Tue, 28 Jun 2016

Package V8 updated to version 1.0.3 with previous version 1.0.2 dated 2016-06-14

Title: Embedded JavaScript Engine for R
Description: An R interface to Google's open source JavaScript engine. V8 is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition. In addition, this package implements typed arrays as specified in ECMA 6 used for high-performance computing and libraries compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between V8 versions 1.0.2 dated 2016-06-14 and 1.0.3 dated 2016-06-28

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More information about V8 at CRAN
Permanent link

New package tempR with initial version 0.9.9.7
Package: tempR
Type: Package
Title: Temporal Sensory Data Analysis
Version: 0.9.9.7
Date: 2016-06-28
Author: J. C. Castura [aut, cre]
Maintainer: J. C. Castura <jcastura@compusense.com>
Description: Analysis and visualization of data from temporal sensory methods, including for temporal check-all-that-apply (TCATA) and temporal dominance of sensations (TDS).
Depends: R (>= 3.3.0)
Imports: grDevices, stats, graphics
License: GPL (>= 2)
LazyData: TRUE
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-28 04:11:25 UTC; jcastura
Repository: CRAN
Date/Publication: 2016-06-28 08:30:01

More information about tempR at CRAN
Permanent link

Package srvyr updated to version 0.1.2 with previous version 0.1.1 dated 2016-04-03

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

Diff between srvyr versions 0.1.1 dated 2016-04-03 and 0.1.2 dated 2016-06-28

 DESCRIPTION                                   |   14 -
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 NEWS.md                                       |    9 
 R/cascade.r                                   |    4 
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More information about srvyr at CRAN
Permanent link

Package simmer updated to version 3.3.0 with previous version 3.2.1 dated 2016-04-29

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, 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>

Diff between simmer versions 3.2.1 dated 2016-04-29 and 3.3.0 dated 2016-06-28

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 simmer-3.3.0/simmer/R/plot.R                                         |   12 
 simmer-3.3.0/simmer/R/simulator.R                                    |  154 +++-
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 simmer-3.3.0/simmer/R/utils.R                                        |    5 
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More information about simmer at CRAN
Permanent link

Package rpf updated to version 0.53 with previous version 0.52 dated 2016-05-04

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], Michael D. Hunter [ctb], Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>

Diff between rpf versions 0.52 dated 2016-05-04 and 0.53 dated 2016-06-28

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More information about rpf at CRAN
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New package rgeospatialquality with initial version 0.3.2
Package: rgeospatialquality
Type: Package
Title: Wrapper for the Geospatial Data Quality REST API
Version: 0.3.2
Date: 2016-06-27
Authors@R: person("Javier", "Otegui", email="javier.otegui@gmail.com", role=c("aut", "cre"))
Description: Provides native wrappers for the functions available via the spatial quality REST API. See <http://bit.ly/bioinformatics_btw057> for more information on the API.
License: MIT + file LICENSE
LazyData: TRUE
Imports: httr (>= 1.0.0), jsonlite (>= 0.9.19), plyr (>= 1.8.3)
RoxygenNote: 5.0.1
Suggests: knitr, roxygen2, rmarkdown, testthat, covr, rgbif (>= 0.9.2), rvertnet, rinat
VignetteBuilder: knitr
URL: https://github.com/ropenscilabs/rgeospatialquality
BugReports: https://github.com/ropenscilabs/rgeospatialquality/issues
NeedsCompilation: no
Packaged: 2016-06-27 20:37:44 UTC; jotegui
Author: Javier Otegui [aut, cre]
Maintainer: Javier Otegui <javier.otegui@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-28 08:28:36

More information about rgeospatialquality at CRAN
Permanent link

New package RcmdrPlugin.BiclustGUI with initial version 1.0.4
Package: RcmdrPlugin.BiclustGUI
Type: Package
Title: 'Rcmdr' Plug-in GUI for Biclustering
Version: 1.0.4
Date: 2016-06-26
Author: De Troyer Ewoud, Otava Martin
Maintainer: De Troyer Ewoud <ewoud.detroyer@uhasselt.be>
Description: A plug-in for R Commander ('Rcmdr'). The package is a Graphical User Interface (GUI) in which several biclustering methods can be executed, followed by diagnostics and plots of the results. Further, the GUI also has the possibility to connect the methods to more general diagnostic packages for biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG', 'isa2', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and 'BcDiag' are also implemented to be able to further investigate results. The GUI also provides a couple of extra utilities to export, save, search through and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific framework for biclustering in which new methods, diagnostics and plots can be added. Scripts were prepared so that R-package developers can freely design their own dialogs in the GUI which can then be added by the maintainer of 'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk' and 'Rcmdr' and are easy to fill in.
License: GPL-3
Depends: biclust, fabia, iBBiG,superbiclust(>= 1.1),BcDiag(>= 1.0.10), rqubic, BicARE, s4vd
Imports: Rcmdr, tcltk, gplots, grDevices, graphics, methods, utils
VignetteBuilder: knitr
Suggests: knitr
NeedsCompilation: no
Packaged: 2016-06-27 05:25:54 UTC; rforge
Repository: CRAN
Repository/R-Forge/Project: biclustgui
Repository/R-Forge/Revision: 78
Repository/R-Forge/DateTimeStamp: 2016-06-27 05:08:48
Date/Publication: 2016-06-28 07:51:05

More information about RcmdrPlugin.BiclustGUI at CRAN
Permanent link

Package MVar.pt updated to version 1.9.1 with previous version 1.9 dated 2016-06-22

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), analise de multiplos fatores (MFA), para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar.pt versions 1.9 dated 2016-06-22 and 1.9.1 dated 2016-06-28

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More information about MVar.pt at CRAN
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Package mkin updated to version 0.9.43 with previous version 0.9.42 dated 2016-03-24

Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006, 2014). 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. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using compiled C functions. 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 <jranke@uni-bremen.de>

Diff between mkin versions 0.9.42 dated 2016-03-24 and 0.9.43 dated 2016-06-28

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Package mdhglm updated to version 1.4 with previous version 1.2 dated 2016-03-17

Title: Multivariate Double Hierarchical Generalized Linear Models
Description: Allows various models for multivariate response variables where each response is assumed to follow double hierarchical generalized linear models. In double hierarchical generalized linear models, the mean, dispersion parameters for variance of random effects, and residual variance can be further modeled as random-effect models.
Author: Youngjo Lee, Marek Molas, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>

Diff between mdhglm versions 1.2 dated 2016-03-17 and 1.4 dated 2016-06-28

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Package FastImputation updated to version 1.3.1 with previous version 1.3 dated 2016-02-15

Title: Learn from Training Data then Quickly Fill in Missing Data
Description: TrainFastImputation() uses training data to describe a multivariate normal distribution that the data approximates or can be transformed into approximating and stores this information as an object of class 'FastImputationPatterns'. FastImputation() function uses this 'FastImputationPatterns' object to impute (make a good guess at) missing data in a single line or a whole data frame of data. This approximates the process used by Amelia [http://gking.harvard.edu/amelia/] but is much faster when filling in values for a single line of data.
Author: Stephen R. Haptonstahl
Maintainer: Stephen R. Haptonstahl <srh@haptonstahl.org>

Diff between FastImputation versions 1.3 dated 2016-02-15 and 1.3.1 dated 2016-06-28

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Package Corbi updated to version 0.3-5 with previous version 0.3-4 dated 2016-06-06

Title: Collection of Rudimentary Bioinformatics Tools
Description: Provides a bundle of basic and fundamental bioinformatics tools, such as network querying and alignment, subnetwork extraction and search.
Author: Ling-Yun Wu [aut, cre], Qiang Huang [aut]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>

Diff between Corbi versions 0.3-4 dated 2016-06-06 and 0.3-5 dated 2016-06-28

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Package checkmate updated to version 1.8.1 with previous version 1.8.0 dated 2016-06-06

Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang <michellang@gmail.com>, Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>

Diff between checkmate versions 1.8.0 dated 2016-06-06 and 1.8.1 dated 2016-06-28

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Package bigrquery updated to version 0.3.0 with previous version 0.2.0 dated 2016-03-03

Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between bigrquery versions 0.2.0 dated 2016-03-03 and 0.3.0 dated 2016-06-28

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Package backports updated to version 1.0.3 with previous version 1.0.2 dated 2016-03-18

Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Provides implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>

Diff between backports versions 1.0.2 dated 2016-03-18 and 1.0.3 dated 2016-06-28

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Mon, 27 Jun 2016

Package rrecsys updated to version 0.9.5.4 with previous version 0.9.5.3 dated 2016-06-21

Title: Environment for Assessing Recommender Systems
Description: Provides implementations of several popular recommendation systems. They can process standard recommendation datasets (user/item matrix) as input and generate rating predictions and recommendation lists. Standard algorithm implementations included in this package are: Global/Item/User-Average baselines, Item-Based KNN, FunkSVD, BPR and weighted ALS. They can be assessed according to the standard offline evaluation methodology for recommender systems using measures such as MAE, RMSE, Precision, Recall, AUC, NDCG, RankScore and coverage measures. The package is intended for rapid prototyping of recommendation algorithms and education purposes.
Author: Ludovik Çoba [aut, cre, cph], Markus Zanker [ctb]
Maintainer: Ludovik Çoba <lcoba@unishk.edu.al>

Diff between rrecsys versions 0.9.5.3 dated 2016-06-21 and 0.9.5.4 dated 2016-06-27

