Sun, 23 Apr 2017

New package welchADF with initial version 0.1
Package: welchADF
Title: Welch-James Statistic for Robust Hypothesis Testing under Heterocedasticity and Non-Normality
Description: Implementation of Johansen's general formulation of Welch-James's statistic with Approximate Degrees of Freedom, which makes it suitable for testing any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Some improvements, namely trimmed means and Winsorized variances, and bootstrapping for calculating an empirical critical value, have been added to the classical formulation. The code departs from a previous SAS implementation by L.M. Lix and H.J. Keselman, available at <http://homepage.usask.ca/~lml321/Program.pdf> and published in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-8986.00060>.
Version: 0.1
Date: 2017-04-23
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
License: LGPL (>= 3)
URL: <http://decsai.ugr.es/~pjvi/r-packages.html>
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-23 16:37:45 UTC; AsusPC
Repository: CRAN
Date/Publication: 2017-04-23 16:50:32 UTC

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New package sidrar with initial version 0.1.1
Package: sidrar
Type: Package
Title: An Interface to IBGE's SIDRA API
Version: 0.1.1
Authors@R: person("Renato", "Prado Siqueira", email = "rpradosiqueira@gmail.com", role = c("aut", "cre"))
Description: Allows the user to connect with IBGE's (Instituto Brasileiro de Geografia e Estatistica, see <http://www.ibge.gov.br/> for more information) SIDRA API in a flexible way. SIDRA is the acronym to "Sistema IBGE de Recuperacao Automatica" and is the system where IBGE turns available aggregate data from their researches.
Depends: R (>= 3.2.0)
License: GPL-3
Encoding: UTF-8
URL: http://github.com/rpradosiqueira/sidrar
BugReports: http://github.com/rpradosiqueira/sidrar/issues
Imports: dplyr, magrittr, RCurl, rjson, rvest, stringr, xml2
RoxygenNote: 6.0.1
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-23 15:25:48 UTC; Renato
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-23 16:43:01 UTC

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New package nat.templatebrains with initial version 0.8.2
Package: nat.templatebrains
Type: Package
Title: NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains
Version: 0.8.2
Authors@R: c(person("Gregory", "Jefferis", , "jefferis@gmail.com", role = c("aut", "cre")), person("James", "Manton", , "ajd.manton@googlemail.com", role = c("aut")))
Description: Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
License: GPL-3
Depends: R (>= 2.10), rgl, nat (>= 1.8.6)
Imports: igraph, digest, rappdirs, memoise
Suggests: testthat (>= 0.10), git2r
URL: https://github.com/jefferislab/nat.templatebrains
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-22 17:52:37 UTC; jdm
Author: Gregory Jefferis [aut, cre], James Manton [aut]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-22 22:24:52 UTC

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Sat, 22 Apr 2017

New package antiword with initial version 1.0
Package: antiword
Type: Package
Title: Extract Text from Microsoft Word Documents
Version: 1.0
Authors@R: c( person("Jeroen", "Ooms", ,"jeroen@berkeley.edu", role = c("aut", "cre")), person("Adri van Os", role = "cph", comment = "Author 'antiword' utility") )
Description: Wraps the 'AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old 'doc' format, not the new xml based 'docx' format.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: sys
RoxygenNote: 6.0.1
URL: https://github.com/ropensci/antiword#readme (devel) http://www.winfield.demon.nl (upstream)
BugReports: http://github.com/ropensci/antiword/issues
NeedsCompilation: yes
Packaged: 2017-04-22 15:56:25 UTC; jeroen
Author: Jeroen Ooms [aut, cre], Adri van Os [cph] (Author 'antiword' utility)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2017-04-22 16:26:34 UTC

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New package startR with initial version 0.0.1
Package: startR
Title: Automatically Retrieve Multidimensional Distributed Data Sets
Version: 0.0.1
Authors@R: c( person("BSC-CNS", role = c("aut", "cph")), person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")))
Description: Tool to automatically fetch, transform and arrange subsets of multidimensional data sets (collections of files) stored in local and/or remote file systems or servers, using multicore capabilities where possible. The tool provides an interface to perceive a collection of data sets as a single large multidimensional data array, and enables the user to request for automatic retrieval, processing and arrangement of subsets of the large array. Wrapper functions to add support for custom file formats can be plugged in/out, making the tool suitable for any research field where large multidimensional data sets are involved.
Depends: R (>= 2.14.1)
Imports: abind, bigmemory, future, parallel
Suggests: easyNCDF, s2dverification
License: LGPL-3
URL: https://earth.bsc.es/gitlab/es/startR/
BugReports: https://earth.bsc.es/gitlab/es/startR/issues
LazyData: true
NeedsCompilation: no
Packaged: 2017-04-22 02:58:45 UTC; nmanubens
Author: BSC-CNS [aut, cph], Nicolau Manubens [aut, cre]
Maintainer: Nicolau Manubens <nicolau.manubens@bsc.es>
Repository: CRAN
Date/Publication: 2017-04-22 04:26:58 UTC

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Fri, 21 Apr 2017

New package wgeesel with initial version 1.0
Package: wgeesel
Type: Package
Title: Weighted Generalized Estimating Equations and Model Selection
Version: 1.0
Date: 2017-04-14
Encoding: UTF-8
Author: Cong Xu <congxu17@gmail.com>, Zheng Li <zheng.li@outlook.com>, Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Description: Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
License: GPL-2
Depends: R (>= 3.0.0)
Imports: MASS, stats, geepack, bindata, PoisNor
NeedsCompilation: no
Packaged: 2017-04-21 19:49:24 UTC; Joe
Repository: CRAN
Date/Publication: 2017-04-21 23:22:25 UTC

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New package SADISA with initial version 1.0
Package: SADISA
Type: Package
Title: Species Abundance Distributions with Independent-Species Assumption
Version: 1.0
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Description: Computes the probability of a set of species abundances of a single or multiple samples of individuals under a mainland-island model. One must specify the mainland (metacommunity) model and the island (local) community model. It assumes that species fluctuate independently. See Haegeman, B. & R.S. Etienne (2017). A general sampling formula for community structure data. Methods in Ecology & Evolution. In press.
License: GPL-3
LazyData: FALSE
RoxygenNote: 5.0.1
Imports: subplex, pracma, DDD
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-21 21:22:10 UTC; rampa
Repository: CRAN
Date/Publication: 2017-04-21 23:08:31 UTC

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New package chemmodlab with initial version 1.0.0
Package: chemmodlab
Type: Package
Title: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models
Version: 1.0.0
Date: 2017-04-21
Authors@R: c( person("Jacqueline", "Hughes-Oliver", email = "hughesol@ncsu.edu", role = c("aut")), person("Jeremy", "Ash", email = "jrash@ncsu.edu", role = c("aut", "cre")), person("Atina", "Brooks", email = "atina.brooks@alumni.ncsu.edu", role = c("aut")) )
Description: Contains a set of methods for fitting models and methods for validating the resulting models. The statistical methodologies comprise a comprehensive collection of approaches whose validity and utility have been accepted by experts in the Cheminformatics field. As promising new methodologies emerge from the statistical and data-mining communities, they will be incorporated into the laboratory. These methods are aimed at discovering quantitative structure-activity relationships (QSARs). However, the user can directly input their own choices of descriptors and responses, so the capability for comparing models is effectively unlimited.
Depends: R (>= 3.1.1)
License: GPL-3
LazyData: TRUE
URL: https://github.com/jrash/ChemModLab
BugReports: https://github.com/jrash/ChemModLab/issues
Imports: class (>= 7.3.14), e1071 (>= 1.6.7), elasticnet (>= 1.1), foreach(>= 1.4.3), lars(>= 1.2), MASS(>= 7.3.45), nnet(>= 7.3.12), pROC(>= 1.8), randomForest(>= 4.6.12), rpart(>= 4.1.10), tree (>= 1.0.37), pls (>= 2.5.0), caret (>= 6.0-71), stats, graphics, grDevices, utils, datasets, methods
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-21 20:23:07 UTC; Vestige
Author: Jacqueline Hughes-Oliver [aut], Jeremy Ash [aut, cre], Atina Brooks [aut]
Maintainer: Jeremy Ash <jrash@ncsu.edu>
Suggests: knitr, rmarkdown
Repository: CRAN
Date/Publication: 2017-04-21 23:23:34 UTC

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New package statGraph with initial version 0.1.0
Package: statGraph
Type: Package
Title: Statistical Methods for Graphs
Author: Suzana S. Santos [aut], Andre Fujita [aut, cre]
Maintainer: Andre Fujita <fujita@ime.usp.br>
Depends: R (>= 2.10.0), stats, graphics
Imports: igraph, MASS
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation, model selection based on the GIC (Graph Information Criterion), statistical tests to discriminate two or more populations of graphs (ANOGVA -Analysis of Graph Variability), correlation between graphs, and clustering of graphs.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
URL: https://www.ime.usp.br/~fujita/software.html
Authors@R: c(person(given="Suzana S.", family="Santos", email="suzana@ime.usp.br", role=c("aut")), person(given="Andre", family="Fujita", email="fujita@ime.usp.br", role=c("aut", "cre")))
Version: 0.1.0
Date: 2017-04-21
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-21 03:55:17 UTC; su
Repository: CRAN
Date/Publication: 2017-04-21 18:43:05 UTC

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New package hoardr with initial version 0.1.0
Package: hoardr
Type: Package
Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.
Version: 0.1.0
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"))
License: MIT + file LICENSE
URL: https://github.com/ropensci/hoardr
BugReports: https://github.com/ropensci/hoardr/issues
VignetteBuilder: knitr
Imports: R6 (>= 2.2.0), rappdirs (>= 0.3.1)
Suggests: roxygen2 (>= 6.0.1), testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-21 15:48:08 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-21 18:27:33 UTC

