Sat, 27 May 2017

Package tablaxlsx updated to version 1.2.2 with previous version 1.2.0 dated 2016-06-13

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

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Package rust updated to version 1.2.0 with previous version 1.1.0 dated 2016-11-18

Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalised ratio-of-uniforms (RU) method to simulate from univariate and (low-dimensional) multivariate continuous distributions. The user specifies the log-density, up to an additive constant. The RU algorithm is applied after relocation of mode of the density to zero, and the user can choose a tuning parameter r. For details see Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random variates via the ratio-of-uniforms method, Statistics and Computing (1991) 1, 129-133. A Box-Cox variable transformation can be used to make the input density suitable for the RU method and to improve efficiency. In the multivariate case rotation of axes can also be used to improve efficiency. From version 1.2.0 the 'Rcpp' package <https://cran.r-project.org/package=Rcpp> can be used to improve efficiency. See the rust website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>

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Package overlap updated to version 0.3.0 with previous version 0.2.7 dated 2017-03-01

Title: Estimates of Coefficient of Overlapping for Animal Activity Patterns
Description: Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Author: Mike Meredith and Martin Ridout
Maintainer: Mike Meredith <mmeredith@wcs.org>

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Package MIICD updated to version 2.4 with previous version 2.3 dated 2016-11-28

Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression with interval censored data or proportional sub-distribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the 'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>

Diff between MIICD versions 2.3 dated 2016-11-28 and 2.4 dated 2017-05-27

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Package heatmaply updated to version 0.10.1 with previous version 0.9.1 dated 2017-04-14

Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Jonathan Sidi [ctb] (https://github.com/yonicd), Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package googleCloudStorageR updated to version 0.3.0 with previous version 0.2.0 dated 2016-09-11

Title: R Interface with Google Cloud Storage
Description: Interact with Google Cloud Storage API in R. Part of the 'cloudyr' project.
Author: Mark Edmondson [aut, cre]
Maintainer: Mark Edmondson <r@sunholo.com>

Diff between googleCloudStorageR versions 0.2.0 dated 2016-09-11 and 0.3.0 dated 2017-05-27

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Package cleanNLP updated to version 1.9.0 with previous version 1.5.2 dated 2017-04-12

Title: A Tidy Data Model for Natural Language Processing
Description: Provides a set of fast tools for converting a textual corpus into a set of normalized tables. Users may make use of a Python back end with 'spaCy' <https://spacy.io> or the Java back end 'CoreNLP' <http://stanfordnlp.github.io/CoreNLP/>. A minimal back end with no external dependencies is also provided. Exposed annotation tasks include tokenization, part of speech tagging, named entity recognition, entity linking, sentiment analysis, dependency parsing, coreference resolution, and word embeddings. Summary statistics regarding token unigram, part of speech tag, and dependency type frequencies are also included to assist with analyses.
Author: Taylor B. Arnold [aut, cre]
Maintainer: Taylor B. Arnold <taylor.arnold@acm.org>

Diff between cleanNLP versions 1.5.2 dated 2017-04-12 and 1.9.0 dated 2017-05-27

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Package BayesianTools updated to version 0.1.2 with previous version 0.1.1 dated 2017-04-05

Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre], Francesco Minunno [aut], Stefan Paul [aut], David Cameron [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

Diff between BayesianTools versions 0.1.1 dated 2017-04-05 and 0.1.2 dated 2017-05-27

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New package survidm with initial version 0.1.0
Package: survidm
Type: Package
Title: Inference and Prediction in an Illness-Death Model
Version: 0.1.0
Date: 2017-05-24
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Description: Newly developed methods for the estimation of several probabilities in an illness-death model. The package can be used to obtain nonparametric and semiparametric estimates for: transition probabilities, occupation probabilities, cumulative incidence function and the sojourn time distributions. Several auxiliary functions are also provided which can be used for marginal estimation of the survival functions.
Depends: R (>= 3.0.0)
Encoding: UTF-8
License: GPL-3
LazyData: true
Imports: KernSmooth, np, survival, doParallel, parallel, doRNG, foreach
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-05-27 12:26:46 UTC; Sestelo
Repository: CRAN
Date/Publication: 2017-05-27 14:05:27 UTC

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New package stratvns with initial version 1.0
Package: stratvns
Type: Package
Title: Optimal Stratification in Stratified Sampling Optimization Algorithm
Version: 1.0
Author: Breno Oliveira, Leonardo Lima and Jose Brito
Maintainer: Jose Brito <jambrito@gmail.com>
Description: An Optimization Algorithm Applied to stratification Problem. It is aims to delimit the population strata and defining the allocation of sample,considering the following objective: minimize the sample size given a fixed precision level. Exhaustive enumeration method is applied in small problems, while in problems with greater complexity the algorithm is based on metaheuristic Variable Neighborhood Decomposition Search with Path Relink.
Depends: Rglpk,snowfall,stratification, sampling, MultAlloc
Encoding: UTF-8
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-27 01:32:32 UTC; AMANDOCA_AMD
Repository: CRAN
Date/Publication: 2017-05-27 14:07:58 UTC

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New package SeerMapper with initial version 1.2.0
Package: SeerMapper
Type: Package
Version: 1.2.0
Date: 2017-05-26
Title: A Quick Way to Map U.S. Rates and Data of U. S. States, Counties, Census Tracts, or Seer Registries using 2000 and 2010 U. S. Census Boundaries
Author: "Jim Pearson" <jpearson@statnetconsulting.com>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Imports: graphics, maptools, RColorBrewer, rgdal, sp, stats, stringr, SeerMapperRegs, SeerMapperEast, SeerMapperWest, SeerMapper2010Regs, SeerMapper2010East, SeerMapper2010West
Depends: R (>= 3.2.0)
Suggests:
Description: Provides an easy way to map seer registry area rate data on a U. S, map. The U. S. data may be mapped at the state, U. S. NCI Seer Register, state/county or census tract level. The function can categorize the data into "n" quantiles, where "n" is 3 to 11 or the caller can specify a cut point list for the categorizes. The caller can also provide the data and the comparison operation to request hatching over any areas. The default operation and value are > 0.05 (p-values). The location id provided in the data determines the geographic level of the mapping. If states, state/counties or census tracts are being mapped, the location ids used must be the U.S. FIPS codes for states (2 digits), state/counties (5 digits) or state/county/census tracts (11 digits). If the location id references the U.S. Seer Registry areas, the Seer Registry area identifier used to link the data to the geographical areas, then the location id is the Seer Registry name or abbreviation. Additional parameters are used to provide control over the drawing of the boundaries at the data's boundary level and higher levels. The package uses modified boundary data from the 2000 and 2010 U. S. Census to reduce the storage requirements and improve drawing speed. The 'SeerMapper' package contains the U. S. Census 2000 and 2010 boundary data for the regional, state, Seer Registry, and county levels. Six supplement packages contain the census tract boundary data (see manual for more details.)
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-05-27 00:31:45 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-05-27 14:09:10 UTC