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New package pim with initial version 2.0.0.2
Package: pim
Type: Package
Title: Fit Probabilistic Index Models
Version: 2.0.0.2
Date: 2016-06-27
Authors@R: c(person("Joris","Meys", email = "Joris.Meys@UGent.be", role = c('aut', 'cre')),person("Jan","De Neve", email = "Jan.DeNeve@UGent.be", role = 'aut'), person("Nick","Sabbe", role = 'aut'))
Author: Joris Meys [aut, cre], Jan De Neve [aut], Nick Sabbe [aut]
Maintainer: Joris Meys <Joris.Meys@UGent.be>
Description: Fit a probabilistic index model as described in Thas et al <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the modeling function has changed in this new version. The old version is still available at R-Forge. You can install the old package using install.packages('pimold', repos = 'http://R-Forge.R-project.org').
Depends: R (>= 3.0), utils
Imports: methods, stats4, nleqslv, BB
License: GPL (>= 2)
URL: http://r-forge.r-project.org/projects/pim/
Collate: 'CreateScoreFun.R' 'DysData.R' 'EngelData.R' 'Estimators.R' 'pim.poset-class.R' 'pim.environment-class.R' 'pim-package.R' 'pim.formula-class.R' 'pim-class.R' 'pim.summary-class.R' 'Extract.pim.summary.R' 'FEVData.R' 'Getters.R' 'Getters_pim.R' 'Getters_pim.formula.R' 'InternalFunctions.R' 'InternalObjects.R' 'LR.R' 'MHData.R' 'P.R' 'SUData.R' 'add.poset.R' 'as.data.frame.pim.environment.R' 'as.matrix.pim.summary.R' 'coef.R' 'confint.pim.R' 'create.poset.R' 'formula.R' 'has.intercept.R' 'is.complete.R' 'make.posfun.R' 'model.matrix.pim.R' 'new.pim.R' 'new.pim.env.R' 'new.pim.formula.R' 'new.pim.poset.R' 'nobs.R' 'penv.R' 'pim.R' 'pim.fit.R' 'pimdata.R' 'poset.R' 'print.R' 'response.R' 'sandwich.estimator.R' 'summary.R' 'vcov.R' 'vcov.estimators.R' 'vcov.internal.R' 'zzz.R'
Suggests: testthat, MASS
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-27 13:02:40 UTC; Joris
Repository: CRAN
Date/Publication: 2016-06-27 17:22:49

More information about pim at CRAN
Permanent link

New package optiSel with initial version 0.1
Package: optiSel
Type: Package
Title: Optimum Contribution Selection and Pedigree Analysis
Version: 0.1
Date: 2016-06-24
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Depends: R (>= 3.2.4)
Imports: GENLIB, Matrix, Rcsdp, alabama, cccp, kinship2, nadiv, nloptr, pedigree, pspline, stringr, MASS, methods, stats
Description: Computation of optimum contributions of selection candidates in animal breeding, genetic contributions, the native effective size, native genome equivalents, the diversity of native alleles, and pedigree completeness. Moreover, functions are provided for preparing and plotting pedigrees.
License: GPL-2
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-06-27 11:51:59 UTC; Robin
Repository: CRAN
Date/Publication: 2016-06-27 17:22:52

More information about optiSel at CRAN
Permanent link

Package meteR updated to version 1.2 with previous version 1.1 dated 2016-02-26

Title: Fitting and Plotting Tools for the Maximum Entropy Theory of Ecology (METE)
Description: Fit and plot macroecological patterns predicted by the Maximum Entropy Theory of Ecology (METE).
Author: Andy Rominger, Cory Merow
Maintainer: Cory Merow <cory.merow@gmail.com>

Diff between meteR versions 1.1 dated 2016-02-26 and 1.2 dated 2016-06-27

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 meteR-1.2/meteR/DESCRIPTION                                                                                 |   14 
 meteR-1.2/meteR/MD5                                                                                         |  178 +---------
 meteR-1.2/meteR/NAMESPACE                                                                                   |    1 
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 meteR-1.2/meteR/R/logLik.meteDist.R                                                                         |   57 ++-
 meteR-1.2/meteR/R/meteDist2Rank.R                                                                           |    5 
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 meteR-1.2/meteR/R/meteSSF.R                                                                                 |    3 
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 meteR-1.2/meteR/R/residuals.meteRelat.R                                                                     |    4 
 meteR-1.2/meteR/R/sad.meteESF.R                                                                             |   14 
 meteR-1.2/meteR/R/sar.R                                                                                     |   18 -
 meteR-1.2/meteR/R/sar_helper_funs.R                                                                         |    2 
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 meteR-1.2/meteR/man/logLikZ.Rd                                                                              |   14 
 meteR-1.2/meteR/man/meteSAR.Rd                                                                              |   14 
 meteR-1.2/meteR/man/mseZ.Rd                                                                                 |   15 
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Package derivmkts updated to version 0.2.1 with previous version 0.2.0 dated 2016-05-08

Title: Functions and R Code to Accompany Derivatives Markets
Description: A set of pricing and expository functions that should be useful in teaching a course on financial derivatives.
Author: Robert McDonald [aut, cre, cph]
Maintainer: Robert McDonald <rmcd1024@gmail.com>

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Package vardpoor updated to version 0.7.0 with previous version 0.6.4 dated 2016-06-16

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>

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Package fastR updated to version 1.0 with previous version 0.10.2 dated 2015-12-18

Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Fast covariance matrix calculation, Mahalanobis distance and column-wise variances are some of the functions.
Author: Michail Tsagris and Manos Papadakis
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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Package nleqslv updated to version 3.0.2 with previous version 3.0.1 dated 2016-05-03

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>

Diff between nleqslv versions 3.0.1 dated 2016-05-03 and 3.0.2 dated 2016-06-27

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Package CUFF updated to version 1.2 with previous version 1.1 dated 2016-06-01

Title: Charles's Utility Function using Formula
Description: Utility functions that provides wrapper to descriptive base functions like cor, mean and table. It makes use of the formula interface to pass variables to functions. It also provides operators to concatenate (%+%), to repeat (%n%) and manage character vectors for nice display.
Author: Charles-Édouard Giguère
Maintainer: Charles-Édouard Giguère <ce.giguere@gmail.com>

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Package Compind updated to version 1.1.2 with previous version 1.1 dated 2015-09-08

Title: Composite Indicators Functions
Description: Contains several functions to enhance approaches to the Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps.
Author: Francesco Vidoli, Elisa Fusco
Maintainer: Francesco Vidoli <fvidoli@gmail.com>

Diff between Compind versions 1.1 dated 2015-09-08 and 1.1.2 dated 2016-06-27

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Package ldamatch updated to version 1.0.1 with previous version 1.0.0 dated 2016-06-21

Title: Selection of Statistically Similar Research Groups
Description: Select statistically similar research groups by backward selection using various robust algorithms, including a heuristic based on linear discriminant analysis, multiple heuristics based on the test statistic, and parallelized exhaustive search.
Author: Kyle Gorman [aut, cre], Geza Kiss [aut]
Maintainer: Kyle Gorman <kylebgorman@gmail.com>

Diff between ldamatch versions 1.0.0 dated 2016-06-21 and 1.0.1 dated 2016-06-27

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New package SeqMADE with initial version 1.0
Package: SeqMADE
Type: Package
Title: Network Module-Based Model in the Differential Expression Analysis for RNA-Seq
Version: 1.0
Date: 2016-06-27
Author: Mingli Lei, Jia Xu, Li-Ching Huang, Lily Wang, Jing Li
Maintainer: Mingli Lei<leimingli2013@sjtu.edu.cn>
Description: A network module-based generalized linear model for differential expression analysis with the count-based sequence data from RNA-Seq.
License: GPL (>= 2)
Depends: R (>= 2.1.0),MASS
Repository: CRAN
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-06-27 03:06:53 UTC; Mingli Lei
Date/Publication: 2016-06-27 06:59:54

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Package rvg updated to version 0.1.0 with previous version 0.0.9 dated 2016-04-29

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 rstudioapi updated to version 0.6 with previous version 0.5 dated 2016-01-24

Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error messages when it's not.
Author: Hadley Wickham [aut], JJ Allaire [aut, cre], Kevin Ushey [ctb], RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>

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New package IntegrateBs with initial version 0.1.0
Package: IntegrateBs
Title: Integration for B-Spline
Version: 0.1.0
Authors@R: person("Yue", "Bai", email = "bai42@wisc.edu", role = c("aut", "cre"))
Maintainer: Yue Bai <bai42@wisc.edu>
Description: Integrated B-spline function.
Depends: R (>= 3.0.2)
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-26 14:03:37 UTC; dudupiggy
Author: Yue Bai [aut, cre]
Repository: CRAN
Date/Publication: 2016-06-27 06:59:52

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Package gkmSVM updated to version 0.70 with previous version 0.65 dated 2015-12-08

Title: Gapped-Kmer Support Vector Machine
Description: Imports the 'gkmSVM' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms.
Author: Mahmoud Ghandi
Maintainer: Mahmoud Ghandi <mghandi@gmail.com>

Diff between gkmSVM versions 0.65 dated 2015-12-08 and 0.70 dated 2016-06-27

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New package fuzzr with initial version 0.1.0
Package: fuzzr
Type: Package
Title: Fuzz-Test R Functions
Version: 0.1.0
Authors@R: person("Matthew", "Lincoln", email = "matthew.d.lincoln@gmail.com", role = c("aut", "cre"))
Description: Test function arguments with a wide array of inputs, and produce reports summarizing messages, warnings, errors, and returned values.
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: assertthat, progress, purrr, tidyr
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/mdlincoln/fuzzr
BugReports: https://github.com/mdlincoln/fuzzr/issues
NeedsCompilation: no
Packaged: 2016-06-26 17:23:31 UTC; admin
Author: Matthew Lincoln [aut, cre]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-27 07:00:02