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New package fasjem with initial version 1.0.0
Package: fasjem
Version: 1.0.0
Date: 2017-04-21
Title: A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models
Authors@R: c(person("Beilun", "Wang", role = c("aut", "cre"), email = "bw4mw@virginia.edu"), person("Yanjun", "Qi", role = "aut", email = "yanjun@virginia.edu"))
Author: Beilun Wang [aut, cre], Yanjun Qi [aut]
Maintainer: Beilun Wang <bw4mw@virginia.edu>
Depends: R (>= 3.0.0)
Description: The FASJEM (A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models) is a joint estimator which is fast and scalable for learning multiple related sparse Gaussian graphical models. For more details, please see <https://www.cs.virginia.edu/yanjun/paperA14/2017_JEM_combined.pdf>.
License: GPL-2
URL: https://www.cs.virginia.edu/~bw4mw, https://github.com/QData/JEM
BugReports: https://github.com/QData/JEM
NeedsCompilation: no
Packaged: 2017-04-21 13:02:25 UTC; beilunwang
Repository: CRAN
Date/Publication: 2017-04-21 18:27:31 UTC

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New package safer with initial version 0.1.0
Package: safer
Type: Package
Title: Encrypt and Decrypt Strings, R Objects and Files
Version: 0.1.0
Authors@R: person("KS", "Srikanth", email = "sri.teach@gmail.com", role = c("aut", "cre"))
Description: A consistent interface to encrypt and decrypt strings, R objects and files using symmetric key encryption.
Imports: sodium (>= 0.4), base64enc (>= 0.1.3), assertthat (>= 0.1)
Depends: R (>= 3.3.2)
License: GPL-3
URL: https://github.com/talegari/safer
BugReports: https://github.com/talegari/safer/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-21 13:39:02 UTC; srik
Author: KS Srikanth [aut, cre]
Maintainer: KS Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-21 13:49:28 UTC

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New package RHMS with initial version 1.0
Package: RHMS
Type: Package
Title: Hydrologic Modelling System for R Users
Version: 1.0
Depends: R (>= 3.0.0), graphics, stats, pso, Hmisc
Date: 2017-03-28
Author: Rezgar Arabzadeh ; Shahab Araghinejad
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>
Description: Hydrologic modelling system provides functionalities to R users to simulate hydrologic events. The packages includes functions to build, simulate, visualize, and calibrating hydrologic features.
License: GPL-2
NeedsCompilation: no
Packaged: 2017-04-21 13:18:58 UTC; parisa
Repository: CRAN
Date/Publication: 2017-04-21 13:50:28 UTC

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New package simMP with initial version 0.17.3
Package: simMP
Type: Package
Title: Simulate Somatic Mutations in Cancer Genomes from Mutational Processes
Version: 0.17.3
Author: Nan Zhou
Maintainer: Nan Zhou <zhnanx@gmail.com>
Description: Simulates somatic single base substitutions carried in cancer genomes. By only providing a human reference genome, substitutions that result from mutational processes operative in every cancer genome can be generated.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, IRanges, XVector
Depends: R (>= 3.0.0), doParallel, utils, foreach, parallel, stats
Suggests: BSgenome.Hsapiens.UCSC.hg38
NeedsCompilation: no
Packaged: 2017-04-21 03:42:12 UTC; mq44741340
Repository: CRAN
Date/Publication: 2017-04-21 06:03:09 UTC

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New package fastDummies with initial version 0.1.0
Package: fastDummies
Type: Package
Title: Fast Creation of Dummy (Binary) Columns from Categorical Variables
Version: 0.1.0
Authors@R: person("Jacob", "Kaplan", email = "jacobkap@sas.upenn.edu", role = c("aut", "cre"))
Description: Creates dummy columns from columns that have categorical variables (character or factor types). This package provides a significant speed increase from creating dummy variables through model.matrix().
Depends: R (>= 2.10)
Imports: data.table
License: GPL
Encoding: UTF-8
LazyData: true
URL: https://github.com/jacobkap/fastDummies
BugReports: https://github.com/jacobkap/fastDummies/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-21 02:25:15 UTC; user
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jacobkap@sas.upenn.edu>
Repository: CRAN
Date/Publication: 2017-04-21 06:04:38 UTC

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Thu, 20 Apr 2017

New package nonmemica with initial version 0.7.1
Package: nonmemica
Type: Package
Title: Create and Evaluate NONMEM Models in a Project Context
Version: 0.7.1
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.
License: GPL-3
LazyData: TRUE
Imports: dplyr, tidyr, xml2, encode, csv, fold, spec, lazyeval, metaplot, magrittr
Suggests: ReporteRs, pander, knitr, wrangle
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-20 16:26:54 UTC; tbergsma
Repository: CRAN
Date/Publication: 2017-04-20 23:16:50 UTC

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New package kernelboot with initial version 0.1.0
Package: kernelboot
Type: Package
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Version: 0.1.0
Date: 2017-04-20
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Description: Smoothed bootstrap and functions for random generation from univariate and multivariate kernel densities. It does not estimate kernel densities.
License: GPL-2
URL: https://github.com/twolodzko/kernelboot
BugReports: https://github.com/twolodzko/kernelboot/issues
Depends: R (>= 3.1.0)
LinkingTo: Rcpp
Imports: Rcpp, future
Suggests: covr, testthat, ks, KernSmooth
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-04-20 12:24:05 UTC; tymoteusz.wolodzko
Repository: CRAN
Date/Publication: 2017-04-20 15:07:38 UTC

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New package dtree with initial version 0.2.3
Package: dtree
Type: Package
Title: Decision Trees
Version: 0.2.3
Author: Ross Jacobucci
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Description: Combines various decision tree algorithms, plus both linear regression and ensemble methods into one package. Allows for the use of both continuous and categorical outcomes. An optional feature is to quantify the (in)stability to the decision tree methods, indicating when results can be trusted and when ensemble methods may be preferential.
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
Depends: rpart, party, evtree, partykit, caret
Suggests: randomForest, tree, MASS, ISLR, matrixStats, plyr, rpart.utils, stringr, pROC
NeedsCompilation: no
Packaged: 2017-04-20 00:08:39 UTC; RJacobucci
Repository: CRAN
Date/Publication: 2017-04-20 15:06:11 UTC

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New package BeSS with initial version 1.0.0
Package: BeSS
Type: Package
Title: Best Subset Selection for Sparse Generalized Linear Model and Cox Model
Version: 1.0.0
Date: 2017-4-12
Author: Canhong Wen, Aijun Zhang, Shijie Quan, Xueqin Wang
Maintainer: Canhong Wen <wencanhong@gmail.com>
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
License: GPL-3
Depends: R (>= 2.0.0)
Imports: Rcpp, Matrix, glmnet, survival
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2017-04-20 13:31:30 UTC; user5
Repository: CRAN
Date/Publication: 2017-04-20 15:06:59 UTC

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New package AHMbook with initial version 0.1.3
Package: AHMbook
Type: Package
Title: Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology'
Version: 0.1.3
Date: 2017-04-20
Depends: R (>= 2.10), unmarked (>= 0.12)
Imports: grDevices, graphics, methods, stats, utils, plotrix, raster, sp, RandomFields, coda
Suggests:
Author: Marc Kery, Andy Royle, Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Description: Provides functions and data sets to accompany the book 'Applied Hierarchical Modeling in Ecology: Analysis of distribution, abundance and species richness in R and BUGS' by Marc Kery and Andy Royle. The first volume appeared early in 2016 (ISBN: 978-0-12-801378-6, <https://www.mbr-pwrc.usgs.gov/pubanalysis/keryroylebook>; the second volume is in preparation and additional functions will be added to this package.
License: GPL (>= 3)
NeedsCompilation: no
URL: https://www.mbr-pwrc.usgs.gov/pubanalysis/keryroylebook/, https://sites.google.com/site/appliedhierarchicalmodeling/home
Packaged: 2017-04-20 09:20:16 UTC; MIKE
Repository: CRAN
Date/Publication: 2017-04-20 15:08:04 UTC

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New package rpatrec with initial version 0.9.1
Package: rpatrec
Type: Package
Title: Recognising Visual Charting Patterns in Time Series Data
Version: 0.9.1
Date: 2017-04-23
Authors@R: person("Stephan", "Maier", email = "sm297@st-andrews.ac.uk", role = c("aut", "cre"))
Description: Generating visual charting patterns and noise, smoothing to find a signal in noisy time series and enabling users to apply their findings to real life data.
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: np, graphics, stats
RoxygenNote: 6.0.1.9000
URL: http://github.com/maiers94/rpatrec
BugReports: http://github.com/maiers94/rpatrec/issues
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-19 20:37:01 UTC; sm297
Author: Stephan Maier [aut, cre]
Maintainer: Stephan Maier <sm297@st-andrews.ac.uk>
Repository: CRAN
Date/Publication: 2017-04-20 08:45:11 UTC

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New package PortfolioOptim with initial version 1.0.3
Package: PortfolioOptim
Title: Small/Large Sample Portfolio Optimization
Version: 1.0.3
Authors@R: c( person("Andrzej", "Palczewski", email = "A.Palczewski@mimuw.edu.pl", role = c("aut", "cre")), person("Aleksandra","Dabrowska",email = "oll.dabrowska@gmail.com", role=c("ctb")))
Description: Two functions for financial portfolio optimization by linear programming are provided. One function implements Benders decomposition algorithm and can be used for very large data sets. The other, applicable for moderate sample sizes, finds optimal portfolio which has the smallest distance to a given benchmark portfolio.
Depends: R (>= 3.3.0)
License: GNU General Public License version 3
Encoding: UTF-8
LazyData: true
Author: Andrzej Palczewski [aut, cre], Aleksandra Dabrowska [ctb]
Maintainer: Andrzej Palczewski <A.Palczewski@mimuw.edu.pl>
Imports: Rglpk
RoxygenNote: 6.0.1
Suggests: mvtnorm, testthat
NeedsCompilation: no
Packaged: 2017-04-20 08:38:45 UTC; apalczew
Repository: CRAN
Date/Publication: 2017-04-20 08:55:52 UTC