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New package polypoly with initial version 0.0.2
Package: polypoly
Title: Helper Functions for Orthogonal Polynomials
Version: 0.0.2
Authors@R: person("Tristan", "Mahr", email = "tristan.mahr@gmail.com", role = c("aut", "cre"))
Description: Tools for reshaping, plotting, and manipulating matrices of orthogonal polynomials.
Depends: R (>= 3.3.3)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/tjmahr/polypoly
BugReports: https://github.com/tjmahr/polypoly/issues
Imports: tibble, reshape2, ggplot2, rlang, stats
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, lme4, splines
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-05-26 18:22:42 UTC; mahr
Author: Tristan Mahr [aut, cre]
Maintainer: Tristan Mahr <tristan.mahr@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-27 14:12:20 UTC

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Package phrasemachine updated to version 1.1.1 with previous version 1.0.0 dated 2016-10-24

Title: Simple Phrase Extraction
Description: Simple noun phrase extraction using part-of-speech information. Takes a collection of un-processed documents as input and returns a set of noun phrases associated with those documents.
Author: Matthew J. Denny, Abram Handler, Brendan O'Connor
Maintainer: Matthew J. Denny <mdenny@psu.edu>

Diff between phrasemachine versions 1.0.0 dated 2016-10-24 and 1.1.1 dated 2017-05-27

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Package nauf updated to version 1.0.1 with previous version 1.0.0 dated 2017-05-09

Title: Regression with NA Values in Unordered Factors
Description: Fits regressions where unordered factors can be set to NA in subsets of the data where they are not applicable or otherwise not contrastive by using sum contrasts and setting NA values to zero.
Author: Christopher D. Eager [aut, cre]
Maintainer: Christopher D. Eager <eagerstats@gmail.com>

Diff between nauf versions 1.0.0 dated 2017-05-09 and 1.0.1 dated 2017-05-27

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New package KarsTS with initial version 1.0
Package: KarsTS
Type: Package
Title: An Interface for Karstic Time Series
Version: 1.0
Date: 2017-05-23
Authors@R: c(person("Marina", "Saez", email = "marinasaez_andreu@hotmail.com",role = c("aut", "cre")),person("David", "Benavente", role = c("ths")),person("Soledad", "Cuezva", role = c("ths")),person("Concepcion", "Pla", role = c("ctb")))
Author: Marina Saez [aut, cre], David Benavente [ths], Soledad Cuezva [ths], Concepcion Pla [ctb]
Maintainer: Marina Saez <marinasaez_andreu@hotmail.com>
Description: An R graphical user interface for karstic time series, based on the 'tcltk' package. Karstic research typically includes CO2 and Rn concentrations and microclimatic measurements. Many of these time series have a strong non-linear behavior. Gaps are often a significant problem because caves are aggressive environments for the apparels. 'KarsTS' provides linear and non-linear analysis and filling methods, as well as tools to manipulate easily time series and gap sets.
License: GPL (>= 2)
Note: Please, cite this package as: Marina Saez (2017). KarsTS: An Interface For Karstic Time Series. R package version 1.0.
RoxygenNote: 6.0.1
Imports: circular, BaylorEdPsych, MVN, tcltk, tcltk2, tkrplot, tseriesChaos, stlplus, tseries, forecast, stinepack, missForest, nonlinearTseries, stats, graphics, utils, zoo, grDevices, rgl, mgcv
NeedsCompilation: no
Packaged: 2017-05-26 13:41:01 UTC; rs
Repository: CRAN
Date/Publication: 2017-05-27 14:26:52 UTC

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New package didrooRFM with initial version 1.0.0
Package: didrooRFM
Title: Compute Recency Frequency Monetary Scores for your Customer Data
Version: 1.0.0
Authors@R: person("Satish", "Hariharan", email = "satish181990@gmail.com", role = c("aut", "cre"))
Description: This hosts the findRFM function which generates RFM scores on a 1-5 point scale for customer transaction data. The function consumes a data frame with Transaction Number, Customer ID, Date of Purchase (in date format) and Amount of Purchase as the attributes. The function returns a data frame with RFM data for the sales information.
Depends: R (>= 3.3.3)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: dplyr
BugReports: https://goo.gl/forms/BU7rb8HmgTSeWZE02
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-27 13:49:57 UTC; didroo
Author: Satish Hariharan [aut, cre]
Maintainer: Satish Hariharan <satish181990@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-27 14:29:07 UTC

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Fri, 26 May 2017

Package tigris updated to version 0.5.3 with previous version 0.5.1 dated 2017-05-09

Title: Load Census TIGER/Line Shapefiles into R
Description: Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre], Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

Diff between tigris versions 0.5.1 dated 2017-05-09 and 0.5.3 dated 2017-05-26

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Package stratbr updated to version 1.2 with previous version 1.1 dated 2017-05-19

Title: Optimal Stratification in Stratified Sampling
Description: An Optimization Algorithm Applied to Stratification Problem.This function aims at constructing optimal strata with an optimization algorithm based on a global optimisation technique called Biased Random Key Genetic Algorithms.
Author: Jose Brito, Pedro Silva and Tomas Veiga
Maintainer: Jose Brito <jambrito@gmail.com>

Diff between stratbr versions 1.1 dated 2017-05-19 and 1.2 dated 2017-05-26

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Package protViz updated to version 0.2.31 with previous version 0.2.28 dated 2017-01-30

Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Description: Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre], Jonas Grossmann [aut], Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

Diff between protViz versions 0.2.28 dated 2017-01-30 and 0.2.31 dated 2017-05-26

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Package mgm updated to version 1.2-0 with previous version 1.1-7 dated 2016-10-20

Title: Estimating Time-Varying k-Order Mixed Graphical Models
Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>

Diff between mgm versions 1.1-7 dated 2016-10-20 and 1.2-0 dated 2017-05-26

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Package InterVA4 updated to version 1.7.4 with previous version 1.7.3 dated 2016-12-24

Title: Replicate and Analyse 'InterVA4'
Description: Provides an R version of the 'InterVA4' software (<http://www.interva.net>) for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark, Peter Byass
Maintainer: Zehang Li <lizehang@uw.edu>

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Package BAS updated to version 1.4.6 with previous version 1.4.5 dated 2017-03-31

Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and generalized linear models using stochastic or deterministic sampling without replacement from posterior distributions. Prior distributions on coefficients are from Zellner's g-prior or mixtures of g-priors corresponding to the Zellner-Siow Cauchy Priors or the mixture of g-priors from Liang et al (2008) <DOI:10.1198/016214507000001337> for linear models or mixtures of g-priors in GLMs of Li and Clyde (2015) <arXiv:1503.06913>. Other model selection criteria include AIC, BIC and Empirical Bayes estimates of g. Sampling probabilities may be updated based on the sampled models using Sampling w/out Replacement or an efficient MCMC algorithm samples models using the BAS tree structure as an efficient hash table. Uniform priors over all models or beta-binomial prior distributions on model size are allowed, and for large p truncated priors on the model space may be used. The user may force variables to always be included. Details behind the sampling algorithm are provided in Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049>. This material is based upon work supported by the National Science Foundation under Grant DMS-1106891. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Author: Merlise Clyde [aut, cre, cph], Michael Littman [ctb], Quanli Wang [ctb], Joyee Ghosh [ctb], Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>

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Package SmartSVA updated to version 0.1.2 with previous version 0.1.1 dated 2016-11-23