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Package future.BatchJobs updated to version 0.12.1 with previous version 0.12.0 dated 2016-06-26

Title: A Future for BatchJobs
Description: Simple parallel and distributed processing using futures that utilizes the 'BatchJobs' framework, e.g. 'fit %<-% { glm(y ~ x + z) }'. This package implements the Future API of the 'future' package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future.BatchJobs versions 0.12.0 dated 2016-06-26 and 0.12.1 dated 2016-06-27

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New package dtplyr with initial version 0.0.1
Package: dtplyr
Title: Data Table Back-End for 'dplyr'
Version: 0.0.1
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph") )
Description: This implements the data table back-end for 'dplyr' so that you can seamlessly use data table and 'dplyr' together.
License: GPL (>= 2)
Imports: dplyr (>= 0.5.0), data.table, lazyeval
Suggests: Lahman, nycflights13, testthat, covr
LazyData: true
RoxygenNote: 5.0.1
URL: https://github.com/hadley/dtplyr
BugReports: https://github.com/hadley/dtplyr/issues
NeedsCompilation: no
Packaged: 2016-06-26 15:50:06 UTC; hadley
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Repository: CRAN
Date/Publication: 2016-06-27 06:59:59

More information about dtplyr at CRAN
Permanent link

Package archivist.github updated to version 0.2.1 with previous version 0.2.0 dated 2016-06-13

Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre], Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>

Diff between archivist.github versions 0.2.0 dated 2016-06-13 and 0.2.1 dated 2016-06-27

 DESCRIPTION |    6 +++---
 MD5         |    8 ++++----
 NEWS.md     |    5 +++++
 R/zzz.R     |   13 ++++++-------
 README.md   |   13 ++++++++++++-
 5 files changed, 30 insertions(+), 15 deletions(-)

More information about archivist.github at CRAN
Permanent link

Sun, 26 Jun 2016

Package survival updated to version 2.39-5 with previous version 2.39-4 dated 2016-05-11

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

Diff between survival versions 2.39-4 dated 2016-05-11 and 2.39-5 dated 2016-06-26

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 survival-2.39-5/survival/R/plot.survfit.R          |    6 
 survival-2.39-5/survival/R/survfit.matrix.R        |   67 ++-------
 survival-2.39-5/survival/R/survfitms.R             |   15 +-
 survival-2.39-5/survival/R/tmerge.R                |   27 ++-
 survival-2.39-5/survival/inst/NEWS.Rd              |   23 +++
 survival-2.39-5/survival/inst/doc/adjcurve.pdf     |binary
 survival-2.39-5/survival/inst/doc/compete.Rnw      |   17 ++
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 survival-2.39-5/survival/inst/doc/splines.R        |   61 +++++---
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 survival-2.39-5/survival/inst/doc/splines.pdf      |binary
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More information about survival at CRAN
Permanent link

Package npROCRegression updated to version 1.0-2 with previous version 1.0-1 dated 2016-06-22

Title: Kernel-Based Nonparametric ROC Regression Modelling
Description: Implements several nonparametric regression approaches for the inclusion of covariate information on the receiver operating characteristic (ROC) framework.
Author: Maria Xose Rodriguez-Alvarez [aut, cre], Javier Roca-Pardinas [aut]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@uvigo.es>

Diff between npROCRegression versions 1.0-1 dated 2016-06-22 and 1.0-2 dated 2016-06-26

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More information about npROCRegression at CRAN
Permanent link

Package magicaxis updated to version 2.0.0 with previous version 1.9.4 dated 2015-06-10

Title: Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>

Diff between magicaxis versions 1.9.4 dated 2015-06-10 and 2.0.0 dated 2016-06-26

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More information about magicaxis at CRAN
Permanent link

Package googlesheets updated to version 0.2.1 with previous version 0.2.0 dated 2016-03-18

Title: Manage Google Spreadsheets from R
Description: Interact with Google Sheets from R.
Author: Jennifer Bryan [aut, cre], Joanna Zhao [aut]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>

Diff between googlesheets versions 0.2.0 dated 2016-03-18 and 0.2.1 dated 2016-06-26

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 googlesheets-0.2.1/googlesheets/R/httr-helpers.R                                     |   21 
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 googlesheets-0.2.1/googlesheets/tests/testthat/test-gs-register.R                    |    2 
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 googlesheets-0.2.1/googlesheets/vignettes/basic-usage.Rmd                            |  349 ++-
 googlesheets-0.2.1/googlesheets/vignettes/formulas-and-formatted-numbers.Rmd         |   46 
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 69 files changed, 2287 insertions(+), 1365 deletions(-)

More information about googlesheets at CRAN
Permanent link

New package future.BatchJobs with initial version 0.12.0
Package: future.BatchJobs
Version: 0.12.0
Depends: R (>= 3.2.0), future (>= 1.0.0)
Imports: BatchJobs (>= 1.6), R.utils
Suggests: listenv, markdown, R.rsp
VignetteBuilder: R.rsp
Title: A Future for BatchJobs
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Simple parallel and distributed processing using futures that utilizes the 'BatchJobs' framework, e.g. 'fit %<-% { glm.fit(x, y) }'. This package implements the Future API of the 'future' package.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/future.BatchJobs
BugReports: https://github.com/HenrikBengtsson/future.BatchJobs/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-26 00:20:15 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-06-26 12:39:35

More information about future.BatchJobs at CRAN
Permanent link

New package tableHTML with initial version 0.2.10
Package: tableHTML
Type: Package
Title: A Tool to Create HTML Tables
Version: 0.2.10
Authors@R: person("Theo", "Boutaris", email = "teoboot2007@hotmail.com", role = c("aut", "cre", "cph"))
URL: https://lyzander.github.io/tableHTML
BugReports: https://github.com/LyzandeR/tableHTML/issues
Depends: R (>= 3.2.0)
Imports: htmltools, magrittr
Description: A tool to easily create and style HTML tables, which are compatible with shiny.
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-25 18:22:36 UTC; teoboot
Author: Theo Boutaris [aut, cre, cph]
Maintainer: Theo Boutaris <teoboot2007@hotmail.com>
Repository: CRAN
Date/Publication: 2016-06-26 09:30:36

More information about tableHTML at CRAN
Permanent link

New package InspectChangepoint with initial version 1.0
Package: InspectChangepoint
Type: Package
Title: High-Dimensional Changepoint Estimation via Sparse Projection
Version: 1.0
Date: 2016-06-24
Author: Tengyao Wang
Maintainer: Tengyao Wang <t.wang@statslab.cam.ac.uk>
Imports: stats, graphics, MASS
Description: Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.
License: GPL-3
NeedsCompilation: no
Packaged: 2016-06-25 17:53:30 UTC; tengyao
Repository: CRAN
Date/Publication: 2016-06-26 09:17:50

More information about InspectChangepoint at CRAN
Permanent link

Package couchDB updated to version 1.4.1 with previous version 1.3.0 dated 2014-09-09

Title: Connect to and Work with CouchDB Databases
Description: Interface to the couchDB document database <http://couchdb.apache.org>.
Author: Aleksander Dietrichson [aut, cre], Frans van Dunn<c3><a9> [ctb]
Maintainer: Aleksander Dietrichson <sasha@xrrch.com>

Diff between couchDB versions 1.3.0 dated 2014-09-09 and 1.4.1 dated 2016-06-26

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More information about couchDB at CRAN
Permanent link

Package XGR updated to version 1.0.2 with previous version 1.0.1 dated 2016-04-22

Title: Exploring Genomic Relations for Precision Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes or SNPs, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks and TF binding sites) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

Diff between XGR versions 1.0.1 dated 2016-04-22 and 1.0.2 dated 2016-06-26

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More information about XGR at CRAN
Permanent link

Package WARN updated to version 1.2-1 with previous version 1.2-0 dated 2016-02-23

Title: Weaning Age Reconstruction with Nitrogen Isotope Analysis
Description: This estimates precise weaning ages for a given skeletal population by analyzing the stable nitrogen isotope ratios of them. Bone collagen turnover rates estimated anew and the approximate Bayesian computation (ABC) were adopted in this package.
Author: Takumi Tsutaya
Maintainer: Takumi Tsutaya <tsutayatakumi@gmail.com>

Diff between WARN versions 1.2-0 dated 2016-02-23 and 1.2-1 dated 2016-06-26

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Package tutorial updated to version 0.4.0 with previous version 0.3.1 dated 2016-05-13

Title: Convert R Markdown Files to DataCamp Light HTML Files
Description: DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light-weight implementation of the DataCamp UI, that allows you to embed interactive exercises inside HTML documents. The tutorial package makes it easy to create these HTML files from R Markdown files. An extension to knitr, tutorial detects appropriately formatted code chunks and replaces them with DataCamp Light readable chunks in the resulting HTML file.
Author: Filip Schouwenaars
Maintainer: Filip Schouwenaars <filip@datacamp.com>

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Package preprocomb updated to version 0.3.0 with previous version 0.2.0 dated 2016-01-01

Title: Tools for Preprocessing Combinations
Description: Preprocessing is often the most time-consuming phase in data analysis and preprocessing transformations interdependent in unexpected ways. This package helps to make preprocessing faster and more effective. It provides an S4 framework for creating and evaluating preprocessing combinations for classification, clustering and outlier detection. The framework supports adding of user-defined preprocessors and preprocessing phases. Default preprocessors can be used for low variance removal, missing value imputation, scaling, outlier removal, noise smoothing, feature selection and class imbalance correction.
Author: Markus Vattulainen
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>

