Mon, 27 Apr 2015

New package VCA with initial version 1.1.1
Package: VCA
Version: 1.1.1
Date: 2015-04-16
Title: Variance Component Analysis
Author: Andre Schuetzenmeister
Maintainer: Andre Schuetzenmeister
Depends: R (>= 3.0.0), stats
Imports: Matrix, numDeriv
Description: ANOVA-type estimation (prediction) of random effects and variance components in linear mixed models, is implemented. Random models, a sub-set of mixed models, can be fit applying a Variance Component Analysis (VCA). This is a special type of analysis frequently used in verifying the precision performance of diagnostics. The Satterthwaite approximation of the total degrees of freedom is implemented. There are several functions for extracting, random effects, fixed effects, variance-covariance matrices of random and fixed effects. Residuals can be extracted as raw, standardized and studentized residuals. Additionally, a variability chart is implemented for visualizing the variability in sub-classes emerging from an experimental design ('varPlot').
License: GPL (>= 3)
Collate: 'plot.R' 'vca.R'
NeedsCompilation: yes
Packaged: 2015-04-16 10:21:45 UTC; schueta6
Repository: CRAN
Date/Publication: 2015-04-27 09:02:57

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Sun, 26 Apr 2015

New package h5 with initial version 0.9
Package: h5
Type: Package
Title: Interface to the 'HDF5' Library
Version: 0.9
Date: 2015-04-22
Authors@R: c(person("Mario", "Annau", role = c("aut", "cre"), email = "mario.annau@gmail.com"))
Copyright: See COPYRIGHTS file.
Description: S4 Interface to the 'HDF5' library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The 'HDF5' format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.
License: BSD_2_clause + file LICENSE
BugReports: https://github.com/mannau/h5/issues
SystemRequirements: libhdf5 (>= 1.8.4) with C++ interface enabled (--enable-cxx=yes)
Depends: R (>= 3.1)
Imports: Rcpp (>= 0.11.5), methods
LinkingTo: Rcpp
Suggests: testthat, roxygen2, RCurl
Collate: 'H5Location-Attribute.R' 'Attribute.R' 'CommonFG.R' 'CommonFG-DataSet.R' 'CommonFG-Group.R' 'DataSet.R' 'DataSpace.R' 'Dataset-Extend.R' 'Dataset-Subset.R' 'H5File.R' 'H5Group.R' 'Helpers.R' 'RcppExports.R' 'h5-package.R'
NeedsCompilation: yes
Packaged: 2015-04-26 17:45:02 UTC; mario
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau
Repository: CRAN
Date/Publication: 2015-04-26 22:45:59

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New package haplotypes with initial version 1.0
Package: haplotypes
Title: Haplotype Inference and Statistical Analysis of Genetic Variation
Version: 1.0
Date: 2015-04-24
Author: Caner Aktas
Maintainer: Caner Aktas
Description: Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and inferring haplotypes from DNA sequences or user provided absolute character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony.
License: GPL-2
URL: http://cran.r-project.org, https://biolsystematics.wordpress.com/r/
Depends: R (>= 3.1.1), methods, network
Suggests: sna
NeedsCompilation: no
Packaged: 2015-04-25 18:32:05 UTC; cnr
Repository: CRAN
Date/Publication: 2015-04-26 09:49:28

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Fri, 24 Apr 2015

New package RJafroc with initial version 0.0.1
Package: RJafroc
Type: Package
Title: Analysis of Data Acquired Using the Receiver Operating Characteristic Paradigm and Its Extensions
Version: 0.0.1
Date: 2015-04-21
Authors@R: c(person("Xuetong", "Zhai", role = c("aut", "cre"), email = "xuetong.zhai@gmail.com"), person("Dev", "Chakraborty", role = c("aut", "ths"), email = "dpc10ster@gmail.com"))
Maintainer: Xuetong Zhai
Depends: tools, xlsx, ggplot2, stringr, utils
Suggests: knitr
VignetteBuilder: knitr
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software.
License: GPL-3
LazyData: true
URL: http://www.devchakraborty.com
Packaged: 2015-04-23 03:52:09 UTC; XuetongZhai
Author: Xuetong Zhai [aut, cre], Dev Chakraborty [aut, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-24 08:18:56

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New package RRTCS with initial version 0.0.1
Package: RRTCS
Type: Package
Title: Randomized Response Techniques for Complex Surveys
Version: 0.0.1
Date: 2015-04-22
Author: Beatriz Cobo Rodríguez, María del Mar Rueda García, Antonio Arcos Cebrián
Maintainer: Beatriz Cobo Rodríguez
Description: Point and interval estimation of linear parameters with data obtained from complex surveys (including stratified and clustered samples) when randomization techniques are used. The randomized response technique was developed to obtain estimates that are more valid when studying sensitive topics. Estimators and variances for 14 randomized response methods for qualitative variables and 7 randomized response methods for quantitative variables are also implemented. In addition, some data sets from surveys with these randomization methods are included in the package.
License: GPL (>= 2)
Encoding: UTF-8
Imports: sampling, samplingVarEst
Packaged: 2015-04-23 18:21:36 UTC; Usuario
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-24 06:50:24

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Wed, 22 Apr 2015

New package treeperm with initial version 1.6
Package: treeperm
Type: Package
Title: Exact and Asymptotic K Sample Permutation Test
Version: 1.6
Date: 2015-04-22
Author: Qiao Kang
Maintainer: Qiao Kang
Depends: R (>= 2.14.1)
Description: An implementation of permutation tests in R, supporting both exact and asymptotic K sample test of data locations. The p value of exact tests is found using tree algorithms. Tree algorithms treat permutations of input data as tree nodes and perform constraint depth-first searches for permutations that fall into the critical region of a test systematically. Pruning of tree search and optimisations at C level enable exact tests for certain large data sets.
License: GPL-2
Packaged: 2015-04-22 16:47:23 UTC; sony
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-22 22:49:55

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New package TickExec with initial version 1.0
Package: TickExec
Type: Package
Title: Execution Functions for Tick Data Back Test
Version: 1.0
Date: 2015-04-20
Author: HKUST
Maintainer: SONG Yang
Description: Functions to execute orders in backtesting using tick data. A testing platform was established by the four major execution functions, namely 'LimitBuy', 'LimitSell', 'MarketSell' and 'MarketSell', which enclosed all tedious aspects (such as queueing for order executions and calculate actual executed volumes) for order execution using tick data. Such that one can focus on the logic of strategies, rather than its execution.
License: GPL-3
Packaged: 2015-04-22 17:17:08 UTC; Ian
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 22:31:08

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New package shinydashboard with initial version 0.4.0
Package: shinydashboard
Title: Create Dashboards with 'Shiny'
Version: 0.4.0
Authors@R: c( person("Winston", "Chang", role = c("aut", "cre"), email = "winston@rstudio.com"), person(family = "RStudio", role = "cph"), person(family = "Almasaeed Studio", role = c("ctb", "cph")), person(family = "Adobe Systems Incorporated", role = c("ctb", "cph"), comment = "Source Sans Pro font") )
Description: Create dashboards with 'Shiny'. This package provides a theme on top of 'Shiny', making it easy to create attractive dashboards.
URL: http://rstudio.github.io/shinydashboard/
Depends: R (>= 3.0)
License: GPL-2 | file LICENSE
Imports: shiny (>= 0.11.1), htmltools (>= 0.2.6)
NeedsCompilation: no
Packaged: 2015-04-22 15:21:29 UTC; winston
Author: Winston Chang [aut, cre], RStudio [cph], Almasaeed Studio [ctb, cph], Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang
Repository: CRAN
Date/Publication: 2015-04-22 23:08:28

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New package emg with initial version 1.0.6
Package: emg
Type: Package
Title: Exponentially Modified Gaussian (EMG) Distribution
Version: 1.0.6
Date: 2015-04-21
Author: Shawn Garbett, Mark Kozdoba
Maintainer: Shawn Garbett
Depends: R (>= 1.8.0), stats, stats4
Description: Provides basic distribution functions for a mixture model of a Gaussian and exponential distribution.
License: GPL-2
LazyLoad: yes
Packaged: 2015-04-22 05:09:58 UTC; sgarbett
NeedsCompilation: no
X-CRAN-Comment: Archived on 2014-08-19 as maintainer address bounced.
Repository: CRAN
Date/Publication: 2015-04-22 22:42:07

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New package discSurv with initial version 1.0.0
Package: discSurv
Version: 1.0.0
Title: Discrete Time Survival Analysis
Date: 2015-04-22
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski
Description: Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.
Imports: functional, Matrix, matrixcalc, mvtnorm, numDeriv, caret, mgcv
Suggests: Ecdat, pec, survival, randomForest
License: GPL-3
LazyLoad: yes
Packaged: 2015-04-22 14:10:33 UTC; Welchowski
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 21:58:21

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New package cellranger with initial version 0.1.0
Package: cellranger
Title: Translate Spreadsheet Cell Ranges to Rows and Columns
Version: 0.1.0
Authors@R: c( person("Jennifer", "Bryan", , "jenny@stat.ubc.ca", c("cre", "aut")), person("Hadley", "Wickham", , "hadley@rstudio.com", "ctb") )
Description: Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/jennybc/cellranger
BugReports: https://github.com/jennybc/cellranger/issues
Suggests: testthat
Packaged: 2015-04-22 17:10:55 UTC; jenny
Author: Jennifer Bryan [cre, aut], Hadley Wickham [ctb]
Maintainer: Jennifer Bryan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 21:58:18

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New package shinyjs with initial version 0.0.3.3
Package: shinyjs
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Version: 0.0.3.3
Authors@R: person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"))
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Many useful JavaScript functions are made available by shinyjs with a simple R interface so that you don't have to write any JavaScript code. Even if you do know JavaScript, shinyjs can be used as convenience functions to avoid dealing with message passing and writing JavaScript code.
URL: https://github.com/daattali/shinyjs
Depends: R (>= 3.1.2)
Imports: shiny (>= 0.11.1)
Suggests: knitr (>= 1.7), testthat (>= 0.9.1)
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-04-21 16:30:06 UTC; Dean
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali
Repository: CRAN
Date/Publication: 2015-04-22 08:07:52

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New package rversions with initial version 1.0.0
Package: rversions
Title: Query R Versions, Including r-release and r-oldrel
Version: 1.0.0
Authors@R: person("Gabor", "Csardi", , "csardi.gabor@gmail.com", role = c("aut", "cre"))
Description: Query the main R SVN repository to find the versions r-release and r-oldrel refer to, and also all previous R versions and their release dates.
License: MIT + file LICENSE
URL: https://github.com/metacran/rversions
BugReports: https://github.com/metacran/rversions/issues
Imports: RCurl, XML
NeedsCompilation: no
Packaged: 2015-04-21 19:50:01 UTC; gaborcsardi
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
Repository: CRAN
Date/Publication: 2015-04-22 08:06:34

