Tue, 03 May 2016

Package vtreat updated to version 0.5.25 with previous version 0.5.23 dated 2016-04-29

Title: Simple Variable Treatment
Description: A data.frame processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical levels, rare categorical levels, new categorical levels (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>

Diff between vtreat versions 0.5.23 dated 2016-04-29 and 0.5.25 dated 2016-05-03

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More information about vtreat at CRAN
Permanent link

Package visNetwork updated to version 1.0.0 with previous version 0.2.1 dated 2016-01-31

Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib, http://visjs.org, http://www.almende.com/home), Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>

Diff between visNetwork versions 0.2.1 dated 2016-01-31 and 1.0.0 dated 2016-05-03

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 visNetwork-1.0.0/visNetwork/DESCRIPTION                                                       |   20 
 visNetwork-1.0.0/visNetwork/LICENSE                                                           |    2 
 visNetwork-1.0.0/visNetwork/MD5                                                               |  351 
 visNetwork-1.0.0/visNetwork/NAMESPACE                                                         |   13 
 visNetwork-1.0.0/visNetwork/NEWS                                                              |   27 
 visNetwork-1.0.0/visNetwork/R/dependencies.R                                                  |   59 
 visNetwork-1.0.0/visNetwork/R/visClustering.R                                                 |    4 
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 visNetwork-1.0.0/visNetwork/R/visFit.R                                                        |    2 
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 visNetwork-1.0.0/visNetwork/README.md                                                         |   14 
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 visNetwork-1.0.0/visNetwork/man/visConfigure.Rd                                               |    7 
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 visNetwork-1.0.0/visNetwork/man/visEdges.Rd                                                   |   15 
 visNetwork-1.0.0/visNetwork/man/visEvents.Rd                                                  |   11 
 visNetwork-1.0.0/visNetwork/man/visExport.Rd                                                  |   16 
 visNetwork-1.0.0/visNetwork/man/visFit.Rd                                                     |   11 
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 visNetwork-1.0.0/visNetwork/man/visNetwork.Rd                                                 |   63 
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 194 files changed, 20775 insertions(+), 19108 deletions(-)

More information about visNetwork at CRAN
Permanent link

Package vardpoor updated to version 0.6.0 with previous version 0.5.9 dated 2016-04-07

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

Diff between vardpoor versions 0.5.9 dated 2016-04-07 and 0.6.0 dated 2016-05-03

 DESCRIPTION             |    8 ++++----
 MD5                     |   24 ++++++++++++------------
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 13 files changed, 58 insertions(+), 58 deletions(-)

More information about vardpoor at CRAN
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Package tseries updated to version 0.10-35 with previous version 0.10-34 dated 2015-02-20

Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut], Kurt Hornik [aut, cre], Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between tseries versions 0.10-34 dated 2015-02-20 and 0.10-35 dated 2016-05-03

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Package TippingPoint updated to version 1.1.0 with previous version 1.0.0 dated 2016-05-02

Title: Enhanced Tipping Point Displays the Results of Sensitivity Analyses for Missing Data
Description: Using the idea of "tipping point" (proposed in Gregory Campbell, Gene Pennello and Lilly Yue(2011) <DOI:10.1080/10543406.2011.550094>) to visualize the results of sensitivity analysis for missing data, the package provides a set of functions to list out all the possible combinations of the values of missing data in two treatment arms, calculate corresponding estimated treatment effects and p values and draw a colored heat-map to visualize them. It could deal with randomized experiments with a binary outcome or a continuous outcome. In addition, the package provides a visualized method to compare various imputation methods by adding the rectangles or convex hulls on the basic plot.
Author: Shengjie Zhang <zhangshengjie@mrbc-nccd.com>, Xikun Han <hanxikun2014@163.com> and Victoria Liublinska <vliublin@g.harvard.edu>
Maintainer: Xikun Han <hanxikun2014@163.com>

Diff between TippingPoint versions 1.0.0 dated 2016-05-02 and 1.1.0 dated 2016-05-03

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Package splusTimeSeries updated to version 1.5.0-74 with previous version 1.5.0-73 dated 2013-09-10

Title: Time Series from S-PLUS
Description: A collection of classes and methods for working with time series. The code was originally available in S-PLUS.
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny <skaluzny@tibco.com>

Diff between splusTimeSeries versions 1.5.0-73 dated 2013-09-10 and 1.5.0-74 dated 2016-05-03

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Package splusTimeDate updated to version 2.5.0-136 with previous version 2.5.0-135 dated 2014-07-21

Title: Times and Dates from S-PLUS
Description: A collection of classes and methods for working with times and dates. The code was originally available in S-PLUS.
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny <skaluzny@tibco.com>

Diff between splusTimeDate versions 2.5.0-135 dated 2014-07-21 and 2.5.0-136 dated 2016-05-03

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Package sommer updated to version 1.5 with previous version 1.4 dated 2016-03-24

Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information, Expectation-Maximization or Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures or other covariance structures in R, but functional as a regular mixed model program.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

Diff between sommer versions 1.4 dated 2016-03-24 and 1.5 dated 2016-05-03

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Package seqminer updated to version 5.2 with previous version 5.0 dated 2015-10-22

Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu <dajiang.liu@gmail.com>, with contributions from Heng Li <lh3@live.co.uk> (Heng Li wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>

Diff between seqminer versions 5.0 dated 2015-10-22 and 5.2 dated 2016-05-03

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Package rsconnect updated to version 0.4.3 with previous version 0.4.2.1 dated 2016-03-29