Title: Fast and Robust Surrogate Variable Analysis
Description: Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures variation of unknown sources (batch effects) for high-dimensional data sets. The algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes a revision on it that achieves more than 10 times faster running time while trading no accuracy loss in return.
Author: Jun Chen <Chen.Jun2@mayo.edu>, Ehsan Behnam <behnamgh@usc.edu>
Maintainer: Jun Chen <Chen.Jun2@mayo.edu>

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Package tictactoe updated to version 0.2.2 with previous version 0.2.0 dated 2016-12-28

Title: Tic-Tac-Toe Game
Description: Implements tic-tac-toe game to play on console, either with human or AI players. Various levels of AI players are trained through the Q-learning algorithm.
Author: Kota Mori [aut, cre]
Maintainer: Kota Mori <kmori05@gmail.com>

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Package AID updated to version 2.0 with previous version 1.9 dated 2017-05-19

Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assess the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

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Package LinkageMapView updated to version 2.1.0 with previous version 2.0.0 dated 2017-04-28

Title: Plot Linkage Group Maps with Quantitative Trait Loci
Description: Produces high resolution, publication ready linkage maps and quantitative trait loci maps. Input can be output from 'R/qtl', simple text or comma delimited files. Output is currently a portable document file.
Author: Lisa Ouellette [aut, cre]
Maintainer: Lisa Ouellette <louellet@uncc.edu>

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Package epanetReader updated to version 0.5.1 with previous version 0.4.0 dated 2016-08-10

Title: Read Epanet Files into R
Description: Reads water network simulation data in 'Epanet' text-based '.inp' and '.rpt' formats into R. Also reads results from 'Epanet-msx'. Provides basic summary information and plots. The README file has a quick introduction. See <http://www2.epa.gov/water-research/epanet> for more information on the 'Epanet' software for modeling hydraulic and water quality behavior of water piping systems.
Author: Bradley J. Eck
Maintainer: Bradley Eck <brad@bradeck.net>

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Package combiter updated to version 1.0.2 with previous version 0.1.0 dated 2016-09-26

Title: Combinatorics Iterators
Description: Provides iterators for combinations, permutations, subsets, and Cartesian product, which allow one to go through all elements without creating a huge set of all possible values.
Author: Kota Mori [aut, cre]
Maintainer: Kota Mori <kmori05@gmail.com>

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 34 files changed, 515 insertions(+), 248 deletions(-)

More information about combiter at CRAN
Permanent link

New package breakfast with initial version 0.1.0
Package: breakfast
Title: Multiple Change-Point Detection and Segmentation
Version: 0.1.0
Authors@R: person("Piotr", "Fryzlewicz", email = "p.fryzlewicz@lse.ac.uk", role = c("aut", "cre"))
Description: Performs multiple change-point detection in data sequences, or data sequence segmentation, using computationally efficient multiscale methods. This version only implements the "Tail-Greedy Unbalanced Haar" change-point detection methodology; more methods will be added in future versions. To start with, see the function segment.mean.
Depends: R (>= 3.4.0)
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: plyr
NeedsCompilation: no
Packaged: 2017-05-26 12:43:53 UTC; piotr
Author: Piotr Fryzlewicz [aut, cre]
Maintainer: Piotr Fryzlewicz <p.fryzlewicz@lse.ac.uk>
Repository: CRAN
Date/Publication: 2017-05-26 13:12:07 UTC

More information about breakfast at CRAN
Permanent link

Package polyCub updated to version 0.6.0 with previous version 0.5-2 dated 2015-02-26

Title: Cubature over Polygonal Domains
Description: The following methods for cubature (numerical integration) over polygonal domains are currently implemented: the two-dimensional midpoint rule as a simple wrapper around as.im.function() from package 'spatstat' (Baddeley and Turner, 2005), the product Gauss cubature by Sommariva and Vianello (2007), an adaptive cubature for isotropic functions via line integrate() along the boundary (Meyer and Held, 2014), and quasi-exact methods specific to the integration of the bivariate Gaussian density over polygonal and circular domains (based on formulae from the Abramowitz and Stegun (1972) handbook). For cubature over simple hypercubes, the packages 'cubature' and 'R2Cuba' are more appropriate.
Author: Sebastian Meyer [aut, cre, trl], Leonhard Held [ths], Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>

Diff between polyCub versions 0.5-2 dated 2015-02-26 and 0.6.0 dated 2017-05-26

 DESCRIPTION                       |   55 +++++++++++++++--------------
 MD5                               |   70 +++++++++++++++++++++-----------------
 NAMESPACE                         |    5 +-
 R/polyCub.SV.R                    |   13 +++----
 R/polyCub.exact.Gauss.R           |   19 +++++-----
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 40 files changed, 249 insertions(+), 221 deletions(-)

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Package mombf updated to version 1.9.5 with previous version 1.9.4 dated 2017-03-08

Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local and Zellner priors. Bayes factors, marginal densities and variable selection in regression setups. Routines to sample, evaluate prior densities, distribution functions and quantiles are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>

Diff between mombf versions 1.9.4 dated 2017-03-08 and 1.9.5 dated 2017-05-26

 ChangeLog             |    6 ++
 DESCRIPTION           |    8 +--
 MD5                   |   16 +++----
 R/modelSelection.R    |   36 +++++++++++++----
 inst/doc/mombf.pdf    |binary
 man/modelSelection.Rd |   10 +++-
 src/do_mombf.h        |    4 -
 src/modelSel.cpp      |  101 ++++++++++++++++++++++++++------------------------
 src/modelSel.h        |    4 -
 9 files changed, 110 insertions(+), 75 deletions(-)

More information about mombf at CRAN
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Package BeSS updated to version 1.0.1 with previous version 1.0.0 dated 2017-04-20

Title: Best Subset Selection for Sparse Generalized Linear Model and Cox Model
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen, Aijun Zhang, Shijie Quan, Xueqin Wang
Maintainer: Canhong Wen <wencanhong@gmail.com>

Diff between BeSS versions 1.0.0 dated 2017-04-20 and 1.0.1 dated 2017-05-26

 DESCRIPTION          |    6 
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More information about BeSS at CRAN
Permanent link

Package magclass updated to version 4.39 with previous version 3.85 dated 2016-07-21

Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial- temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).
Author: Jan Philipp Dietrich, Benjamin Bodirsky, Misko Stevanovic, Lavinia Baumstark, Christoph Bertram, Markus Bonsch, Anastasis Giannousakis, Florian Humpenoeder, David Klein, Ina Neher, Michaja Pehl, Anselm Schultes, Xiaoxi Wang
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>

Diff between magclass versions 3.85 dated 2016-07-21 and 4.39 dated 2017-05-26

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Package quanteda updated to version 0.9.9-65 with previous version 0.9.9-50 dated 2017-04-20

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible framework for for the management, processing, and quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre, cph], Kohei Watanabe [ctb], Paul Nulty [ctb], Adam Obeng [ctb], Haiyan Wang [ctb], Benjamin Lauderdale [ctb], Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

Diff between quanteda versions 0.9.9-50 dated 2017-04-20 and 0.9.9-65 dated 2017-05-26

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Package optiSel updated to version 0.9.1 with previous version 0.9 dated 2017-05-24

Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>

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New package geometa with initial version 0.1-0
Package: geometa
Type: Package
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Version: 0.1-0
Date: 2017-05-24
Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Description: Provides facilities to handle reading and writing of geographic metadata defined with OGC/ISO 19115 and 19139 (XML) standards.
Depends: R (>= 3.1.0)
Imports: R6, XML
Suggests: testthat, roxygen2
License: MIT + file LICENSE
URL: https://github.com/eblondel/geometa/wiki
BugReports: https://github.com/eblondel/geometa/issues
LazyLoad: yes
NeedsCompilation: no
Packaged: 2017-05-25 12:31:35 UTC; Emmanuel
Repository: CRAN
Date/Publication: 2017-05-25 15:22:29

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New package walrus with initial version 1.0.0
Package: walrus
Type: Package
Title: Robust Statistical Methods
Version: 1.0.0
Author: Jonathon Love, Patrick Mair
Maintainer: Jonathon Love <jon@thon.cc>
Description: A toolbox of common robust statistical tests, including robust descriptives, robust t-tests, and robust ANOVA. It is also available as a module for 'jamovi' (see <https://www.jamovi.org> for more information). Walrus is based on the WRS2 package by Patrick Mair, which is in turn based on the scripts and work of Rand Wilcox. These analyses are described in depth in the book 'Introduction to Robust Estimation & Hypothesis Testing'.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: WRS2, ggplot2, jmvcore (>= 0.5.5), R6
Suggests: MASS
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-26 01:30:42 UTC; jonathon
Repository: CRAN
Date/Publication: 2017-05-26 06:07:05 UTC

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Package sparklyr updated to version 0.5.5 with previous version 0.5.4 dated 2017-04-25

Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data processing, see <http://spark.apache.org>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut, cre], Kevin Ushey [aut], JJ Allaire [aut], RStudio [cph], The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>

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Package snowFT updated to version 1.5-0 with previous version 1.4-0 dated 2015-06-25

Title: Fault Tolerant Simple Network of Workstations
Description: Extension of the snow package supporting fault tolerant and reproducible applications, as well as supporting easy-to-use parallel programming - only one function is needed.
Author: Hana Sevcikova, A. J. Rossini
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package preText updated to version 0.5.0 with previous version 0.4.4 dated 2016-10-08

Title: Diagnostics to Assess the Effects of Text Preprocessing Decisions
Description: Functions to assess the effects of different text preprocessing decisions on the inferences drawn from the resulting document-term matrices they generate.
Author: Matthew J. Denny <mdenny@psu.edu>, Arthur Spirling <as9934@nyu.edu>,
Maintainer: Matthew J. Denny <mdenny@psu.edu>

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Package ldbod updated to version 0.1.2 with previous version 0.1.1 dated 2016-12-22

Title: Local Density-Based Outlier Detection
Description: Flexible procedures to compute local density-based outlier scores for ranking outliers. Both exact and approximate nearest neighbor search can be implemented, while also accommodating multiple neighborhood sizes and four different local density-based methods. It allows for referencing a random subsample of the input data or a user specified reference data set to compute outlier scores against, so both unsupervised and semi-supervised outlier detection can be implemented.
Author: Kristopher Williams
Maintainer: Kristopher Williams <kristopher.williams83@gmail.com>

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Package knotR updated to version 1.0-2 with previous version 1.0-1 dated 2016-09-30

Title: Knot Diagrams using Bezier Curves
Description: Makes nice pictures of knots using Bezier curves and numerical optimization.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package icRSF updated to version 1.1 with previous version 1.0 dated 2016-01-20

Title: A Modified Random Survival Forest Algorithm
Description: Implements a modification to the Random Survival Forests algorithm for obtaining variable importance in high dimensional datasets. The proposed algorithm is appropriate for settings in which a silent event is observed through sequentially administered, error-prone self-reports or laboratory based diagnostic tests. The modified algorithm incorporates a formal likelihood framework that accommodates sequentially administered, error-prone self-reports or laboratory based diagnostic tests. The original Random Survival Forests algorithm is modified by the introduction of a new splitting criterion based on a likelihood ratio test statistic.
Author: Hui Xu and Raji Balasubramanian
Maintainer: Hui Xu <huix@schoolph.umass.edu>

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Package future updated to version 1.5.0 with previous version 1.4.0 dated 2017-03-13

Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use `x %<-% { expression }` with `plan(multiprocess)`. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, on in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implements additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future versions 1.4.0 dated 2017-03-13 and 1.5.0 dated 2017-05-26

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Package fpp2 updated to version 2.1 with previous version 2.0 dated 2017-02-23

Title: Data for "Forecasting: Principles and Practice" (2nd Edition)
Description: All data sets required for the examples and exercises in the book "Forecasting: principles and practice" by Rob J Hyndman and George Athanasopoulos <http://OTexts.org/fpp2/>. All packages required to run the examples are also loaded.
Author: Rob Hyndman [aut, cre, cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between fpp2 versions 2.0 dated 2017-02-23 and 2.1 dated 2017-05-26

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More information about fpp2 at CRAN
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Package configr updated to version 0.2.3 with previous version 0.2.2 dated 2017-04-30

Title: An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

Diff between configr versions 0.2.2 dated 2017-04-30 and 0.2.3 dated 2017-05-26

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New package CharFun with initial version 0.1.0
Package: CharFun
Type: Package
Title: Numerical Computation Cumulative Distribution Function and Probability Density Function from Characteristic Function
Version: 0.1.0
Author: Ľudmila Šimková
Maintainer: Ľudmila Šimková <ludula.simkova@gmail.com>
Description: The Characteristic Functions Toolbox (CharFun) consists of a set of algorithms for evaluating selected characteristic functions and algorithms for numerical inversion of the (combined and/or compound) characteristic functions, used to evaluate the probability density function (PDF) and the cumulative distribution function (CDF).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Imports: Bessel
NeedsCompilation: no
Packaged: 2017-05-25 23:20:43 UTC; ludula
Repository: CRAN
Date/Publication: 2017-05-26 06:08:30 UTC

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Thu, 25 May 2017

Package tensorflow updated to version 0.8.1 with previous version 0.7 dated 2017-03-22

Title: R Interface to TensorFlow
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
Author: JJ Allaire [aut, cre] (R interface), RStudio [cph], Dirk Eddelbuettel [ctb, cph], Nick Golding [ctb, cph], Yuan Tang [ctb, cph], Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between tensorflow versions 0.7 dated 2017-03-22 and 0.8.1 dated 2017-05-25

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Package gge updated to version 1.2 with previous version 1.1 dated 2016-10-07

Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and GGB (genotype plus genotype-by-block-of-environments) models.
Author: Kevin Wright [aut, cre], Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>

Diff between gge versions 1.1 dated 2016-10-07 and 1.2 dated 2017-05-25

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Package spaMM updated to version 2.1.0 with previous version 2.0.0 dated 2017-04-06

Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference in mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Variation in residual variance is handled and can be modelled as a linear model. The algorithms are currently various Laplace approximations methods for likelihood or restricted likelihood, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [aut], GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between spaMM versions 2.0.0 dated 2017-04-06 and 2.1.0 dated 2017-05-25

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Package rtdists updated to version 0.7-3 with previous version 0.6-6 dated 2016-07-15