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New package antaresViz with initial version 0.8
Package: antaresViz
Type: Package
Title: Antares Visualizations
Version: 0.8
Date: 2017-04-06
Authors@R: c( person("Francois", "Guillem", , "francois.guillem@rte-france.com", role = c("aut", "cre")), person("Jalal-Edine", "ZAWAM", , "jalal-edine.zawam@rte-france.com", role = "ctb"), person("RTE", role = "cph") )
Maintainer: Francois Guillem <francois.guillem@rte-france.com>
Description: Visualize results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations.
URL: https://github.com/rte-antares-rpackage/antaresViz
BugReports: https://github.com/rte-antares-rpackage/antaresViz/issues
License: GPL (>= 2) | file LICENSE
LazyData: TRUE
Encoding: UTF-8
Depends: antaresRead (>= 0.14.0), antaresProcessing (>= 0.5.0)
Imports: dygraphs (>= 1.1.1), shiny (>= 0.13.0), miniUI, magrittr, plotly (>= 4.5.6), tibble, htmltools, htmlwidgets (>= 0.7.0), manipulateWidget (>= 0.5.1), leaflet (>= 1.0), sp, webshot, data.table, methods, lubridate, geojsonio, graphics, stats
RoxygenNote: 6.0.1
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2017-04-20 08:22:13 UTC; franguil
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Repository: CRAN
Date/Publication: 2017-04-20 08:33:58 UTC

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Wed, 19 Apr 2017

New package timekit with initial version 0.1.0
Package: timekit
Type: Package
Title: Simplified and Extensible Time Series Coercion Tools
Version: 0.1.0
Date: 2017-04-19
Authors@R: c( person("Matt", "Dancho", email = "mdancho@business-science.io", role = c("aut", "cre")), person("Davis", "Vaughan", email = "dvaughan@business-science.io", role = c("aut")) )
Description: Coerces between time-based tibbles ('tbl') and the primary time series object classes including 'xts', 'zoo', and 'ts'. Additionally, provides methods for maintaining the non-regularized time index during coercion to regularized time series objects.
URL: https://github.com/business-science/timekit
BugReports: https://github.com/business-science/timekit/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: devtools (>= 1.12.0), dplyr (>= 0.5.0), forcats (>= 0.2.0), forecast (>= 0.8.0), lazyeval (>= 0.2.0), lubridate (>= 1.6.0), purrr (>= 0.2.2), quantmod (>= 0.4-8), readr (>= 1.0.0), scales (<= 0.4.1), tibble (>= 1.2), tidyquant (>= 0.5.0), tidyr (>= 0.6.1), timeSeries (>= 3022.101.2), tseries (>= 0.10-37), TTR (>= 0.23-1), xts (>= 0.9-7), zoo (>= 1.7-14)
Suggests: knitr, rmarkdown, testthat, stringr, tidyverse
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-19 20:10:30 UTC; mdanc
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Repository: CRAN
Date/Publication: 2017-04-19 20:16:34 UTC

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New package DescToolsAddIns with initial version 0.9
Package: DescToolsAddIns
Type: Package
Title: Some Functions to be Used as Shortcuts in RStudio
Version: 0.9
Date: 2017-04-19
Author: Andri Signorell
Maintainer: Andri Signorell <andri@signorell.net>
Description: RStudio as of recently offers the option to define addins and assign shortcuts to them. This package contains AddIns for a few most used functions in an analysts (at least mine) daily work (like str(), example(), plot(), head(), view(), Desc()). Most of these functions will get the current selection in RStudio's editor window and send the specific command to the console while instantly executing it. Assigning shortcuts to these AddIns will spare you quite a few keystrokes.
Depends: base, stats, R (>= 3.1.1)
Imports: DescTools, rstudioapi
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2017-04-19 19:33:45 UTC; Andri
Repository: CRAN
Date/Publication: 2017-04-19 19:58:09 UTC

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New package simule with initial version 1.0.0
Package: simule
Version: 1.0.0
Date: 2017-04-18
Title: A Constrained L1 Minimization Approach for Estimating Multiple Sparse Gaussian or Nonparanormal Graphical Models
Authors@R: c(person("Beilun", "Wang", role = c("aut", "cre"), email = "bw4mw@virginia.edu"), person("Yanjun", "Qi", role = "aut", email = "yanjun@virginia.edu"))
Author: Beilun Wang [aut, cre], Yanjun Qi [aut]
Maintainer: Beilun Wang <bw4mw@virginia.edu>
Depends: R (>= 3.0.0), lpSolve, pcaPP
Suggests: parallel
Description: The SIMULE (Shared and Individual parts of MULtiple graphs Explicitly) is a generalized method for estimating multiple related graphs with shared and individual pattern among graphs. For more details, please see <arXiv:1605.03468>.
License: GPL-2
URL: https://www.cs.virginia.edu/~bw4mw, https://github.com/QData/SIMULE
BugReports: https://github.com/QData/SIMULE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-19 14:46:03 UTC; beilunwang
Repository: CRAN
Date/Publication: 2017-04-19 15:49:35 UTC

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New package RNAseqNet with initial version 0.1.0
Package: RNAseqNet
Type: Package
Title: Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation
Version: 0.1.0
Date: 2017-04-19
Authors@R: c(person("Alyssa", "Imbert", role = c("aut"), email="alyssa.imbert@inra.fr"), person("Nathalie", "Villa-Vialaneix", role = c("aut", "cre"), email="nathalie.villa-vialaneix@inra.fr"))
Maintainer: Nathalie Villa-Vialaneix <nathalie.villa-vialaneix@inra.fr>
Description: Infer log-linear Poisson Graphical Model with an auxiliary data set. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset. Standard log-linear Poisson graphical model can also be used for the inference and the Stability Approach for Regularization Selection (StARS) is implemented to drive the selection of the regularization parameter.
License: GPL (>= 3)
Repository: CRAN
Depends: R (>= 3.1.0), ggplot2
Imports: igraph (>= 1.0), hot.deck, PoiClaClu, glmnet
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-19 13:49:29 UTC; nathalie
Author: Alyssa Imbert [aut], Nathalie Villa-Vialaneix [aut, cre]
Date/Publication: 2017-04-19 15:51:49 UTC

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New package PCADSC with initial version 0.8.0
Package: PCADSC
Type: Package
Title: Tools for Principal Component Analysis-Based Data Structure Comparisons
Version: 0.8.0
Authors@R: c(person("Anne H.", "Petersen", , email="ahpe@sund.ku.dk", role=c("aut", "cre")), person("Bo", "Markussen", , email="bomar@math.ku.dk", role=c("aut")))
Description: A suite of non-parametric, visual tools for assessing differences in data structures for two datasets that contain different observations of the same variables. These tools are all based on Principal Component Analysis (PCA) and thus effectively address differences in the structures of the covariance matrices of the two datasets. The PCASDC tools consist of easy-to-use, intuitive plots that each focus on different aspects of the PCA decompositions. The cumulative eigenvalue (CE) plot describes differences in the variance components (eigenvalues) of the deconstructed covariance matrices. The angle plot presents the information loss when moving from the PCA decomposition of one dataset to the PCA decomposition of the other. The chroma plot describes the loading patterns of the two datasets, thereby presenting the relative weighting and importance of the variables from the original dataset.
Depends: R (>= 3.2.2)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: reshape2, methods, pander, ggplot2, Matrix
RoxygenNote: 5.0.1
URL: https://github.com/annepetersen1/PCADSC
BugReports: https://github.com/annepetersen1/PCADSC/issues
NeedsCompilation: no
Packaged: 2017-04-19 10:00:23 UTC; zms499
Author: Anne H. Petersen [aut, cre], Bo Markussen [aut]
Maintainer: Anne H. Petersen <ahpe@sund.ku.dk>
Repository: CRAN
Date/Publication: 2017-04-19 10:07:43 UTC

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New package CHMM with initial version 0.1.0
Package: CHMM
Type: Package
Title: Coupled Hidden Markov Models
Version: 0.1.0
Authors@R: c( person("Xiaoqiang", "Wang", email = "xiaoqiang.wang@sdu.edu.cn", role = "aut"), person("Julie", "Aubert", email = "julie.aubert@agroparistech.fr", role = c("aut","cre")) )
Description: An exact and a variational inference for coupled Hidden Markov Models applied to the joint detection of copy number variations.
Depends: R (>= 3.1.0)
Imports: mclust
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-04-18 14:47:08 UTC; aubert
Author: Xiaoqiang Wang [aut], Julie Aubert [aut, cre]
Maintainer: Julie Aubert <julie.aubert@agroparistech.fr>
Repository: CRAN
Date/Publication: 2017-04-19 10:07:41 UTC