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Package simLife updated to version 0.2.3 with previous version 0.2.1 dated 2016-06-25

Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

Diff between simLife versions 0.2.1 dated 2016-06-25 and 0.2.3 dated 2016-06-26

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Sat, 25 Jun 2016

Package proxy updated to version 0.4-16 with previous version 0.4-15 dated 2015-07-08

Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre], Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package MALDIquant updated to version 1.15 with previous version 1.14 dated 2015-11-18

Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

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Package Gmedian updated to version 1.2.1 with previous version 1.2 dated 2016-04-20

Title: Geometric Median, k-Median Clustering and Robust Median PCA
Description: Fast algorithms for robust estimation with large samples of multivariate observations. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.
Author: Herve Cardot
Maintainer: Herve Cardot <herve.cardot@u-bourgogne.fr>

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New package doFuture with initial version 0.2.0
Package: doFuture
Version: 0.2.0
Title: Foreach Parallel Adaptor using the Future API of the 'future' Package
Depends: future (>= 1.0.0), foreach (>= 1.4.3), iterators (>= 1.0.8)
Suggests: doRNG (>= 1.6), markdown, R.rsp
VignetteBuilder: R.rsp
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Provides a '%dopar%' adaptor such that any type of futures can be used as backends for the 'foreach' framework.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/doFuture
BugReports: https://github.com/HenrikBengtsson/doFuture/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-25 17:25:07 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-06-25 19:53:58

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Package tidytext updated to version 0.1.1 with previous version 0.1.0 dated 2016-04-28

Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using 'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb], David Robinson [aut], Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>

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Package statar updated to version 0.6.2 with previous version 0.6.1 dated 2016-05-20

Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize', 'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>

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New package SPEDInstabR with initial version 1.0
Package: SPEDInstabR
Version: 1.0
Date: 2016-06-23
Title: Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept
Author: Cstor Guisande Gonzlez
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>
Description: From output files obtained from the software ModestR, the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
License: GPL (>= 2)
Encoding: latin1
Depends: R (>= 3.1.1), beanplot, raster, plotrix, TeachingDemos
Repository: CRAN
Packaged: 2016-06-23 20:23:34 UTC; castor
NeedsCompilation: no
Date/Publication: 2016-06-25 19:07:30

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Package simLife updated to version 0.2.1 with previous version 0.2 dated 2016-05-31

Title: Simulation of Fatigue Lifetimes
Description: Provides methods for simulation and analysis of a very general fatigue lifetime model for (metal matrix) composite materials.
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>

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Package rstanarm updated to version 2.10.1 with previous version 2.9.0-4 dated 2016-05-24

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Trustees of Columbia University [cph], R Core Deveopment Team [cph] (R/pp_data.R, R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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New package MixSIAR with initial version 3.1.6
Package: MixSIAR
Title: Bayesian Mixing Models in R
Version: 3.1.6
Authors@R: c( person("Brian", "Stock", email = "b1stock@ucsd.edu", role = c("cre","aut")), person("Brice", "Semmens", email = "semmens@ucsd.edu", role = "aut"), person("Eric", "Ward", role = "ctb"), person("Andrew", "Parnell", role = "ctb"), person("Andrew", "Jackson", role = "ctb"), person("Donald", "Phillips", role = "ctb"), person("Jon", "Moore", role = "ctb"), person("Stuart", "Bearhop", role = "ctb"), person("Richard", "Inger", role = "ctb"))
Description: Creates and runs Bayesian mixing models to analyze biotracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR', and includes both GUI (graphical user interface) and script versions.
Depends: R (>= 3.2.3)
Imports: ggplot2 (>= 1.0.1), rjags (>= 4-4), R2jags (>= 0.5-7), MASS (>= 7.3), RColorBrewer (>= 1.1), reshape (>= 0.8), reshape2 (>= 1.4.1), lattice (>= 0.20), compositions (>= 1.40), ggmcmc (>= 0.7.2), coda (>= 0.18-1)
Suggests: gWidgets (>= 0.0-54), gWidgetsRGtk2 (>= 0.0-83), splancs (>= 2.01-38), knitr, rmarkdown, testthat
SystemRequirements: JAGS (>= 4.1) for the script version, both JAGS and GTK+ for the GUI version. For install instructions, see manual at <https://github.com/brianstock/MixSIAR/blob/master/inst/mixsiar_manual_3.1_small.pdf>
URL: https://github.com/brianstock/MixSIAR
BugReports: https://github.com/brianstock/MixSIAR/issues
License: GPL-3
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-25 00:38:37 UTC; brian
Author: Brian Stock [cre, aut], Brice Semmens [aut], Eric Ward [ctb], Andrew Parnell [ctb], Andrew Jackson [ctb], Donald Phillips [ctb], Jon Moore [ctb], Stuart Bearhop [ctb], Richard Inger [ctb]
Maintainer: Brian Stock <b1stock@ucsd.edu>
Repository: CRAN
Date/Publication: 2016-06-25 19:07:27

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Package metricTester updated to version 1.2.2 with previous version 1.0.2 dated 2016-05-10

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and performance of phylogenetic metrics and null models.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

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Package ks updated to version 1.10.4 with previous version 1.10.3 dated 2016-04-04

Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>

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Package GSIF updated to version 0.5-2 with previous version 0.5-1 dated 2016-05-03

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 googleAuthR updated to version 0.3.1 with previous version 0.3.0 dated 2016-05-09

Title: Easy Authentication with Google OAuth2 API
Description: Create R functions that interact with OAuth2 Google APIs easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre], Jennifer Bryan [ctb], Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

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Package ddpcr updated to version 1.4 with previous version 1.3 dated 2016-06-05

Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package benchmarkme updated to version 0.3.0 with previous version 0.2.3 dated 2016-02-26

Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>

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New package BACCT with initial version 1.0
Package: BACCT
Type: Package
Title: Bayesian Augmented Control for Clinical Trials
Version: 1.0
Date: 2016-06-24
Authors@R: c( person("Hongtao", "Zhang", role = c("aut", "cre"), email = "hongtao.zhang@abbvie.com"), person("Qi", "Tang", role = "aut", email = "qi.tang@abbvie.com") )
Description: Implements the Bayesian Augmented Control (BAC, a.k.a. Bayesian historical data borrowing) method under clinical trial setting by calling 'Just Another Gibbs Sampler' ('JAGS') software. In addition, the 'BACCT' package evaluates user-specified decision rules by computing the type-I error/power, or probability of correct go/no-go decision at interim look. The evaluation can be presented numerically or graphically. Users need to have 'JAGS' 4.0.0 or newer installed due to a compatibility issue with 'rjags' package. Currently, the package implements the BAC method for binary outcome only. Support for continuous and survival endpoints will be added in future releases. We would like to thank AbbVie's Statistical Innovation group and Clinical Statistics group for their support in developing the 'BACCT' package.
Depends: R (>= 2.10)
Imports: rjags, ggplot2, reshape2
License: GPL (>= 3)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-24 19:05:19 UTC; zhanghx5
Author: Hongtao Zhang [aut, cre], Qi Tang [aut]
Maintainer: Hongtao Zhang <hongtao.zhang@abbvie.com>
Repository: CRAN
Date/Publication: 2016-06-25 19:07:22

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Package asymmetry updated to version 1.1 with previous version 1.0 dated 2016-04-26

Title: The Slide-Vector Model for Multidimensional Scaling of Asymmetric Data
Description: The slide-vector model is provided in this package together with functions for the analysis and graphical display of asymmetry. The slide vector model is a scaling model for asymmetric data. A distance model is fitted to the symmetric part of the data whereas the asymmetric part of the data is represented by projections of the coordinates onto the slide-vector. The slide-vector points in the direction of large asymmetries in the data. The distance is modified in such a way that the distance between two points that are parallel to the slide-vector is larger in the direction of this vector. The distance is smaller in the opposite direction. If the line connecting two points is perpendicular to the slide-vector the difference between the two projections is zero. In this case the distance between the two points is symmetric. The algorithm for fitting this model is derived from the majorization approach to multidimensional scaling.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>

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Package AnalyzeTS updated to version 2.0 with previous version 1.9 dated 2016-05-26

Title: Analyze (Fuzzy) Time Series
Description: Analyze (fuzzy) time series, calculate AIC value of common time series models and propose the best model. Fuzzy time series can be analyzed by "Chen", "Sing", "Heuristic" and "Chen-Hsu" models. The Abbasov-Mamedova model and an improved version of the Abbasov-Mamedova model is included as well.
Author: Tran Thi Ngoc Han, Doan Hai Nghi, Mai Thi Hong Diem, Nguyen Thi Diem My, Hong Viet Minh, Vo Van Tai.
Maintainer: Hong Viet Minh <hongvietminh@gmail.com>

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Fri, 24 Jun 2016

Package validate updated to version 0.1.5 with previous version 0.1.4 dated 2016-04-15

Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront data with them and analyze or visualize the results. The package supports rules that are per-field, in-record, cross-record or cross-dataset. Rules can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut], Edwin de Jonge [aut], Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package UpSetR updated to version 1.2.2 with previous version 1.2.1 dated 2016-06-01

Title: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.
Author: Jake Conway [cre], Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>

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Package TraMineR updated to version 1.8-12 with previous version 1.8-11.1 dated 2016-01-29

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph], Nicolas Muller [aut], Reto Buergin [aut], Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