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Mon, 20 Apr 2015

New package xml2 with initial version 0.1.0
Package: xml2
Version: 0.1.0
Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre")), person("Jeroen", "Ooms", role = "ctb"), person("RStudio", role = "cph"), person("R Foundation", role = "ctb", comment = "Copy of R-project homepage cached as example") )
Depends: R (>= 3.1.0)
Imports: Rcpp
LinkingTo: Rcpp (>= 0.11.4.6), BH
Suggests: testthat, curl
License: GPL (>= 2)
Packaged: 2015-04-20 19:36:32 UTC; hadley
Author: Hadley Wickham [aut, cre], Jeroen Ooms [ctb], RStudio [cph], R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-20 22:43:45

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New package RSocrata with initial version 1.6.0-12
Package: RSocrata
Title: Download 'Socrata' Data Sets as R Data Frames
Description: Provides easier interaction with Socrata open data portals \url{http://dev.socrata.com}. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format. Manages throttling by 'Socrata'.
Version: 1.6.0-12
Date: 2015-4-20
URL: https://github.com/Chicago/RSocrata
BugReports: https://github.com/Chicago/RSocrata/issues
Depends: httr (>= 0.3), jsonlite (>= 0.9.14), mime (>= 0.2)
Imports: curl (>= 0.5)
Suggests: RUnit
Author: Hugh Devlin, Ph. D. and Tom Schenk, Jr.
Maintainer: "Tom Schenk Jr."
License: MIT + file LICENSE
Packaged: 2015-04-20 17:03:19 UTC; 362222
NeedsCompilation: no
X-CRAN-Comment: Archived on 2014-12-07 as maintainer address bounced.
Repository: CRAN
Date/Publication: 2015-04-20 22:13:33

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New package rLiDAR with initial version 0.1
Package: rLiDAR
Type: Package
Title: LiDAR Data Processing and Visualization
Version: 0.1
Author: Carlos A. Silva, Nicholas L. Crookston, Andrew T. Hudak, Lee A. Vierling
Maintainer: Carlos A. Silva
Depends: R (>= 3.1.2)
Imports: spatstat,sp,deldir,plyr,raster,geometry,rgl,bitops
Description: Set of tools for reading, processing and visualizing small set of LiDAR (Light Detection and Ranging) data for forest inventory applications.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: rlidar
Repository/R-Forge/Revision: 115
Repository/R-Forge/DateTimeStamp: 2015-04-16 04:49:32
Date/Publication: 2015-04-20 17:52:06
Packaged: 2015-04-16 05:10:18 UTC; rforge
NeedsCompilation: no

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New package GWLelast with initial version 1.0
Package: GWLelast
Type: Package
Title: Geographically Weighted Logistic Elastic Net Regression
Version: 1.0
Date: 2015-04-20
Author: Daisuke Yoneoka, Eiko Saito
Maintainer: Daisuke Yoneoka
Description: Fit a geographically weighted logistic elastic net regression.
License: GPL-2
Suggests: testthat
Imports: doParallel,geosphere,sp,spgwr,glmnet,doMC,foreach
Packaged: 2015-04-20 03:55:57 UTC; Daisuke
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-20 14:25:06

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New package ADPclust with initial version 0.6.3
Package: ADPclust
Type: Package
Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast Clustering Using Adaptive Density Peak Detection). The work is built and improved upon Rodriguez and Laio[2014]'s idea. ADPclust clusters data by finding density peaks in a density-distance plot generated from local multivariate Gaussian density estimation. It includes an automatic centroids selection and parameter optimization algorithm, which finds the number of clusters and cluster centroids by comparing average silhouettes on a grid of testing clustering results; It also includes an user interactive algorithm that allows the user to manually selects cluster centroids from a two dimensional "density-distance plot".
Version: 0.6.3
Author: Yifan "Ethan" Xu , Xiao-Feng Wang
Maintainer: Yifan "Ethan" Xu
Depends: R (>= 2.14.0),
Imports: dplyr, cluster, fields, knitr
VignetteBuilder: knitr
License: GPL (>= 2)
LazyData: true
Packaged: 2015-04-20 03:40:54 UTC; yifanxu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-20 14:17:36

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New package synRNASeqNet with initial version 1.0
Package: synRNASeqNet
Type: Package
Title: Synthetic RNA-Seq Network Generation and Mutual Information Estimates
Version: 1.0
Date: 2015-04-07
Author: Luciano Garofano, Stefano Maria Pagnotta, Michele Ceccarelli
Maintainer: Luciano Garofano
Depends: R (>= 3.1.1), parallel, parmigene, GenKern, igraph
URL: https://github.com/lucgar/synRNASeqNet
Imports: KernSmooth
Description: It implements various estimators of mutual information, such as the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, the shrinkage estimator, and the Chao-Shen estimator. It also offers wrappers to the kNN and kernel density estimators. Furthermore, it provides various index of performance evaluation such as precision, recall, FPR, F-Score, ROC-PR Curves and so on. Lastly, it provides a brand new way of generating synthetic RNA-Seq Network with known dependence structure.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2015-04-20 08:45:39 UTC; luciano
Repository: CRAN
Date/Publication: 2015-04-20 11:55:18

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Sun, 19 Apr 2015

New package WikipediaR with initial version 1.0
Package: WikipediaR
Type: Package
Title: R-Based Wikipedia Client
Version: 1.0
Date: 2015-04-13
Authors@R: c(person("Avner", "Bar-Hen", role = c("aut", "cre"), email = "Avner.Bar-Hen@mi.parisdescartes.fr"), person("Louise", "Baschet", role = "ctb"), person("Francois-Xavier", "Jollois", role = "ctb"), person("Jeremie", "Riou", role = "ctb") )
Maintainer: Avner Bar-Hen
Description: Provides an interface to the Wikipedia web application programming interface (API), using internet connection. Three functions provide details for a specific Wikipedia page: all links that are present, all pages that link to, all the contributions (revisions for main pages, and discussions for talk pages). Two functions provide details for a specific user: all contributions, and general information (as name, gender, rights or groups). It provides additional information compared to others packages, as 'WikipediR'. It does not need login. The multiplex network that can be constructed from the results of the functions of 'WikipediaR' can be modeled as Stochastic Block Model as in Barbillon P., Donnet, S., Lazega E., and Bar-Hen A.: "Stochastic Block Models for Multiplex networks: an application to networks of researchers", ArXiv 1501.06444, http://arxiv.org/abs/1501.06444.
License: GPL (> 2)
Depends: R (>= 2.10.0), XML (>= 2.6.3)
URL: http://www.r-project.org
Repository: CRAN
Packaged: 2015-04-17 14:44:06 UTC; Louise
Author: Avner Bar-Hen [aut, cre], Louise Baschet [ctb], Francois-Xavier Jollois [ctb], Jeremie Riou [ctb]
NeedsCompilation: no
Date/Publication: 2015-04-19 22:10:18

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New package tdr with initial version 0.11
Package: tdr
Type: Package
Title: Target Diagram
Version: 0.11
Date: 2015-04-18
Encoding: UTF-8
Authors@R: person("Oscar", "Perpinan Lamigueiro", email="oscar.perpinan@gmail.com", role=c('cre', 'aut'))
Description: Implementation of target diagrams using 'lattice' and 'ggplot2' graphics. Target diagrams provide a graphical overview of the respective contributions of the unbiased RMSE and MBE to the total RMSE (Jolliff, J. et al., 2009. "Summary Diagrams for Coupled Hydrodynamic-Ecosystem Model Skill Assessment." Journal of Marine Systems 76: 64–82.)
URL: http://github.com/oscarperpinan/tdr
BugReports: https://github.com/oscarperpinan/tdr/issues
License: GPL-2
Depends: lattice, ggplot2
Imports: RColorBrewer
Suggests: latticeExtra
Packaged: 2015-04-19 08:18:13 UTC; oscar
Author: Oscar Perpinan Lamigueiro [cre, aut]
Maintainer: Oscar Perpinan Lamigueiro
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-19 22:12:15

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New package timeSeq with initial version 1.0.0
Package: timeSeq
Type: Package
Title: Nonparallel Differential Expressed Genes
Version: 1.0.0
Date: 2015-04-19
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao
Description: Uses a negative binomial mixed-effects (NBME) model to detect nonparallel differential expression(NPDE) genes and parallel differential expression(PDE) genes in the time course RNA-seq data.
Depends: R (>= 3.0.1)
Imports: parallel, gss, lattice, pheatmap, doParallel, foreach, reshape, edgeR
License: GPL (>= 2)
Packaged: 2015-04-19 01:56:33 UTC; gaofan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-19 07:55:48

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New package PortfolioAnalytics with initial version 1.0.3636
Package: PortfolioAnalytics
Type: Package
Title: Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios
Authors@R: c( person(given=c("Brian","G."),family="Peterson",role=c("cre","aut","cph"), email="brian@braverock.com") , person(given="Peter",family="Carl",role=c("aut","cph"), email="peter@braverock.com") , person(given="Kris",family="Boudt",role=c("ctb","cph")) , person(given="Ross",family="Bennett",role=c("ctb","cph")) , person(given="Hezky",family="Varon",role="ctb") , person(given="Guy",family="Yollin",role="ctb") , person(given="R. Douglas",family="Martin",role="ctb") )
Version: 1.0.3636
Date: 2015-04-18
Maintainer: Brian G. Peterson
Description: Portfolio optimization and analysis routines and graphics.
Depends: R (>= 2.14.0), zoo, xts (>= 0.8), foreach, PerformanceAnalytics (>= 1.1.0)
Suggests: quantmod, DEoptim(>= 2.2.1), iterators, fGarch, Rglpk, quadprog, ROI (>= 0.1.0), ROI.plugin.glpk (>= 0.0.2), ROI.plugin.quadprog (>= 0.0.2), ROI.plugin.symphony (>= 0.0.2), pso, GenSA, corpcor, testthat, nloptr (>= 1.0.0), MASS, robustbase
License: GPL
Copyright: (c) 2004-2015
NeedsCompilation: yes
Packaged: 2015-04-19 01:37:19.121143 UTC; brian
Author: Brian G. Peterson [cre, aut, cph], Peter Carl [aut, cph], Kris Boudt [ctb, cph], Ross Bennett [ctb, cph], Hezky Varon [ctb], Guy Yollin [ctb], R. Douglas Martin [ctb]
Repository: CRAN
Date/Publication: 2015-04-19 07:38:57

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Sat, 18 Apr 2015

New package TDCor with initial version 0.1-1
Package: TDCor
Type: Package
Title: Gene Network Inference from Time-Series Transcriptomic Data
Version: 0.1-1
Date: 2015-04-08
Author: Julien Lavenus
Maintainer: Mikael Lucas
Imports: parallel
Depends: R (>= 3.1.2), deSolve
Description: The Time-Delay Correlation algorithm (TDCor) reconstructs the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developed to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset which was used in this study is included in the package to illustrate how to use it.
License: GPL (>= 2)
Packaged: 2015-04-08 19:28:20.092 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 17:19:35

