-26

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Package lpSolve updated to version 5.6.10 with previous version 5.6.9 dated 2014-06-20

Title: Interface to Lp_solve v. 5.5 to solve linear/integer programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Samuel E. Buttrey

Diff between lpSolve versions 5.6.9 dated 2014-06-20 and 5.6.10 dated 2014-07-26

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Package infotheo updated to version 1.2.0 with previous version 1.1.1 dated 2012-12-10

Title: Information-Theoretic Measures
Description: This package implements various measures of information theory based on several entropy estimators.
Author: Patrick E. Meyer
Maintainer: Patrick E. Meyer

Diff between infotheo versions 1.1.1 dated 2012-12-10 and 1.2.0 dated 2014-07-26

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Package DiscML updated to version 1.0.1 with previous version 1.0 dated 2014-05-02

Title: DiscML: An R package for estimating evolutionary rates of discrete characters using maximum likelihood
Description: DiscML performs rate estimation using maximum likelihood with the options to correct for unobservable data, to implement a Gamma-distribution for rate variation, and to estimate the prior root probabilities from the empirical data.
Author: Tane Kim, Weilong Hao
Maintainer: Weilong Hao

Diff between DiscML versions 1.0 dated 2014-05-02 and 1.0.1 dated 2014-07-26

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Package cvxclustr updated to version 1.1.0 with previous version 1.0.0 dated 2013-04-30

Title: Splitting methods for convex clustering
Description: Alternating Minimization Algorithm (AMA) and Alternating Direction Method of Multipliers (ADMM) splitting methods for convex clustering.
Author: Eric C. Chi, Kenneth Lange
Maintainer: Eric C. Chi

Diff between cvxclustr versions 1.0.0 dated 2013-04-30 and 1.1.0 dated 2014-07-26

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Fri, 25 Jul 2014

Package MRCV updated to version 0.3-2 with previous version 0.3-1 dated 2014-04-10

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 dcGOR updated to version 1.0.2 with previous version 1.0.0 dated 2014-07-02

Title: an R package tailored to the needs of analysing ontologies and annotations on protein domains
Description: The 'dcGOR' package is intended to provide the wider bioinformatics community with the use of the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a variety of ontologies on functions, phenotypes, diseases and more. With the package, users are expected to easily analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; enrichment analysis and visual outputs; semantic similarity between annotated domains from ontology term semantic similarity; random walk with restart upon domain-domain (semantic) networks; and high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang

Diff between dcGOR versions 1.0.0 dated 2014-07-02 and 1.0.2 dated 2014-07-25

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Package AppliedPredictiveModeling updated to version 1.1-6 with previous version 1.1-5 dated 2014-02-03

Title: Functions and Data Sets for 'Applied Predictive Modeling'
Description: A few functions and several data set for the Springer book 'Applied Predictive Modeling'
Author: Max Kuhn, Kjell Johnson
Maintainer: Max Kuhn

Diff between AppliedPredictiveModeling versions 1.1-5 dated 2014-02-03 and 1.1-6 dated 2014-07-25

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Package Rankcluster updated to version 0.92.9 with previous version 0.92 dated 2014-02-12

Title: Model-based clustering for multivariate partial ranking data
Description: This package proposes a model-based clustering algorithm for ranking data. Multivariate rankings as well as partial rankings are taken into account. This algorithm is based on an extension of the Insertion Sorting Rank (ISR) model for ranking data, which is a meaningful and effective model parametrized by a position parameter (the modal ranking, quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity of the rank population is modelled by a mixture of ISR, whereas conditional independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez

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Package quantregGrowth updated to version 0.3-0 with previous version 0.1-3 dated 2014-07-02

Title: Growth charts via regression quantiles
Description: Fits non-crossing regression quantiles as a function of linear covariates and a smooth terms via B-splines with quadratic penalties.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo

Diff between quantregGrowth versions 0.1-3 dated 2014-07-02 and 0.3-0 dated 2014-07-25

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Package MSBVAR updated to version 0.9-1 with previous version 0.9-0 dated 2014-06-02

Title: Markov-Switching, Bayesian, Vector Autoregression Models
Description: Provides methods for estimating frequentist and Bayesian Vector Autoregression (VAR) models and Markov-switching Bayesian VAR (MSBVAR). Functions for reduced form and structural VAR models are also available. Includes methods for the generating posterior inferences for these models, forecasts, impulse responses (using likelihood-based error bands), and forecast error decompositions. Also includes utility functions for plotting forecasts and impulse responses, and generating draws from Wishart and singular multivariate normal densities. Current version includes functionality to build and evaluate models with Markov switching.
Author: Patrick Brandt [aut, cre], W. Ryan Davis [cre]
Maintainer: Patrick Brandt

Diff between MSBVAR versions 0.9-0 dated 2014-06-02 and 0.9-1 dated 2014-07-25

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Package rngWELL updated to version 0.10-3 with previous version 0.10-2 dated 2013-06-11