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Package Thermimage updated to version 2.1.1 with previous version 2.1 dated 2016-05-18

Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations.
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>

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Package sparsediscrim updated to version 0.2.3 with previous version 0.2 dated 2014-03-31

Title: Sparse and Regularized Discriminant Analysis
Description: A collection of sparse and regularized discriminant analysis methods intended for small-sample, high-dimensional data sets. The package features the High-Dimensional Regularized Discriminant Analysis classifier.
Author: John A. Ramey <johnramey@gmail.com>
Maintainer: John A. Ramey <johnramey@gmail.com>

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 sparsediscrim-0.2.3/sparsediscrim/man/generate_intraclass.Rd       |   85 +--
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 sparsediscrim-0.2.3/sparsediscrim/man/quadform.Rd                  |   20 
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 sparsediscrim-0.2.3/sparsediscrim/man/regdiscrim_estimates.Rd      |   84 +--
 sparsediscrim-0.2.3/sparsediscrim/man/risk_stein.Rd                |   45 -
 sparsediscrim-0.2.3/sparsediscrim/man/sdlda.Rd                     |  174 +++----
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 sparsediscrim-0.2.3/sparsediscrim/man/smdlda.Rd                    |  156 ++----
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 sparsediscrim-0.2.3/sparsediscrim/man/solve_chol.Rd                |    8 
 sparsediscrim-0.2.3/sparsediscrim/man/tong_mean_shrinkage.Rd       |   24 
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More information about sparsediscrim at CRAN
Permanent link

Package SpaDES updated to version 1.2.0 with previous version 1.1.4 dated 2016-04-20

Title: Develop and Run Spatially Explicit Discrete Event Simulation Models
Description: Easily implement a variety of simulation models, with a focus on spatially explicit agent based models. These include raster-based, event-based, and agent-based models. The core simulation components are built upon a discrete event simulation framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules. Included are numerous tools to visualize raster and other maps. The suggested package `fastshp` can be installed with `install.packages("fastshp", repos="http://rforge.net", type="source")`.
Author: Alex M Chubaty [aut, cre], Eliot J B McIntire [aut], Yong Luo [ctb], Steve Cumming [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>

Diff between SpaDES versions 1.1.4 dated 2016-04-20 and 1.2.0 dated 2016-06-24

 DESCRIPTION                                                      |   24 
 MD5                                                              |  468 
 NAMESPACE                                                        |  989 -
 NEWS                                                             |  483 
 R/SELES.R                                                        |  555 
 R/agent.R                                                        |  176 
 R/check.R                                                        |  546 
 R/checkpoint.R                                                   |  676 -
 R/copy.R                                                         |   78 
 R/environment.R                                                  |  408 
 R/experiment.R                                                   | 1321 +-
 R/helpers.R                                                      |  259 
 R/initialize.R                                                   |  719 -
 R/load.R                                                         |  610 -
 R/mapReduce.R                                                    |  164 
 R/mergeRaster.R                                                  |only
 R/misc-methods.R                                                 | 1452 +-
 R/module-dependencies-class.R                                    |  450 
 R/module-dependencies-methods.R                                  |  536 
 R/module-repository.R                                            |  899 -
 R/module-template.R                                              | 1564 +-
 R/moduleCoverage.R                                               |  300 
 R/moduleMetadata.R                                               |  152 
 R/movement.R                                                     |  252 
 R/neighbourhood.R                                                | 1547 +-
 R/numerical-comparisons.R                                        |   72 
 R/plotting-classes.R                                             |  580 -
 R/plotting-colours.R                                             | 1144 +
 R/plotting-diagrams.R                                            |  612 -
 R/plotting-helpers.R                                             | 1516 +-
 R/plotting-other.R                                               |  768 -
 R/plotting.R                                                     | 3980 +++---
 R/priority.R                                                     |   86 
 R/probability.R                                                  |   94 
 R/progress.R                                                     |  234 
 R/save.R                                                         |  296 
 R/shine.R                                                        |  694 -
 R/simList-accessors.R                                            | 5777 +++++-----
 R/simList-class.R                                                |  512 
 R/simulation.R                                                   | 2000 +--
 R/spades-classes.R                                               |   72 
 R/spades-package.R                                               |  843 -
 R/splitRaster.R                                                  |  281 
 R/spread-process.R                                               | 2021 ++-
 R/times.R                                                        |  907 -
 R/zzz.R                                                          |   30 
 README.md                                                        |  149 
 build/vignette.rds                                               |binary
 demo/00Index                                                     |    4 
 demo/spades-simulation.R                                         |  102 
 inst/doc/i-introduction.R                                        |   78 
 inst/doc/i-introduction.Rmd                                      |  660 -
 inst/doc/i-introduction.html                                     |  740 -
 inst/doc/ii-modules.R                                            |  705 -
 inst/doc/ii-modules.Rmd                                          | 1617 +-
 inst/doc/ii-modules.html                                         | 2081 +--
 inst/doc/iii-plotting.R                                          |  306 
 inst/doc/iii-plotting.Rmd                                        |  824 -
 inst/doc/iii-plotting.html                                       |  771 -
 inst/examples                                                    |only
 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R   |   44 
 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd |   88 
 inst/sampleModules/caribouMovement/caribouMovement.R             |  308 
 inst/sampleModules/fireSpread/fireSpread.R                       |  368 
 inst/sampleModules/randomLandscapes/randomLandscapes.R           |  232 
 man/Plot.Rd                                                      |  621 -
 man/SELESagentLocation.Rd                                        |   58 
 man/SELESnumAgents.Rd                                            |   60 
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 man/SpaDES-package.Rd                                            |  802 -
 man/addDepends.Rd                                                |   58 
 man/adj.Rd                                                       |  198 
 man/append_attr.Rd                                               |   78 
 man/arrangeViewports.Rd                                          |   48 
 man/arrangement-class.Rd                                         |  144 
 man/assignSpaDES.Rd                                              |   66 
 man/cache.Rd                                                     |  103 
 man/changeObjEnv.Rd                                              |  124 
 man/checkModule.Rd                                               |   58 
 man/checkObject.Rd                                               |  112 
 man/checkParams.Rd                                               |   72 
 man/checkPath.Rd                                                 |   76 
 man/checkpoint.Rd                                                |  102 
 man/checksums.Rd                                                 |   92 
 man/cir.Rd                                                       |  248 
 man/classFilter.Rd                                               |  202 
 man/clearPlot.Rd                                                 |   80 
 man/clearStubArtifacts.Rd                                        |   58 
 man/copy.Rd                                                      |   58 
 man/crw.Rd                                                       |  154 
 man/defineModule.Rd                                              |  114 
 man/defineParameter.Rd                                           |  108 
 man/depsEdgeList.Rd                                              |   72 
 man/depsGraph.Rd                                                 |   68 
 man/depsLoadOrder.Rd                                             |   68 
 man/depsPruneEdges.Rd                                            |   54 
 man/dev.Rd                                                       |   63 
 man/digest.Rd                                                    |   54 
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 man/distances.Rd                                                 |only
 man/divergentColors.Rd                                           |   98 
 man/doEvent.Rd                                                   |   86 
 man/downloadData.Rd                                              |   70 
 man/downloadModule.Rd                                            |  128 
 man/dwrpnorm2.Rd                                                 |   88 
 man/emptyEventList.Rd                                            |  120 
 man/emptyMetadata.Rd                                             |   48 
 man/equalExtent.Rd                                               |   44 
 man/eventDiagram.Rd                                              |  110 
 man/existsSpaDES.Rd                                              |   52 
 man/experiment.Rd                                                |  821 -
 man/fileExt.Rd                                                   |   42 
 man/fileName.Rd                                                  |   42 
 man/fileTable.Rd                                                 |   74 
 man/fillInputRows.Rd                                             |   34 
 man/fillOutputRows.Rd                                            |   34 
 man/findFactors.Rd                                               |   38 
 man/findObjects.Rd                                               |only
 man/ganttStatus.Rd                                               |   58 
 man/gaussmap.Rd                                                  |   98 
 man/getColors.Rd                                                 |   68 
 man/getFileName.Rd                                               |   54 
 man/getModuleVersion.Rd                                          |   58 
 man/getSpaDES.Rd                                                 |   48 
 man/grid-functions.Rd                                            |   46 
 man/heading.Rd                                                   |  128 
 man/identifyGrobToPlot.Rd                                        |   78 
 man/inRange.Rd                                                   |   60 
 man/initialize-method.Rd                                         |   34 
 man/initiateAgents.Rd                                            |  161 
 man/inputObjects.Rd                                              |   62 
 man/layerNames.Rd                                                |   90 
 man/loadFiles.Rd                                                 |  176 
 man/loadPackages.Rd                                              |  102 
 man/ls-method.Rd                                                 |   58 
 man/ls_str-method.Rd                                             |   58 
 man/makeColorMatrix.Rd                                           |  110 
 man/makeDigestible.Rd                                            |   88 
 man/makeLayout.Rd                                                |   66 
 man/makeLines.Rd                                                 |  115 
 man/makeList.Rd                                                  |   54 
 man/makeSpadesPlot.Rd                                            |   88 
 man/makeViewports.Rd                                             |   56 
 man/maxTimeunit.Rd                                               |   52 
 man/mergeRaster.Rd                                               |only
 man/minTimeunit.Rd                                               |   54 
 man/moduleCoverage.Rd                                            |  128 
 man/moduleDeps-class.Rd                                          |  146 
 man/moduleDiagram.Rd                                             |   80 
 man/moduleMetadata.Rd                                            |   82 
 man/newModule.Rd                                                 |  232 
 man/newPlot.Rd                                                   |   58 
 man/newProgressBar.Rd                                            |   50 
 man/nlayers.Rd                                                   |   77 
 man/normPath.Rd                                                  |   68 
 man/objectDiagram.Rd                                             |   68 
 man/objectNames.Rd                                               |   64 
 man/openModules.Rd                                               |  106 
 man/packages.Rd                                                  |   50 
 man/paddedFloatToChar.Rd                                         |   72 
 man/parseArgs.Rd                                                 |   58 
 man/parseModule.Rd                                               |   54 
 man/patchSize.Rd                                                 |   30 
 man/plotGrob.Rd                                                  |  215 
 man/prepareRaster.Rd                                             |   66 
 man/priority.Rd                                                  |   64 
 man/randomPolygons.Rd                                            |  109 
 man/rasterToMemory.Rd                                            |   62 
 man/rasterizeReduce.Rd                                           |  120 
 man/rings.Rd                                                     |only
 man/rndstr.Rd                                                    |  130 
 man/saveFiles.Rd                                                 |  138 
 man/scheduleEvent.Rd                                             |  132 
 man/setColors.Rd                                                 |  194 
 man/shine.Rd                                                     |  136 
 man/show-method.Rd                                               |   32 
 man/sim2gantt.Rd                                                 |   72 
 man/simDeps-class.Rd                                             |   44 
 man/simInit.Rd                                                   |  390 
 man/simList-accessors-envir.Rd                                   |   96 
 man/simList-accessors-events.Rd                                  |  194 
 man/simList-accessors-inout.Rd                                   |  610 -
 man/simList-accessors-modules.Rd                                 |  174 
 man/simList-accessors-objects.Rd                                 |  158 
 man/simList-accessors-params.Rd                                  |  300 
 man/simList-accessors-paths.Rd                                   |  210 
 man/simList-accessors-times.Rd                                   |  343 
 man/simList-class.Rd                                             |  222 
 man/simList_-class.Rd                                            |   46 
 man/sortDotsFirst.Rd                                             |   48 
 man/spades-classes.Rd                                            |   90 
 man/spades.Rd                                                    |  214 
 man/spadesEnv.Rd                                                 |   30 
 man/spadesGrob-class.Rd                                          |  102 
 man/spadesMaps.Rd                                                |   50 
 man/spadesMouseClicks.Rd                                         |  136 
 man/spadesPlot-class.Rd                                          |   96 
 man/spadesPlotObjects-class.Rd                                   |   44 
 man/spadesPlottables-class.Rd                                    |   46 
 man/spadesTime.Rd                                                |  160 
 man/spatialObjects-class.Rd                                      |   46 
 man/specnumperpatch-probs.Rd                                     |   82 
 man/splitRaster.Rd                                               |  203 
 man/spread.Rd                                                    |  699 -
 man/timeConversion.Rd                                            |  186 
 man/unittrim.Rd                                                  |   44 
 man/unparsed.Rd                                                  |   50 
 man/updateList.Rd                                                |  104 
 man/updateSpadesPlot.Rd                                          |   62 
 man/versionWarning.Rd                                            |   74 
 man/wrap.Rd                                                      |  172 
 man/zipModule.Rd                                                 |   80 
 tests/test-all.R                                                 |    4 
 tests/testthat/test-Plot.R                                       | 1240 +-
 tests/testthat/test-adj.R                                        |  635 -
 tests/testthat/test-checkPath.R                                  |  144 
 tests/testthat/test-checkpoint.R                                 |   76 
 tests/testthat/test-downloadModule.R                             |  193 
 tests/testthat/test-environment.R                                |   22 
 tests/testthat/test-examples.R                                   |    6 
 tests/testthat/test-experiment.R                                 |  406 
 tests/testthat/test-inRange.R                                    |   38 
 tests/testthat/test-load.R                                       |  571 
 tests/testthat/test-mapReduce.R                                  |  206 
 tests/testthat/test-module-deps-methods.R                        |  302 
 tests/testthat/test-module-template.R                            |   94 
 tests/testthat/test-paths.R                                      |  112 
 tests/testthat/test-save.R                                       |  195 
 tests/testthat/test-simList.R                                    |  441 
 tests/testthat/test-simulation.R                                 |  220 
 tests/testthat/test-splitRaster.R                                |only
 tests/testthat/test-spread.R                                     | 1175 +-
 tests/testthat/test-timeunits.R                                  |  214 
 tests/testthat/test-updateList.R                                 |   32 
 vignettes/bibliography.bib                                       |  270 
 vignettes/i-introduction.Rmd                                     |  660 -
 vignettes/ii-modules.Rmd                                         | 1617 +-
 vignettes/iii-plotting.Rmd                                       |  824 -
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More information about SpaDES at CRAN
Permanent link