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New package leaflet.minicharts with initial version 0.1.0
Package: leaflet.minicharts
Type: Package
Title: Minicharts for Interactive Maps
Version: 0.1.0
Authors@R: c( person("Francois", "Guillem", , "francois.guillem@rte-france.com", role = c("aut", "cre")), person("Jalal-Edine", "ZAWAM", , "jalal-edine.zawam@rte-france.com", role = "ctb"), person("RTE", role = "cph") )
Maintainer: Francois Guillem <francois.guillem@rte-france.com>
Description: Add and modify small charts on an interactive map created with package 'leaflet'. These charts can be used to represent at same time multiple variables on a single map.
License: GPL (>= 2) | file LICENSE
Depends: R (>= 2.10)
Imports: leaflet, htmltools
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, dplyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-19 08:32:02 UTC; franguil
Author: Francois Guillem [aut, cre], Jalal-Edine ZAWAM [ctb], RTE [cph]
Repository: CRAN
Date/Publication: 2017-04-19 08:40:56 UTC

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New package DA.MRFA with initial version 1.1
Package: DA.MRFA
Type: Package
Title: Dimensionality Assessment using Minimum Rank Factor Analysis
Version: 1.1
Date: 2017-04-18
Author: David Navarro-Gonzalez, Urbano Lorenzo-Seva
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>
Description: Performs Parallel Analysis for assessing the dimensionality of a set of variables using Minimum Rank Factor Analysis (see Timmerman & Lorenzo-Seva (2011) <DOI:10.1037/a0023353> and ten Berge & Kiers (1991) <DOI:10.1007/BF02294464> for more information). The package also includes the option to compute Minimum Rank Factor Analysis by itself, as well as the Greater Lower Bound calculation.
Depends: R (>= 2.10)
Imports: stats, Matrix, optimbase, psych
Suggests: PCovR
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
RoxygenNote: 6.0.1
Packaged: 2017-04-19 07:12:14 UTC; dng
Repository: CRAN
Date/Publication: 2017-04-19 08:32:25 UTC

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New package ompr.roi with initial version 0.6.0
Package: ompr.roi
Type: Package
Title: A Solver for 'ompr' that Uses the R Optimization Infrastructure ('ROI')
Version: 0.6.0
Authors@R: person("Dirk", "Schumacher", email = "mail@dirk-schumacher.net", role = c("aut", "cre", "cph"))
Description: A solver for 'ompr' based on the R Optimization Infrastructure ('ROI'). The package makes all solvers in 'ROI' available to solve 'ompr' models. Please see the 'ompr' website <https://dirkschumacher.github.io/ompr> and package docs for more information and examples on how to use it.
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
URL: https://github.com/dirkschumacher/ompr.roi
BugReports: https://github.com/dirkschumacher/ompr.roi/issues
Depends: R (>= 3.2.0)
Imports: ROI, ompr
Suggests: testthat, magrittr, ROI.plugin.glpk
ByteCompile: Yes
NeedsCompilation: no
Packaged: 2017-04-19 06:04:56 UTC; dirkschumacher
Author: Dirk Schumacher [aut, cre, cph]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Repository: CRAN
Date/Publication: 2017-04-19 07:06:33 UTC

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New package preseqR with initial version 3.0.1
Package: preseqR
Type: Package
Title: Predicting the Number of Species in a Random Sample
Version: 3.0.1
Date: 2017-04-10
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>
Description: The relation between the number of species and the number of individuals in a random sample is a classic problem back to Fisher (1943) <doi:10.2307/1411>. We generalize this problem to estimate the number of species represented at least r times in a random sample. In particular when r=1, it becomes the classic problem. We use a mixture of Poisson processes to model sampling procedures and apply a nonparametric empirical Bayes approach to obtain an estimator. For more information on preseqR, see Deng C, Daley T and Smith AD (2015) <doi:10.1007/s40484-015-0049-7> and Deng C and Smith AD (2016) <arXiv:1607.02804v2>.
License: GPL-3
Imports: polynom, graphics, stats
NeedsCompilation: yes
Packaged: 2017-04-18 23:51:37 UTC; JAKE
Repository: CRAN
Date/Publication: 2017-04-19 04:26:12 UTC

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Tue, 18 Apr 2017

New package ReinforcementLearning with initial version 1.0.0
Package: ReinforcementLearning
Type: Package
Title: Model-Free Reinforcement Learning
Version: 1.0.0
Date: 2017-04-17
Authors@R: c(person("Nicolas", "Proellochs", email="nicolas.proellochs@is.uni-freiburg.de", role=c("aut", "cre")), person("Stefan", "Feuerriegel", email="stefan.feuerriegel@is.uni-freiburg.de", role=c("aut")))
Maintainer: Nicolas Proellochs <nicolas.proellochs@is.uni-freiburg.de>
Description: Performs model-free reinforcement learning in R. This implementation enables the learning of an optimal policy based on sample sequences consisting of states, actions and rewards. In addition, it supplies multiple predefined reinforcement learning algorithms, such as experience replay.
License: MIT + file LICENSE
Depends: R (>= 3.2.0)
Imports: ggplot2, hash (>= 2.0), data.table
Suggests: testthat, knitr, rmarkdown
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-18 17:03:48 UTC; Nic
Author: Nicolas Proellochs [aut, cre], Stefan Feuerriegel [aut]
Repository: CRAN
Date/Publication: 2017-04-18 17:40:53 UTC

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New package RcppQuantuccia with initial version 0.0.1
Package: RcppQuantuccia
Type: Package
Title: R Bindings to the 'Quantuccia' Header-Only Essentials of 'QuantLib'
Version: 0.0.1
Date: 2017-04-17
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Description: 'QuantLib' bindings are provided for R using 'Rcpp' and the header-only 'Quantuccia' variant (put together by Peter Caspers) offering an essential subset of 'QuantLib'. See the included file 'AUTHORS' for a full list of contributors to both 'QuantLib' and 'Quantuccia'.
License: GPL (>= 2)
Imports: Rcpp
LinkingTo: Rcpp, BH
RoxygenNote: 6.0.1
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2017-04-18 13:08:07.26676 UTC; edd
Repository: CRAN
Date/Publication: 2017-04-18 17:42:20 UTC

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New package TSGSIS with initial version 0.1
Package: TSGSIS
Title: Two Stage-Grouped Sure Independence Screening
Description: To provide a high dimensional grouped variable selection approach for detection of whole-genome SNP effects and SNP-SNP interactions, as described in Fang et al. (2017, under review).
Version: 0.1
Author: Yao-Hwei Fang, Jie-Huei Wang, and Chao A. Hsiung
Maintainer: Yao-Hwei Fang <yhfang@nhri.org.tw>
Date: 2017-04-18
Depends: R (>= 3.2.3), glmnet, MASS, stats
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Repository: CRAN
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-18 01:08:21 UTC; lulu
Date/Publication: 2017-04-18 06:43:40 UTC

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New package WLreg with initial version 1.0.0
Package: WLreg
Type: Package
Version: 1.0.0
Date: 2017-04-18
Title: Regression Analysis Based on Win Loss Endpoints
Description: Use various regression models for the analysis of win loss endpoints adjusting for non-binary and multivariate covariates.
Authors@R: c( person(given="Xiaodong", family="Luo", email = "Xiaodong.Luo@sanofi.com", role =c("aut", "cre")), person("Sanofi", role = "cph"))
Depends: R (>= 3.1.2)
Imports: inline, stats, survival
License: GPL (>= 2)
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: yes
Packaged: 2017-04-18 02:46:58 UTC; Administrator
Author: Xiaodong Luo [aut, cre], Sanofi [cph]
Maintainer: Xiaodong Luo <Xiaodong.Luo@sanofi.com>
Repository: CRAN
Date/Publication: 2017-04-18 05:29:06 UTC

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Mon, 17 Apr 2017

New package CADStat with initial version 3.0.7
Package: CADStat
Version: 3.0.7
Date: 2017-04-17
Title: Provides a GUI to Several Statistical Methods
Author: Lester Yuan, Tom Stockton, Doug Bronson, Pasha Minallah, and Mark Fitzgerald
Maintainer: David Rebhuhn <rebhuhn.david@epa.gov>
Depends: R (>= 2.15.0), JGR (>= 1.7-10)
Imports: rJava, XML, lattice, bio.infer, gdata, gmodels, quantreg, rpart, JavaGD, car, MASS, iplots, SparseM, MatrixModels, gtools, png, pbkrtest, lme4, minqa, Rcpp, nloptr
Description: Using Java GUI for R (JGR), CADStat provides a user interface for several statistical methods - scatterplot, boxplot, linear regression, generalized linear regression, quantile regression, conditional probability calculations, and regression trees.
License: GPL (>= 2)
URL: http://www.rforge.net/CADStat/
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-17 20:00:51 UTC; drebhuhn
Repository: CRAN
Date/Publication: 2017-04-17 23:25:59 UTC

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New package l1kdeconv with initial version 1.1.0
Package: l1kdeconv
Type: Package
Title: Deconvolution for LINCS L1000 Data
Version: 1.1.0
Date: 2017-04-15
Author: Zhao Li[aut], Peng Yu[aut, cre]
Maintainer: Zhao Li <lizhao.informatics@gmail.com>
Description: LINCS L1000 is a high-througphput technology that allows the gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses. We present a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model (AGMM). Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv shows more stable and better performance than methods commonly used in LINCS L1000 data deconvolution.
Imports: stats
License: GPL (>= 2)
Depends: R (>= 3.2.0)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-17 22:28:29 UTC; zhao
Repository: CRAN
Date/Publication: 2017-04-17 23:00:19 UTC

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New package icosa with initial version 0.9.80
Package: icosa
Title: Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra
Version: 0.9.80
Authors@R: person("Adam T.", "Kocsis", email = "adam.kocsis@outlook.com", role = c("aut", "cre"))
Description: Employs triangular tessellation to refine icosahedra defined in 3d space. The procedures can be set to provide a grid with a custom resolution. Both the primary triangular and their inverted penta- hexagonal grids are available for implementation. Additional functions are provided to position points (latitude-longitude data) on the grids, to allow 2D and 3D plotting, use raster data and shapefiles.
Depends: R (>= 3.2.2), rgl
Date: 2017-04-17
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 5.0.1
LinkingTo: Rcpp
Imports: Rcpp, sp, raster, igraph, rgdal, methods
NeedsCompilation: yes
Packaged: 2017-04-17 17:45:10 UTC; kocsis
Author: Adam T. Kocsis [aut, cre]
Maintainer: Adam T. Kocsis <adam.kocsis@outlook.com>
Repository: CRAN
Date/Publication: 2017-04-17 22:54:10 UTC