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New package crimelinkage with initial version 0.0.3
Package: crimelinkage
Title: Statistical Methods for Crime Series Linkage
Version: 0.0.3
Authors@R: c( person("Michael", "Porter", email = "mporter@cba.ua.edu", role = c("aut", "cre")), person("Brian", "Reich", email = "brian_reich@ncsu.edu", role = "aut"))
Description: Statistical Methods for Crime Series Linkage. This package provides code for criminal case linkage, crime series identification, crime series clustering, and suspect identification.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
Date: 2015-04-16
BugReports:
Imports: igraph, geosphere
Suggests: fields, knitr, gbm
VignetteBuilder: knitr
Packaged: 2015-04-18 12:50:50 UTC; mdporter
Author: Michael Porter [aut, cre], Brian Reich [aut]
Maintainer: Michael Porter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 17:19:39

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New package plaqr with initial version 1.0
Package: plaqr
Title: Partially Linear Additive Quantile Regression
Description: Estimation, prediction, thresholding, and plotting for partially linear additive quantile regression. Intuitive functions for fitting and plotting partially linear additive quantile regression models. Uses and works with functions from the 'quantreg' package.
Version: 1.0
Authors@R: person("Adam", "Maidman", role = c("cre","aut"), email = "maidm004@umn.edu")
Maintainer: Adam Maidman
Depends: R (>= 3.0), quantreg, splines
License: GPL (>= 2)
Repository: CRAN
Date/Publication: 2015-04-18 10:59:33
Packaged: 2015-04-17 14:49:00 UTC; maidm004
Author: Adam Maidman [cre, aut]
NeedsCompilation: no

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New package NPC with initial version 1.0.0
Package: NPC
Type: Package
Title: Nonparametric Combination of Hypothesis Tests
Version: 1.0.0
Authors@R: person("Devin", "Caughey", email="devin.caughey@gmail.com", role=c("aut", "cre"))
Depends: R (>= 3.1.1)
LazyData: true
Description: An implementation of nonparametric combination of hypothesis tests. This package performs nonparametric combination (Pesarin and Salmaso 2010), a permutation-based procedure for jointly testing multiple hypotheses. The tests are conducted under the global "sharp" null hypothesis of no effects, and the component tests are combined on the metric of their p-values. A key feature of nonparametric combination is that it accounts for the dependence among tests under the null hypothesis. In addition to the "NPC" function, which performs nonparametric combination itself, the package also contains a number of helper functions, many of which calculate a test statistic given an input of data.
License: GPL-3
Imports: permute, dplyr, coin, matlab
Suggests: car, mvtnorm, plyr, xtable
Packaged: 2015-04-17 13:04:24 UTC; justin
Author: Devin Caughey [aut, cre]
Maintainer: Devin Caughey
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:55:51

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New package gbm2sas with initial version 1.0
Package: gbm2sas
Type: Package
Title: Convert GBM Object Trees to SAS Code
Version: 1.0
Date: 2015-04-10
Author: John R. Dixon
Maintainer: John R. Dixon
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
License: GPL-3
Depends: gbm
Packaged: 2015-04-16 15:33:56 UTC; i800146
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:56:14

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New package BivarP with initial version 1.0
Package: BivarP
Type: Package
Title: Estimating the Parameters of Some Bivariate Distributions
Version: 1.0
Date: 2015-04-17
Author: Josef Brejcha
Maintainer: Josef Brejcha
Depends: dfoptim, survival, copula
Description: Parameter estimation of bivariate distribution functions modeled as a Archimedean copula function. The input data may contain values from right censored. Used marginal distributions are two-parameter. Methods for density, distribution, survival, random sample generation.
License: GPL (>= 3)
LazyData: TRUE
Packaged: 2015-04-17 10:31:40 UTC; brch
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-18 08:55:28

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Fri, 17 Apr 2015

New package marl with initial version 1.0
Package: marl
Type: Package
Title: Multivariate Analysis Based on Relative Likelihoods
Version: 1.0
Date: 2015-04-09
Author: Milan Bimali
Maintainer: Milan Bimali
Description: Functions provided allow data simulation; construction of weighted relative likelihood functions; clustering and principal component analysis based on weighted relative likelihood functions.
License: GPL-2
Packaged: 2015-04-16 22:20:48 UTC; Milan Bimali
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-17 10:41:30

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Thu, 16 Apr 2015

New package multimark with initial version 1.1.3
Package: multimark
Type: Package
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive Marks
Version: 1.1.3
Date: 2015-04-15
Depends: R (>= 3.0.0)
Imports: parallel, statmod, Matrix, RMark, coda, methods, Brobdingnag, mvtnorm
Authors@R: c(person("Brett T.", "McClintock", email = "brett.mcclintock@noaa.gov",role = c("aut", "cre")),person("Acho", "Arnold",role = c("ctb","cph"), comment = "C original matrix library, https://github.com/najela/matrix.h"),person("Barry", "Brown",role = "ctb", comment = "Fortran original ranlib library"),person("James", "Lovato",role = "ctb", comment = "Fortran original ranlib library"),person("John", "Burkardt",role = "ctb", comment = "C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib"),person("Cleve", "Moler",role = "ctb", comment = "C original linpack library, http://www.kkant.net/geist/ranlib/"))
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive "marks", such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo.
License: GPL-2
LazyData: yes
ByteCompile: TRUE
Packaged: 2015-04-16 19:16:16 UTC; Brett McClintock
Author: Brett T. McClintock [aut, cre], Acho Arnold [ctb, cph] (C original matrix library, https://github.com/najela/matrix.h), Barry Brown [ctb] (Fortran original ranlib library), James Lovato [ctb] (Fortran original ranlib library), John Burkardt [ctb] (C original ranlib library, http://people.sc.fsu.edu/~jburkardt/c_src/ranlib), Cleve Moler [ctb] (C original linpack library, http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-16 23:32:32

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New package qclust with initial version 1.0
Package: qclust
Type: Package
Title: Robust Estimation of Gaussian Mixture Models
Version: 1.0
Date: 2015-04-15
Author: Yichen Qin, Carey E. Priebe
Maintainer: Yichen Qin
Description: Robust estimation of Gaussian mixture models fitted by modified EM algorithm, robust clustering and classification.
Depends: mclust, mvtnorm
URL: http://homepages.uc.edu/~qinyn/qclust/
License: GPL-2
Packaged: 2015-04-16 16:10:36 UTC; qyc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-16 19:53:55

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New package dga with initial version 1.2
Package: dga
Type: Package
Title: Capture-Recapture Estimation using Bayesian Model Averaging
Version: 1.2
Date: 2015-04-16
Author: James Johndrow, Kristian Lum, and Patrick Ball
Maintainer: Kristian Lum
Description: Performs Bayesian model averaging for capture-recapture. This includes code to stratify records, check the strata for suitable overlap to be used for capture-recapture, and some functions to plot the estimated population size.
License: GPL (>= 2)
LazyLoad: yes
Imports: chron
Packaged: 2015-04-16 14:42:17 UTC; kristianlum
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-16 19:53:41

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Wed, 15 Apr 2015

New package rdrop2 with initial version 0.6
Package: rdrop2
Title: Programmatic Interface to the Dropbox API
Version: 0.6
Authors@R: person("Karthik", "Ram", , "karthik.ram@gmail.com", c("aut", "cre"))
Description: Provides full programmatic access to the Dropbox file hosting platform (dropbox.com), including support for all standard file operations.
Depends: R (>= 3.1.1)
License: MIT + file LICENSE
LazyData: true
Imports: assertthat, data.table, dplyr, httr, jsonlite, magrittr
Suggests: testthat, uuid
Packaged: 2015-04-15 15:27:51 UTC; karthik
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:09

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New package multiway with initial version 1.0-0
Package: multiway
Type: Package
Title: Component Models for Multi-Way Data
Version: 1.0-0
Date: 2015-04-15
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
Depends: parallel
Description: Fits multi-way component models via alternating least squares algorithms with optional constraints (orthogonality and non-negativity). Fit models include Individual Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component Analysis, and Tucker Factor Analysis.
License: GPL (>= 2)
Packaged: 2015-04-15 05:13:48 UTC; Nate
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:04

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New package forecTheta with initial version 1.0
Package: forecTheta
Type: Package
Title: Forecasting Time Series by Theta Method
Version: 1.0
Date: 2015-03-30
Author: Jose Augusto Fioruci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fioruci
Depends: R (>= 3.0.2), forecast, parallel
Description: Routines for forecasting univariate time series using Theta Method and Optimised Theta Method (Fioruci et al, 2015). Contains two cross-validation routines of Tashman (2000).
License: GPL (>= 2)
URL: http://arxiv.org/abs/1503.03529
Packaged: 2015-04-15 14:02:41 UTC; Augusto
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 21:41:01

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New package boxr with initial version 0.2.5
Package: boxr
Type: Package
Title: Interface for the 'Box.com API'
Version: 0.2.5
Date: 2015-04-15
Authors@R: person("Brendan", "Rocks", email = "rocks.brendan@gmail.com", role = c("aut", "cre"))
URL: https://github.com/brendan-R/boxr/
BugReports: https://github.com/brendan-R/boxr/issues
Description: An R interface for the remote file hosting service 'Box' (https://www.box.com/).In addition to uploading and downloading files, this package includes functions which mirror base R operations for local files, (e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git' style functions for entire directories (e.g. box_fetch(), box_push()).
License: MIT + file LICENSE
Imports: httr, httpuv, assertthat, stringr, dplyr, digest, jsonlite
Suggests: testthat, knitr
VignetteBuilder: knitr
Packaged: 2015-04-15 20:04:04 UTC; brendan.rocks
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 22:11:41

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New package blockmodels with initial version 1.0.4
Package: blockmodels
Type: Package
Title: Latent and Stochastic Block Model Estimation by a 'V-EM' Algorithm
Version: 1.0.4
Date: 2015-04-15
Author: INRA, Jean-Benoist Leger
Maintainer: Jean-Benoist Leger
Description: Latent and Stochastic Block Model estimation by a V-EM algorithm Various probability distribution are provided (Bernoulli, Poisson...), with or without covariates.
License: LGPL-2.1
Depends: Rcpp (>= 0.10.6), parallel, methods, digest
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2015-04-15 14:53:48 UTC; jleger
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-15 21:33:16