Package rstan updated to version 2.10.1 with previous version 2.9.0-3 dated 2016-02-11

Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), Hadley Wickham [cph] (R/rtools.R), Joel de Guzman [cph] (Boost), John Fletcher [cph] (Boost), Thomas Heller [cph] (Boost), Eric Niebler [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between rstan versions 2.9.0-3 dated 2016-02-11 and 2.10.1 dated 2016-06-24

 rstan-2.10.1/rstan/DESCRIPTION                                       |   57 
 rstan-2.10.1/rstan/MD5                                               |  189 -
 rstan-2.10.1/rstan/NAMESPACE                                         |    1 
 rstan-2.10.1/rstan/R/AllClass.R                                      |    2 
 rstan-2.10.1/rstan/R/Rcpp_module_def.R                               |    2 
 rstan-2.10.1/rstan/R/chains.R                                        |    2 
 rstan-2.10.1/rstan/R/cxxdso-class.R                                  |    8 
 rstan-2.10.1/rstan/R/cxxfunplus.R                                    |    6 
 rstan-2.10.1/rstan/R/expose_stan_functions.R                         |   23 
 rstan-2.10.1/rstan/R/git_rstan_head.R                                |    3 
 rstan-2.10.1/rstan/R/lookup.R                                        |    6 
 rstan-2.10.1/rstan/R/makefile_op.R                                   |    2 
 rstan-2.10.1/rstan/R/misc.R                                          |   12 
 rstan-2.10.1/rstan/R/monitor.R                                       |    2 
 rstan-2.10.1/rstan/R/options.R                                       |    2 
 rstan-2.10.1/rstan/R/pairs.R                                         |   16 
 rstan-2.10.1/rstan/R/plugin.R                                        |   34 
 rstan-2.10.1/rstan/R/rstan.R                                         |    2 
 rstan-2.10.1/rstan/R/rstan_package_skeleton.R                        |   22 
 rstan-2.10.1/rstan/R/rtools.R                                        |    2 
 rstan-2.10.1/rstan/R/stan_csv.R                                      |    4 
 rstan-2.10.1/rstan/R/stan_demo.R                                     |   11 
 rstan-2.10.1/rstan/R/stan_plot.R                                     |   42 
 rstan-2.10.1/rstan/R/stan_plot_helpers.R                             |   42 
 rstan-2.10.1/rstan/R/stanc.R                                         |    8 
 rstan-2.10.1/rstan/R/stanfit-class.R                                 |   24 
 rstan-2.10.1/rstan/R/stanmodel-class.R                               |   32 
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 rstan-2.10.1/rstan/src/misc.cpp                                      |    2 
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More information about rstan at CRAN
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Package Fragman updated to version 1.0.5 with previous version 1.0.4 dated 2016-04-25

Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

Diff between Fragman versions 1.0.4 dated 2016-04-25 and 1.0.5 dated 2016-06-24

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Package chunked updated to version 0.3 with previous version 0.2.1 dated 2016-04-07

Title: Chunkwise Text-File Processing for 'dplyr'
Description: Text data can be processed chunkwise using 'dplyr' commands. These are recorded and executed per data chunk, so large files can be processed with limited memory using the 'LaF' package.
Author: Edwin de Jonge
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

Diff between chunked versions 0.2.1 dated 2016-04-07 and 0.3 dated 2016-06-24

 DESCRIPTION                 |   12 ++++++------
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More information about chunked at CRAN
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New package dlstats with initial version 0.0.5
Package: dlstats
Title: Download Stats of R Packages
Version: 0.0.5
Authors@R: c(person(given = "Guangchuang", family = "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")) )
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages. Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <http://cranlogs.r-pkg.org>. 'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Depends: R (>= 3.3.0)
Imports: jsonlite, magrittr, utils
Suggests: ggplot2, knitr, tidyr
License: Artistic-2.0
VignetteBuilder: knitr
ByteCompile: true
Encoding: UTF-8
LazyData: true
URL: https://github.com/GuangchuangYu/dlstats
BugReports: https://github.com/GuangchuangYu/dlstats/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-23 01:35:10 UTC; guangchuangyu
Author: Guangchuang Yu [aut, cre]
Repository: CRAN
Date/Publication: 2016-06-24 20:17:40

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Package broom updated to version 0.4.1 with previous version 0.4.0 dated 2015-11-30

Title: Convert Statistical Analysis Objects into Tidy Data Frames
Description: Convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>