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New package glue with initial version 1.0.0
Package: glue
Title: Interpreted String Literals
Version: 1.0.0
Authors@R: person("Jim", "Hester", email = "james.f.hester@gmail.com", role = c("aut", "cre"))
Description: An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/stable/manual/strings/#triple-quoted-string-literals>.
Depends: R (>= 3.0.0)
Suggests: testthat, covr, magrittr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-04-17 18:33:26 UTC; jhester
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-17 22:29:19 UTC

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New package metaplot with initial version 0.1.1
Package: metaplot
Type: Package
Title: Formalized Plots for Self-Describing Data
Version: 0.1.1
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Description: Creates fully-annotated plots with minimum guidance. Since the data is self-describing, less effort is needed for creating the plot. Generally expects data of class folded (see fold package). If attributes GUIDE and LABEL are present, they will be used to create formal axis labels. Several aesthetics are supported, such as reference lines, unity lines, smooths, and log transformations.
Imports: encode, lattice, magrittr, lazyeval, dplyr, fold,
Suggests: spec, tidyr, csv
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-17 17:19:39 UTC; tbergsma
Repository: CRAN
Date/Publication: 2017-04-17 18:30:57 UTC

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New package reportROC with initial version 1.0
Package: reportROC
Type: Package
Title: An Easy Way to Report ROC Analysis
Version: 1.0
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Description: Provides an easy way to report the results of ROC analysis, including: 1. an ROC curve. 2. the value of Cutoff, SEN (sensitivity), SPE (specificity), AUC (Area Under Curve), AUC.SE (the standard error of AUC), PLR (positive likelihood ratio), NLR (negative likelihood ratio), PPV (positive predictive value), NPV (negative predictive value).
License: GPL-3
Depends: R (>= 3.3.3)
Imports: pROC
LazyData: TRUE
NeedsCompilation: no
Packaged: 2017-04-17 15:07:44 UTC; dgdzc
Repository: CRAN
Date/Publication: 2017-04-17 17:38:13 UTC

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New package ompr with initial version 0.6.0
Package: ompr
Type: Package
Title: Model and Solve Mixed Integer Linear Programs
Version: 0.6.0
Authors@R: person("Dirk", "Schumacher", email = "mail@dirk-schumacher.net", role = c("aut", "cre", "cph"))
Description: Model mixed integer linear programs in an algebraic way directly in R. The model is solver-independent and thus offers the possibility to solve a model with different solvers. It currently only supports linear constraints and objective functions. See the 'ompr' website <https://dirkschumacher.github.io/ompr> for more information, documentation and examples.
License: GPL-3 | file LICENSE
LazyData: TRUE
RoxygenNote: 6.0.1
URL: https://github.com/dirkschumacher/ompr
BugReports: https://github.com/dirkschumacher/ompr/issues
Depends: R (>= 3.2.0)
Imports: dplyr, lazyeval, Rcpp
Suggests: magrittr, testthat
ByteCompile: Yes
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2017-04-17 13:59:07 UTC; dirkschumacher
Author: Dirk Schumacher [aut, cre, cph]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Repository: CRAN
Date/Publication: 2017-04-17 14:52:25 UTC

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New package Inventorymodel with initial version 1.0.3
Encoding: latin1
Package: Inventorymodel
Title: Inventory Models
Version: 1.0.3
Date: 2017-04-17
Author: Alejandro Saavedra Nieves
Maintainer: Alejandro Saavedra Nieves <alejandro.saavedra.nieves@gmail.com>
Depends: R(>= 2.15.0),e1071, GameTheoryAllocation
Description: Determination of the optimal policy in inventory problems from a game-theoretic perspective.
License: GPL-2
LazyLoad: yes
Packaged: 2017-04-17 08:44:03 UTC; Alejandro
Repository: CRAN
Date/Publication: 2017-04-17 15:27:07 UTC
NeedsCompilation: no

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Sun, 16 Apr 2017

New package mro with initial version 0.1.1
Package: mro
Type: Package
Title: Multiple Correlation
Version: 0.1.1
Author: Abirami S
Maintainer: Abirami S <abirami89@gmail.com>
Description: Computes multiple correlation coefficient when the data matrix is given and tests its significance.
Depends: R (>= 3.1.0), MASS,matrixcalc
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-16 15:29:21 UTC; Sampath
Repository: CRAN
Date/Publication: 2017-04-16 16:24:55 UTC

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New package corpus with initial version 0.2-0
Package: corpus
Version: 0.2-0
Date: 2017-04-15
Title: Text Corpus Analysis
Author: Patrick O. Perry
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Description: Text corpus data analysis, with full support for UTF8-encoded Unicode text. The package provides the ability to seamlessly read and process text from large JSON files without holding all of the data in memory simultaneously.
Suggests: testthat
LazyData: Yes
License: Apache License (== 2.0) | file LICENSE
URL: https://github.com/patperry/r-corpus
BugReports: https://github.com/patperry/r-corpus/issues
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2017-04-15 23:31:41 UTC; ptrck
Repository: CRAN
Date/Publication: 2017-04-16 10:09:37 UTC

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Sat, 15 Apr 2017

New package MODIStsp with initial version 1.3.2
Package: MODIStsp
Title: A Tool for Automating Download and Preprocessing of MODIS Land Products Data
Type: Package
Version: 1.3.2
Date: 2017-04-14
Authors@R: c(person("Lorenzo", "Busetto", email = "lbusett@gmail.com", role = c("aut", "cre")), person("Luigi", "Ranghetti", email = "ranghetti.l@irea.cnr.it", role = c("aut")))
Description: Allows automating the creation of time series of rasters derived from MODIS Satellite Land Products data. It performs several typical preprocessing steps such as download, mosaicking, reprojection and resize of data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional Quality Indicators should be extracted from aggregated MODIS Quality Assurance layers and, in the case of Surface Reflectance products , which Spectral Indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing to automatically update time series related to a MODIS product whenever a new image is available.
License: GPL-3
Depends: R (>= 3.1.3)
Imports: bitops (>= 1.0-6), data.table (>= 1.9.6), gdalUtils (>= 2.0.1.7), gWidgets (>= 0.0-54), gWidgetsRGtk2 (>= 0.0-83), hash (>= 2.2.6), httr (>= 1.1.0), pacman, plyr (>= 1.8.3), raster (>= 2.5-2), RCurl (>= 1.95-4.8), rgdal (>= 1.0-3), rgeos (>= 0.3-8), RJSONIO (>= 1.3.0), sp (>= 1.2-2), stringr (>= 1.0.0), xts (>= 0.9-7), XML (>= 3.98-1.1)
Suggests: knitr, rmarkdown, png, grid
SystemRequirements: Cairo >= 1.0.0, ATK (>= 1.10.0), Pango (>= 1.10.0), GTK+ (>= 2.8.0), GLib (>= 2.8.0), Curl, GDAL (>= 1.6.3), PROJ.4 (>= 4.4.9)
URL: https://github.com/lbusett/MODIStsp
BugReports: https://github.com/lbusett/MODIStsp/issues
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-15 15:43:05 UTC; LB_laptop
Author: Lorenzo Busetto [aut, cre], Luigi Ranghetti [aut]
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-15 20:31:21 UTC

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New package bigKRLS with initial version 1.5.1
Package: bigKRLS
Type: Package
Title: Optimized Kernel Regularized Least Squares
Version: 1.5.1
Date: 2017-04-14
Author: Pete Mohanty and Robert B. Shaffer
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>
Description: Functions for Kernel-Regularized Least Squares optimized for speed and memory usage are provided along with visualization tools. For working papers, sample code, and recent presentations visit <https://sites.google.com/site/petemohanty/software/>.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.4), biganalytics, bigalgebra, shiny, parallel, ggplot2
LinkingTo: Rcpp, RcppArmadillo, bigmemory, BH
Depends: R (>= 3.3.0), bigmemory
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-04-15 05:49:10 UTC; mohanty
Repository: CRAN
Date/Publication: 2017-04-15 06:36:34 UTC

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New package shinymaterial with initial version 0.1.0
Package: shinymaterial
Type: Package
Title: Implement Material Design in Shiny Applications
Version: 0.1.0
Authors@R: c( person("Eric", "Anderson", role = c("aut", "cre"), email = "eric.ray.anderson@gmail.com"), person("Alvin", "Wang", role = c("ctb", "cph"), comment = "Materialize CSS library"), person("Alan", "Chang", role = c("ctb", "cph"), comment = "Materialize CSS library"), person("Alex", "Mark", role = c("ctb", "cph"), comment = "Materialize CSS library"), person("Kevin", "Louie", role = c("ctb", "cph"), comment = "Materialize CSS library") )
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Description: Allows shiny developers to incorporate UI elements based on Google's Material design. See <https://material.io/guidelines/> for more information.
URL: https://ericrayanderson.shinyapps.io/shinymaterial/
License: GPL-3 | file LICENSE
Imports: shiny (>= 0.7.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-14 19:58:37 UTC; ericanderson
Author: Eric Anderson [aut, cre], Alvin Wang [ctb, cph] (Materialize CSS library), Alan Chang [ctb, cph] (Materialize CSS library), Alex Mark [ctb, cph] (Materialize CSS library), Kevin Louie [ctb, cph] (Materialize CSS library)
Repository: CRAN
Date/Publication: 2017-04-15 05:14:08 UTC