Title: Deployment Interface for R Markdown Documents and Shiny Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'RStudio Connect'. Supported content types include R Markdown documents, Shiny applications, plots, and static web content.
Author: JJ Allaire
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between rsconnect versions 0.4.2.1 dated 2016-03-29 and 0.4.3 dated 2016-05-03

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Package RLumModel updated to version 0.1.1 with previous version 0.1.0 dated 2016-02-03

Title: Modelling Ordinary Differential Equations Leading to Luminescence
Description: A collection of function to simulate luminescence signals in the mineral quartz based on published models.
Author: Johannes Friedrich [aut, trl, cre], Sebastian Kreutzer [aut, ths], Christoph Schmidt [aut, ths]
Maintainer: Johannes Friedrich <johannes.friedrich@uni-bayreuth.de>

Diff between RLumModel versions 0.1.0 dated 2016-02-03 and 0.1.1 dated 2016-05-03

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Package repo updated to version 2.0.2 with previous version 1.0 dated 2015-08-03

Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with annotations, tags, dependency notes, provenance traces. It also provides navigation tools to easily locate, load and edit previously stored resources.
Author: Francesco Napolitano <franapoli@gmail.com>
Maintainer: Francesco Napolitano <franapoli@gmail.com>

Diff between repo versions 1.0 dated 2015-08-03 and 2.0.2 dated 2016-05-03

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Package RecordLinkage updated to version 0.4-9 with previous version 0.4-8 dated 2015-05-28

Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain.
Author: Andreas Borg <borga@uni-mainz.de>, Murat Sariyar <murat.sariyar@charite.de>
Maintainer: Andreas Borg <borga@uni-mainz.de>

Diff between RecordLinkage versions 0.4-8 dated 2015-05-28 and 0.4-9 dated 2016-05-03

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Package recommenderlabJester updated to version 0.1-2 with previous version 0.1-1 dated 2015-07-14

Title: Jester Dataset for 'recommenderlab'
Description: Provides the Jester Dataset for package recommenderlab.
Author: Michael Hahsler
Maintainer: Michael Hahsler <mhahsler@smu.edu>

Diff between recommenderlabJester versions 0.1-1 dated 2015-07-14 and 0.1-2 dated 2016-05-03

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Package plotKML updated to version 0.5-6 with previous version 0.5-5 dated 2016-01-06

Title: Visualization of Spatial and Spatio-Temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>

Diff between plotKML versions 0.5-5 dated 2016-01-06 and 0.5-6 dated 2016-05-03

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Package phenology updated to version 5.1 with previous version 4.2.4 dated 2015-06-30

Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between phenology versions 4.2.4 dated 2015-06-30 and 5.1 dated 2016-05-03

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Package optmatch updated to version 0.9-6 with previous version 0.9-5 dated 2015-07-30

Title: Functions for Optimal Matching
Description: Distance based bipartite matching using the RELAX-IV minimum cost flow solver, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, and Peter Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas <dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>

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Package nproc updated to version 0.4 with previous version 0.1 dated 2016-02-13

Title: Neyman-Pearson Receiver Operator Curve
Description: Given a sample of class 0 and class 1 and a classification method, the package generates the corresponding Neyman-Pearson classifier with a pre-specified type-I error control and Neyman-Pearson Receiver Operator Curve.
Author: Yang Feng, Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>

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Package nleqslv updated to version 3.0.1 with previous version 3.0 dated 2016-01-28

Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>

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Package netcoh updated to version 0.2 with previous version 0.1 dated 2016-03-03

Title: Statistical Modeling with Network Cohesion
Description: Model fitting procedures for regression with network cohesion effects, when a network connecting sample individuals is available in a regression problem. In the future, other commonly used statistical models will be added, such as gaussian graphical model.
Author: Tianxi Li, Elizaveta Levina, Ji Zhu
Maintainer: Tianxi Li <tianxili@umich.edu>

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Package Matrix updated to version 1.2-6 with previous version 1.2-5 dated 2016-04-17

Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>

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Package lawn updated to version 0.1.7 with previous version 0.1.6 dated 2016-03-04

Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (http://turfjs.org/) for 'geospatial' analysis. The package revolves around using 'GeoJSON' data. Functions are included for creating 'GeoJSON' data objects, measuring aspects of 'GeoJSON', and combining, transforming, and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre], Jeff Hollister [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package lamW updated to version 1.1.1 with previous version 1.1.0 dated 2016-03-16

Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package jqr updated to version 0.2.2 with previous version 0.2.0 dated 2016-03-23

Title: Client for 'jq', a JSON Processor
Description: Client for 'jq', a JSON processor (<http://stedolan.github.io/jq/>), written in C. 'jq' allows the following with JSON data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.
Author: Rich FitzJohn [aut], Scott Chamberlain [aut, cre], Stefan Milton Bache [aut], Stephen Dolan [aut, cph] (jq library), jq contributors [ctb] (jq library; authors listed in inst/AUTHORS.jq), Free Software Foundation [ctb, cph] (parser code in src/parser.c), David M Gay [ctb, cph] (code in src/jv_dtoa.c)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package InvariantCausalPrediction updated to version 0.6-1 with previous version 0.6-0 dated 2016-04-12

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

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Package Hmisc updated to version 3.17-4 with previous version 3.17-3 dated 2016-04-03

Title: Harrell Miscellaneous
Description: Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