Diff between broom versions 0.4.0 dated 2015-11-30 and 0.4.1 dated 2016-06-24

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Permanent link

New package BTR with initial version 1.2.3
Package: BTR
Type: Package
Title: Training and Analysing Asynchronous Boolean Models
Version: 1.2.3
Date: 2016-6-23
Author: Chee Yee Lim
Maintainer: Chee Yee Lim <cyl49@cam.ac.uk>
Description: Tools for inferring asynchronous Boolean models from single-cell expression data.
Depends: R (>= 3.0.3), methods
Imports: parallel, Rcpp (>= 0.11.4), foreach (>= 1.4.1), doParallel (>= 1.0.8), poweRlaw (>= 0.30.0), diptest (>= 0.75-7), igraph (>= 1.0.1), infotheo (>= 1.2.0), entropy (>= 1.2.1)
LinkingTo: Rcpp
License: GPL-3
LazyData: true
Suggests: bnlearn (>= 3.8.1), knitr, rmarkdown
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-24 15:44:44 UTC; cylim
Repository: CRAN
Date/Publication: 2016-06-24 19:13:51

More information about BTR at CRAN
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Package unfoldr updated to version 0.5.8 with previous version 0.5.7 dated 2016-06-24

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, spherocylinders 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>

Diff between unfoldr versions 0.5.7 dated 2016-06-24 and 0.5.8 dated 2016-06-24

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 src/GeometricPrimitives.h   |   23 +++----
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 src/Intersector.h           |  135 ++++++++++++++++++++------------------------
 src/SimCylinder.cpp         |    2 
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Package rtson updated to version 1.2 with previous version 1.1 dated 2015-12-02

Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>

Diff between rtson versions 1.1 dated 2015-12-02 and 1.2 dated 2016-06-24

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 MD5                         |   18 +++---
 NAMESPACE                   |    2 
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Package dplyr updated to version 0.5.0 with previous version 0.4.3 dated 2015-09-01

Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre], Romain Francois [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between dplyr versions 0.4.3 dated 2015-09-01 and 0.5.0 dated 2016-06-24

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Package devtools updated to version 1.12.0 with previous version 1.11.1 dated 2016-04-21

Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package BerlinData (with last version 1.0.1) was removed from CRAN

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

2014-12-08 1.0.1
2014-05-11 1.0.0

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Package xml2 updated to version 1.0.0 with previous version 0.1.2 dated 2015-09-01

Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre], James Hester [aut], Jeroen Ooms [ctb], RStudio [cph], R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package searchConsoleR updated to version 0.2.1 with previous version 0.2.0 dated 2016-04-03

Title: Google Search Console R Client
Description: Provides an interface with the Google Search Console, formally called Google Webmaster Tools.
Author: Mark Edmondson [aut, cre], Jennifer Bryan [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>

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New package NoiseFiltersR with initial version 0.1.0
Package: NoiseFiltersR
Type: Package
Title: Label Noise Filters for Data Preprocessing in Classification
Version: 0.1.0
Authors@R: c( person("Pablo", "Morales", email = "pablomoralvarez@gmail.com", role = c("aut")), person("Julian", "Luengo", email = "julianlm@decsai.ugr.es", role = c("aut","cre")), person("Luis P.F.", "Garcia", role = c("aut")), person("Ana C.", "Lorena", role = c("aut")), person("Andre C.P.L.F.", "de Carvalho", role = c("aut")), person("Francisco", "Herrera", role = c("aut")))
Description: An extensive implementation of state-of-the-art and classical algorithms to preprocess label noise in classification problems.
License: GPL-3
LazyData: TRUE
Imports: RWeka, kknn, nnet, caret, e1071, rpart, randomForest, MASS, rJava, stats, utils
Depends: R (>= 3.3.0)
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-24 10:17:13 UTC; pablo
Author: Pablo Morales [aut], Julian Luengo [aut, cre], Luis P.F. Garcia [aut], Ana C. Lorena [aut], Andre C.P.L.F. de Carvalho [aut], Francisco Herrera [aut]
Maintainer: Julian Luengo <julianlm@decsai.ugr.es>
Repository: CRAN
Date/Publication: 2016-06-24 12:34:50

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Package extraDistr updated to version 1.7.2 with previous version 1.7.1 dated 2016-06-18

Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>

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 extraDistr-1.7.2/extraDistr/src/logarithmic-series-distribution.cpp     |    5 
 extraDistr-1.7.2/extraDistr/src/mixture-of-normal-distributions.cpp     |   18 -
 extraDistr-1.7.2/extraDistr/src/mixture-of-poisson-distributions.cpp    |   18 -
 extraDistr-1.7.2/extraDistr/src/multinomial-distribution.cpp            |   14 
 extraDistr-1.7.2/extraDistr/src/non-standard-t-distribution.cpp         |    2 
 extraDistr-1.7.2/extraDistr/src/non-standart-beta-distribution.cpp      |    2 
 extraDistr-1.7.2/extraDistr/src/pareto-distribution.cpp                 |    2 
 extraDistr-1.7.2/extraDistr/src/proportion-distribution.cpp             |    2 
 extraDistr-1.7.2/extraDistr/src/shared.cpp                              |    2 
 extraDistr-1.7.2/extraDistr/src/slash-distribution.cpp                  |    5 
 77 files changed, 554 insertions(+), 400 deletions(-)

More information about extraDistr at CRAN
Permanent link

New package conclust with initial version 1.0
Package: conclust
Type: Package
Title: Pairwise Constraints Clustering
Version: 1.0
Date: 2016-06-22
Author: Tran Khanh Hiep, Nguyen Minh Duc
Maintainer: Tran Khanh Hiep <hieptkse03059@fpt.edu.vn>
Description: There are 3 main functions in this package: ckmeans(), lcvqe() and mpckm(). They take an unlabeled dataset and two lists of must-link and cannot-link constraints as input and produce a clustering as output.
License: GPL-3
NeedsCompilation: no
Packaged: 2016-06-24 10:06:02 UTC; Hiep
Repository: CRAN
Date/Publication: 2016-06-24 12:20:11

More information about conclust at CRAN
Permanent link

Package XLConnectJars updated to version 0.2-12 with previous version 0.2-9 dated 2014-08-14

Title: JAR Dependencies for the XLConnect Package
Description: Provides external JAR dependencies for the XLConnect package.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI, Apache XMLBeans)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>

Diff between XLConnectJars versions 0.2-9 dated 2014-08-14 and 0.2-12 dated 2016-06-24

 XLConnectJars-0.2-12/XLConnectJars/DESCRIPTION                     |   14 +++++-----
 XLConnectJars-0.2-12/XLConnectJars/MD5                             |   12 ++++----
 XLConnectJars-0.2-12/XLConnectJars/NEWS                            |    3 ++
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 XLConnectJars-0.2-9/XLConnectJars/inst/java/ooxml-schemas-1.1.jar  |only
 8 files changed, 20 insertions(+), 18 deletions(-)

More information about XLConnectJars at CRAN
Permanent link

Package XLConnect updated to version 0.2-12 with previous version 0.2-11 dated 2015-03-01

Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons Codec), Stephen Colebourne [ctb, cph] (Joda-Time Java library), Graph Builder [ctb, cph] (Curvesapi Java library)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>

Diff between XLConnect versions 0.2-11 dated 2015-03-01 and 0.2-12 dated 2016-06-24

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 XLConnect-0.2-12/XLConnect/DESCRIPTION                                         |   19 
 XLConnect-0.2-12/XLConnect/MD5                                                 |  276 +++++----
 XLConnect-0.2-12/XLConnect/NAMESPACE                                           |    1 
 XLConnect-0.2-12/XLConnect/NEWS                                                |   17 
 XLConnect-0.2-12/XLConnect/R/XLConnectSettings.R                               |    6 
 XLConnect-0.2-12/XLConnect/R/aref.R                                            |    2 
 XLConnect-0.2-12/XLConnect/R/aref2idx.R                                        |    2 
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 XLConnect-0.2-12/XLConnect/R/classToXlcType.R                                  |    2 
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 XLConnect-0.2-12/XLConnect/R/constants.R                                       |    2 
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 XLConnect-0.2-12/XLConnect/inst/unitTests/runit.writeAndReadWorksheet.R        |  280 +++++-----
 XLConnect-0.2-12/XLConnect/java/README                                         |   10 
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 145 files changed, 649 insertions(+), 517 deletions(-)

More information about XLConnect at CRAN
Permanent link

Package timetools updated to version 1.8.0 with previous version 1.7.4 dated 2016-03-24

Title: Seasonal/Sequential (Instants/Durations, Even or not) Time Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>

Diff between timetools versions 1.7.4 dated 2016-03-24 and 1.8.0 dated 2016-06-24

 DESCRIPTION               |    8 ++++----
 MD5                       |   12 ++++++------
 R/TimeInstantDataFrame.R  |   42 +++++++++++++++++++++++++++++++++++++++---
 R/TimeIntervalDataFrame.R |   42 +++++++++++++++++++++++++++++++++++++++---
 R/split.R                 |    4 ++--
 README                    |   10 ++++++++++
 man/timetools-package.Rd  |    4 ++--
 7 files changed, 102 insertions(+), 20 deletions(-)

More information about timetools at CRAN
Permanent link

New package VetResearchLMM with initial version 0.1.0
Package: VetResearchLMM
Type: Package
Title: Linear Mixed Models - An Introduction with Applications in Veterinary Research
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Luc", "Duchateau"), email = "Luc.Duchateau@ugent.be", role = "ctb") , person(c("Paul", "Janssen"), email = "paul.janssen@uhasselt.be", role = "ctb") , person(c("John", "Rowlands"), email = " ", role = "ctb") )
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: R Codes and Datasets for Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998). Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
Depends: R (>= 3.1)
Imports: ggplot2, lme4, nlme, lmerTest, multcomp
License: GPL-2
URL:
LazyData: TRUE
RoxygenNote: 5.0.1.9000
NeedsCompilation: no
Packaged: 2016-06-23 03:40:45 UTC; yaseen
Author: Muhammad Yaseen [aut, cre], Luc Duchateau [ctb], Paul Janssen [ctb], John Rowlands [ctb]
Repository: CRAN
Date/Publication: 2016-06-24 09:53:26