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Fri, 14 Apr 2017

New package bayesCL with initial version 0.0.1
Package: bayesCL
Version: 0.0.1
Date: 2017-04-10
Title: Bayesian Inference on a GPU using OpenCL
Author: Rok Cesnovar, Erik Strumbelj
Maintainer: Rok Cesnovar <rok.cesnovar@fri.uni-lj.si>
Description: Bayesian Inference on a GPU. The package currently supports sampling from PolyaGamma, Multinomial logit and Bayesian lasso.
License: GPL (>= 3)
Depends: R (>= 2.14.0)
Packaged: 2017-04-10 12:23:01 UTC; rok
NeedsCompilation: yes
SystemRequirements: OpenCL library; single-precision AMD or Nvidia GPU;
Repository: CRAN
Date/Publication: 2017-04-14 21:38:23 UTC
RoxygenNote: 6.0.1

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New package StatPerMeCo with initial version 0.1.0
Package: StatPerMeCo
Type: Package
Title: Statistical Performance Measures to Evaluate Covariance Matrix Estimates
Version: 0.1.0
Date: 2017-04-13
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Description: Statistical performance measures used in the econometric literature to evaluate conditional covariance/correlation matrix estimates (MSE, MAE, Euclidean distance, Frobenius distance, Stein distance, asymmetric loss function, eigenvalue loss function and the loss function defined in Eq. (4.6) of Engle et al. (2016) <doi:10.2139/ssrn.2814555>). Additionally, compute Eq. (3.1) and (4.2) of Li et al. (2016) <doi:10.1080/07350015.2015.1092975> to compare the factor loading matrix. The statistical performance measures implemented have been previously used in, for instance, Laurent et al. (2012) <doi:10.1002/jae.1248>, Amendola et al. (2015) <doi:10.1002/for.2322> and Becker et al. (2015) <doi:10.1016/j.ijforecast.2013.11.007>.
License: GPL (>= 2)
Note: The author acknowledges financial support from Sao Paulo Research Foundation (FAPESP) grant 2016/18599-4
NeedsCompilation: no
Packaged: 2017-04-14 17:27:22 UTC; ctruciosm
Repository: CRAN
Date/Publication: 2017-04-14 18:05:37 UTC

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New package thankr with initial version 1.0.0
Package: thankr
Type: Package
Title: Find Out Who Maintains the Packages you Use
Version: 1.0.0
Authors@R: c(person("Dirk", "Schumacher", email = "mail@dirk-schumacher.net", role = c("aut", "cre")))
Description: Find out who maintains the packages you use in your current session or in your package library and maybe say 'thank you'.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: tools, utils
Suggests: testthat, covr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-14 15:55:03 UTC; dirkschumacher
Author: Dirk Schumacher [aut, cre]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Repository: CRAN
Date/Publication: 2017-04-14 16:13:27 UTC

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New package SeerMapper2010West with initial version 1.2.0
Package: SeerMapper2010West
Type: Package
Version: 1.2.0
Date: 2017-04-13
Title: Supplemental U.S. 2010 Census Tract Boundaries for 14 Western States without Seer Registries for 'SeerMapper'
Author: "Jim Pearson" <jpearson@statnetconsulting.com> with data provided by "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2010 census tract boundaries for the 14 states without Seer Registries that are west of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. 2010 Census data and is in public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-14 15:16:19 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-14 15:47:16 UTC

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New package EpiILM with initial version 1.0
Package: EpiILM
Type: Package
Title: Spatial and Network Based Individual Level Models for Epidemics
Version: 1.0
Date: 2017-04-14
Author: Vineetha Warriyar. K. V.
Maintainer: Vineetha <vineethawarriyar.kod@ucalgary.ca>
Description: Provides tools for simulating from individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
License: GPL (>= 2)
Depends: graphics, grDevices, stats, utils, R (>= 3.2.0)
NeedsCompilation: yes
Packaged: 2017-04-14 15:26:17 UTC; Vineetha
Repository: CRAN
Date/Publication: 2017-04-14 15:47:11 UTC

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New package SeerMapper2010East with initial version 1.2.0
Package: SeerMapper2010East
Type: Package
Version: 1.2.0
Date: 2017-04-12
Title: Supplemental U. S. 2010 Census Tract Boundaries for 23 Eastern States without Registries for 'SeerMapper'
Author: "Jim Pearson" <jpearson@statnetconsulting.com> with data provided by "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2010 census tract boundary package for 23 states without Seer Registries that are east of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. Census data and is in public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-14 01:14:52 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-14 14:37:32 UTC

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New package networktools with initial version 1.0.0
Package: networktools
Title: Assorted Tools for Identifying Important Nodes in Networks (Impact, Expected Influence)
Version: 1.0.0
Authors@R: person("Payton", "Jones", email = "payton_jones@g.harvard.edu", role = c("aut", "cre"))
Description: Includes assorted tools for network analysis. Specifically, includes functions for calculating impact statistics, which aim to identify how each node impacts the overall network structure (global strength impact, network structure impact, edge impact), and for calculating and visualizing expected influence.
Depends: R (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: qgraph,igraph,IsingFit,reshape2,nnet,ggplot2,gridExtra,stats,graphics,utils,NetworkComparisonTest,devtools
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: http://github.com/paytonjjones/networktools
BugReports: http://github.com/paytonjjones/networktools/issues
NeedsCompilation: no
Packaged: 2017-04-14 01:04:37 UTC; payto
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <payton_jones@g.harvard.edu>
Repository: CRAN
Date/Publication: 2017-04-14 14:37:33 UTC

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New package docuSignr with initial version 0.0.1
Package: docuSignr
Title: Connect to 'DocuSign' API
Version: 0.0.1
Authors@R: c( person("Carl", "Ganz", email = "carl@cannadatasolutions.com", role = c("aut", "cre")), person("CannaData Solutions", role = "cph") )
Description: Connect to the 'DocuSign' Rest API <https://www.docusign.com/p/RESTAPIGuide/RESTAPIGuide.htm>, which supports embedded signing, and sending of documents.
Depends: R (>= 3.2.2)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: httr, jsonlite, magrittr
RoxygenNote: 6.0.1
Suggests: testthat, covr
URL: https://github.com/CannaData/docuSignr
BugReports: https://github.com/CannaData/docuSignr/issues
NeedsCompilation: no
Packaged: 2017-04-14 05:03:16 UTC; carl
Author: Carl Ganz [aut, cre], CannaData Solutions [cph]
Maintainer: Carl Ganz <carl@cannadatasolutions.com>
Repository: CRAN
Date/Publication: 2017-04-14 14:04:40 UTC

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Thu, 13 Apr 2017

New package tubern with initial version 0.1.0
Package: tubern
Title: R Client for the YouTube Analytics and Reporting API
Version: 0.1.0
Authors@R: person("Gaurav", "Sood", email = "gsood07@gmail.com", role = c("aut", "cre"))
Maintainer: Gaurav Sood <gsood07@gmail.com>
Description: Get statistics and reports from YouTube. To learn more about the YouTube Analytics and Reporting API, see <https://developers.google.com/youtube/reporting/>.
URL: http://github.com/soodoku/tubern
BugReports: http://github.com/soodoku/tubern/issues
Depends: R (>= 3.2.0)
License: MIT + file LICENSE
LazyData: true
Imports: httr, jsonlite
VignetteBuilder: knitr
Suggests: knitr (>= 1.11), testthat, rmarkdown, xml2
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-13 22:33:45 UTC; gsood
Author: Gaurav Sood [aut, cre]
Repository: CRAN
Date/Publication: 2017-04-13 22:44:46 UTC

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New package fold with initial version 0.1
Package: fold
Type: Package
Title: A Self-Describing Dataset Format and Interface
Version: 0.1
Date: 2017-04-13
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Description: Defines a compact data format that includes metadata. The function fold() creates the format by converting from data.frame, and unfold() converts back. The predictability of the folded format supports reusability of data processing tools, while the presence of embedded metadata improves portability, interpretability, and efficiency.
License: GPL-3
LazyData: TRUE
Imports: tidyr, dplyr, lazyeval, encode, csv
Suggests: magrittr, wrangle
Depends: R (>= 2.10)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-13 21:20:55 UTC; tbergsma
Repository: CRAN
Date/Publication: 2017-04-13 22:27:32 UTC

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New package spup with initial version 0.1-0
Package: spup
Type: Package
Title: Uncertainty Propagation Analysis
Version: 0.1-0
Date: 2017-04-06
Authors@R: c(person("Kasia", "Sawicka", email = "kasia.sawicka@wur.nl", role = c("aut", "cre")), person("Gerard", "Heuvelink", email = "gerard.heuvelink@wur.nl", role = c("aut")), person("Dennis", "Walvoort", email = "dennis.walvoort@wur.nl", role = c("ctb")), person("Stefan", "van Dam", email = "stefan.vandam@wur.nl", role = c("ctb")) )
Description: Uncertainty propagation analysis in spatial environmental modelling following methodology described in Heuvelink et al. (2017) <doi:10.1080/13658810601063951> and Brown and Heuvelink (2007) <doi:10.1016/j.cageo.2006.06.015>. The package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model outputs. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques. Uncertain variables are described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is accommodated for. The MC realizations may be used as input to the environmental models called from R, or externally.
Depends: R (>= 3.3.3)
Imports: graphics, gstat, magrittr, methods, mvtnorm, purrr, raster, whisker
Suggests: dplyr, GGally, gridExtra, knitr, readr, sp
License: GPL (>= 3)
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-13 09:33:20 UTC; sawic002
Author: Kasia Sawicka [aut, cre], Gerard Heuvelink [aut], Dennis Walvoort [ctb], Stefan van Dam [ctb]
Maintainer: Kasia Sawicka <kasia.sawicka@wur.nl>
Repository: CRAN
Date/Publication: 2017-04-13 21:21:06 UTC