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New package apex with initial version 1.0.0
Package: apex
Title: Phylogenetic Methods for Multiple Gene Data
Version: 1.0.0
Authors@R: c(TJ=person("Thibaut", "Jombart", , "t.jombart@imperial.ac.uk", role = c("aut", "cre")), ZK=person("Zhian Namir", "Kamvar", email = "kamvarz@science.oregonstate.edu", role = c("aut")), KS=person("Klaus", "Schliep", email="klaus.schliep@umb.edu", role = c("aut")), RH=person("Rebecca", "Harris", email="rbharris@uw.edu", role = c("aut")))
Description: Toolkit for the analysis of multiple gene data. Apex implements the new S4 classes "multidna", "multiphyDat" and associated methods to handle aligned DNA sequences from multiple genes.
Depends: R (>= 3.1.3), methods, ape, phangorn
Imports: adegenet
License: GPL (>= 2)
LazyData: true
Collate: doc.R internal.R multidna.class.R multiphyDat.class.R show.R multidna.constructor.R multiphyDat.constructor.R accessors.R handling.R plot.R readfiles.R datasets.R dist.R getTree.R exports.R
VignetteBuilder: knitr
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2015-04-15 14:57:02 UTC; thibaut
Author: Thibaut Jombart [aut, cre], Zhian Namir Kamvar [aut], Klaus Schliep [aut], Rebecca Harris [aut]
Maintainer: Thibaut Jombart
Repository: CRAN
Date/Publication: 2015-04-15 21:32:16

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New package REST with initial version 1.0.1
Package: REST
Type: Package
Title: RcmdrPlugin Easy Script Templates
Version: 1.0.1
Date: 2015-04-15
Author: De Troyer Ewoud
Maintainer: De Troyer Ewoud
Description: Contains easy scripts which can be used to quickly create GUI windows for 'Rcmdr' Plugins. No knowledge about Tcl/Tk is required to make use of these scripts (These scripts are a generalisation of the template scripts in the 'RcmdrPlugin.BiclustGUI' package).
License: GPL-3
Imports: Rcmdr, tcltk
VignetteBuilder: knitr
Suggests: knitr
Repository: CRAN
Repository/R-Forge/Project: rest
Repository/R-Forge/Revision: 23
Repository/R-Forge/DateTimeStamp: 2015-04-15 09:28:36
Date/Publication: 2015-04-15 20:46:38
Packaged: 2015-04-15 09:45:45 UTC; rforge
NeedsCompilation: no

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New package ggtern with initial version 1.0.5.0
Package: ggtern
Type: Package
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Version: 1.0.5.0
Date: 2015-04-15
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton
Description: Extends the functionality of ggplot2, providing the capability to plot ternary diagrams for (subset of) the ggplot2 geometries. Additionally, ggtern has implemented several NEW geometries which are unavailable to the standard ggplot2 release. For further examples and documentation, please proceed to the ggtern website.
License: GPL-2
Depends: ggplot2(>= 1.0.0.0)
Imports: plyr, gtable, scales, reshape2, proto, MASS, sp, grid
URL: http://www.ggtern.com
Collate: 'onLoad.R' 'ggtern-package.R' 'aaa.R' 'utilities-help.R' 'gg-internal.R' 'statnew.R' 'geom.R' 'data.R' 'element_ternary.R' 'utilities.R' 'tern-stop.R' 'strip-unapproved.R' 'coord-tern.R' 'global.R' 'theme-defaults.R' 'theme-elements.R' 'theme.R' 'theme-noarrows.R' 'theme-arrowlength.R' 'theme-showsecondary.R' 'theme-showtitles.R' 'theme-showlabels.R' 'theme-showgrid.R' 'theme-convenience.R' 'theme-ticksoutside.R' 'theme-arrowbaseline.R' 'labs-pcnt.R' 'labs-new.R' 'log-ratio-trans.R' 'mahalanobis.R' 'tern-clockwise.R' 'aes.R' 'scales.R' 'panel.R' 'ggtern.R' 'kde2d-weighted.R' 'ggtern-build.R' 'plot-construction.R' 'tern-render.R' 'tern-limits.R' 'geom-smooth.R' 'geom-segment.R' 'geom-Tline.R' 'geom-Lline.R' 'geom-Rline.R' 'geom-confidence.R' 'geom-density2d.R' 'geom-errorbarT.R' 'geom-errorbarL.R' 'geom-errorbarR.R' 'stat-smooth.R' 'stat-density-2d.R' 'stat-Tline.R' 'stat-Lline.R' 'stat-Rline.R' 'TRL-line.R' 'multiplot.R' 'ggsave.R' 'point-in-sequence.R'
Packaged: 2015-04-15 12:02:22 UTC; nick
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 20:54:01

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New package embryogrowth with initial version 6.0
Package: embryogrowth
Type: Package
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Version: 6.0
Date: 2015-04-15
Author: Marc Girondot
Maintainer: Marc Girondot
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Depends: deSolve, parallel, HelpersMG, coda, polynom, R (>= 2.14.2)
Suggests: entropy, numDeriv, shiny
License: GPL-2
LazyData: yes
LazyLoad: yes
Encoding: UTF-8
Packaged: 2015-04-15 11:20:06 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 20:51:33

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New package cernn with initial version 0.1
Package: cernn
Title: Covariance Estimation Regularized by Nuclear Norm Penalties
Description: An implementation of the covariance estimation method proposed in Chi and Lange (2014), "Stable estimation of a covariance matrix guided by nuclear norm penalties," Computational Statistics and Data Analysis 80:117-128.
Version: 0.1
Maintainer: Eric C. Chi
Author: Eric C. Chi
Depends: R (>= 3.1.3)
License: MIT + file LICENSE
LazyData: true
Packaged: 2015-04-15 03:49:42 UTC; ericchi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 12:38:20

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Tue, 14 Apr 2015

New package SPRT with initial version 1.0
Package: SPRT
Type: Package
Title: Wald's Sequential Probability Ratio Test
Version: 1.0
Date: 2015-04-14
Author: Stephane Mikael Bottine
Maintainer: Stephane Mikael Bottine
Description: Perform Wald's Sequential Probability Ratio Test on variables with a Normal, Bernoulli, Exponential and Poisson distribution. Plot acceptance and continuation regions, or create your own with the help of closures.
License: BSD_2_clause + file LICENSE
Packaged: 2015-04-14 15:26:52 UTC; BOTTINES
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-15 01:01:11

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New package sivipm with initial version 1.0-0
Package: sivipm
Version: 1.0-0
Date: 2015-04-15
Title: Sensitivity Indices with Dependent Inputs
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier
Depends: methods, seqinr
Description: Sensitivity indices with dependent correlated inputs, using a method based on PLS regression.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: yes
Packaged: 2015-04-14 11:34:27 UTC; abouvier
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-14 16:28:43

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New package readxl with initial version 0.1.0
Package: readxl
Title: Read Excel Files
Version: 0.1.0
Authors@R: c( person("Hadley", "Wickham", ,"hadley@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph", comment = "Copyright holder of all R code and all C/C++ code without explicit copyright attribution"), person("Marcin", "Kalicinski", role = c("ctb", "cph"), comment = "Author of included RapidXML code"), person("Komarov Valery", role = c("ctb", "cph"), comment = "Author of included libxls code"), person("Christophe Leitienne", role = c("ctb", "cph"), comment = "Author of included libxls code"), person("Bob Colbert", role = c("ctb", "cph"), comment = "Author of included libxls code"), person("David Hoerl", role = c("ctb", "cph"), comment = "Author of included libxls code") )
Description: Import excel files into R. Supports '.xls' via the embedded 'libxls' C library (http://sourceforge.net/projects/libxls/) and '.xlsx' via the embedded 'RapidXML' C++ library (http://rapidxml.sourceforge.net). Works on Windows, Mac and Linux without external dependencies.
License: GPL-3 + file LICENSE
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp (>= 0.11.5)
Suggests: testthat
Packaged: 2015-04-14 13:24:38 UTC; hadley
Author: Hadley Wickham [aut, cre], RStudio [cph] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code)
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-14 16:28:42

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New package adegraphics with initial version 1.0-1
Package: adegraphics
Type: Package
Title: An S4 Lattice-Based Package for the Representation of Multivariate Data
Version: 1.0-1
Date: 2015-04-14
Author: Stéphane Dray and Aurélie Siberchicot , with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Depends: R (>= 3.0.2)
License: GPL (>= 2)
Imports: ade4, grid, KernSmooth, lattice, methods, RColorBrewer, sp (>= 1.0-16)
Suggests: Guerry, maptools, pixmap, spdep, splancs
Collate: adeGsenv.R parameter.R utils.R utilstriangle.R genericMethod.R utilsclass.R panelfunctions.R ADEg.R ADEgS.R utilsADEgS.R ADEg.C1.R C1.barchart.R C1.curve.R C1.density.R C1.gauss.R C1.dotplot.R C1.hist.R C1.interval.R ADEg.S1.R S1.boxplot.R S1.class.R S1.distri.R S1.label.R S1.match.R ADEg.S2.R S2.arrow.R S2.class.R S2.corcircle.R S2.density.R S2.distri.R S2.image.R S2.label.R S2.logo.R S2.match.R S2.traject.R S2.value.R ADEg.T.R T.image.R T.value.R T.cont.R ADEg.Tr.R Tr.class.R Tr.label.R Tr.match.R Tr.traject.R ade4-kplot.R ade4-scatter.R ade4-plot.R s.hist.R multiplot.R s.Spatial.R utilskey.R
URL: http://pbil.univ-lyon1.fr/ADE-4, Mailing list: http://listes.univ-lyon1.fr/wws/info/adelist
Encoding: UTF-8
Repository: CRAN
Repository/R-Forge/Project: ade4
Repository/R-Forge/Revision: 798
Repository/R-Forge/DateTimeStamp: 2015-04-14 07:33:51
Date/Publication: 2015-04-14 13:47:29
Packaged: 2015-04-14 07:46:17 UTC; rforge
NeedsCompilation: no

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New package PGRdup with initial version 0.2
Package: PGRdup
Title: Discover Probable Duplicates in Plant Genetic Resources (PGR) Collections
Version: 0.2
Authors@R: c( person(c("J.", "Aravind"), email = "aravindj@nbpgr.ernet.in", role = c("aut", "cre")), person(c("J.", "Radhamani"), email = "radhamani@nbpgr.ernet.in", role = "aut"), person(c("Kalyani", "Srinivasan"), email = "kalyani@nbpgr.ernet.in", role = "aut"), person(c("B.", "Ananda", "Subhash"), email = "anandasubhash@gmail.com", role = "aut"), person(c("R.", "K.", "Tyagi"), email = "rktyagi@nbpgr.ernet.in", role = "aut"))
Description: Provides functions to aid the identification of probable/possible duplicates in Plant Genetic Resources (PGR) collections using 'passport databases' comprising of information records of each constituent sample. These include methods for cleaning the data, creation of a searchable Keyword in Context (KWIC) index of keywords associated with sample records and the identification of nearly identical records with similar information by fuzzy, phonetic and semantic matching of keywords.
Depends: R (>= 3.0.2)
Imports: data.table (>= 1.9.3), igraph, stringdist (>= 0.5), stringi
Copyright: 2014, ICAR-NBPGR
License: GPL-2 | GPL-3
LazyData: true
Packaged: 2015-04-14 07:02:17 UTC; sony
Author: J. Aravind [aut, cre], J. Radhamani [aut], Kalyani Srinivasan [aut], B. Ananda Subhash [aut], R. K. Tyagi [aut]
Maintainer: J. Aravind
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-14 09:25:54