More information about VetResearchLMM at CRAN
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Package StanHeaders updated to version 2.10.0-2 with previous version 2.10.0 dated 2016-06-22

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between StanHeaders versions 2.10.0 dated 2016-06-22 and 2.10.0-2 dated 2016-06-24

 StanHeaders-2.10.0-2/StanHeaders/DESCRIPTION                            |    8 
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More information about StanHeaders at CRAN
Permanent link

New package synthACS with initial version 0.4.4
Package: synthACS
Title: Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data
Version: 0.4.4
Authors@R: person("Alex", "Whitworth",,email = "whitworth.alex@gmail.com", c("aut", "cre"))
Description: Firstly provides a wrapper to library(acs) to access numerous American Community Survey (ACS) base tables which may be of interest to many researchers. Secondly, it builds synthetic micro-datasets of ACS data at any specified geographic level with 10 default individual attributes. Thirdly, the package provides functionality for users to add additional ACS & non-ACS data attributes to micro-datasets based on macro population characteristics. And finally, the package also conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default.
Depends: R (>= 3.2.3), acs (>= 1.2), data.table (>= 1.9.6)
Imports: Rcpp
License: MIT + file LICENSE
LazyData: true
Suggests: testthat, tigris (>= 0.3), sp (>= 1.2), leaflet (>= 1.0), shiny (>= 0.13), rgdal (>= 1.1)
RoxygenNote: 5.0.1
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-06-23 17:55:20 UTC; awhitworth
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-24 09:53:55

More information about synthACS at CRAN
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Package ranger updated to version 0.5.0 with previous version 0.4.0 dated 2016-04-07

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>

Diff between ranger versions 0.4.0 dated 2016-04-07 and 0.5.0 dated 2016-06-24

 DESCRIPTION                              |   20 -
 MD5                                      |   83 ++--
 NAMESPACE                                |    2 
 NEWS                                     |    8 
 R/RcppExports.R                          |    4 
 R/getTerminalNodeIDs.R                   |    2 
 R/holdoutRF.R                            |only
 R/importance.R                           |   89 ++++
 R/predict.R                              |   78 ++--
 R/print.R                                |    1 
 R/ranger.R                               |  228 +++++++++--
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 man/ranger.Rd                            |   58 ++
 src/AAA_check_cpp11.cpp                  |    3 
 src/Forest.cpp                           |  102 +++--
 src/Forest.h                             |   18 
 src/ForestProbability.cpp                |   11 
 src/RcppExports.cpp                      |    9 
 src/Tree.cpp                             |  115 +++--
 src/Tree.h                               |    8 
 src/TreeClassification.cpp               |    4 
 src/TreeProbability.cpp                  |  142 ++++---
 src/TreeProbability.h                    |   12 
 src/TreeRegression.cpp                   |  121 ++++++
 src/TreeRegression.h                     |    9 
 src/TreeSurvival.cpp                     |  142 ++++++-
 src/TreeSurvival.h                       |    2 
 src/globals.h                            |   25 +
 src/rangerCpp.cpp                        |    4 
 src/utility.cpp                          |  302 +++++++++++++++
 src/utility.h                            |  171 ++++++++
 src/version.h                            |    2 
 tests/testthat/test_char.R               |only
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 tests/testthat/test_csrf.R               |   10 
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 tests/testthat/test_predict.R            |only
 tests/testthat/test_print.R              |only
 tests/testthat/test_probability.R        |only
 tests/testthat/test_ranger.R             |  601 ++-----------------------------
 tests/testthat/test_regression.R         |only
 tests/testthat/test_seed.R               |only
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 tests/testthat/test_survival.R           |only
 tests/testthat/test_unordered.R          |only
 51 files changed, 1496 insertions(+), 898 deletions(-)

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Package randomLCA updated to version 1.0-9 with previous version 1.0-8 dated 2016-05-20

Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>

Diff between randomLCA versions 1.0-8 dated 2016-05-20 and 1.0-9 dated 2016-06-24

 DESCRIPTION                |   12 -
 MD5                        |   28 +--
 NAMESPACE                  |    1 
 R/fitAdaptRandom.R         |   57 ++++---
 R/fitAdaptRandom2.R        |   79 ++++++----
 R/fitFixed.R               |  345 ++++++++++++++++++++++-----------------------
 R/outcomeProbs.R           |   12 -
 R/randomLCA.R              |    9 -
 build/vignette.rds         |binary
 inst/NEWS                  |   12 +
 man/randomLCA.Rd           |    2 
 src/bernoulliprob.c        |   11 -
 src/bernoulliprobrandom.c  |   18 +-
 src/bernoulliprobrandom2.c |   18 +-
 src/lcemalgorith.c         |   21 +-
 15 files changed, 340 insertions(+), 285 deletions(-)

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Package mirtCAT updated to version 0.9 with previous version 0.8 dated 2016-02-24

Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R. Package also contains tools useful for performing Monte Carlo simulations for studying the behaviour of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between mirtCAT versions 0.8 dated 2016-02-24 and 0.9 dated 2016-06-24

 DESCRIPTION                         |   12 ++---
 MD5                                 |   36 ++++++++--------
 NEWS.md                             |    6 ++
 R/ShinyGUIClass.R                   |   10 ++++
 R/findNextCATItem.R                 |   29 ++++++++-----
 R/generate.mirt_object.R            |    2 
 R/generate_pattern.R                |    4 -
 R/mirtCAT.R                         |    5 ++
 R/selection_criteria.R              |   74 +++++++++-------------------------
 R/server.R                          |    9 +---
 R/util.R                            |   10 ++++
 build/vignette.rds                  |binary
 man/findNextItem.Rd                 |   12 ++++-
 man/mirtCAT.Rd                      |    5 ++
 tests/GUI-tests/GUI-tests.R         |    5 ++
 tests/tests/test-mirtCAT_classify.R |   10 ++--
 tests/tests/test-mirtCAT_multi.R    |   11 +----
 tests/tests/test-mirtCAT_ordered.R  |   20 ++++-----
 tests/tests/test-mirtCAT_uni.R      |   78 ++++++++++++++++++------------------
 19 files changed, 178 insertions(+), 160 deletions(-)

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Package overlapping updated to version 1.3 with previous version 1.2 dated 2016-02-08

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more empirical distributions.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

Diff between overlapping versions 1.2 dated 2016-02-08 and 1.3 dated 2016-06-24

 DESCRIPTION       |    8 ++++----
 MD5               |   12 ++++++------
 NEWS              |    6 ++++++
 R/final.plot.R    |   10 ++++++----
 R/overlap.R       |    7 ++++---
 man/cutnumeric.Rd |    2 +-
 man/overlap.Rd    |    1 +
 7 files changed, 28 insertions(+), 18 deletions(-)

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Package mirt updated to version 1.18 with previous version 1.17.1 dated 2016-04-27

Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using unidimensional and multidimensional latent trait models under the Item Response Theory paradigm. Exploratory and confirmatory models can be estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier analyses are available for modeling item testlets. Multiple group analysis and mixed effects designs also are available for detecting differential item and test functioning as well as modelling item and person covariates.
Author: Phil Chalmers [aut, cre, cph], Joshua Pritikin [ctb], Alexander Robitzsch [ctb], Mateusz Zoltak [ctb], KwonHyun Kim [ctb], Carl F. Falk [ctb], Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between mirt versions 1.17.1 dated 2016-04-27 and 1.18 dated 2016-06-24

 DESCRIPTION                         |    8 -
 MD5                                 |   96 +++++++++---------
 NAMESPACE                           |    2 
 NEWS.md                             |   26 +++++
 R/02-item_methods.R                 |  187 +++++++++++++++++++++---------------
 R/03-estimation.R                   |  124 +++++++++++++++--------
 R/DTF.R                             |    4 
 R/Discrete-methods.R                |    6 -
 R/EMstep.group.R                    |   32 +++---
 R/EMstep.utils.R                    |   45 ++++++--
 R/LoadPars.R                        |  118 ++++++++++++----------
 R/MHRM.group.R                      |   29 +++++
 R/MultipleGroup-methods.R           |    1 
 R/PLCI.mirt.R                       |  139 +++++++++++++++++++++-----
 R/PrepData.R                        |   46 ++++----
 R/SE.methods.R                      |   21 ++--
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 R/mirt.R                            |   25 ++--
 R/model.elements.R                  |    9 -
 R/simdata.R                         |   15 +-
 R/utils.R                           |   65 ++++++++++--
 build/vignette.rds                  |binary
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 src/dpars.cpp                       |   80 +++++++++++++--
 src/traceLinePts.cpp                |   16 +--
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 tests/extratests/test-02-wideData.R |    6 -
 tests/tests/test-01-mirtOne.R       |    2 
 tests/tests/test-02-mirtTwo.R       |    8 -
 tests/tests/test-03-bfactor.R       |   10 -
 tests/tests/test-04-multipleGroup.R |   40 +++----
 tests/tests/test-06-confmirtTwo.R   |   14 +-
 tests/tests/test-07-mixedmirt.R     |   34 +++---
 tests/tests/test-09-mirt.model.R    |    5 
 tests/tests/test-10-extras.R        |   31 ++---
 tests/tests/test-11-discrete.R      |   17 +--
 51 files changed, 964 insertions(+), 557 deletions(-)

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