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Package GSIF updated to version 0.5-1 with previous version 0.4-7 dated 2015-07-20

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [ctb], Gerard Heuvelink [ctb], Brendan Malone [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>

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Package geoR updated to version 1.7-5.2 with previous version 1.7-5.1 dated 2015-04-23

Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including traditional, likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr <paulojus@ufpr.br> and Peter J. Diggle <p.diggle@lancaster.ac.uk>
Maintainer: Paulo J. Ribeiro Jr <paulojus@ufpr.br>

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Package emuR updated to version 0.1.8 with previous version 0.1.7 dated 2016-03-31

Title: Main Package of the EMU Speech Database Management System
Description: Provides the next iteration of the EMU Speech Database Management System (EMU_SDMS) with database management, data extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre], Klaus Jaensch [aut, ctb], Steve Cassidy [aut, ctb], Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>

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Package eemR updated to version 0.1.3 with previous version 0.1.2 dated 2016-02-04

Title: Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data
Description: Provides various tools to calculate EEM fluorescence metrics and preprocess EEM for PARAFAC analysis.
Author: Philippe Massicotte [aut, cre]
Maintainer: Philippe Massicotte <pm@bios.au.dk>

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Package DBI updated to version 0.4 with previous version 0.3.1 dated 2014-09-24

Title: R Database Interface
Description: A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
Author: R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between DBI versions 0.3.1 dated 2014-09-24 and 0.4 dated 2016-05-03

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Package aSPU updated to version 1.42 with previous version 1.41 dated 2016-03-21

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single SNP association with summary statistics ('MTaSPUs'), (7) Multiple traits-`SNP' set association with summary statistics(`MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics(`MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

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Mon, 02 May 2016

Package tablaxlsx updated to version 1.1.0 with previous version 1.0.9 dated 2016-04-06

Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>

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Package shuffle updated to version 1.0.1 with previous version 1.0 dated 2014-01-07

Title: The Shuffle Estimator for Explainable Variance
Description: Implementation of the shuffle estimator, a non-parametric estimator for signal and noise variance under mild noise correlations.
Author: Yuval Benjamini
Maintainer: Yuval Benjamini <yuvalbenj@gmail.com>

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Package rcorpora updated to version 1.2.0 with previous version 1.1.1 dated 2015-07-12

Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data. It contains all data sets from https://github.com/dariusk/corpora. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Cole Willsea, Matthew Rothenberg, Karl Swedberg, Daniel D. Beck, Javier Arce, Matthew Hokanson, Casey Kolderup, Nathaniel Mitchell, Mark Sample, Nathan Lachenmyer, Aaron Marriner, Greg Kennedy, Greg Borenstein, Peter Organisciak, Rachel White, Tod Robbins, John Wiseman, M. Nowak, Alice Maz, Allison Parrish, Andrew Gorman, Colin Mitchell, David Whitten, Mary Dickson, Michael R. Bernstein, Parker Higgins, Patrick Rodriguez, Ross Barclay, Ross Binden, Ryan Freebern, Justin Alford, Brian Detweiler, Ed Lea, John Ohno, Alexandra Murray, Sean May, Will Hankinson, Brett O'Connor, Brian Jones, Casey Olson, Edward Loveall, Felix Laurie von Massenbach, Garrett Miller, Grant Williamson, Jacob Fauber, Joe Mahoney, Jordan Killpack, Kay Belardinelli, K.Adam White, Kyle McDonald, Andy Dayton, Adam Malantonio, Marcos Wright-Kuhns, Mark Wunsch, Max Bittker, Michael Dewberry, Nathan Black, Noah Kantrowitz, Noah Swartz, Ranjit Bhatnagar, Rob Huzzey, Russell Horton, Vincent Bruijn, Virginia Murdoch, Zac Moody, Scott Grant, Tariq Ali
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

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Package rasclass updated to version 0.2.2 with previous version 0.2.1 dated 2012-01-23

Title: Supervised Raster Image Classification
Description: Software to perform supervised and pixel based raster image classification. It has been designed to facilitate land-cover analysis. Five classification algorithms can be used: Maximum Likelihood Classification, Multinomial Logistic Regression, Neural Networks, Random Forests and Support Vector Machines. The output includes the classified raster and standard classification accuracy assessment such as the accuracy matrix, the overall accuracy and the kappa coefficient. An option for in-sample verification is available.
Author: Daniel Wiesmann <daniel.wiesmann@tecnico.ulisboa.pt> and David Quinn <djq@urbmet.com>
Maintainer: Daniel Wiesmann <daniel.wiesmann@tecnico.ulisboa.pt>

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Package lessR updated to version 3.4.8 with previous version 3.4.6 dated 2016-03-28

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package FunChisq updated to version 2.3.1 with previous version 2.2.4 dated 2016-04-22

Title: Chi-Square and Exact Tests for Non-Parametric Functional Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies using asymptotic chi-square or exact statistics. These tests were motivated to reveal evidence for causality based on functional dependencies. They include asymptotic functional chi-square tests, an exact functional test, a comparative functional chi-square test, and also a comparative chi-square test. The normalized non-constant functional chi-square test was used by Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. For continuous data, these tests offer an advantage over regression analysis when a parametric functional form cannot be assumed; for categorical data, they provide a novel means to assess directional dependencies impossible with classical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package eva updated to version 0.2.2 with previous version 0.2.1 dated 2016-04-05