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Mon, 13 Apr 2015

New package L1pack with initial version 0.3
Package: L1pack
Title: Routines for L1 Estimation
Version: 0.3
Date: 2015-04-13
Author: Felipe Osorio
Maintainer: Felipe Osorio
Description: L1 estimation for linear regression and random number generation for the multivariate Laplace distribution.
URL: http://www.ies.ucv.cl/l1pack/
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-04-13 21:11:54 UTC; ligges
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-13 23:11:54

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New package smds with initial version 1.0
Package: smds
Type: Package
Title: Symbolic Multidimensional Scaling
Version: 1.0
Date: 2015-04-10
Author: Yoshikazu Terada, Patrick J. F. Groenen
Maintainer: Yoshikazu Terada
Depends: R (>= 1.8.0), MASS
Description: Symbolic multidimensional scaling for interval-valued dissimilarities. The hypersphere model and the hyperbox model are available.
License: GPL (>= 2)
Packaged: 2015-04-13 08:12:52 UTC; terada
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-13 12:50:14

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Sun, 12 Apr 2015

New package csrplus with initial version 1.03-0
Package: csrplus
Title: Methods to Test Hypotheses on the Distribution of Spatial Point Processes
Date: 2015-04-02
Version: 1.03-0
Author: Sarah Smith
Maintainer: Sarah Smith
Description: Includes two functions to evaluate the hypothesis of complete spatial randomness (csr) in point processes. The function 'mwin' calculates quadrat counts to estimate the intensity of a spatial point process through the moving window approach proposed by Bailey and Gatrell (1995). Event counts are computed within a window of a set size over a fine lattice of points within the region of observation. The function 'pielou' uses the nearest neighbor test statistic and asymptotic distribution proposed by Pielou (1959) to compare the observed point process to one generated under csr. The value can be compared to that given by the more widely used test proposed by Clark and Evans (1954).
Depends: R (>= 3.0.2)
License: GPL-2
Imports: sp
LazyData: true
Packaged: 2015-04-12 15:19:24 UTC; sarsmith
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-12 22:58:23

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New package mongolite with initial version 0.2
Package: mongolite
Type: Package
Title: Streaming 'MongoDB' Client for R
Description: R bindings to the high-performance 'MongoDB' C driver and high-level IO tools in the same spirit as 'jsonlite'.
Version: 0.2
Date: 2015-04-10
Authors@R: c( person("Jeroen", "Ooms", ,"jeroen.ooms@stat.ucla.edu", role = c("aut", "cre")), person("MongoDB, Inc", role = "cph", comment = "Author of mongo-c-driver") )
Maintainer: Jeroen Ooms
Imports: jsonlite (>= 0.9.16)
License: Apache License 2.0
URL: https://github.com/jeroenooms/mongolite, https://github.com/mongodb/mongo-c-driver
BugReports: https://github.com/jeroenooms/mongolite/issues
SystemRequirements: OpenSSL: libssl-dev (deb) or openssl-devel (rpm) or libssl_dev (csw). SASL: libsasl2-dev (deb) or cyrus-sasl-devel (rpm) or sasl_dev (csw).
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2015-04-11 19:36:59 UTC; jeroen
Author: Jeroen Ooms [aut, cre], MongoDB, Inc [cph] (Author of mongo-c-driver)
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-12 09:01:19

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Sat, 11 Apr 2015

New package saturnin with initial version 1.0
Package: saturnin
Type: Package
Title: Spanning Trees Used for Network Inference
Version: 1.0
Date: 2015-04-10
Author: Loïc Schwaller
Maintainer: Loïc Schwaller
Description: Bayesian inference of graphical model structures using spanning trees.
Suggests: parallel
License: GPL-2
Encoding: UTF-8
Packaged: 2015-04-11 17:29:09 UTC; loic
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-12 00:52:57

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Fri, 10 Apr 2015

New package mvmesh with initial version 1.0
Package: mvmesh
Type: Package
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Version: 1.0
Date: 2015-04-10
Author: John P. Nolan
Maintainer: John P. Nolan
Depends: R (>= 3.0), rcdd, rgl
Description: Define, manipulate and plot meshes on simplices, spheres, balls, and rectangles for use in multivariate statistics. Directional and other multivariate histograms are provided.
License: GPL (>= 3)
Packaged: 2015-04-10 18:22:55 UTC; jpnolan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-11 01:19:14

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New package VIFCP with initial version 1.0
Package: VIFCP
Version: 1.0
Title: Detecting Change-Points via VIFCP Method
Author: Xiaoping shi, Xiangsheng Wang, Dongwei Wei, Yuehua Wu
Maintainer: Dongwei Wei
Depends: R (>= 3.1.3)
License: LGPL-3
Description: Contains a function to support the paper 'A sequential multiple change-point detection procedure via VIF regression' (in print).
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-04-10 18:09:09 UTC; Dongwei
Date/Publication: 2015-04-11 00:17:23

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New package MIIVsem with initial version 0.1
Package: MIIVsem
Title: Two Stage Least Squares with Model Implied Instremental Search
Version: 0.1
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher
Description: Functions for estimating structural equation models using a model-implied instrumental variable (MIIV) search and two stage least squares (2SLS) estimator (MIIV-2SLS).
Depends: R (>= 3.1.2), lavaan
License: GPL-2
LazyData: true
Packaged: 2015-04-10 15:27:49 UTC; macuser
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-11 00:51:17

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New package data.tree with initial version 0.1.6
Package: data.tree
Type: Package
Title: Hierarchical Data Structures
Version: 0.1.6
Date: 2015-04-10
Author: Christoph Glur
Maintainer: Christoph Glur
VignetteBuilder: knitr
Imports: R6
Suggests: testthat, magrittr, knitr
Description: Create tree structures from hierarchical data, and use the utility methods to traverse the tree in various orders. Aggregate, print, convert to and from data.frame, and apply functions to your tree data. Useful for decision trees, machine learning, finance, and many other applications.
License: GPL (>= 2)
URL: http://github.com/gluc/data.tree
BugReports: http://github.com/gluc/data.tree/issues
Depends: R (>= 3.0)
Packaged: 2015-04-10 11:41:56 UTC; gluc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-10 15:06:00

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New package BayesLCA with initial version 1.7
Package: BayesLCA
Type: Package
Title: Bayesian Latent Class Analysis
Version: 1.7
Date: 2015-04-10
Depends: e1071, coda
Authors@R: c( person( "Arthur", "White", email = "arwhite@tcd.ie", role = c( "aut", "cre" ), comment = "Previous email address: arthur.white@ucdconnect.ie" ), person( "Thomas Brendan", "Murphy", email = "brendan.murphy@ucd.ie", role = c( "aut", "ths" ) ) )
Description: Bayesian Latent Class Analysis using several different methods.
License: GPL (>= 2)
Imports: fields, nlme, MCMCpack
Packaged: 2015-04-10 12:35:07 UTC; arthur
Author: Arthur White [aut, cre] (Previous email address: arthur.white@ucdconnect.ie), Thomas Brendan Murphy [aut, ths]
Maintainer: Arthur White
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-10 14:41:32

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New package seroincidence with initial version 1.0.3
Package: seroincidence
Type: Package
Title: Estimating Infection Rates from Serological Data
Version: 1.0.3
Date: 2015-04-10
Authors@R: c(person(given = "Peter", family = "Teunis", email = "peter.teunis@rivm.nl", role = c("aut"), comment = "Author of the method and original code"), person(given = "Daniel", family = "Lewandowski", email = "daniel@nextpagesoft.net", role = c("com", "ctb"), comment = "Creator of the R package"), person(given = "Chantal", family = "Quinten", email = "seroincidence@ecdc.europa.eu", role = c("ctb", "cre"), comment = "Project manager and the package maintainer"))
Maintainer: Chantal Quinten
Description: Translates antibody levels measured in a (cross-sectional) population sample into an estimate of the frequency with which seroconversions (infections) occur in the sampled population.
License: GPL-3
Suggests: testthat, knitr
VignetteBuilder: knitr
LazyData: true
Encoding: UTF-8
URL: http://www.ecdc.europa.eu/en/data-tools/seroincidence-calculator-tool/Pages/default.aspx
NeedsCompilation: no
Packaged: 2015-04-10 07:45:41 UTC; daniel
Author: Peter Teunis [aut] (Author of the method and original code), Daniel Lewandowski [com, ctb] (Creator of the R package), Chantal Quinten [ctb, cre] (Project manager and the package maintainer)
Repository: CRAN
Date/Publication: 2015-04-10 12:16:55

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New package rkafkajars with initial version 1.0
Package: rkafkajars
Type: Package
Title: External Jars Required for Package 'rkafka'
Version: 1.0
Date: 2015-04-10
Author: Shruti Gupta [aut,cre], Coda Hale and Yammer Inc.[ctb,cph],Sun Microsystems Inc.[ctb,cph],Marc Prud'hommeaux[ctb,cph],Paul Holser[ctb],Junit[ctb,cph],The Apache Software Foundation [ctb,cph],Stefan Groschupf[ctb,cph],Taro L.Saito[ctb],EPFL Typesafe Inc.[ctb,cph],QOS.ch[ctb,cph]
Maintainer: Shruti Gupta
Description: The 'rkafkajars' package collects all the external jars required for the 'rkafka' package.
Depends: rJava
Imports: RUnit
SystemRequirements: Oracle Java 7
Copyright: See file COPYRIGHTS
License: Apache License 2.0 | file LICENSE
Packaged: 2015-04-10 09:17:20 UTC; shrutigupta34
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-10 12:16:52

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New package bentcableAR with initial version 0.3.0
Package: bentcableAR
Type: Package
Title: Bent-Cable Regression for Independent Data or Autoregressive Time Series
Version: 0.3.0
Date: 2015-04-10
Author: Grace Chiu , CSIRO, CSIT Bldg, ANU Campus, Acton, ACT 2601, Australia
Maintainer: Grace Chiu
Description: Included are two main interfaces for fitting and diagnosing bent-cable regressions for autoregressive time-series data or independent data (time series or otherwise): 'bentcable.ar()' and 'bentcable.dev.plot()'. Some components in the package can also be used as stand-alone functions. The bent cable (linear-quadratic-linear) generalizes the broken stick (linear-linear), which is also handled by this package. Version 0.2 corrects a glitch in the computation of confidence intervals for the CTP. References that were updated from Versions 0.2.1 and 0.2.2 appear in Version 0.2.3 and up. Version 0.3.0 improves robustness of the error-message producing mechanism. It is the author's intention to distribute any future updates via GitHub.
License: GPL (>= 3)
Packaged: 2015-04-10 07:32:33 UTC; gchiu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-10 12:16:48