Title: Response Time Distributions
Description: Provides response time distributions (density/PDF, distribution function/CDF, quantile function, and random generation): (a) Ratcliff diffusion model (Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C code by Andreas and Jochen Voss and (b) linear ballistic accumulator (LBA; Brown & Heathcote, 2008, <doi:10.1016/j.cogpsych.2007.12.002>) with different distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre], Scott Brown [aut], Matthew Gretton [aut], Andrew Heathcote [aut], Andreas Voss [ctb], Jochen Voss [ctb], Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann+rtdists@gmail.com>

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Package afex updated to version 0.18-0 with previous version 0.17-8 dated 2017-04-13

Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre], Ben Bolker [aut], Jake Westfall [aut], Frederik Aust [aut], Søren Højsgaard [ctb], John Fox [ctb], Michael A. Lawrence [ctb], Ulf Mertens [ctb], Jonathan Love [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>

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Package useful updated to version 1.2.2 with previous version 1.2.1 dated 2016-06-29

Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a data.frame, constructing formulas from text and building design and response matrices.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>

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Package spray updated to version 1.0-3 with previous version 1.0 dated 2016-03-11

Title: Sparse Arrays and Multivariate Polynomials
Description: Sparse arrays interpreted as multivariate polynomials.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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New package simglm with initial version 0.5.0
Package: simglm
Type: Package
Authors@R: person("Brandon", "LeBeau", email = "lebebr01+simglm@gmail.com", role = c("aut", "cre"))
Version: 0.5.0
License: MIT + file LICENSE
Title: Simulate Models Based on the Generalized Linear Model
Description: Easily simulates regression models, including both simple regression and generalized linear mixed models with up to three level of nesting. Power simulations that are flexible allowing the specification of missing data, unbalanced designs, and different random error distributions are built into the package.
Depends: R (>= 3.3.0), stats, Matrix, dplyr, purrr, tidyr, tibble
Suggests: knitr, lme4, nlme, testthat, shiny, e1071, ggplot2
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
NeedsCompilation: no
Packaged: 2017-05-25 17:27:11 UTC; lebeb
Repository: CRAN
Date/Publication: 2017-05-25 21:51:16 UTC

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New package rdoxygen with initial version 1.0.0
Package: rdoxygen
Title: Create Doxygen Documentation for Source Code
Version: 1.0.0
Authors@R: c( person("Clemens", "Schmid", email = "clemens@nevrome.de", role = c("cre", "cph", "aut")) )
Maintainer: Clemens Schmid <clemens@nevrome.de>
Description: Create doxygen documentation for source code in R packages. Includes a RStudio Addin, that allows to trigger the doxygenize process.
Date: 2017-05-23
Depends: R (>= 3.3.3)
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/nevrome/rdoxygen
BugReports: https://github.com/nevrome/rdoxygen/issues
RoxygenNote: 6.0.1
Imports: devtools (>= 1.12.0)
Suggests: testthat
SystemRequirements: doxygen
NeedsCompilation: yes
Packaged: 2017-05-25 21:11:20 UTC; clemens
Author: Clemens Schmid [cre, cph, aut]
Repository: CRAN
Date/Publication: 2017-05-25 21:39:04 UTC

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Package Mediana updated to version 1.0.5 with previous version 1.0.4 dated 2017-02-07

Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based on the Clinical Scenario Evaluation (CSE) approach. The package supports a broad class of data models (including clinical trials with continuous, binary, survival-type and count-type endpoints as well as multivariate outcomes that are based on combinations of different endpoints), analysis strategies and commonly used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>

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Package gaston updated to version 1.5 with previous version 1.4.9 dated 2016-11-29

Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>

Diff between gaston versions 1.4.9 dated 2016-11-29 and 1.5 dated 2017-05-25

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New package fcm with initial version 0.1.1
Package: fcm
Type: Package
Title: Inference of Fuzzy Cognitive Maps (FCMs)
Version: 0.1.1
Date: 2017-05-25
Author: Zoumpoulia Dikopoulou <dikopoulia@gmail.com> <zoumpolia.dikopoulou@uhasselt.be>, Elpiniki Papageorgiou <epapageorgiou@teiste.gr>, <e.i.papageorgiou75@gmail.com>
Maintainer: Zoumpoulia Dikopoulou <dikopoulia@gmail.com>
Description: Provides a selection of 6 different inference rules and 4 threshold functions in order to obtain the inference of the FCM (Fuzzy Cognitive Map). Moreover, the 'fcm' package returns a data frame of the concepts' values of each state after the inference procedure. Fuzzy cognitive maps were introduced by Kosko (1986) <doi:10.1002/int.4550010405> providing ideal causal cognition tools for modeling and simulating dynamic systems.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: reshape2, ggplot2
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2017-05-25 21:31:49 UTC; lucp8904
Repository: CRAN
Date/Publication: 2017-05-25 21:46:07 UTC

More information about fcm at CRAN
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Package fasjem updated to version 1.1.0 with previous version 1.0.0 dated 2017-04-21

Title: A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models
Description: The FASJEM (A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models) is a joint estimator which is fast and scalable for learning multiple related sparse Gaussian graphical models. For more details, please see <https://www.cs.virginia.edu/yanjun/paperA14/2017_JEM_combined.pdf>.
Author: Beilun Wang [aut, cre], Yanjun Qi [aut]
Maintainer: Beilun Wang <bw4mw@virginia.edu>

Diff between fasjem versions 1.0.0 dated 2017-04-21 and 1.1.0 dated 2017-05-25

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Package BioInstaller updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-25

Title: Lightweight Biology Software Installer
Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>

Diff between BioInstaller versions 0.1.0 dated 2017-04-25 and 0.1.1 dated 2017-05-25

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New package apng with initial version 1.0
Package: apng
Type: Package
Title: Convert Png Files into Animated Png
Version: 1.0
Date: 2017-05-23
Author: Quinten Stokkink
Maintainer: Quinten Stokkink <q.a.stokkink@tudelft.nl>
Depends: bitops
Description: Convert several png files into an animated png file. This package exports only a single function `apng'. Call the apng function with a vector of file names (which should be png files) to convert them to a single animated png file.
License: GPL-3 | file LICENSE
NeedsCompilation: no
Packaged: 2017-05-25 20:16:56 UTC; quinten
Repository: CRAN
Date/Publication: 2017-05-25 21:37:00 UTC

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Package soilphysics updated to version 3.1 with previous version 3.0 dated 2016-01-11

Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

Diff between soilphysics versions 3.0 dated 2016-01-11 and 3.1 dated 2017-05-25

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Package wgeesel updated to version 1.3 with previous version 1.2 dated 2017-05-04

Title: Weighted Generalized Estimating Equations and Model Selection
Description: Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
Author: Cong Xu <congxu17@gmail.com>, Zheng Li <zheng.li@outlook.com>, Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>

Diff between wgeesel versions 1.2 dated 2017-05-04 and 1.3 dated 2017-05-25

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Package NHMSAR updated to version 1.5 with previous version 1.4 dated 2016-04-24

Title: Non-Homogeneous Markov Switching Autoregressive Models
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations. Penalization methods are implemented for Markov Switching Vector Autoregressive Models of order 1 only. Most functions of the package handle missing values.
Author: Valerie Monbet
Maintainer: Valerie Monbet <valerie.monbet@gmail.com>