Title: Extreme Value Analysis with Goodness-of-Fit Testing
Description: Goodness-of-fit tests for selection of r in the r-largest order statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the peaks-over-threshold approach. Random number generation and density functions for the GEVr distribution. Profile likelihood for return level estimation using the GEVr and Generalized Pareto distributions. P-value adjustments for sequential, multiple testing error control.
Author: Brian Bader [aut, cre], Jun Yan [ctb]
Maintainer: Brian Bader <brianbader@mail.com>

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Sun, 01 May 2016

Package unfoldr updated to version 0.5 with previous version 0.3 dated 2015-07-07

Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in the estimation of the joint size-shape-orientation distribution of spheroidal shaped particles based on the same measured quantities of corresponding planar section profiles. A single trivariate discretized version of the (stereological) integral equation in the case of prolate and oblate spheroids is solved numerically by the EM algorithm. The estimation of diameter distribution of spheres from planar sections (Wicksell's corpuscle problem) is also implemented. Further, the package provides routines for the simulation of a Poisson germ- grain process with either spheroids or spheres as grains together with functions for planar sections. For the purpose of exact simulation a bivariate size-shape distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

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Package sensitivity updated to version 1.12 with previous version 1.11.1 dated 2015-06-12

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Khalid Boumhaout, Sebastien Da Veiga, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Bernardo Ramos, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

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Package rio updated to version 0.4.0 with previous version 0.3.0 dated 2016-01-14

Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Jason Becker [ctb], Chung-hong Chan [aut], Geoffrey CH Chan [ctb], Thomas J. Leeper [aut, cre], Christopher Gandrud [ctb], Andrew MacDonald [ctb], Ista Zahn [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package opencpu updated to version 1.5.6 with previous version 1.5.4 dated 2016-03-08

Title: Embedded Scientific Computing and Reproducible Research with R
Description: The OpenCPU system exposes an http API for embedded scientific computing with R. The server can run either as a single-user development server within the interactive R session, or as a multi-user linux stack based on rApache and NGINX. The current R package implements the core of the system. When loaded in R, it automatically initiates the single-user server and displays the web address in the console. The OpenCPU website has more detailed API documentation.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package MLmetrics updated to version 1.1.0 with previous version 1.0.0 dated 2015-05-02

Title: Machine Learning Evaluation Metrics
Description: A collection of evaluation metrics, including loss, score and utility functions, that measure regression, classification and ranking performance.
Author: Yachen Yan [aut, cre]
Maintainer: Yachen Yan <yanyachen21@gmail.com>

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Package HelpersMG updated to version 1.5 with previous version 1.4 dated 2016-01-08

Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 1.4 dated 2016-01-08 and 1.5 dated 2016-05-01

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Package biwavelet updated to version 0.19.1 with previous version 0.17.10 dated 2015-05-05

Title: Conduct Univariate and Bivariate Wavelet Analyses
Description: This is a port of the WTC MATLAB package written by Aslak Grinsted and the wavelet program written by Christopher Torrence and Gibert P. Compo. This package can be used to perform univariate and bivariate (cross-wavelet, wavelet coherence, wavelet clustering) analyses.
Author: Tarik C. Gouhier, Aslak Grinsted, Viliam Simko
Maintainer: Tarik C. Gouhier <tarik.gouhier@gmail.com>

Diff between biwavelet versions 0.17.10 dated 2015-05-05 and 0.19.1 dated 2016-05-01

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Permanent link

Package clusterSEs updated to version 2.2 with previous version 2.1 dated 2015-08-05

Title: Calculate Cluster-Robust p-Values and Confidence Intervals
Description: Calculate p-values and confidence intervals using cluster-adjusted t-statistics (based on Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)), pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics (the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of Economics and Statistics 90(3)). Procedures are included for use with GLM, ivreg, plm (pooling or fixed effects), and mlogit models.
Author: Justin Esarey [aut, cre]
Maintainer: Justin Esarey <justin@justinesarey.com>

Diff between clusterSEs versions 2.1 dated 2015-08-05 and 2.2 dated 2016-05-01

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Sat, 30 Apr 2016

Package StressStrength updated to version 1.0.2 with previous version 1.0.1 dated 2014-11-25

Title: Computation and Estimation of Reliability of Stress-Strength Models
Description: Reliability of (normal) stress-strength models and for building two-sided or one-sided confidence intervals according to different approximate procedures.
Author: Alessandro Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo <dott.inchingolo_r@libero.it>
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>

Diff between StressStrength versions 1.0.1 dated 2014-11-25 and 1.0.2 dated 2016-04-30

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Package rmarkdown updated to version 0.9.6 with previous version 0.9.5 dated 2016-02-22

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package phangorn updated to version 2.0.3 with previous version 2.0.2 dated 2016-01-22

Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

Diff between phangorn versions 2.0.2 dated 2016-01-22 and 2.0.3 dated 2016-04-30

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More information about phangorn at CRAN
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Package mpoly updated to version 1.0.1 with previous version 1.0.0 dated 2015-12-31

Title: Symbolic Computation and More with Multivariate Polynomials
Description: Symbolic computing with multivariate polynomials in R.
Author: David Kahle [aut, cre]
Maintainer: David Kahle <david.kahle@gmail.com>

Diff between mpoly versions 1.0.0 dated 2015-12-31 and 1.0.1 dated 2016-04-30

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More information about mpoly at CRAN
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Package DiscreteLaplace updated to version 1.1.1 with previous version 1.1 dated 2015-07-27