Title: toolbox for WELL random number generators.
Description: It is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software. But this package is not intended to be used directly, you are strongly __encouraged__ to use the 'randtoolbox' package, which depends on this package.
Author: all C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R port by Christophe Dutang and Petr Savicky .
Maintainer: Christophe Dutang

Diff between rngWELL versions 0.10-2 dated 2013-06-11 and 0.10-3 dated 2014-07-25

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Package ClustVarLV updated to version 1.3 with previous version 1.2 dated 2014-04-04

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

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Package TreeSimGM updated to version 1.2 with previous version 1.1 dated 2013-02-21

Title: Simulating Phylogenetic Trees under a General Model
Description: The package is a flexible simulation tool for phylogenetic trees under a general model. It is possible to assume any probability distribution for the waiting time until speciation and extinction independently. Thus, TreeSimGM allows to simulate stochastic phylogenetic trees using any probability distribution and parameters for speciation and extinction. The speciation modes have all binary splits and are: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. Those two modes were inspired by allopatric and peripatric speciation respectively.Both models (symmetric and asymmetric) were created and implemented so that different processes (distributions) for speciation and extinction could be independently and explicitly specified. It is also possible to have an implicit extinction process by setting the extinction rate to zero.
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen

Diff between TreeSimGM versions 1.1 dated 2013-02-21 and 1.2 dated 2014-07-25

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Package RandomFields updated to version 3.0.30 with previous version 3.0.10 dated 2014-01-21

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [aut], Sebastian Gross [aut], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather

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 RandomFields-3.0.30/RandomFields/man/RPschlather.Rd                       |   39 
 RandomFields-3.0.30/RandomFields/man/RPsmith.Rd                           |   50 
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 RandomFields-3.0.30/RandomFields/man/RRdistr.Rd                           |    9 
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 RandomFields-3.0.30/RandomFields/man/RRrectangular.Rd                     |    7 
 RandomFields-3.0.30/RandomFields/man/RRspherical.Rd                       |   27 
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 RandomFields-3.0.30/RandomFields/man/Sequential.Rd                        |   13 
 RandomFields-3.0.30/RandomFields/man/Specific.Rd                          |   33 
 RandomFields-3.0.30/RandomFields/man/Spectral.Rd                          |   19 
 RandomFields-3.0.30/RandomFields/man/Tbm.Rd                               |   25 
 RandomFields-3.0.30/RandomFields/man/conventional2RFspDataFrame.Rd        |   15 
 RandomFields-3.0.30/RandomFields/man/fitgauss.Rd                          |   35 
 RandomFields-3.0.30/RandomFields/man/internal.Rd                          |   35 
 RandomFields-3.0.30/RandomFields/man/obsolete.Rd                          |   12 
 RandomFields-3.0.30/RandomFields/man/papers.GSPSJ06.Rd                    |   18 
 RandomFields-3.0.30/RandomFields/man/papers.Rd                            |   17 
 RandomFields-3.0.30/RandomFields/man/papers.S02.Rd                        |   52 
 RandomFields-3.0.30/RandomFields/man/papers.S10.Rd                        |  106 
 RandomFields-3.0.30/RandomFields/man/papers.SBS14.Rd                      |   99 
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 RandomFields-3.0.30/RandomFields/man/plot-method.Rd                       |   75 
 RandomFields-3.0.30/RandomFields/man/soil.Rd                              |   41 
 RandomFields-3.0.30/RandomFields/man/weather.Rd                           |  175 
 RandomFields-3.0.30/RandomFields/src/Brown.cc                             | 1477 +++--
 RandomFields-3.0.30/RandomFields/src/Covariance.h                         |   42 
 RandomFields-3.0.30/RandomFields/src/D.H.cc                               |    4 
 RandomFields-3.0.30/RandomFields/src/Families.cc                          |  648 +-
 RandomFields-3.0.30/RandomFields/src/Gneiting.cc                          |   62 
 RandomFields-3.0.30/RandomFields/src/Huetchen.cc                          |  726 +-
 RandomFields-3.0.30/RandomFields/src/InternalCov.cc                       |  553 +
 RandomFields-3.0.30/RandomFields/src/KeyInfo.cc                           |  245 
 RandomFields-3.0.30/RandomFields/src/MLE.cc                               |   94 
 RandomFields-3.0.30/RandomFields/src/PoissonPolygon.cc                    |  133 
 RandomFields-3.0.30/RandomFields/src/PoissonPolygon.h                     |    1 
 RandomFields-3.0.30/RandomFields/src/Primitive.cc                         |  907 ++-
 RandomFields-3.0.30/RandomFields/src/RF.h                                 |  545 +
 RandomFields-3.0.30/RandomFields/src/RandomFields.h                       |   13 
 RandomFields-3.0.30/RandomFields/src/Specific.cc                          |   60 
 RandomFields-3.0.30/RandomFields/src/Xempvario.cc                         |   14 
 RandomFields-3.0.30/RandomFields/src/auxiliary.cc                         |  103 
 RandomFields-3.0.30/RandomFields/src/basic.h                              |    8 
 RandomFields-3.0.30/RandomFields/src/circulant.cc                         |  127 
 RandomFields-3.0.30/RandomFields/src/direct.cc                            |  111 
 RandomFields-3.0.30/RandomFields/src/empvario.cc                          |  581 +-
 RandomFields-3.0.30/RandomFields/src/error.h                              |    5 
 RandomFields-3.0.30/RandomFields/src/extremes.cc                          |  910 ++-
 RandomFields-3.0.30/RandomFields/src/families.h                           |   21 
 RandomFields-3.0.30/RandomFields/src/fftVario.cc                          |  466 -
 RandomFields-3.0.30/RandomFields/src/gauss.cc                             |  470 +
 RandomFields-3.0.30/RandomFields/src/getNset.cc                           |  464 +
 RandomFields-3.0.30/RandomFields/src/hyperplan.cc                         |   21 
 RandomFields-3.0.30/RandomFields/src/initNerror.cc                        |  491 +
 RandomFields-3.0.30/RandomFields/src/kriging.cc                           |    4 
 RandomFields-3.0.30/RandomFields/src/nugget.cc                            |   43 
 RandomFields-3.0.30/RandomFields/src/operator.cc                          |  699 +-
 RandomFields-3.0.30/RandomFields/src/plusmalS.cc                          | 1684 ++++--
 RandomFields-3.0.30/RandomFields/src/primitive.h                          |   17 
 RandomFields-3.0.30/RandomFields/src/randomshape.h                        |   30 
 RandomFields-3.0.30/RandomFields/src/sequential.cc                        |   21 
 RandomFields-3.0.30/RandomFields/src/simu.cc                              |  535 +
 RandomFields-3.0.30/RandomFields/src/spectral.cc                          |   44 
 RandomFields-3.0.30/RandomFields/src/startGetNset.cc                      |  281 -
 RandomFields-3.0.30/RandomFields/src/tbm.cc                               |  264 
 RandomFields-3.0.30/RandomFields/src/trend.cc                             |  119 
 RandomFields-3.0.30/RandomFields/src/userinterfaces.cc                    |  496 +
 RandomFields-3.0.30/RandomFields/src/variogramAndCo.cc                    |   85 
 253 files changed, 17805 insertions(+), 11008 deletions(-)