Diff between NHMSAR versions 1.4 dated 2016-04-24 and 1.5 dated 2017-05-25

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Package neat updated to version 1.1 with previous version 1.0 dated 2016-09-07

Title: Efficient Network Enrichment Analysis Test
Description: Includes functions and examples to compute NEAT, the Network Enrichment Analysis Test described in Signorelli et al. (2016, <DOI:10.1186/s12859-016-1203-6>).
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>

Diff between neat versions 1.0 dated 2016-09-07 and 1.1 dated 2017-05-25

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Package IsoplotR updated to version 0.13 with previous version 0.12 dated 2017-05-07

Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith' plots). Constructs Re-Os, Sm-Nd, Lu-Hf and Rb-Sr isochrons. Future versions will include functionality for K-Ar, Pb-Pb and U-series dating methods.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 0.12 dated 2017-05-07 and 0.13 dated 2017-05-25

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Permanent link

Package biotools updated to version 3.1 with previous version 3.0 dated 2016-02-03

Title: Tools for Biometry and Applied Statistics in Agricultural Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations. Mantel's permutation test can be found in this package. A new approach for calculating its power is implemented. biotools also contains the new tests for genetic covariance components. An approach for predicting spatial gene diversity is implemented.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

Diff between biotools versions 3.0 dated 2016-02-03 and 3.1 dated 2017-05-25

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New package Xplortext with initial version 1.00
Package: Xplortext
Type: Package
Title: Statistical Analysis of Textual Data
Version: 1.00
Date: 2017-05-24
Author: Monica Bcue-Bertaut, Ramn Alvarez-Esteban, Josep-Anton Snchez- Espigares
Maintainer: Ramn Alvarez-Esteban <ramon.alvarez@unileon.es>
Description: A complete set of functions devoted to statistical analysis of documents.
License: GPL (>= 2.0)
Depends: R (>= 3.4.0), FactoMineR(>= 1.35), ggplot2(>= 2.2.1)
Imports: tm, stringr, slam, stats, graphics, gridExtra, utils
URL: http://www.xplortext.org
Encoding: latin1
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-25 12:27:46 UTC; Usuario
Repository: CRAN
Date/Publication: 2017-05-25 14:33:20 UTC

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Package corpus updated to version 0.5.1 with previous version 0.5.0 dated 2017-05-23

Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, and for computing term occurrence frequencies.
Author: Patrick O. Perry [aut, cre], Martin Porter and Richard Boulton [ctb, cph] (Snowball), Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

Diff between corpus versions 0.5.0 dated 2017-05-23 and 0.5.1 dated 2017-05-25

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New package timelineR with initial version 0.1.0
Package: timelineR
Title: Visualization for Time Series Data
Version: 0.1.0
Authors@R: c( person("Mohsin", "Vindhani", email = "mohsin@systeminsights.com", role = c("aut", "cre")), person("Alex", "Joseph", email = "alex@systeminsights.com", role = c("aut")), person("Ananthapadmanabhan", email = "ananthu@systeminsights.com", role = c("aut")), person("Subramanyam", "Ravishankar", email = "subramanyam@systeminsights.com", role = c("aut")) )
Maintainer: Mohsin Vindhani <mohsin@systeminsights.com>
Description: Helps to visualize multi-variate time-series having numeric and factor variables. You can use the package for visual analysis of data by plotting the data for each variable in the desired order and study interaction between a factor and a numeric variable by creating overlapping plots.
Depends: R (>= 3.3.0)
Imports: dplyr, lubridate, stringr, futile.logger, ggplot2, gtable, grid, mtconnectR
Suggests: testthat, knitr, rmarkdown
License: AGPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-05-25 05:19:06 UTC; mohsinvindhani
Author: Mohsin Vindhani [aut, cre], Alex Joseph [aut], Ananthapadmanabhan [aut], Subramanyam Ravishankar [aut]
Repository: CRAN
Date/Publication: 2017-05-25 07:57:12 UTC

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Package simule updated to version 1.1.0 with previous version 1.0.0 dated 2017-04-19

Title: A Constrained L1 Minimization Approach for Estimating Multiple Sparse Gaussian or Nonparanormal Graphical Models
Description: The SIMULE (Shared and Individual parts of MULtiple graphs Explicitly) is a generalized method for estimating multiple related graphs with shared and individual pattern among graphs. For more details, please see <arXiv:1605.03468>.
Author: Beilun Wang [aut, cre], Yanjun Qi [aut]
Maintainer: Beilun Wang <bw4mw@virginia.edu>

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Package shallot updated to version 0.3.2 with previous version 0.3.1 dated 2017-05-12

Title: Random Partition Distribution Indexed by Pairwise Information
Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior simulation. We hope in the future to add posterior simulation with a user-supplied likelihood. Supporting functions for partition estimation and plotting are also planned.
Author: David B. Dahl [aut, cre], The Apache Software Foundation [ctb, cph]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

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Package rscala updated to version 2.2.2 with previous version 2.2.0 dated 2017-05-24

Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala <http://www.scala-lang.org/> interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions in the 2.10.x, 2.11.x, and 2.12.x series are supported.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between rscala versions 2.2.0 dated 2017-05-24 and 2.2.2 dated 2017-05-25

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Package RQGIS updated to version 1.0.0 with previous version 0.2.0 dated 2017-01-18

Title: Integrating R with QGIS
Description: Establishes an interface between R and 'QGIS', i.e. it allows the user to access 'QGIS' functionalities from the R console. It achieves this by using the 'QGIS' Python API via the command line. Hence, RQGIS extends R's statistical power by the incredible vast geo-functionality of 'QGIS' (including also 'GDAL', 'SAGA'- and 'GRASS'-GIS among other third-party providers). This in turn creates a powerful environment for advanced and innovative (geo-)statistical geocomputing. 'QGIS' is licensed under GPL version 2 or greater and is available from <http://www.qgis.org/en/site/>.
Author: Jannes Muenchow [aut, cre], Patrick Schratz [aut]
Maintainer: Jannes Muenchow <jannes.muenchow@uni-jena.de>

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Package Rfacebook updated to version 0.6.15 with previous version 0.6.11 dated 2017-01-04

Title: Access to Facebook API via R
Description: Provides an interface to the Facebook API.
Author: Pablo Barbera <pbarbera@usc.edu>, Michael Piccirilli <mrp2181@columbia.edu>, Andrew Geisler, Wouter van Atteveldt
Maintainer: Pablo Barbera <pbarbera@usc.edu>

Diff between Rfacebook versions 0.6.11 dated 2017-01-04 and 0.6.15 dated 2017-05-25

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Package kableExtra updated to version 0.2.1 with previous version 0.2.0 dated 2017-05-23

Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: A collection of functions to help build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre], Will Beasley [ctb], Yihui Xie [ctb], Thomas Travison [ctb], GuangChuang Yu [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>

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Package gamlss updated to version 5.0-2 with previous version 5.0-1 dated 2016-11-21

Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting Generalized Additive Models for Location Scale and Shape.
Author: Mikis Stasinopoulos [aut, cre, cph], Bob Rigby [aut], Vlasios Voudouris [ctb], Calliope Akantziliotou [ctb], Marco Enea [ctb], Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <mikis.stasinopoulos@gamlss.org>