Title: Discrete Laplace Distributions
Description: Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
Author: Alessandro Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo <dott.inchingolo_r@libero.it>
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>

Diff between DiscreteLaplace versions 1.1 dated 2015-07-27 and 1.1.1 dated 2016-04-30

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Package DiscreteInverseWeibull updated to version 1.0.2 with previous version 1.0.1 dated 2014-11-25

Title: Discrete Inverse Weibull Distribution
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the discrete inverse Weibull distribution.
Author: Alessandro Barbiero, Riccardo Inchingolo, Mario Samigli
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>

Diff between DiscreteInverseWeibull versions 1.0.1 dated 2014-11-25 and 1.0.2 dated 2016-04-30

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Permanent link

Package BWStest updated to version 0.2.0 with previous version 0.1.0 dated 2016-04-08

Title: Baumgartner Weiss Schindler Test of Equal Distributions
Description: Performs the 'Baumgartner-Weiss-Schindler' two-sample test of equal probability distributions.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

Diff between BWStest versions 0.1.0 dated 2016-04-08 and 0.2.0 dated 2016-04-30

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Permanent link

Package berryFunctions updated to version 1.10.0 with previous version 1.9.0 dated 2015-10-10

Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scatterpoints by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>

Diff between berryFunctions versions 1.9.0 dated 2015-10-10 and 1.10.0 dated 2016-04-30

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More information about berryFunctions at CRAN
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Fri, 29 Apr 2016

Package IAT updated to version 0.3 with previous version 0.2 dated 2014-07-12

Title: Cleaning and Visualizing Implicit Association Test (IAT) Data
Description: Implements the standard D-Scoring algorithm (Greenwald, Banaji, & Nosek, 2003) for Implicit Association Test (IAT) data and includes plotting capabilities for exploring raw IAT data.
Author: Dan Martin <dpmartin42@gmail.com>
Maintainer: Dan Martin <dpmartin42@gmail.com>

Diff between IAT versions 0.2 dated 2014-07-12 and 0.3 dated 2016-04-29

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More information about IAT at CRAN
Permanent link

Package soilDB updated to version 1.8 with previous version 1.7 dated 2016-02-16

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J. Skovlin, and S. Roecker
Maintainer: D.E. Beaudette <dylan.beaudette@ca.usda.gov>

Diff between soilDB versions 1.7 dated 2016-02-16 and 1.8 dated 2016-04-29

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More information about soilDB at CRAN
Permanent link

Package simmer updated to version 3.2.1 with previous version 3.2.0 dated 2016-04-04

Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation (DES) package for R. Designed to be a generic framework like SimPy or SimJulia, it leverages the use of Rcpp to boost the performance and turning DES in R feasible. As a noteworthy characteristic, simmer exploits the concept of trajectory: a common path in the simulation model for entities of the same type.
Author: Bart Smeets [aut], Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>

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Package quantregForest updated to version 1.3 with previous version 1.2 dated 2016-03-22

Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble method for estimation of conditional quantiles. It is particularly well suited for high-dimensional data. Predictor variables of mixed classes can be handled. The package is dependent on the package randomForests, written by Andy Liaw.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

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Package pcIRT updated to version 0.2.2 with previous version 0.2 dated 2015-07-17

Title: IRT Models for Polytomous and Continuous Item Responses
Description: Estimates the multidimensional polytomous Rasch model (Rasch, 1961) and the Continuous Rating Scale model (Mueller, 1987).
Author: Christine Hohensinn
Maintainer: Christine Hohensinn <christine.hohensinn@univie.ac.at>

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Package nycflights13 updated to version 0.2.0 with previous version 0.1 dated 2014-07-22

Title: Flights that Departed NYC in 2013
Description: Airline on-time data for all flights departing NYC in 2013. Also includes useful 'metadata' on airlines, airports, weather, and planes.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package npregfast updated to version 1.3.0 with previous version 1.2.1 dated 2016-02-16

Title: Nonparametric Estimation of Regression Models with Factor-by-Curve Interactions
Description: A method for obtain nonparametric estimates of regression models with or without factor-by-curve interactions using local polynomial kernel smoothers or splines. Additionally, a parametric model (allometric model) can be estimated.
Author: Marta Sestelo [aut, cre], Nora M. Villanueva [aut], Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>

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Package multiplex updated to version 1.9 with previous version 1.8.2 dated 2016-03-08

Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with this package. Among other things, it is possible to create and manipulate multivariate network data with different formats, and there are effective ways available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup or the semiring structure together with the relational bundles occurring in different types of multivariate network data sets. As well an algebraic approach for two-mode networks is made through Galois derivations between families of the pair of subsets.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>

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Package googleformr updated to version 0.0.3 with previous version 0.0.2 dated 2016-03-26

Title: Collect Data Programmatically by POST Methods to Google Forms
Description: GET and POST data to Google Forms; an API to Google Forms, allowing users to POST data securely to Google Forms without needing authentication or permissioning.
Author: Steve Simpson [aut, cre]
Maintainer: Steve Simpson <steven.troy.simpson@gmail.com>

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Package GetTDData updated to version 1.2 with previous version 1.1 dated 2016-04-13

Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package fastclime updated to version 1.4.1 with previous version 1.4 dated 2016-04-18