More information about RandomFields at CRAN
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Package mime updated to version 0.1.2 with previous version 0.1.1 dated 2014-05-12

Title: Map filenames to MIME types
Description: This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between mime versions 0.1.1 dated 2014-05-12 and 0.1.2 dated 2014-07-25

 DESCRIPTION |    8 ++++----
 MD5         |    9 +++++----
 NEWS        |    7 +++++++
 R/mime.R    |    5 +++--
 R/mimemap.R |    2 +-
 tests       |only
 6 files changed, 20 insertions(+), 11 deletions(-)

More information about mime at CRAN
Permanent link

Package markdown updated to version 0.7.2 with previous version 0.7 dated 2014-05-12

Title: Markdown rendering for R
Description: Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. This package provides R bindings to the Sundown markdown rendering library.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie

Diff between markdown versions 0.7 dated 2014-05-12 and 0.7.2 dated 2014-07-25

 DESCRIPTION                     |    8 +-
 MD5                             |   20 ++---
 NEWS                            |   10 ++
 R/renderMarkdown.R              |   26 +++----
 build/vignette.rds              |binary
 inst/doc/markdown-examples.R    |  120 ++++++++++++++++++++++++++++++++++-
 inst/doc/markdown-examples.html |    3 
 inst/doc/markdown-output.R      |  137 +++++++++++++++++++++++++++++++++++++++-
 inst/doc/markdown-output.html   |    3 
 man/markdownToHTML.Rd           |    4 -
 tests/tests.Rout.save           |    2 
 11 files changed, 293 insertions(+), 40 deletions(-)

More information about markdown at CRAN
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Package inTrees updated to version 1.1 with previous version 1.0 dated 2014-07-14

Title: Interpret Tree Ensembles
Description: For tree ensembles such as random forests, regularized random forests and gradient boosted trees, this package provides functions for: extracting, measuring and pruning rules; selecting a compact rule set; summarizing rules into a learner; calculating frequent variable interactions; formatting rules in latex code.
Author: Houtao Deng
Maintainer: Houtao Deng