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 81 files changed, 1196 insertions(+), 1043 deletions(-)

More information about gamlss at CRAN
Permanent link

New package coga with initial version 0.1.0
Package: coga
Title: Convolution of Gamma Distributions
Version: 0.1.0
Date: 2017-05-22
Authors@R: c( person("Chaoran", "Hu", email = "chaoran.hu@uconn.edu", role = c("aut", "cre")), person("Vladimir", "Pozdnyakov", email = "vladimir.pozdnyakov@uconn.edu", role = "ths"), person("Jun", "Yan", email = "jun.yan@uconn.edu", role = "ths"))
Description: Convolution of gamma distributions in R. The convolution of gamma distributions is the sum of series of gamma distributions and all gamma distributions here can have different parameters. This package can calculate density, distribution function and do simulation work.
Depends: R (>= 3.3.1)
License: GPL (>= 3.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat, microbenchmark
VignetteBuilder: knitr
Imports: stats, Rcpp
LinkingTo: Rcpp
BugReports: https://bitbucket.org/chaoranhu/coga/issues
URL: https://bitbucket.org/chaoranhu/coga
NeedsCompilation: yes
Packaged: 2017-05-24 21:50:16 UTC; ChaoranHu
Author: Chaoran Hu [aut, cre], Vladimir Pozdnyakov [ths], Jun Yan [ths]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>
Repository: CRAN
Date/Publication: 2017-05-25 07:37:38 UTC

More information about coga at CRAN
Permanent link

Package bamboo updated to version 0.9.18 with previous version 0.9.17 dated 2017-05-15

Title: Protein Secondary Structure Prediction Using the Bamboo Method
Description: Implementation of the Bamboo methods described in Li, Dahl, Vannucci, Joo, and Tsai (2014) <DOI:10.1371/journal.pone.0109832>.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between bamboo versions 0.9.17 dated 2017-05-15 and 0.9.18 dated 2017-05-25

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 12 files changed, 31 insertions(+), 29 deletions(-)

More information about bamboo at CRAN
Permanent link

Wed, 24 May 2017

Package RGoogleFit updated to version 0.3.0 with previous version 0.2.0 dated 2016-09-20

Title: R Interface to Google Fit API
Description: Provides interface to Google Fit REST API v1 (see <https://developers.google.com/fit/rest/v1/reference/>).
Author: Marcin Szymanski
Maintainer: Marcin Szymanski <ms32035@gmail.com>

Diff between RGoogleFit versions 0.2.0 dated 2016-09-20 and 0.3.0 dated 2017-05-24

 DESCRIPTION               |    8 ++++----
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 13 files changed, 51 insertions(+), 29 deletions(-)

More information about RGoogleFit at CRAN
Permanent link

Package RAMP updated to version 2.0.1 with previous version 1.9 dated 2016-12-18

Title: Regularized Generalized Linear Models with Interaction Effects
Description: Provides an efficient procedure for fitting the entire solution path for high-dimensional regularized quadratic generalized linear models with interactions effects under the strong or weak heredity constraint.
Author: Yang Feng, Ning Hao and Hao Helen Zhang
Maintainer: Yang Feng <yang.feng@columbia.edu>

Diff between RAMP versions 1.9 dated 2016-12-18 and 2.0.1 dated 2017-05-24

 DESCRIPTION                 |   10 +++++-----
 MD5                         |   13 +++++++------
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More information about RAMP at CRAN
Permanent link

Package segmented updated to version 0.5-2.0 with previous version 0.5-1.4 dated 2015-11-04

Title: Regression Models with Break-Points / Change-Points Estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>

Diff between segmented versions 0.5-1.4 dated 2015-11-04 and 0.5-2.0 dated 2017-05-24

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 NAMESPACE                |    3 +-
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More information about segmented at CRAN
Permanent link

Package polmineR updated to version 0.7.3 with previous version 0.7.2 dated 2017-03-24

Title: Toolkit for Corpus Analysis
Description: Library for corpus analysis using the Corpus Workbench as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create partitions and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document term matrices, term co- occurrence matrices etc.) can be created based on the indexed corpora.
Author: Andreas Blaette
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

Diff between polmineR versions 0.7.2 dated 2017-03-24 and 0.7.3 dated 2017-05-24

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Package eechidna updated to version 1.1 with previous version 0.1 dated 2016-05-23

Title: Exploring Election and Census Highly Informative Data Nationally for Australia
Description: Data from the 2013 and 2016 Australian Federal Election (House of Representatives) and the 2011 Australian Census. Includes tools for visualizing and analysing the data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission) 2016.
Author: Di Cook [aut], Anthony Ebert [aut], Heike Hofmann [aut], Rob Hyndman [aut], Thomas Lumley [aut], Ben Marwick [aut, cre], Carson Sievert [aut], Mingzhu Sun [aut], Dilini Talagala [aut], Nicholas Tierney [aut], Nathaniel Tomasetti [aut], Earo Wang [aut], Fang Zhou [aut], Commonwealth of Australia AEC [cph]
Maintainer: Ben Marwick <benmarwick@gmail.com>

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Package BDgraph updated to version 2.37 with previous version 2.36 dated 2017-04-28

Title: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889> and Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>

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Package amen updated to version 1.3 with previous version 1.1 dated 2015-06-26

Title: Additive and Multiplicative Effects Models for Networks and Relational Data
Description: Analysis of dyadic network and relational data using additive and multiplicative effects (AME) models. The basic model includes regression terms, the covariance structure of the social relations model (Warner, Kenny and Stoto (1979) <DOI:10.1037/0022-3514.37.10.1742>, Wong (1982) <DOI:10.2307/2287296>), and multiplicative factor models (Hoff(2009) <DOI:10.1007/s10588-008-9040-4>). Four different link functions accommodate different relational data structures, including binary/network data (bin), normal relational data (nrm), ordinal relational data (ord) and data from fixed-rank nomination schemes (frn). Several of these link functions are discussed in Hoff, Fosdick, Volfovsky and Stovel (2013) <DOI:10.1017/nws.2013.17>. Development of this software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff <peter.hoff@duke.edu>

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Package x.ent updated to version 1.1.7 with previous version 1.1.6 dated 2016-11-30

Title: eXtraction of ENTity
Description: Provides a tool for extracting information (entities and relations between them) in text datasets. It also emphasizes the results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. 'x.ent' uses parsing with Perl functions and JavaScript to define user preferences through a browser and R to display and support analysis of the results extracted. Local grammars are defined and compiled with the tool Unitex, a tool developed by University Paris Est that supports multiple languages. See ?xconfig for an introduction.
Author: Nicolas Turenne [aut], Tien T. Phan [aut, cre]
Maintainer: Tien T. Phan <phantien84@gmail.com>

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Package wally updated to version 1.0.9 with previous version 1.0.8 dated 2017-05-17