Title: A Fast Solver for Parameterized LP Problems, Constrained L1 Minimization Approach to Sparse Precision Matrix Estimation and Dantzig Selector
Description: Provides a method of recovering the precision matrix efficiently and solving for the dantzig selector by applying the parametric simplex method. The computation is based on a linear optimization solver. It also contains a generic LP solver and a parameterized LP solver using parametric simplex method.
Author: Haotian Pang, Di Qi, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang <hpang@princeton.edu>

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Package vtreat updated to version 0.5.23 with previous version 0.5.22 dated 2016-01-07

Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>

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Package qgraph updated to version 1.3.3 with previous version 1.3.2 dated 2016-01-19

Title: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package mvabund updated to version 3.11.9 with previous version 3.11.7 dated 2016-03-31

Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. See 'mvabund-package.Rd' for details of overall package organization. The package is implemented with the Gnu Scientific Library (http://www.gnu.org/software/gsl/) and Rcpp (http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>

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Package mipfp updated to version 3.0-1 with previous version 3.0 dated 2016-04-22

Title: Multidimensional Iterative Proportional Fitting and Alternative Models
Description: An implementation of the iterative proportional fitting (IPFP), maximum likelihood, minimum chi-square and weighted least squares procedures for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional). The package also provides an application of the IPFP to simulate multivariate Bernoulli distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>

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Package evaluate updated to version 0.9 with previous version 0.8.3 dated 2016-03-04

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

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Package daff updated to version 0.2.0 with previous version 0.1.4 dated 2015-04-18

Title: Diff, Patch and Merge for Data.frames
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff. The V8 package is used to wrap the 'daff.js' JavaScript library which is included in the package.
Author: Paul Fitzpatrick [aut] (JavaScript original, http://paulfitz.github.io/daff/), Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package convoSPAT updated to version 1.1 with previous version 1.0 dated 2015-09-28

Title: Convolution-Based Nonstationary Spatial Modeling
Description: Fits convolution-based nonstationary Gaussian process models to point-referenced spatial data. The nonstationary covariance function allows the user to specify the underlying correlation structure and which spatial dependence parameters should be allowed to vary over space: the anisotropy, nugget variance, and process variance. The parameters are estimated via maximum likelihood, using a local likelihood approach. Also provided are functions to fit stationary spatial models for comparison, calculate the kriging predictor and standard errors, and create various plots to visualize nonstationarity.
Author: Mark D. Risser [aut, cre]
Maintainer: Mark D. Risser <markdrisser@gmail.com>

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Package UBL updated to version 0.0.4 with previous version 0.0.3 dated 2016-04-25

Title: An Implementation of Several Approaches to Utility-Based Learning for Both Classification and Regression Tasks
Description: Provides a set of functions that can be used to obtain better predictive performance on cost-sensitive and cost/benefits tasks (for both regression and classification). This includes re-sampling approaches, cost-based methods, special purpose evaluation metrics as well as specific learning systems.
Author: Paula Branco [aut, cre], Rita Ribeiro [aut, ctb], Luis Torgo [aut, ctb]
Maintainer: Paula Branco <paobranco@gmail.com>

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Package twang updated to version 1.4-9.5 with previous version 1.4-9.3 dated 2015-02-02

Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score estimating and weighting, nonresponse weighting, and diagnosis of the weights. This package was originally developed by Drs. Ridgeway, McCaffrey, and Morral. Burgette, Griffin and McCaffrey updated the package during 2011-2016.
Author: Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, Lane Burgette <burgette@rand.org>
Maintainer: Lane Burgette <burgette@rand.org>

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Package rvg updated to version 0.0.9 with previous version 0.0.8 dated 2016-03-04

Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for 'SVG', 'DrawingML' for Microsoft Word, PowerPoint and Excel.
Author: David Gohel [aut, cre], Bob Rudis [ctb] (the javascript code used by function set_attr), Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package remoter updated to version 0.3-2 with previous version 0.2-0 dated 2016-02-04

Title: Remote R: Control a Remote R Session from a Local One
Description: A set of utilities for controlling a remote R session from a local one. Simply set up a server (see package vignette for more details) and connect to it from your local R session, including 'RStudio'. Network communication is handled by the 'ZeroMQ' library by way of the 'pbdZMQ' package. The client/server framework is a custom 'REPL'.
Author: Drew Schmidt [aut, cre], Wei-Chen Chen [aut]
Maintainer: Drew Schmidt <wrathematics@gmail.com>

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Package fmrs updated to version 1.0-7 with previous version 1.0-5 dated 2016-03-27

Title: Variable Selection in Finite Mixture of AFT Regression and FMR
Description: Provides parameter estimation as well as variable selection in Finite Mixture of Accelerated Failure Time Regression and Finite Mixture of Regression Models. Furthermore, this package provides Ridge Regression and Elastic Net.
Author: Farhad Shokoohi <shokoohi@icloud.com> Abbas Khalili Masoud Asgharian Shili Lin
Maintainer: Farhad Shokoohi <shokoohi@icloud.com>

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Thu, 28 Apr 2016

Package MDplot updated to version 0.3.1 with previous version 0.3 dated 2016-02-18

Title: Visualising Molecular Dynamics Analyses
Description: Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis.
Author: Christian Margreitter [aut, cre]
Maintainer: Christian Margreitter <christian.margreitter@gmail.com>

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Package glmmLasso updated to version 1.4.3 with previous version 1.4.1 dated 2016-03-01

Title: Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

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Package fda.usc updated to version 1.2.3 with previous version 1.2.2 dated 2015-12-10

Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut], Manuel Oviedo de la Fuente [aut, cre], Pedro Galeano [ctb], Alicia Nieto [ctb], Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>