Diff between inTrees versions 1.0 dated 2014-07-14 and 1.1 dated 2014-07-25

 DESCRIPTION             |   11 --
 MD5                     |   68 ++++++-------
 NAMESPACE               |    3 
 NEWS                    |    8 +
 R/GBM2List.R            |   26 ++--
 R/Num2Level.R           |   17 +--
 R/RF2List.R             |   17 +--
 R/applyLearner.R        |   30 ++---
 R/buildLearner.R        |  118 ++++++++++------------
 R/computeRuleInfor.R    |    9 -
 R/dataSimulate.R        |   80 ++++++++-------
 R/dicretizeVector.R     |   33 ++----
 R/extractRules.R        |   54 ++++------
 R/formatGBM.R           |   44 +++-----
 R/getFreqPattern.R      |   80 ++++++++-------
 R/getRuleMetric.R       |   32 +++---
 R/getTypeX.R            |   18 +--
 R/inTrees-internal.R    |  251 +++++++++++++++++++++++-------------------------
 R/lookupRule.R          |   21 +---
 R/measureRule.R         |   64 ++++++------
 R/presentRules.R        |   46 +++-----
 R/pruneRule.R           |   14 +-
 R/pruneSingleRule.R     |   50 +++++----
 R/rule2Table.R          |   16 +--
 R/ruleList2Exec.R       |   14 +-
 R/selectRuleRRF.R       |   30 ++---
 R/singleRuleList2Exec.R |   36 +++---
 R/sortRule.R            |   11 +-
 R/treeVisit.R           |  130 ++++++++++++------------
 R/voteAllRules.R        |only
 man/buildLearner.Rd     |   19 +--
 man/dataSimulate.Rd     |   45 +++-----
 man/measureRule.Rd      |    5 
 man/pruneRule.Rd        |   28 ++---
 man/pruneSingleRule.Rd  |   20 ++-
 man/voteAllRules.Rd     |only
 36 files changed, 714 insertions(+), 734 deletions(-)

More information about inTrees at CRAN
Permanent link

Package animation updated to version 2.3 with previous version 2.2 dated 2013-04-14

Title: A gallery of animations in statistics and utilities to create animations
Description: This package contains a variety of functions for animations in statistics, covering areas such as probability theory, mathematical statistics, multivariate statistics, nonparametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions might be helpful in teaching statistics and data analysis. Also provided in this package are several approaches to save animations to various formats, e.g. Flash, GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(), saveLatex(), and saveVideo() respectively). PDF animations can be inserted into Sweave/knitr easily.
Author: Lijia Yu [ctb], Weicheng Zhu [ctb], Yihui Xie [cre, aut]
Maintainer: Yihui Xie