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New package SeerMapper2010Regs with initial version 1.2.0
Package: SeerMapper2010Regs
Type: Package
Version: 1.2.0
Date: 2017-04-13
Title: Supplemental U. S. 2010 Census Tract Boundaries for 15 States with Seer Registries for 'SeerMapper'
Author: "Jim Pearson" <jpearson@statnetconsulting.com> with data provided by "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2010 census tract boundaries of the 15 states containing Seer Registries for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. 2010 Census data and is in public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-13 00:28:07 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-13 21:27:26 UTC

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New package PRIMME with initial version 2.1-0
Package: PRIMME
Type: Package
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Version: 2.1-0
Date: 2017-04-11
Authors@R: c(person("Eloy", "Romero", role=c("aut", "cre"), email="eloy@cs.wm.edu"), person("Andreas", "Stathopoulos", role="aut", email="andreas@cs.wm.edu"), person("College of William & Mary", role="cph"))
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Description: R interface to PRIMME, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix. It can also compute singular values and vectors of a square or rectangular matrix. It can find largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence.
URL: https://github.com/primme/primme
BugReports: https://github.com/primme/primme/issues
Imports: Rcpp
LinkingTo: Rcpp, Matrix
Suggests: Matrix
SystemRequirements: A POSIX system. Currently Linux and OS X are known to work. GNU make.
NeedsCompilation: yes
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.0.1
Packaged: 2017-04-13 13:53:08 UTC; eloy
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], College of William & Mary [cph]
Repository: CRAN
Date/Publication: 2017-04-13 21:32:02 UTC

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New package phantom with initial version 0.1.0
Package: phantom
Title: Gene Set Pareto Heterogeneity Analysis of Time-Course Gene Expression Data
Version: 0.1.0
Author: c(person("Jinghua","Gu",role = c("aut","cre"), email = "Jinghua.Gu@bswhealth.org"), person("Xuan","Wang"), role = "aut", email = "Xuan.Wang@bswhealth.org", person("Jinyan","Chan", role = c("aut","cre"),email = "Jinayn.Chan@bswhealth.org"), person("Nicole","Baldwin"), role = "aut",email = "Nicole.Baldwin@bswhealth.org", person("Jacob","Turner"), role = "aut",email = "Jacob.Turner@bswhealth.org")
Maintainer: Jinyan Chan <Jinyan.Chan@bswhealth.org>
Description: Pareto front based statistical tool for detecting heterogeneity in gene sets and biological modules from time-course data.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.1)
Imports: Rcpp (>= 0.12.3), cluster (>= 1.15.3), NMF (>= 0.20.6), MASS (>= 7.3-35), Matrix (>= 1.1-4), RColorBrewer (>= 1.1-2), gplots (>= 2.16.0)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1.9000
NeedsCompilation: yes
Packaged: 2017-04-13 20:26:58 UTC; Mia
Repository: CRAN
Date/Publication: 2017-04-13 21:11:18 UTC

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New package ordinalForest with initial version 1.0
Package: ordinalForest
Type: Package
Title: Ordinal Forests: Prediction and Class Width Inference with Ordinal Target Variables
Version: 1.0
Date: 2017-04-13
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Imports: ranger, combinat, ggplot2
Description: Ordinal forests (OF) are a method for ordinal regression with high-dimensional and low-dimensional data that is able to predict the values of the ordinal target variable for new observations and at the same time estimate the relative widths of the classes of the ordinal target variable. Using a (permutation-based) variable importance measure it is moreover possible to rank the importances of the covariates. OF will be presented in an upcoming technical report by Hornung et al.. The main functions of the package are: ordfor() (construction of OF), predict.ordfor() (prediction of the target variable values of new observations), and plot.ordfor() (visualization of the estimated relative widths of the classes of the ordinal target variable).
License: GPL-2
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-13 15:51:15 UTC; hornung
Repository: CRAN
Date/Publication: 2017-04-13 21:00:25 UTC

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New package ldhmm with initial version 0.1.0
Package: ldhmm
Type: Package
Title: Hidden Markov Model for Return Time-Series Based on Lambda Distribution
Version: 0.1.0
Date: 2017-04-13
Authors@R: person(given = c("Stephen", "H-T."), family = "Lihn", email = "stevelihn@gmail.com", role = c("aut", "cre"))
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Description: Hidden Markov Model (HMM) based on symmetric lambda distribution framework is implemented for the study of return time-series in the financial market. Major features in the S&P500 index, such as regime identification, volatility clustering, and anti-correlation between return and volatility, can be extracted from HMM cleanly. Univariate symmetric lambda distribution is essentially a location-scale family of power-exponential distribution. Such distribution is suitable for describing highly leptokurtic time series obtained from the financial market. It provides a theoretically solid foundation to explore such data where the normal distribution is not adequate. The HMM implementation follows closely the book: "Hidden Markov Models for Time Series", by Zucchini, MacDonald, Langrock (2016).
Depends: R (>= 3.3.1)
Imports: stats, utils, ecd, xts, zoo, moments, parallel, graphics, methods
Suggests: knitr, testthat, depmixS4, roxygen2, scales, shape
License: Artistic-2.0
Encoding: latin1
LazyData: true
RoxygenNote: 5.0.1
Collate: 'ldhmm-calc_stats_from_obs.R' 'ldhmm-numericOrNull-class.R' 'ldhmm-package.R' 'ldhmm-class.R' 'ldhmm-conditional_prob.R' 'ldhmm-constructor.R' 'ldhmm-decoding.R' 'ldhmm-forecast_prob.R' 'ldhmm-forecast_state.R' 'ldhmm-ld_stats.R' 'ldhmm-log_forward.R' 'ldhmm-mle.R' 'ldhmm-mllk.R' 'ldhmm-n2w.R' 'ldhmm-pseudo_residuals.R' 'ldhmm-state_ld.R' 'ldhmm-state_pdf.R' 'ldhmm-ts_abs_acf.R' 'ldhmm-viterbi.R' 'ldhmm-w2n.R' 'ldhmm.ts_log_rtn.R'
NeedsCompilation: no
Packaged: 2017-04-13 17:41:57 UTC; slihn
Repository: CRAN
Date/Publication: 2017-04-13 20:54:51 UTC

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New package fpest with initial version 0.1.1
Package: fpest
Type: Package
Title: Estimating Finite Population Total
Version: 0.1.1
Author: S.Sampath
Maintainer: S.Sampath <sampath1959@gmail.com>
Description: Given the values of sampled units and selection probabilities the desraj function in the package computes the estimated value of the total as well as estimated variance.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-13 08:18:50 UTC; UOM
Repository: CRAN
Date/Publication: 2017-04-13 21:00:27 UTC

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New package horserule with initial version 0.1.0
Package: horserule
Type: Package
Title: Flexible Non-Linear Regression with the HorseRule Algorithm
Version: 0.1.0
Date: 2017-04-12
Author: Malte Nalenz <malte.nlz@googlemail.com>, Mattias Villani <mattias.villani@liu.se>
Maintainer: Malte Nalenz <malte.nlz@googlemail.com>
Description: Implementation of the HorseRule model a flexible tree based Bayesian regression method for linear and nonlinear regression and classification described in Nalenz & Villani (2017) <arXiv:1702.05008>.
Imports: mvnfast, MASS, randomForest, gbm, inTrees, ggplot2, BayesLogit, grDevices, RColorBrewer, stats
License: GPL-3
RoxygenNote: 6.0.1
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2017-04-13 08:14:31 UTC; maltenlz
Repository: CRAN
Date/Publication: 2017-04-13 17:47:39 UTC

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Wed, 12 Apr 2017

New package rarhsmm with initial version 1.0.1
Package: rarhsmm
Type: Package
Title: Regularized Autoregressive Hidden Semi Markov Model
Version: 1.0.1
Date: 2017-04-13
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun Xu <zekunxu@gmail.com>
Description: Fit Gaussian hidden Markov (or semi-Markov) models with / without autoregressive coefficients and with / without regularization. The fitting algorithm for the hidden Markov model is illustrated by Rabiner (1989) <doi:10.1109/5.18626>. The shrinkage estimation on the covariance matrices is based on the graphical lasso method by Freedman (2007) <doi:10.1093/biostatistics/kxm045>. The shrinkage estimation on the autoregressive coefficients uses the elastic net shrinkage detailed in Zou (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Depends: R(>= 3.0.0)
License: GPL
LazyData: TRUE
Imports: glmnet
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-12 15:53:57 UTC; xuzekun
Repository: CRAN
Date/Publication: 2017-04-12 23:16:50 UTC

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New package R2ucare with initial version 1.0.0
Package: R2ucare
Maintainer: Olivier Gimenez <olivier.gimenez@cefe.cnrs.fr>
License: GPL (>= 2)
Title: Goodness-of-Fit Tests for Capture-Recapture Models
Author: Olivier Gimenez, Jean-Dominique Lebreton, Remi Choquet, Roger Pradel
Description: Performs goodness-of-fit tests for capture-recapture models. Also contains several functions to process capture-recapture data.
Version: 1.0.0
URL: https://github.com/oliviergimenez/R2ucare
Depends: R (>= 3.3.0)
Suggests: knitr, rmarkdown
Imports: stringr, RMark, stats, utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-12 22:11:13 UTC; gimenez
Repository: CRAN
Date/Publication: 2017-04-13 00:09:48 UTC