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Package parsec updated to version 1.1.1 with previous version 1.1 dated 2015-06-22

Title: Partial Orders in Socio-Economics
Description: Implements basic partial order tools for multidimensional poverty evaluation with ordinal variables. Its main goal is to provide socio-economic scholars with an integrated set of elementary functions for multidimensional poverty evaluation, based on ordinal information. The package is organized in four main parts. The first two comprise functions for data management and basic partial order analysis; the third and the fourth are devoted to evaluation and implement both the poset-based approach and a more classical counting procedure.
Author: Alberto Arcagni [aut, cre], Marco Fattore [ctb]
Maintainer: Alberto Arcagni <alberto.arcagni@unimib.it>

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Package imager updated to version 0.20 with previous version 0.15 dated 2016-01-07

Title: Image Processing Library Based on CImg
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R.
Author: Simon Barthelme [aut, cre], Antoine Cecchi [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>

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Package IBDsim updated to version 0.9-6 with previous version 0.9-5 dated 2015-07-03

Title: Simulation of Chromosomal Regions Shared by Family Members
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>

Diff between IBDsim versions 0.9-5 dated 2015-07-03 and 0.9-6 dated 2016-04-28

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Package HiCfeat updated to version 1.1 with previous version 1.0 dated 2015-10-05

Title: Multiple Logistic Regression for 3D Chromatin Domain Border Analysis
Description: We propose a multiple logistic regression model to assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

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Package GFD updated to version 0.2.2 with previous version 0.1.4 dated 2016-01-14

Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic, a permuted version thereof as well as the ANOVA-type statistic for general factorial designs, even with non-normal error terms and/or heteroscedastic variances, for crossed designs with an arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>

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Wed, 27 Apr 2016

Package syuzhet updated to version 1.0.0 with previous version 0.2.0 dated 2015-02-21

Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs from text using three sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include "syuzhet" (default) developed in the Nebraska Literary Lab "afinn" developed by Finn {\AA}rup Nielsen, "bing" developed by Minqing Hu and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in README.md and in the documentation for the "get_sentiment" function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>

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Package robotstxt updated to version 0.3.2 with previous version 0.1.2 dated 2016-02-08

Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Description: Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, scrapers, ...) are allowed to access specific resources on a domain.
Author: Peter Meissner [aut, cre], Oliver Keys [ctb], Rich Fitz John [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

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Package paramlink updated to version 0.9-8 with previous version 0.9-7 dated 2015-07-03

Title: Parametric Linkage Analysis in R
Description: Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>

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Package midrangeMCP updated to version 1.2 with previous version 1.1 dated 2016-02-21

Title: Multiple Comparisons Procedures Based on Studentized Midrange and Range Distributions
Description: Apply tests of multiple comparisons based on studentized midrange and range distributions. The tests are: Tukey Midrange test, Student-Newman- Keuls Midrange test, Skott-Knott Midrange test and Skott-Knott Range test.
Author: Ben Deivide [aut, cre], Daniel Furtado [aut]
Maintainer: Ben Deivide <ben.deivide@gmail.com>

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Package ismev updated to version 1.41 with previous version 1.40 dated 2014-12-24

Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in `An Introduction to Statistical Modeling of Extreme Values' by Stuart Coles. The functions may be divided into the following groups; maxima/minima, order statistics, peaks over thresholds and point processes.
Author: Original S functions written by Janet E. Heffernan with R port and R documentation provided by Alec G. Stephenson.
Maintainer: Eric Gilleland <ericg@ucar.edu>

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Package imputeTS updated to version 1.5 with previous version 0.4 dated 2015-12-04

Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

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Package gcerisk updated to version 16.1.3 with previous version 16.1.2 dated 2016-03-04

Title: Generalized Competing Event Model
Description: Generalized competing event model based on Cox PH model and Fine-Gray model. This function is designed to develop optimized risk-stratification methods for competing risks data, such as described in: 1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F, and Mell LK.(2014) <DOI:10.1016/j.ijrobp.2014.03.047>. Validated competing event model for thestage I-II endometrial cancer population. Int J Radiat Oncol Biol Phys.89:888-98. 2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose BS, Shen H, Vaida F, Murphy JD, and Mell LK.(2016) <DOI:10.1200/JCO.2015.65.0739>. Improved method to stratify elderly cancer patients at risk for competing events. J Clin Oncol.in press.
Author: Hanjie Shen <has072@ucsd.edu>, Ruben Carmona <ruben.carmona13@gmail.com>, Loren Mell <lmell@ucsd.edu>
Maintainer: Hanjie Shen <shenhanjie0418@gmail.com>

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Package funtimes updated to version 2.2 with previous version 2.1 dated 2016-01-16

Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich; Yulia R. Gel; Xingyu Wang; Calvin Chu
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>

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Package multisensi updated to version 2.0 with previous version 1.0-8 dated 2015-02-17

Title: Multivariate Sensitivity Analysis
Description: Functions to perform sensitivity analysis on a model with multivariate output.
Author: Caroline Bidot <caroline.bidot@jouy.inra.fr>, Matieyendou Lamboni <clamboni@yahoo.fr>, Hervé Monod <herve.monod@jouy.inra.fr>
Maintainer: Caroline Bidot <caroline.bidot@jouy.inra.fr>

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Package CopyDetect updated to version 1.2 with previous version 1.1 dated 2014-06-11