Diff between animation versions 2.2 dated 2013-04-14 and 2.3 dated 2014-07-25

 animation-2.2/animation/R/ani.stop.R                                 |only
 animation-2.2/animation/R/animation-defunct.R                        |only
 animation-2.2/animation/inst/misc/scianimator/css/shCore.css         |only
 animation-2.2/animation/inst/misc/scianimator/css/shThemeDefault.css |only
 animation-2.2/animation/inst/misc/scianimator/js/shAutoloader.js     |only
 animation-2.2/animation/inst/misc/scianimator/js/shBrushR.js         |only
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 animation-2.2/animation/man/ani.stop.Rd                              |only
 animation-2.2/animation/man/animation-defunct.Rd                     |only
 animation-2.2/animation/readme.md                                    |only
 animation-2.2/animation/tests/flash-animation.r                      |only
 animation-2.2/animation/tests/gif-animation.r                        |only
 animation-2.2/animation/tests/html-animation.r                       |only
 animation-2.3/animation/DESCRIPTION                                  |   54 -
 animation-2.3/animation/MD5                                          |  282 +++---
 animation-2.3/animation/NAMESPACE                                    |   52 +
 animation-2.3/animation/NEWS                                         |   35 
 animation-2.3/animation/R/BM.circle.R                                |   48 -
 animation-2.3/animation/R/MC.hitormiss.R                             |   91 +-
 animation-2.3/animation/R/MC.samplemean.R                            |  100 +-
 animation-2.3/animation/R/Rosling.bubbles.R                          |   32 
 animation-2.3/animation/R/ani.options.R                              |  409 ++++------
 animation-2.3/animation/R/ani.pause.R                                |   27 
 animation-2.3/animation/R/ani.record.R                               |  133 +--
 animation-2.3/animation/R/ani.start.R                                |   59 -
 animation-2.3/animation/R/animation-package.R                        |   39 
 animation-2.3/animation/R/bisection.method.R                         |  151 +--
 animation-2.3/animation/R/boot.iid.R                                 |  126 +--
 animation-2.3/animation/R/boot.lowess.R                              |   55 -
 animation-2.3/animation/R/brownian.motion.R                          |   50 -
 animation-2.3/animation/R/buffon.needle.R                            |   11 
 animation-2.3/animation/R/clt.ani.R                                  |  128 +--
 animation-2.3/animation/R/conf.int.R                                 |   40 
 animation-2.3/animation/R/cv.ani.R                                   |   69 -
 animation-2.3/animation/R/cv.nfeaturesLDA.R                          |  190 ++--
 animation-2.3/animation/R/ecol.death.sim.R                           |   92 +-
 animation-2.3/animation/R/flip.coin.R                                |  151 +--
 animation-2.3/animation/R/g.brownian.motion.R                        |  123 +--
 animation-2.3/animation/R/grad.desc.R                                |   49 -
 animation-2.3/animation/R/im.convert.R                               |  302 +++----
 animation-2.3/animation/R/kfcv.R                                     |   33 
 animation-2.3/animation/R/kmeans.ani.R                               |  155 +--
 animation-2.3/animation/R/knn.ani.R                                  |  274 +++---
 animation-2.3/animation/R/least.squares.R                            |  180 ++--
 animation-2.3/animation/R/lln.ani.R                                  |   93 +-
 animation-2.3/animation/R/moving.block.R                             |   95 +-
 animation-2.3/animation/R/mwar.ani.R                                 |  139 +--
 animation-2.3/animation/R/newton.method.R                            |  152 +--
 animation-2.3/animation/R/pdftk.R                                    |   66 -
 animation-2.3/animation/R/price.ani.R                                |   89 +-
 animation-2.3/animation/R/qpdf.R                                     |   55 -
 animation-2.3/animation/R/quincunx.R                                 |  127 +--
 animation-2.3/animation/R/quincunx2.R                                |only
 animation-2.3/animation/R/sample.cluster.R                           |   27 
 animation-2.3/animation/R/sample.ratio.R                             |   35 
 animation-2.3/animation/R/sample.simple.R                            |   25 
 animation-2.3/animation/R/sample.strat.R                             |   26 
 animation-2.3/animation/R/sample.system.R                            |   22 
 animation-2.3/animation/R/saveGIF.R                                  |   56 -
 animation-2.3/animation/R/saveHTML.R                                 |  144 ++-
 animation-2.3/animation/R/saveLatex.R                                |  159 +--
 animation-2.3/animation/R/saveSWF.R                                  |  102 +-
 animation-2.3/animation/R/saveVideo.R                                |   65 -
 animation-2.3/animation/R/sim.qqnorm.R                               |   10 
 animation-2.3/animation/R/utils.R                                    |only
 animation-2.3/animation/R/vi.grid.illusion.R                         |   21 
 animation-2.3/animation/R/vi.lilac.chaser.R                          |   14 
 animation-2.3/animation/R/zzz.R                                      |    8 
 animation-2.3/animation/README.md                                    |only
 animation-2.3/animation/demo/CLEvsLAL.R                              |  117 +-
 animation-2.3/animation/demo/IBM.R                                   |   54 -
 animation-2.3/animation/demo/Mandelbrot.R                            |   42 -
 animation-2.3/animation/demo/Sierpinski.R                            |   48 -
 animation-2.3/animation/demo/Sweave_animation.R                      |   14 
 animation-2.3/animation/demo/Xmas.R                                  |   30 
 animation-2.3/animation/demo/Xmas2.R                                 |   40 
 animation-2.3/animation/demo/Xmas_card.R                             |   38 
 animation-2.3/animation/demo/busybees.R                              |   64 -
 animation-2.3/animation/demo/elephant.R                              |   62 -
 animation-2.3/animation/demo/fire.R                                  |   66 -
 animation-2.3/animation/demo/fireworks.R                             |  157 ++-
 animation-2.3/animation/demo/flowers.R                               |   16 
 animation-2.3/animation/demo/game_of_life.R                          |  125 +--
 animation-2.3/animation/demo/ggobi_animation.R                       |   28 
 animation-2.3/animation/demo/hanoi.R                                 |   64 -
 animation-2.3/animation/demo/jumpingHorse.R                          |   76 -
 animation-2.3/animation/demo/pollen.R                                |   33 
 animation-2.3/animation/demo/recur.leaf.R                            |   40 
 animation-2.3/animation/demo/recur.snow.R                            |   68 -
 animation-2.3/animation/demo/recur.tree.R                            |  119 +-
 animation-2.3/animation/demo/rgl_animation.R                         |   55 -
 animation-2.3/animation/demo/use_Cairo.R                             |   28 
 animation-2.3/animation/demo/wordrotation.R                          |    8 
 animation-2.3/animation/inst/misc/scianimator/index.html             |   15 
 animation-2.3/animation/man/BM.circle.Rd                             |   38 
 animation-2.3/animation/man/CLELAL09.Rd                              |   35 
 animation-2.3/animation/man/HuSpeech.Rd                              |   13 
 animation-2.3/animation/man/MC.hitormiss.Rd                          |   64 -
 animation-2.3/animation/man/MC.samplemean.Rd                         |   84 --
 animation-2.3/animation/man/ObamaSpeech.Rd                           |    8 
 animation-2.3/animation/man/Rosling.bubbles.Rd                       |   90 +-
 animation-2.3/animation/man/ani.options.Rd                           |  333 +++-----
 animation-2.3/animation/man/ani.pause.Rd                             |   19 
 animation-2.3/animation/man/ani.record.Rd                            |  109 +-
 animation-2.3/animation/man/ani.start.Rd                             |   48 -
 animation-2.3/animation/man/animation-package.Rd                     |  151 +--
 animation-2.3/animation/man/bisection.method.Rd                      |  100 +-
 animation-2.3/animation/man/boot.iid.Rd                              |   97 +-
 animation-2.3/animation/man/boot.lowess.Rd                           |   31 
 animation-2.3/animation/man/brownian.motion.Rd                       |   58 -
 animation-2.3/animation/man/buffon.needle.Rd                         |  133 +--
 animation-2.3/animation/man/clt.ani.Rd                               |  101 +-
 animation-2.3/animation/man/conf.int.Rd                              |   72 -
 animation-2.3/animation/man/convert.Rd                               |  160 +--
 animation-2.3/animation/man/cv.ani.Rd                                |   73 -
 animation-2.3/animation/man/cv.nfeaturesLDA.Rd                       |  122 +-
 animation-2.3/animation/man/ecol.death.sim.Rd                        |   54 -
 animation-2.3/animation/man/flip.coin.Rd                             |  105 +-
 animation-2.3/animation/man/g.brownian.motion.Rd                     |   65 -
 animation-2.3/animation/man/grad.desc.Rd                             |  150 +--
 animation-2.3/animation/man/iatemp.Rd                                |    5 
 animation-2.3/animation/man/kfcv.Rd                                  |   22 
 animation-2.3/animation/man/kmeans.ani.Rd                            |  106 +-
 animation-2.3/animation/man/knn.ani.Rd                               |  132 +--
 animation-2.3/animation/man/least.squares.Rd                         |   99 +-
 animation-2.3/animation/man/lln.ani.Rd                               |   66 -
 animation-2.3/animation/man/moving.block.Rd                          |  119 +-
 animation-2.3/animation/man/mwar.ani.Rd                              |   82 --
 animation-2.3/animation/man/newton.method.Rd                         |   96 +-
 animation-2.3/animation/man/pageview.Rd                              |    6 
 animation-2.3/animation/man/pdftk.Rd                                 |   41 -
 animation-2.3/animation/man/pollen.Rd                                |    8 
 animation-2.3/animation/man/price.ani.Rd                             |   30 
 animation-2.3/animation/man/qpdf.Rd                                  |   34 
 animation-2.3/animation/man/quincunx.Rd                              |  105 +-
 animation-2.3/animation/man/sample.cluster.Rd                        |   38 
 animation-2.3/animation/man/sample.ratio.Rd                          |   60 -
 animation-2.3/animation/man/sample.simple.Rd                         |   38 
 animation-2.3/animation/man/sample.strat.Rd                          |   43 -
 animation-2.3/animation/man/sample.system.Rd                         |   36 
 animation-2.3/animation/man/saveGIF.Rd                               |  158 +--
 animation-2.3/animation/man/saveHTML.Rd                              |  225 ++---
 animation-2.3/animation/man/saveLatex.Rd                             |  242 ++---
 animation-2.3/animation/man/saveSWF.Rd                               |  103 +-
 animation-2.3/animation/man/saveVideo.Rd                             |   84 --
 animation-2.3/animation/man/sim.qqnorm.Rd                            |   46 -
 animation-2.3/animation/man/vanke1127.Rd                             |   10 
 animation-2.3/animation/man/vi.grid.illusion.Rd                      |   39 
 animation-2.3/animation/man/vi.lilac.chaser.Rd                       |   34 
 animation-2.3/animation/tests/run-all.R                              |only
 animation-2.3/animation/tests/testit                                 |only
 151 files changed, 5109 insertions(+), 5788 deletions(-)