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New package qrng with initial version 0.0-1
Package: qrng
Version: 0.0-1
Encoding: UTF-8
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in high dimensions.
Authors@R: c(person(given = "Marius", family = "Hofert", role = c("aut", "cre"), email = "marius.hofert@uwaterloo.ca"), person(given = "Christiane", family = "Lemieux", role = "aut", email = "clemieux@uwaterloo.ca"))
Author: Marius Hofert [aut, cre], Christiane Lemieux [aut]
Maintainer: Marius Hofert
Depends: R (>= 3.0.0)
Imports:
Suggests:
Enhances:
License: GPL-2 | GPL-3
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-10 10:51:22
Packaged: 2015-04-10 04:47:58 UTC; mhofert

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Thu, 09 Apr 2015

New package RandomFieldsUtils with initial version 0.0.1
Package: RandomFieldsUtils
Version: 0.0.1
Title: Utilities for the Simulation and Analysis of Random Fields
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb]
Maintainer: Martin Schlather
Depends: R (>= 3.1)
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
License: GPL (>= 3)
URL: http://ms.math.uni-mannheim.de/de/publications/software
Packaged: 2015-04-09 19:17:44 UTC; schlather
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-10 01:24:12

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New package emov with initial version 0.1
Package: emov
Version: 0.1
Date: 2015-04-09
Title: Eye Movement Analysis Package for Fixation and Saccade Detection
Author: Simon Schwab
Maintainer: Simon Schwab
Depends: R (>= 1.8.0)
Description: An R package for fixation and saccade detection in eye movement recordings. Eye movements consist of alternating saccades and fixations. This package implements a dispersion-based algorithm (I-DT) proposed by Salvucci & Goldberg (2000) which detects fixation duration and position.
License: GPL-3
URL: https://github.com/schw4b/emov
BugReports: https://github.com/schw4b/emov/issues
Packaged: 2015-04-09 08:37:19 UTC; simon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 12:04:18

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New package denovolyzeR with initial version 0.1.0
Package: denovolyzeR
Title: Statistical Analyses of De Novo Genetic Variants
Version: 0.1.0
Date: 2015-04-01
Authors@R: c( person("James","Ware",email="j.ware@imperial.ac.uk",role=c("aut","cre")), person("Jason","Homsy",role="ctb"), person("Kaitlin","Samocha",role="ctb") )
Description: An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework. denovolyzeR provides a suite of functions to implement these analyses for the interpretation of de novo variation in human disease.
Depends: R (>= 3.1.0)
Imports: dplyr (>= 0.3), reshape (>= 0.8)
License: GPL-3
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
URL: http://jamesware.github.io/denovolyzeR
BugReports: http://github.com/jamesware/denovolyzeR/issues
Packaged: 2015-04-09 06:35:00 UTC; jamesware
Author: James Ware [aut, cre], Jason Homsy [ctb], Kaitlin Samocha [ctb]
Maintainer: James Ware
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 12:03:44

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Wed, 08 Apr 2015

New package phenology with initial version 4.1
Package: phenology
Type: Package
Title: Tools to Manage a Parametric Function that Describes Phenology
Version: 4.1
Date: 2015-04-08
Author: Marc Girondot
Maintainer: Marc Girondot
Depends: fields, zoo, coda, HelpersMG, shiny, R (>= 2.14.0)
Description: Functions used to fit and test the phenology of species based on counts.
License: GPL-2
LazyData: yes
LazyLoad: yes
URL: http://max2.ese.u-psud.fr/epc/conservation/Girondot/Publications/Marine_Turtles_Nesting_Season.html
Encoding: UTF-8
Packaged: 2015-04-08 15:03:36 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 01:18:00

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New package readr with initial version 0.1.0
Package: readr
Version: 0.1.0
Title: Read Tabular Data
Description: Read flat/tabular text files from disk.
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre")), person("Romain", "Francois", role = "aut"), person("R Core Team", role = "ctb", comment = "Date time code adapted from R"), person("RStudio", role = "cph"))
Encoding: UTF-8
Depends: R (>= 3.0.2)
LinkingTo: Rcpp, BH
Imports: Rcpp (>= 0.11.5), curl
Suggests: testthat, knitr, DiagrammeR
License: GPL (>= 2)
VignetteBuilder: knitr
Packaged: 2015-04-08 20:31:26 UTC; hadley
Author: Hadley Wickham [aut, cre], Romain Francois [aut], R Core Team [ctb] (Date time code adapted from R), RStudio [cph]
Maintainer: Hadley Wickham
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-09 01:03:53

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New package qwraps2 with initial version 0.1
Package: qwraps2
Title: Quick Wraps 2
Version: 0.1
Authors@R: person("Peter", "DeWitt", , "dewittpe@gmail.com", role = c("aut", "cre"))
Description: A collection of (wrapper) functions the creator found useful for quickly placing data summaries and formatted regression results into .Rnw or .Rmd files. Functions for generating commonly used graphics, such as receiver operating curves or Bland-Altman plots, are also provided by 'qwraps2'. 'qwraps2' is a updated version of an package 'qwraps'. The original version 'qwraps' was never submitted to CRAN but can be found at https://github.com/dewittpe/qwraps. The implementation and limited scope of the functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally different from 'qwraps'.
Depends: R (>= 3.1.3)
License: GPL-2
LazyData: true
Imports: dplyr, ggplot2
Packaged: 2015-04-08 16:48:55 UTC; dewittp
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-09 00:40:15

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New package groupRemMap with initial version 0.1-0
Package: groupRemMap
Version: 0.1-0
Date: 2015-03-25
Title: Regularized Multivariate Regression for Identifying Master Predictors Using the GroupRemMap Penalty
Author: Xianlong Wang , Li Qin, Hexin Zhang, Yuzheng Zhang, Li Hsu, Pei Wang
Maintainer: Xianlong Wang
Description: An implementation of the GroupRemMap penalty for fitting regularized multivariate response regression models under the high-dimension-low-sample-size setting. When the predictors naturally fall into groups, the GroupRemMap penalty encourages procedure to select groups of predictors, while control for the overall sparsity of the final model.
License: GPL (>= 2)
Packaged: 2015-04-08 16:58:29 UTC; xwan2
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-09 01:07:16

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New package retrosheet with initial version 1.0
Package: retrosheet
Type: Package
Title: Import 'Retrosheet' Data as a Structured R Object
Version: 1.0
Authors@R: c(person("Richard", "Scriven", email = "rmscriven@gmail.com", role = c("aut", "cre")), person("Ananda", "Mahto", email = "mrdwab@gmail.com", role = "ctb"))
Date: 2015-03-17
Maintainer: Richard Scriven
Description: A collection of tools for importing the professional baseball data available from http://www.retrosheet.org. In particular, the event (play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested event as a structured R object. It will also retrieve the game-log, roster, and schedule files if requested.
URL: http://github.com/rmscriven/retrosheet
Depends: R (>= 2.10)
License: GPL (>= 2)
Imports: RCurl (>= 1.95-4.5), XML (>= 3.98-1.1), data.table(>= 1.9.4)
Note: Notice regarding the transfer of data from Retrosheet: The information used here was obtained free of charge from and is copyrighted by Retrosheet. Interested parties may contact Retrosheet at "www.retrosheet.org".
Packaged: 2015-04-08 05:54:37 UTC; richard
Author: Richard Scriven [aut, cre], Ananda Mahto [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 12:17:55

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New package pairsD3 with initial version 0.0.6
Package: pairsD3
Title: D3 Scatterplot Matrices
Version: 0.0.6
Authors@R: person("Garth", "Tarr", , "garth.tarr@gmail.com", role = c("aut", "cre"))
Description: Creates an interactive scatterplot matrix using the D3 JavaScript library. See for more information on D3.
Depends: R (>= 3.1.2)
License: GPL (>= 3)
Date: 2015-04-08
URL: http://github.com/garthtarr/pairsD3/
LazyData: true
Imports: htmlwidgets (>= 0.3.2), shiny
Suggests: knitr
Packaged: 2015-04-08 09:31:43 UTC; garthtarr
Author: Garth Tarr [aut, cre]
Maintainer: Garth Tarr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 11:53:10

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New package TROM with initial version 1.0
Package: TROM
Type: Package
Title: Transcriptome Overlap Measure
Version: 1.0
Date: 2015-04-07
Author: Jingyi Jessica Li , Wei Li
Maintainer: Jingyi Jessica Li
Depends: R (>= 2.10), lattice, methods, topGO
Imports: AnnotationDbi, openxlsx, GO.db, gtools, RColorBrewer, gplots
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples.
License: GPL-2
Packaged: 2015-04-08 03:21:23 UTC; Think
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 07:25:04

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New package cqrReg with initial version 1.2
Package: cqrReg
Type: Package
Title: Quantile, Composite Quantile Regression and Regularized Versions
Version: 1.2
Date: 2015-04-07
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
License: GPL (>= 2)
Depends: Rcpp (>= 0.10.0),quantreg,R (>= 2.6)
LinkingTo: Rcpp,RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-04-07 23:31:21 UTC; billy
Repository: CRAN
Date/Publication: 2015-04-08 07:35:09

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Tue, 07 Apr 2015

New package esaBcv with initial version 1.0.1
Package: esaBcv
Title: Estimate Number of Latent Factors and Factor Matrix for Factor Analysis
Version: 1.0.1
Authors@R: c(person(c("Art", "B."), "Owen", role = c("aut")), person("Jingshu", "Wang", email = "wangjingshususan@gmail.com", role = c("aut", "cre")) )
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Depends: R (>= 3.1.3)
License: GPL (>= 2)
LazyData: true
Imports: corpcor, svd
Suggests: MASS
Packaged: 2015-04-07 18:23:26 UTC; jingshu
Author: Art B. Owen [aut], Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-08 00:53:20

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New package quanteda with initial version 0.7.2
Package: quanteda
Type: Package
Title: Quantitative Analysis of Textual Data
Authors@R: c( person("Kenneth", "Benoit", email = "kbenoit@lse.ac.uk", role = c("aut", "cre")), person("Paul", "Nulty", email = "paul.nulty@gmail.com", role = "aut"), person("Pablo", "Barberá", email = "pablo.barbera@nyu.edu", role = "ctb"), person("Kohei", "Watanabe", email = "watanabe.kohei@gmail.com", role = "ctb"), person("Benjamin", "Lauderdale", email = "B.E.lauderdale@lse.ac.uk", role = "ctb"))
Author: Kenneth Benoit [aut, cre], Paul Nulty [aut], Pablo Barberá [ctb], Kohei Watanabe [ctb], Benjamin Lauderdale [ctb]
Version: 0.7.2
Date: 2015-04-05
Description: A fast, flexible toolset for for the management, processing, and quantitative analysis of textual data in R.
License: GPL-3
Depends: R (>= 3.0)
Imports: methods, Matrix (>= 1.1), data.table (>= 1.9.3), SnowballC, wordcloud, proxy, Rcpp, ca
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, lda, topicmodels, jsonlite (>= 0.9.10), streamR, tm, slam, ggplot2
URL: http://github.com/kbenoit/quanteda
Encoding: UTF-8
BugReports: https://github.com/kbenoit/quanteda/issues
LazyData: TRUE
VignetteBuilder: knitr
Collate: 'RcppExports.R' 'clean.R' 'dictionaryFunctions.R' 'collocations.R' 'converters.R' 'corpus-sources-S4.R' 'corpus.R' 'dataDocs.R' 'describe-texts.R' 'dfm-classes.R' 'dfm-main.R' 'distance.R' 'gui.R' 'kwic.R' 'lexdiv.R' 'ngrams.R' 'onLoad.R' 'plots.R' 'quanteda-package.R' 'resample.R' 'settings.R' 'stopwords.R' 'syllables.R' 'textmodel-ca.R' 'textmodel-generics.R' 'textmodel-wordfish.R' 'textmodel-wordscores.R' 'tokenize.R'
Packaged: 2015-04-07 12:03:05 UTC; kbenoit
Maintainer: Kenneth Benoit
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-07 16:00:23