Title: Computing Statistical Indices to Detect Answer Copying on Multiple-Choice Tests
Description: Contains several IRT and non-IRT based statistical indices proposed in the literature for detecting answer copying on multiple-choice examinations. Includes the indices that have been shown as effective and reliable based on the simulation studies. Provides results for the Omega index, Generalized Binomial Test, K index, K1 and K2 indices, and S1 and S2 indices.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>

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Package slackr updated to version 1.4.1 with previous version 1.2 dated 2014-09-08

Title: Send Messages, Images, R Objects and Files to 'Slack' Channels/Users
Description: 'Slack' <http://slack.com/> provides a service for teams to collaborate by sharing messages, images, links, files and more. Functions are provided that make it possible to interact with the 'Slack' platform 'API'. When you need to share information or data from R, rather than resort to copy/ paste in e-mails or other services like 'Skype' <http://www.skype.com/>, you can use this package to send well-formatted output from multiple R objects and expressions to all teammates at the same time with little effort. You can also send images from the current graphics device, R objects (as RData), and upload files.
Author: Bob Rudis [aut, cre], Jay Jacobs [ctb], David Severski [ctb], Quinn Weber [ctb], Konrad Karczewski [ctb], Shinya Uryu [ctb], Gregory Jefferis [ctb], Ed Niles [ctb], Rick Saporta [ctb]
Maintainer: Bob Rudis <bob@rudis.net>

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Package SimDesign updated to version 0.9 with previous version 0.8 dated 2016-03-22

Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R. The package controls the structure and back-end of Monte Carlo simulations by utilizing a general generate-analyse-summarise strategy. The functions provided control common simulation issues such as re-simulating non-convergent results, support parallel back-end and MPI distributed computations, save and restore temporary files, aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package saeSim updated to version 0.8.0 with previous version 0.7.0 dated 2015-02-16

Title: Simulation Tools for Small Area Estimation
Description: Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre], Timo Schmid [aut]
Maintainer: Sebastian Warnholz <Sebastian.Warnholz@fu-berlin.de>

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Package rfUtilities updated to version 2.0-0 with previous version 1.0-2 dated 2015-09-29

Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance correction, significance test, cross validation and partial dependency plots.
Author: Jeffrey S. Evans [cre, aut], Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

Diff between rfUtilities versions 1.0-2 dated 2015-09-29 and 2.0-0 dated 2016-04-27

 DESCRIPTION                         |   12 +-
 MD5                                 |   82 ++++++++++++-----
 NAMESPACE                           |   35 ++++++-
 R/accuracy.R                        |only
 R/multi.collinear.R                 |   12 +-
 R/occurrence.threshold.R            |only
 R/plot.occurrence.threshold.R       |only
 R/plot.rf.cv.R                      |only
 R/plot.rf.modelSel.R                |only
 R/plot.significance.R               |only
 R/print.accuracy.R                  |only
 R/print.occurrence.threshold.R      |only
 R/print.rf.cv.R                     |only
 R/print.rf.fit.R                    |only
 R/print.rf.modelSel.R               |only
 R/print.significance.R              |only
 R/rf.class.sensitivity.R            |   52 +++++-----
 R/rf.classBalance.R                 |   80 ++++++++--------
 R/rf.crossValidation.R              |  173 ++++++++++++++++++++----------------
 R/rf.imp.freq.R                     |   10 +-
 R/rf.modelSel.R                     |  121 +++++++++++++------------
 R/rf.partial.ci.R                   |   23 ++--
 R/rf.partial.prob.R                 |   14 +-
 R/rf.regression.fit.R               |only
 R/rf.significance.R                 |  128 +++++++++++---------------
 R/rfu.news.R                        |only
 R/summary.accuracy.R                |only
 R/summary.occurrence.threshold.R    |only
 R/summary.rf.cv.R                   |only
 R/summary.rf.modelSel.R             |only
 R/summary.significance.R            |only
 R/zzz.R                             |only
 inst/CITATION                       |    4 
 inst/NEWS                           |   43 +++++++-
 man/accuracy.Rd                     |only
 man/multi.collinear.Rd              |   10 +-
 man/occurrence.threshold.Rd         |only
 man/plot.occurrence.threshold.Rd    |only
 man/plot.rf.cv.Rd                   |only
 man/plot.rf.modelSel.Rd             |only
 man/plot.significance.Rd            |only
 man/print.accuracy.Rd               |only
 man/print.occurrence.threshold.Rd   |only
 man/print.rf.cv.Rd                  |only
 man/print.rf.modelSel.Rd            |only
 man/print.significance.Rd           |only
 man/rf.class.sensitivity.Rd         |   22 ++--
 man/rf.classBalance.Rd              |   21 +---
 man/rf.crossValidation.Rd           |   59 ++++++++----
 man/rf.imp.freq.Rd                  |   12 +-
 man/rf.modelSel.Rd                  |   43 ++++----
 man/rf.partial.ci.Rd                |    9 +
 man/rf.partial.prob.Rd              |    5 -
 man/rf.regression.fit.Rd            |only
 man/rf.significance.Rd              |   22 ++--
 man/rfu.news.Rd                     |only
 man/summary.accuracy.Rd             |only
 man/summary.occurrence.threshold.Rd |only
 man/summary.rf.cv.Rd                |only
 man/summary.rf.modelSel.Rd          |only
 man/summary.significance.Rd         |only
 61 files changed, 570 insertions(+), 422 deletions(-)

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