More information about animation at CRAN
Permanent link

Thu, 24 Jul 2014

Package pocrm updated to version 0.8 with previous version 0.7 dated 2014-03-11

Title: Dose-finding in drug combination Phase I trials using the partial order continual reassessment method (PO-CRM).
Description: This package provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) for use in Phase I trials of combinations of agents. It also provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Varhegyi, Nikole (nev4g)"

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Package bold updated to version 0.1.2 with previous version 0.1.0 dated 2014-05-28

Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by Bold Systems for genetic barcode data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain

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Package multcomp updated to version 1.3-5 with previous version 1.3-4 dated 2014-07-09

Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre], Frank Bretz [aut], Peter Westfall [aut], Richard M. Heiberger [ctb], Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn

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Package simPH updated to version 1.2.2 with previous version 1.2.1 dated 2014-05-16

Title: Tools for simulating and plotting quantities of interest estimated from Cox Proportional Hazards models
Description: The package simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

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Package RItools updated to version 0.1-12 with previous version 0.1-11 dated 2011-03-05

Title: Randomization inference tools
Description: Tools for randomization inference.
Author: Jake Bowers , Mark Fredrickson , and Ben Hansen
Maintainer: Jake Bowers

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Package dlnm updated to version 2.1.2 with previous version 2.1.0 dated 2014-05-21

Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify and run distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini

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Package tables updated to version 0.7.79 with previous version 0.7.64 dated 2013-11-12

Title: Formula-driven table generation
Description: Computes and displays complex tables of summary statistics
Author: Duncan Murdoch
Maintainer: Duncan Murdoch

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Package rebmix updated to version 2.6.1 with previous version 2.6.0 dated 2014-06-25

Title: The Rebmix Package
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

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Package randtoolbox updated to version 1.15 with previous version 1.14 dated 2013-06-11

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 Power2Stage updated to version 0.1-4 with previous version 0.1-3 dated 2014-07-02

Title: Power and Sample size distribution of 2-stage BE studies via simulations
Description: Contains functions to calculate power and sample size distribution of 2-stage BE studies with a 2x2 crossover design according to Potvin et.al. / Montague et. al. modified to include a futility Nmax and modified to do the sample size estimation step with PE and mse of stage 1 as well as the power calculation steps according to Karalis & Macheras. The third function calculates power and sample size distribution of 2-stage BE studies with a futility criterion for the point estimator of T/R from stage 1. The fourth function calculates power of non-adaptive group sequential (2-stage) BE studies. The fifth function calculates power and sample size distribution of 2-stage BE studies in 2 parallel groups.
Author: Detlew Labes [aut, cre], Helmut Schuetz [ctb]
Maintainer: Detlew Labes

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Package mkin updated to version 0.9-32 with previous version 0.9-31 dated 2014-07-14

Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data
Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers and a choice of the optimisation methods made available by the FME package (default is a Levenberg-Marquardt variant). Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb], René Lehmann [ctb], Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke

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Package ManyTests updated to version 1.1 with previous version 1.0 dated 2014-03-31

Title: Multiple testing procedures of Cox (2011) and Wang and Cox (2007).
Description: Performs the multiple testing procedures of Cox (2011) and Wang and Cox (2007).
Author: Christiana Kartsonaki
Maintainer: Christiana Kartsonaki

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Package lmerTest updated to version 2.0-11 with previous version 2.0-6 dated 2014-02-24

Title: Tests for random and fixed effects for linear mixed effect models (lmer objects of lme4 package).
Description: The package provides different kinds of tests on lmer objects (of lme4 package). The tests comprise type 3 and type 1 F tests for fixed effects, LRT tests for random effects, calculation of population means for fixed factors with confidence intervals and corresponding plots. Package also provides backward elimination of non-significant effects
Author: Alexandra Kuznetsova [aut, cre], Per Bruun Brockhoff [aut, ths], Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova

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Package imguR updated to version 1.0.0 with previous version 0.1.5 dated 2012-10-15

Title: Imgur API Client Package for R
Description: A package to share plots using the image hosting service Imgur.com
Author: Thomas J. Leeper [aut, cre], Aaron Statham [ctb], Yihui Xie [ctb]
Maintainer: Thomas J. Leeper

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Package spuRs updated to version 2.0.0 with previous version 1.0.5 dated 2012-08-03

Title: Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R".
Description: This package provides functions and datasets from the book "Introduction to Scientific Programming and Simulation Using R".
Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Maintainer: Andrew Robinson

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Package sensitivitymw updated to version 1.1 with previous version 1.0 dated 2014-05-13

Title: Sensitivity analysis using weighted M-statistics
Description: Sensitivity analysis analysis in matched observational studies with multiple controls using weighted M-statistics to increase design sensitivity.
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum

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Package poppr updated to version 1.1.0 with previous version 1.0.6 dated 2014-03-05

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

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Permanent link

Wed, 23 Jul 2014

Package mada updated to version 0.5.6 with previous version 0.5.5 dated 2014-01-01

Title: Meta-Analysis of Diagnostic Accuracy (mada)
Description: This package provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler

Diff between mada versions 0.5.5 dated 2014-01-01 and 0.5.6 dated 2014-07-23

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More information about mada at CRAN
Permanent link

Package CAvariants updated to version 2.1 with previous version 2.0 dated 2014-06-26

Title: Correspondence Analysis Variants
Description: Six variants of two-way correspondence analysis can be performed, simple ca singly ordered ca doubly ordered ca non symmetrical ca singly ordered non symmetrical ca doubly ordered non symmetrical ca
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo

Diff between CAvariants versions 2.0 dated 2014-06-26 and 2.1 dated 2014-07-23

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More information about CAvariants at CRAN
Permanent link

Package pitchRx updated to version 1.5 with previous version 1.4 dated 2014-05-27

Title: Tools for Harnessing MLBAM Gameday data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced Media's Gameday data (as well as store it in a remote database). The Gameday website hosts a wealth of data in XML format, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball's flight path from a pitcher's hand to home plate. With pitchRx, one can easily create animations and interactive 3D scatterplots of the baseball's flight path. PITCHf/x data is also commonly used to generate a static plot of baseball locations at the moment they cross home plate. These plots, sometimes called strike-zone plots, can also refer to a plot of event probabilities over the same region. pitchRx provides an easy and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert
Maintainer: Carson Sievert