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New package HelpersMG with initial version 1.0
Package: HelpersMG
Type: Package
Title: Tools for Earth Meteorological Analysis
Version: 1.0
Date: 2015-04-07
Author: Marc Girondot
Maintainer: Marc Girondot
Depends: coda, R (>= 2.14.0)
Suggests: RNetCDF, ncdf4, ncdf, maps, XML
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct daily time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
License: GPL-2
LazyData: yes
LazyLoad: yes
Encoding: UTF-8
Packaged: 2015-04-07 13:27:22 UTC; marc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-07 15:40:53

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New package rcorpora with initial version 1.0.0
Package: rcorpora
Title: A Collection of Small Text Corpuses of Interesting Data
Version: 1.0.0
Maintainer: Gabor Csardi
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson, Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup, Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern, Ross Barclay, Ross Binden, Justin Alford, Cole Willsea, Andrew Gorman, Javier Arce, Patrick Rodriguez, Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody, Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black, Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell, Michael Dewberry, Joe Mahoney
Description: A collection of small text corpuses of interesting data. It contains all data sets from the fantastic https://github.com/dariusk/corpora repository. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
License: CC0
Imports: jsonlite
URL: https://github.com/gaborcsardi/rcorpora
BugReports: https://github.com/gaborcsardi/rcorpora/issues
NeedsCompilation: no
Packaged: 2015-04-07 02:22:26 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2015-04-07 09:10:08

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Mon, 06 Apr 2015

New package pssm with initial version 1.0
Package: pssm
Version: 1.0
Type: Package
Date: 2015-03-18
Title: Piecewise Exponential Model for Time to Progression and Time from Progression to Death
Author: David A. Schoenfeld [aut, cre]
Maintainer: David A. Schoenfeld
Description: Estimates parameters of a piecewise exponential model for time to progression and time from progression to death with interval censoring of the time to progression and covariates for each distribution using proportional hazards.
License: GPL-2
Imports: MASS, abind, numDeriv, MHadaptive
Depends: methods
Collate: 'pssm.generate.data.R' 'llikef.R' 'rprog.R' 'rsurv.R' 'startv.R' 'generic_functions.R' 'pssm.R' 'pssm.survivalcurv.R' 'pssm.simulate.R' 'pssm.power.R' 'pssm.noninferiority.boundary.R'
Packaged: 2015-04-06 17:43:39 UTC; das15
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-07 00:30:38

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New package ngramrr with initial version 0.1.1
Package: ngramrr
Title: A Simple General Purpose N-Gram Tokenizer
Version: 0.1.1
Date: 2015-04-05
Author: Chung-hong Chan
Maintainer: Chung-hong Chan
Description: A simple n-gram (contiguous sequences of n items from a given sequence of text) tokenizer to be used with the 'tm' package with no 'rJava'/'RWeka' dependency.
URL: https://github.com/chainsawriot/ngramrr
Depends: R (>= 3.0.0)
License: GPL-2
LazyData: true
Imports: tau
Suggests: tm, testthat, magrittr
Packaged: 2015-04-05 12:58:30 UTC; chainsaw
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-06 07:36:48

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Sun, 05 Apr 2015

New package zooaRch with initial version 1.0
Package: zooaRch
Type: Package
Title: Analytical Tools for Zooarchaeological Data
Version: 1.0
Date: 2015-03-15
Author: Erik Otarola-Castillo, Jesse Wolfhagen, Max D. Price
Maintainer: Erik Otarola-Castillo
Description: The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.
Depends: ggplot2
License: GPL (>= 2)
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-04-04 23:45:57 UTC; EOC
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-05 08:26:30

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Sat, 04 Apr 2015

New package SOUP with initial version 1.1
Package: SOUP
Version: 1.1
Date: 2015-04-03
Title: Stochastic Ordering Using Permutations (and Pairwise Comparisons)
Authors@R: person("Federico", "Mattiello", role = c("aut", "cre"), email = "federico.mattiello@gmail.com")
Author: Federico Mattiello [aut, cre]
Maintainer: Federico Mattiello
Depends: R (>= 3.0.0), methods, tensor
Suggests: flip
Description: Construct a ranking of a set of treatments/groups by gathering together information coming from several response variables. It can be used with both balanced and unbalanced experiments (with almost all test statistics) as well as in presence of either continuous covariates or a stratifying (categorical) variable.
License: GPL (>= 2)
Collate: 'NPC.R' 'PermSpace.R' 'RankResults.R' 'SOUP.R' 'multiplicity.R' 'simpleAD.R' 'simpleHotelling.R' 'simpleMeanDiff.R' 'simpleTtest.R' 'strataAD.R' 'strataLmCoef.R' 'strataMeanDiff.R' 'strataTtest.R' 't2p.R' 'utilities.R' 'PValueMat.R' 'SoupObject.R' 'rankingRule.R' 'iterNPC.r'
Packaged: 2015-04-04 13:01:17 UTC; Federico
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-04 16:14:05

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New package crunch with initial version 1.0.2
Package: crunch
Type: Package
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Version: 1.0.2
Date: 2015-04-03
Authors@R: c(person("Neal", "Richardson", role = c("aut", "cre"), email = "neal@crunch.io"))
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson
URL: https://github.com/Crunch-io/rcrunch
BugReports: https://github.com/Crunch-io/rcrunch/issues
License: LGPL (>= 3)
LazyLoad: yes
Depends: R (>= 3.0.0)
Imports: httr, RJSONIO, methods, RCurl
Suggests: knitr, testthat
VignetteBuilder: knitr
Packaged: 2015-04-03 23:00:29 UTC; npr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-04 07:32:57

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Fri, 03 Apr 2015

New package shapeR with initial version 0.1-3
Package: shapeR
Type: Package
Title: Collection and Analysis of Otolith Shape Data
Version: 0.1-3
Date: 2015-04-02
Authors@R: c(person("Lisa Anne", "Libungan", role = c("aut", "cre"), email = "lisa.libungan@gmail.com"), person("Snaebjorn", "Palsson", role = c("aut", "ths"), email = "snaebj@hi.is"))
Maintainer: Lisa Anne Libungan
Depends: R (>= 3.0.2)
Imports: gplots, jpeg, pixmap, wavethresh, methods, vegan, MASS
Description: Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.
License: GPL (>= 2)
URL: https://github.com/lisalibungan/shapeR, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102
LazyDataCompression: yes
Packaged: 2015-04-03 12:52:19 UTC; lal
Author: Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 22:48:14

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New package fpCompare with initial version 0.1.0
Package: fpCompare
Type: Package
Title: Reliable Comparison of Floating Point Numbers
URL: https://github.com/PredictiveEcology/fpCompare
Version: 0.1.0
Date: 2015-04-03
Authors@R: c( person("Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada", role="cph"), person(c("Alex", "M"), "Chubaty", email="achubaty@NRCan.gc.ca", role=c("aut", "cre")) )
Description: Comparisons of floating point numbers are problematic due to errors associated with the binary representation of decimal numbers. Despite being aware of these problems, people still use numerical methods that fail to account for these and other rounding errors (this pitfall is the first to be highlighted in Circle 1 of Burns (2012) [The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)). This package provides four new relational operators useful for performing floating point number comparisons with a set tolerance.
Depends: R (>= 3.1.2)
Suggests: knitr, testthat
License: GPL-3
VignetteBuilder: knitr
ByteCompile: yes
BugReports: https://github.com/PredictiveEcology/fpCompare/issues
Packaged: 2015-04-03 20:35:16 UTC; achubaty
Author: Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph], Alex M Chubaty [aut, cre]
Maintainer: Alex M Chubaty
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 23:11:17

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New package EcoSimR with initial version 0.1.0
Package: EcoSimR
Type: Package
Title: Null Model Analysis for Ecological Data
Version: 0.1.0
Date: 2015-04-02
BugReports: https://github.com/GotelliLab/EcoSimR/issues
Authors@R: c(person("Nick", "Gotelli", role = c("aut"), email = "ngotelli@uvm.edu"), person("Edmund", "Hart", role = c("aut","cre"), email = "edmund.m.hart@gmail.com"), person("Aaron", "Ellison", role = c("aut"), email = "aellison@fas.harvard.edu") )
LazyLoad: yes
LazyData: yes
Description: Given a site by species interaction matrix, users can make inferences about species interactions by performance hypothesis comparing test statistics against a null distribution. The current package provides algorithms and metrics for niche-overlap, body size ratios and species co-occurrence. Users can also integrate their own algorithms and metrics within these frameworks or completely novel null models. Detailed explanations about the underlying assumptions of null model analysis in ecology can be found at http://ecosimr.org.
License: MIT + file LICENSE
Depends: MASS
Suggests: testthat, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-04-03 17:57:52 UTC; edmundhart
Author: Nick Gotelli [aut], Edmund Hart [aut, cre], Aaron Ellison [aut]
Maintainer: Edmund Hart
Repository: CRAN
Date/Publication: 2015-04-03 22:09:00

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New package thsls with initial version 0.1
Package: thsls
Type: Package
Title: Three-Stage Least Squares Estimation for Systems of Simultaneous Equations
Version: 0.1
Date: 2015-04-03
Author: Zaghdoudi Taha
Maintainer: Zaghdoudi Taha
Description: Fit the Simultaneous Systems of Linear Equations using Three-stage Least Squares.
License: GPL-3
LazyData: TRUE
Imports: Formula
Packaged: 2015-04-03 14:49:32 UTC; Taha
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 20:04:55