Title: The Wally Calibration Plot for Risk Prediction Models
Description: A prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. A calibration plot provides a simple, yet useful, way of assessing the calibration assumption. The Wally plot consists of a sequence of usual calibration plots. Among the plots contained within the sequence, one is the actual calibration plot which has been obtained from the data and the others are obtained from similar simulated data under the calibration assumption. It provides the investigator with a direct visual understanding of the shape and sampling variability that are common under the calibration assumption. The original calibration plot from the data is included randomly among the simulated calibration plots, similarly to a police lineup. If the original calibration plot is not easily identified then the calibration assumption is not contradicted by the data. The method handles the common situations in which the data contain censored observations and occurrences of competing events.
Author: Paul F Blanche <paulfblanche@gmail.com>, Thomas A. Gerds <tag@biostat.ku.dk>
Maintainer: Paul F. Blanche <paulfblanche@gmail.com>

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Package TriadSim updated to version 0.1.1 with previous version 0.0.1 dated 2017-05-12

Title: Simulating Triad Genomewide Genotypes
Description: Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
Author: Min Shi [aut, cre]
Maintainer: Min Shi <shi2@niehs.nih.gov>

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Package spant updated to version 0.2.0 with previous version 0.1.0 dated 2017-04-26

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data.
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

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Package meta updated to version 4.8-2 with previous version 4.8-1 dated 2017-03-17

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed); - generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between meta versions 4.8-1 dated 2017-03-17 and 4.8-2 dated 2017-05-24

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Package manipulateWidget updated to version 0.6.0 with previous version 0.5.1 dated 2017-01-27

Title: Add Even More Interactivity to Interactive Charts
Description: Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.
Author: Francois Guillem [aut, cre], RTE [cph], JJ Allaire [ctb]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between manipulateWidget versions 0.5.1 dated 2017-01-27 and 0.6.0 dated 2017-05-24

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Package jtools updated to version 0.4.5 with previous version 0.4.4 dated 2017-03-26

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written for the purpose of more efficiently understanding and sharing the results of (primarily) regression analyses. There are a number of functions focused specifically on the interpretation and presentation of interactions in linear models. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <long.1377@osu.edu>

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Permanent link

Package antaresProcessing updated to version 0.10.2 with previous version 0.10.1 dated 2017-04-20

Title: Antares Results Processing
Description: Process results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>

Diff between antaresProcessing versions 0.10.1 dated 2017-04-20 and 0.10.2 dated 2017-05-24

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Permanent link

Package sdcMicro updated to version 5.0.2 with previous version 5.0.1 dated 2017-03-14

Title: Statistical Disclosure Control Methods for Anonymization of Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly confidential. This package can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. In addition, various risk estimation methods are included. Note that the package includes a graphical user interface that allows to use various methods of this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between sdcMicro versions 5.0.1 dated 2017-03-14 and 5.0.2 dated 2017-05-24

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More information about sdcMicro at CRAN
Permanent link

Package rbcb updated to version 0.1.1 with previous version 0.1.0 dated 2017-03-22

Title: R Interface to Brazilian Central Bank Web Services
Description: The Brazilian Central Bank API delivers many datasets which regard economic activity, regional economy, international economy, public finances, credit indicators and many more. For more information please see <http://dadosabertos.bcb.gov.br/>. These datasets can be accessed through 'rbcb' functions and can be obtained in different data structures common to R ('tibble', 'data.frame', 'xts', ...).
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>

Diff between rbcb versions 0.1.0 dated 2017-03-22 and 0.1.1 dated 2017-05-24

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Package funrar updated to version 1.1.0 with previous version 1.0.3 dated 2017-05-05

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity.
Author: Matthias Grenié [aut, cre], Pierre Denelle [aut], Caroline Tucker [aut]
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>

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More information about funrar at CRAN
Permanent link

Package optiSel updated to version 0.9 with previous version 0.8.1 dated 2017-04-25

Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>

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 man/opticont.Rd                 |   12 ++--
 man/opticont4mb.Rd              |  117 ++++++----------------------------------
 man/plot.HaploFreq.Rd           |   21 ++++---
 man/sampleIndiv.Rd              |only
 src/RcppExports.cpp             |    9 ++-
 src/init.c                      |    2 
 src/rcpp_completeness.cpp       |    2 
 src/rcpp_genecont.cpp           |   71 +++++++++++++++++++-----
 src/rcpp_segIBD.cpp             |    8 +-
 src/rcpp_segIBDandN.cpp         |   10 +--
 src/rcpp_segIBDandNVersion2.cpp |   10 +--
 src/rcpp_segN.cpp               |    6 +-
 vignettes/ocs-vignette.Rmd      |   17 +++++
 vignettes/seg-vignette.Rmd      |    4 -
 37 files changed, 316 insertions(+), 267 deletions(-)

More information about optiSel at CRAN
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Package ARTP2 updated to version 0.9.32 with previous version 0.9.30 dated 2016-07-11

Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Maintainer: Han Zhang <han.zhang2@nih.gov>

Diff between ARTP2 versions 0.9.30 dated 2016-07-11 and 0.9.32 dated 2017-05-24

 ARTP2-0.9.30/ARTP2/src/Makevars                 |only
 ARTP2-0.9.30/ARTP2/src/artp2.cpp                |only
 ARTP2-0.9.30/ARTP2/src/test.cpp                 |only
 ARTP2-0.9.32/ARTP2/DESCRIPTION                  |   12 +++---
 ARTP2-0.9.32/ARTP2/MD5                          |   46 +++++++++++++-----------
 ARTP2-0.9.32/ARTP2/NAMESPACE                    |    2 -
 ARTP2-0.9.32/ARTP2/R/artp2.R                    |    2 -
 ARTP2-0.9.32/ARTP2/R/extract.reference.allele.R |   14 ++++++-
 ARTP2-0.9.32/ARTP2/R/load.summary.files.R       |    5 ++
 ARTP2-0.9.32/ARTP2/R/load.summary.statistics.R  |    3 +
 ARTP2-0.9.32/ARTP2/R/recover.stat.R             |    4 ++
 ARTP2-0.9.32/ARTP2/R/test.R                     |    2 -
 ARTP2-0.9.32/ARTP2/cleanup                      |only
 ARTP2-0.9.32/ARTP2/configure                    |only
 ARTP2-0.9.32/ARTP2/configure.ac                 |only
 ARTP2-0.9.32/ARTP2/data/data.rda                |binary
 ARTP2-0.9.32/ARTP2/data/geno.rda                |binary
 ARTP2-0.9.32/ARTP2/data/pathway.rda             |binary
 ARTP2-0.9.32/ARTP2/data/ref.geno.rda            |binary
 ARTP2-0.9.32/ARTP2/data/subj.id.rda             |binary
 ARTP2-0.9.32/ARTP2/man/meta.Rd                  |    2 -
 ARTP2-0.9.32/ARTP2/man/rARTP.Rd                 |   22 ++++++++++-
 ARTP2-0.9.32/ARTP2/man/sARTP.Rd                 |   22 +++++++----
 ARTP2-0.9.32/ARTP2/man/warm.start.Rd            |    2 +
 ARTP2-0.9.32/ARTP2/src/ARTP2_init.c             |only
 ARTP2-0.9.32/ARTP2/src/Makevars.in              |only
 ARTP2-0.9.32/ARTP2/src/artp2_main.cpp           |only
 ARTP2-0.9.32/ARTP2/src/test_c.cpp               |only
 ARTP2-0.9.32/ARTP2/src/util.h                   |    2 -
 29 files changed, 97 insertions(+), 43 deletions(-)

More information about ARTP2 at CRAN
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