Diff between pitchRx versions 1.4 dated 2014-05-27 and 1.5 dated 2014-07-23

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More information about pitchRx at CRAN
Permanent link

Package ecoengine updated to version 1.4 with previous version 1.3 dated 2014-04-14

Title: Programmatic interface to the API serving UC Berkeley's Natural History Data
Description: The ecoengine (http://ecoengine.berkeley.edu/) provides access to more than 2 million georeferenced specimen records from the Berkeley Natural History Museums. http://bnhm.berkeley.edu/
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram

Diff between ecoengine versions 1.3 dated 2014-04-14 and 1.4 dated 2014-07-23

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More information about ecoengine at CRAN
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Package survsim updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-21

Title: Simulation of simple and complex survival data
Description: Simulation of simple and complex survival data
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler

Diff between survsim versions 1.1.1 dated 2014-07-21 and 1.1.2 dated 2014-07-23

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Package rnaseqWrapper updated to version 1.0-1 with previous version 1.0 dated 2014-07-17

Title: Wrapper for several R packages and scripts to automate RNA-seq analysis
Description: This package is designed to streamline several of the common steps for RNA-seq analysis, including differential expression and variant discovery. For the development build, or to contribute changes to this package, please see our repository at https://bitbucket.org/petersmp/rnaseqwrapper/
Author: Mark Peterson
Maintainer: Mark Peterson

Diff between rnaseqWrapper versions 1.0 dated 2014-07-17 and 1.0-1 dated 2014-07-23

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Package miscFuncs updated to version 1.2-6 with previous version 1.2-4 dated 2013-12-14

Title: Miscellaneous Useful Functions
Description: LaTeX tables, Kalman filter, web scraping, development tools, relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor

Diff between miscFuncs versions 1.2-4 dated 2013-12-14 and 1.2-6 dated 2014-07-23

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More information about miscFuncs at CRAN
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Package hglm updated to version 2.0-8 with previous version 2.0-4 dated 2014-01-21

Title: Hierarchical Generalized Linear Models
Description: The hglm package is used to fit hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen

Diff between hglm versions 2.0-4 dated 2014-01-21 and 2.0-8 dated 2014-07-23

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Package nontarget updated to version 1.3 with previous version 1.2 dated 2012-10-18

Title: Detecting, combining and filtering isotope, adduct and homologue series relations in high-resolution mass spectrometry (HRMS) data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos

Diff between nontarget versions 1.2 dated 2012-10-18 and 1.3 dated 2014-07-23

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Permanent link

Package frailtypack updated to version 2.6.1 with previous version 2.6 dated 2014-03-24

Title: General Frailty models: shared, joint and nested frailty models with prediction
Description: Frailtypack fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. Prediction values are available. Left truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata (max=2) are allowed. In each model, the random effects have a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

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More information about frailtypack at CRAN
Permanent link

Package Epi updated to version 1.1.67 with previous version 1.1.65 dated 2014-06-24

Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation and manipulation of multistate data - the Lexis suite of functions. Includes interfaces to mstate, etm and cmprsk packages. Also contains functions for Age-Period-Cohort modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well some epidemiological datasets.
Author: Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Maintainer: Bendix Carstensen

Diff between Epi versions 1.1.65 dated 2014-06-24 and 1.1.67 dated 2014-07-23

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Package pdfetch updated to version 0.1.4 with previous version 0.1.3 dated 2014-04-19

Title: Fetch economic and financial time series data from public sources
Description: A package for downloading economic and financial time series from public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart

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Package IBDhaploRtools updated to version 1.7 with previous version 1.5 dated 2013-03-21

Title: Functions for the Analysis of IBD Haplo output
Description: IBDhaploRtools consists of several functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson

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Package hts updated to version 4.4 with previous version 4.3 dated 2014-06-10

Title: Hierarchical and grouped time series
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Roman A Ahmed and Han Lin Shang to earlier versions of the package
Maintainer: Rob J Hyndman

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Tue, 22 Jul 2014

Package sweSCB updated to version 0.3.5 with previous version 0.3.4 dated 2014-04-15

Title: An R interface to the web API of Statistics Sweden
Description: Interface for the REST API of Statistics Sweden. The package offers methods to fetch information about the data hierarchy stored behind the API; extract metadata; fetch actual data; and clean up the results.
Author: Love Hansson, Thomas Reinholdsson, Mans Magnusson
Maintainer: Mans Magnusson

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Package spartan updated to version 2.0 with previous version 1.3 dated 2014-03-19

Title: Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk.Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

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Package SIS updated to version 0.7-3 with previous version 0.7-2 dated 2014-05-06

Title: Sure Independence Screening
Description: (Iterative) Sure Independence Screening for Generalized Linear Models and Cox's Proportional Hazards Models
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana

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