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New package RKEAjars with initial version 5.0-1
Package: RKEAjars
Version: 5.0-1
Title: R/KEA Interface Jars
Authors@R: c(person("Kurt", "Hornik", role = c("aut", "cre"), email = "Kurt.Hornik@R-project.org"), person("Eibe", "Frank", role = c("ctb", "cph"), comment = "KEA Java library"), person("Olena", "Medelyan", role = c("ctb", "cph"), comment = "KEA Java library"), person("The Apache Software Foundation", role = c("ctb", "cph"), comment = "Apache Commons Logging and Apache Jena Java libraries"), person("International Business Machines Corporation and others", role = c("ctb", "cph"), comment = "International Components for Unicode for Java (ICU4J)"), person("Martin", "Porter", role = c("ctb", "cph"), comment = "Snowball base"), person("Richard", "Boulton", role = c("ctb", "cph"), comment = "Snowball Java library"), person("University of Waikato", role = c("ctb", "cph"), comment = "Weka Java library"))
Description: External jars required for package RKEA.
Imports: rJava (>= 0.6-3)
SystemRequirements: Java (>= 5.0)
License: GPL-2
Packaged: 2015-04-03 15:14:37 UTC; hornik
Author: Kurt Hornik [aut, cre], Eibe Frank [ctb, cph] (KEA Java library), Olena Medelyan [ctb, cph] (KEA Java library), The Apache Software Foundation [ctb, cph] (Apache Commons Logging and Apache Jena Java libraries), International Business Machines Corporation and others [ctb, cph] (International Components for Unicode for Java (ICU4J)), Martin Porter [ctb, cph] (Snowball base), Richard Boulton [ctb, cph] (Snowball Java library), University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 17:27:47

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New package hgm with initial version 1.11
Package: hgm
Type: Package
Depends: R (>= 2.6.0), deSolve
Title: Holonomic Gradient Method and Gradient Descent
Version: 1.11
Date: 2015-03-26
Author: Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta Nishiyama
Maintainer: Nobuki Takayama
Description: The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization constants of unnormalized probability distributions by utilizing holonomic systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method to find maximal likelihood estimates by utilizing the HGM.
License: GPL-2
LazyLoad: yes
URL: http://www.openxm.org
Packaged: 2015-04-02 23:09:09 UTC; taka
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-03 07:48:02

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Thu, 02 Apr 2015

New package PhyloMeasures with initial version 1.0
Package: PhyloMeasures
Type: Package
Title: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures
Version: 1.0
Date: 2015-03-26
Authors@R: c(person("Constantinos", "Tsirogiannis", role = c("aut", "cre"), email = "analekta@gmail.com"), person("Brody", "Sandel", role = "aut"))
Author: Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Maintainer: Constantinos Tsirogiannis
Description: Given a phylogenetic tree T and a sample S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers the implementations of efficient algorithms for several such measures. Most importantly, the package includes algorithms for computing exactly and efficiently the expectation and the variance of these measures, which are essential for null model comparisons. Efficient computation of richness-standardized versions of these metrics, such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures are also available in this package. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure.
License: GPL-3
Imports: ape
LazyLoad: yes
Packaged: 2015-04-02 11:13:51 UTC; constant
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-03 01:46:13

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New package stcm with initial version 0.1.0
Package: stcm
Title: Tools for Inference with Set-Theoretic Comparative Methods
Authors@R: person("Chris", "Krogslund", role = c("aut", "cre"), email = "ckrogslund@berkeley.edu")
Version: 0.1.0
Date: 2015-04-01
Description: Provides a number of functions for carrying out inference with set-theoretic comparative methods, including facilities for examining causal paths, assessing the sensitivity of results to measurement and model specification error, and performing Random Forest Comparative Analysis.
Depends: R (>= 3.1.1),
License: GPL (>= 3)
LazyData: yes
Imports: QCA, plyr, ggplot2, XML, randomForest, caret, dendextend, magrittr
Maintainer: Chris Krogslund
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-04-02 18:01:47 UTC; chris
Author: Chris Krogslund [aut, cre]
Date/Publication: 2015-04-03 01:00:07

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New package mra with initial version 2.16.4
Package: mra
Type: Package
Title: Analysis of Mark-Recapture Data
Version: 2.16.4
Date: 2015-03-30
Authors@R: c( person("Trent", "McDonald", email="tmcdonald@west-inc.com", role=c("cre","aut")), person("Eric", "Regehr", email="eric_regehr@fws.gov", role=c("ctb")), person("Jeff", "Bromaghin", email="jbromaghin@usgs.gov", role=c("ctb")) )
Author: Trent McDonald [cre, aut], Eric Regehr [ctb], Jeff Bromaghin [ctb]
Maintainer: Trent McDonald
Description: Analysis of mark-recapture data using covariates. Models: CJS open population; Huggin's closed population. Link functions: logit, sine, hazard. Model selection and model averaging routines. Plot methods. Simulation routine. CJS methods produce estimates of population size using the Horvitz-Thompson estimator.
License: GNU General Public License
BugReports: https://github.com/tmcd82070/MRA/issues
Packaged: 2015-03-30 19:42:02 UTC; tmcdonald
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-02 15:00:47

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New package Thermimage with initial version 1.0
Package: Thermimage
Type: Package
Title: Functions for Handling Thermal Images
Version: 1.0
Date: 2015-03-26
Author: Glenn J. Tattersall, PhD
Maintainer: Glenn J. Tattersall
Description: A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature.
License: GPL-2
Depends: R (>= 2.10)
LazyData: TRUE
Repository: CRAN
URL: http://github.com/gtatters/Thermimage
BugReports: http://github.com/gtatters/Thermimage/issues
Packaged: 2015-04-01 21:12:12 UTC; GlennTattersall
NeedsCompilation: no
Date/Publication: 2015-04-02 07:56:52

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New package HighDimOut with initial version 1.0.0
Package: HighDimOut
Type: Package
Title: Outlier Detection Algorithms for High-Dimensional Data
Version: 1.0.0
Date: 2015-03-30
Author: Cheng Fan
Maintainer: Cheng Fan
Depends: R (>= 3.0.1)
Imports: foreach, DMwR, plyr, proxy, FNN, ggplot2
Suggests: knitr
VignetteBuilder: knitr
LazyData: true
Description: Three high-dimensional outlier detection algorithms and a outlier unification scheme are implemented in this package. The angle-based outlier detection (ABOD) algorithm is based on the work of Kriegel, Schubert, and Zimek [2008]. The subspace outlier detection (SOD) algorithm is based on the work of Kriegel, Kroger, Schubert, and Zimek [2009]. The feature bagging-based outlier detection (FBOD) algorithm is based on the work of Lazarevic and Kumar [2005]. The outlier unification scheme is based on the work of Kriegel, Kroger, Schubert, and Zimek [2011].
License: GPL-3
Packaged: 2015-04-02 05:40:26 UTC; mac
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-02 08:02:28

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Wed, 01 Apr 2015

New package SWMPr with initial version 2.0.0
Package: SWMPr
Type: Package
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Version: 2.0.0
Date: 2015-4-1
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck
Description: Tools for retrieving, organizing, and analyzing environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System. These tools address common challenges associated with continuous time series data for environmental decision making.
BugReports: https://github.com/fawda123/SWMPr/issues
License: CC0
Imports: data.table, httr, ggmap, gridExtra, maptools, oce, dplyr, reshape2, tictoc, tidyr, wq, XML
LazyData: true
Depends: R (>= 3.1.1), ggplot2, zoo
Authors@R: person(given = "Marcus W.", family = "Beck", role = c("aut","cre"), email = "mbafs2012@gmail.com")
Packaged: 2015-04-01 18:27:11 UTC; MBeck
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-01 23:58:53

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New package MCMC4Extremes with initial version 1.0
Package: MCMC4Extremes
Type: Package
Title: Posterior Distribution of Extreme Value Models in R
Version: 1.0
Date: 2015-03-14
Authors@R: c(person("Fernando Ferraz", "do Nascimento", email = "fernandofn@ufpi.edu.br", role = c("aut", "cre")), person("Wyara Vanesa", "Moura e Silva", email = "wyaravms@hotmail.com", role = c("aut", "ctb")))
Author: Fernando Ferraz do Nascimento [aut, cre], Wyara Vanesa Moura e Silva [aut, ctb]
Maintainer: Fernando Ferraz do Nascimento
Depends: R (>= 3.0), evir
Description: Provides some function to perform posterior estimation for some distribution, with emphasis to extreme value distributions.It contains some extreme datasets, and functions that perform the runs of posterior points of the GPD and GEV distribution. The package calculate some important extreme measures like return level for each t periods of time, and some plots as the predictive distribution, and return level plots.
License: GPL-2
Packaged: 2015-04-01 11:21:29 UTC; WYARAVMS
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-02 00:04:49

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New package DiffCorr with initial version 0.4.1
Package: DiffCorr
Type: Package
Title: Analyzing and Visualizing Differential Correlation Networks in Biological Data
Version: 0.4.1
Date: 2015-03-31
Author: Atsushi Fukushima, Kozo Nishida
Maintainer: Atsushi Fukushima
Depends: pcaMethods, igraph, fdrtool, multtest
Description: A method for identifying pattern changes between 2 experimental conditions in correlation networks (e.g., gene co-expression networks), which builds on a commonly used association measure, such as Pearson's correlation coefficient. This package includes functions to calculate correlation matrices for high-dimensional dataset and to test differential correlation, which means the changes in the correlation relationship among variables (e.g., genes and metabolites) between 2 experimental conditions.
License: GPL (> 3)
Packaged: 2015-03-31 08:49:09 UTC; fuku
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-02 00:07:09

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New package HarmonicRegression with initial version 1.0
Package: HarmonicRegression
Type: Package
Title: Harmonic Regression to One or more Time Series
Version: 1.0
Date: 2015-04-01
Author: Paal O. Westermark
Maintainer: Paal O. Westermark
Description: Fits the first harmonics in a Fourier expansion to one or more time series. Trend elimination can be performed. Computed values include estimates of amplitudes and phases, as well as confidence intervals and p-values for the null hypothesis of Gaussian noise.
License: MIT + file LICENSE
VignetteBuilder: knitr
Suggests: knitr
Depends: R (>= 2.10)
Packaged: 2015-04-01 16:32:51 UTC; westerm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-01 19:27:09

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New package gazepath with initial version 1.0
Package: gazepath
Type: Package
Title: Gazepath Transforms Eye-Tracking Data into Fixations and Saccades
Version: 1.0
Date: 2015-03-03
Author: Daan van Renswoude
Maintainer: Daan van Renswoude
Description: Eye-tracking data must be transformed into fixations and saccades before it can be analyzed. This package provides a non-parametric speed-based approach to do this on a trial basis. The method is especially useful when there are large differences in data quality, as the thresholds are adjusted accordingly. The same pre-processing procedure can be applied to all participants, while accounting for individual differences in data quality.
License: GPL-2
Repository: CRAN
Repository/R-Forge/Project: gazepatterns
Repository/R-Forge/Revision: 36
Repository/R-Forge/DateTimeStamp: 2015-04-01 12:54:43
Date/Publication: 2015-04-01 19:39:54
Packaged: 2015-04-01 13:05:17 UTC; rforge
Depends: R (>= 2.10)
NeedsCompilation: no

More information about gazepath at CRAN
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New package PopVar with initial version 1.0
Package: PopVar
Title: Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation
Version: 1.0
Date: 2015-02-20
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede
Depends: R (>= 3.0.1), utils
Imports: BGLR, qtl, rrBLUP
License: GPL-3
LazyData: true
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Packaged: 2015-03-31 22:29:51 UTC; tylertiede
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-01 07:50:38

More information about PopVar at CRAN
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