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New package SeerMapperWest with initial version 1.2.0
Package: SeerMapperWest
Type: Package
Version: 1.2.0
Date: 2017-04-12
Title: Supplemental U.S. 2000 Census Tract Boundaries for 14 Western States without Seer Registries for 'SeerMapper'
Author: "Jim Pearson" <jpearson@statnetconsulting.com> with data provided by "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2000 census tract boundaries for the 14 states without Seer Registries that are west of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. Census data and is in the public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-12 19:43:55 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-12 23:10:58 UTC

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New package cbanalysis with initial version 0.1.0
Package: cbanalysis
Type: Package
Title: Coffee Break Descriptive Analysis
Version: 0.1.0
Authors@R: person("Sandip Kumar", "Gupta", email = "sandip_nitj@yahoo.co.in", role = c("aut", "cre"))
Maintainer: Sandip Kumar Gupta <sandip_nitj@yahoo.co.in>
Description: Contains function which subsets the input data frame based on the variable types and returns list of data frames.
License: GPL-2
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-12 17:22:51 UTC; Sandip
Author: Sandip Kumar Gupta [aut, cre]
Repository: CRAN
Date/Publication: 2017-04-12 23:08:42 UTC

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New package ROI.plugin.clp with initial version 0.1
Package: ROI.plugin.clp
Version: 0.1
Date: 2017-04-10
Title: 'Clp (Coin-or linear programming)' Plugin for the 'R' Optimization Interface
Authors@R: c(person("Benoit", "Thieurmel", role = c("aut", "cre"), email = "benoit.thieurmel@datastorm.fr"))
Description: Enhances the R Optimization Infrastructure (ROI) package by registering the COIN-OR Clp open-source solver from the COIN-OR suite <https://projects.coin-or.org/>. It allows for solving linear programming with continuous objective variables keeping sparse constraints definition.
Imports: methods, stats, ROI (>= 0.2-1), clpAPI, slam, Matrix
License: EPL
URL: https://github.com/datastorm-open/ROI.plugin.clp, https://projects.coin-or.org/Clp
NeedsCompilation: no
RoxygenNote: 6.0.1
Suggests: testthat
Packaged: 2017-04-12 14:24:22 UTC; Datastorm
Author: Benoit Thieurmel [aut, cre]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Repository: CRAN
Date/Publication: 2017-04-12 14:40:48 UTC

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New package SeerMapperEast with initial version 1.2.0
Package: SeerMapperEast
Type: Package
Version: 1.2.0
Date: 2017-04-10
Title: Supplemental U. S. 2000 Census Tract Boundaries for 23 Eastern States without Seer Registries
Author: "Jim Pearson" <jpearson@statnetconsulting.com> with data provided by "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2000 census tract boundaries for the 23 states without Seer Registries that are east of the Mississippi river for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. Census data and is in the public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-12 07:09:24 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-12 14:15:09 UTC

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New package optrcdmaeAT with initial version 1.0.0
Package: optrcdmaeAT
Version: 1.0.0
Date: 2017-04-12
Title: Optimal Row-Column Designs for Two-Colour cDNA Microarray Experiments
Author: Legesse Kassa Debusho, Dibaba Bayisa Gemechu, and Linda Haines
Maintainer: Dibaba Bayisa Gemechu <diboobayu@gmail.com>
Depends: R (>= 3.3.2), MASS, Matrix, igraph, tcltk
License: GPL-2
Description: Computes A-, MV-, D- and E-optimal or near-optimal row-column designs for two-colour cDNA microarray experiments using the linear fixed effects and mixed effects models where the interest is in a comparison of all pairwise treatment contrasts. The algorithms used in this package are based on the array exchange and treatment exchange algorithms adopted from Debusho, Gemechu and Haines (2016, unpublished) algorithms after adjusting for the row-column designs setup. The package also provides an optional method of using the graphical user interface (GUI) R package tcltk to ensure that it is user friendly.
NeedsCompilation: no
Packaged: 2017-04-12 11:01:58 UTC; Dibaba B Gemechu
Repository: CRAN
Date/Publication: 2017-04-12 14:24:01 UTC

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New package marcher with initial version 0.0-2
Package: marcher
Type: Package
Title: Migration and Range Change Estimation in R
Version: 0.0-2
Authors@R: c(person("Eliezer", "Gurarie", role = c("aut", "cre"), email = "egurarie@umd.edu"), person("Farid", "Cheraghi", role = "aut"))
Description: A set of tools for likelihood-based estimation, model selection and testing of two- and three-range shift and migration models for animal movement data as described in Gurarie et al. (2017) <doi: 10.1111/1365-2656.12674>. Provided movement data (X, Y and Time), including irregularly sampled data, functions estimate the time, duration and location of one or two range shifts, as well as the ranging area and auto-correlation structure of the movment. Tests assess, for example, whether the shift was "significant", and whether a two-shift migration was a true return migration.
License: GPL-2
Depends: R (>= 3.3.0)
Imports: stats, Matrix, graphics, grDevices, plyr, mvtnorm, RColorBrewer, minpack.lm, zoo, numDeriv, magrittr, scales
VignetteBuilder: knitr
BugReports: https://github.com/EliGurarie/marcher/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, lubridate
NeedsCompilation: no
Packaged: 2017-04-12 02:31:07 UTC; Farid
Author: Eliezer Gurarie [aut, cre], Farid Cheraghi [aut]
Maintainer: Eliezer Gurarie <egurarie@umd.edu>
Repository: CRAN
Date/Publication: 2017-04-12 14:26:18 UTC

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New package BisRNA with initial version 0.2.1
Package: BisRNA
Type: Package
Title: Analysis of RNA Cytosine-5 Methylation
Version: 0.2.1
Author: Carine Legrand
Maintainer: Carine Legrand <c.legrand@dkfz.de>
Description: Bisulfite-treated RNA non-conversion in a set of samples is analysed as follows: each sample's Poisson parameter is estimated, and non-conversion p-values are calculated for each sample and adjusted for multiple testing. Finally, combined non-conversion p-value and standard error of the non-conversion are calculated on the intersection of the set of samples. A low combined non-conversion p-value points to methylation of the corresponding RNA cytosine, or another event blocking bisulfite conversion.
Date: 2017-04-11
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 3.3.2)
Imports: MASS, knitr, graphics, stats, utils
Suggests: IHW, testthat
NeedsCompilation: no
Packaged: 2017-04-12 10:55:19 UTC; legrand
Repository: CRAN
Date/Publication: 2017-04-12 14:13:34 UTC

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Tue, 11 Apr 2017

New package GLIDE with initial version 1.0.1
Package: GLIDE
Type: Package
Title: Global and Individual Tests for Direct Effects
Version: 1.0.1
Date: 2017-04-07
Authors@R: c(person("James", "Dai", role = c("aut", "cre"), email = "jdai@fredhutch.org"), person("Xiaoyu", "Wang", role = c("aut")))
Author: James Dai [aut, cre], Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Description: Functions evaluate global and individual tests for direct effects in Mendelian randomization studies.
Depends: R (>= 2.10)
Imports: MASS,foreach,parallel,doParallel
LazyLoad: no
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2017-04-11 16:27:47 UTC; xwang234
Repository: CRAN
Date/Publication: 2017-04-11 22:54:13 UTC

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New package DCA with initial version 1.0
Package: DCA
Type: Package
Title: Dynamic Correlation Analysis for High Dimensional Data
Version: 1.0
Date: 2017-04-07
Author: Tianwei Yu <tianwei.yu@emory.edu>
Maintainer: Tianwei Yu <tianwei.yu@emory.edu>
Description: Finding dominant latent signals that regulate dynamic correlation between many pairs of variables.
Imports: methods, GPArotation, PMA, coin, elasticnet, locfdr, modeest, mvtnorm,
License: GPL-2
Packaged: 2017-04-10 17:25:21 UTC; tyu8
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2017-04-11 21:04:59 UTC

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New package GADAG with initial version 0.99.0
Package: GADAG
Type: Package
Title: A Genetic Algorithm for Learning Directed Acyclic Graphs
Version: 0.99.0
Date: 2017-04-07
Author: Magali Champion, Victor Picheny and Matthieu Vignes
Maintainer: Magali Champion <magali.champion@parisdescartes.fr>
Description: Sparse large Directed Acyclic Graphs learning with a combination of a convex program and a tailored genetic algorithm (see Champion et al. (2017) <https://hal.archives-ouvertes.fr/hal-01172745v2/document>).
License: GPL-2
Depends: igraph, MASS
Imports: Rcpp (>= 0.12.5)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2017-04-11 12:36:50 UTC; magali
RoxygenNote: 6.0.1
Repository: CRAN
Date/Publication: 2017-04-11 13:52:58 UTC

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New package fuzzywuzzyR with initial version 1.0.0
Package: fuzzywuzzyR
Type: Package
Title: Fuzzy String Matching
Version: 1.0.0
Date: 2017-04-11
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Description: Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
License: GPL-2
SystemRequirements: Python (>= 2.4), difflib, fuzzywuzzy ( >=0.15.0 ), python-Levenshtein ( >=0.12.0 ). Detailed installation instructions for each operating system can be found in the README file.
Depends: R(>= 3.2.3)
Imports: reticulate, R6
Suggests: testthat, covr, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-11 12:55:33 UTC; lampros
Repository: CRAN
Date/Publication: 2017-04-11 13:52:56 UTC

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New package vocaldia with initial version 0.8.0
License: GPL-3
LazyData: true
Package: vocaldia
Type: Package
Title: Create and Manipulate Vocalisation Diagrams
Version: 0.8.0
Date: 2017-04-03
Authors@R: person("Saturnino", "Luz", email = "luzs@acm.org", role = c("aut", "cre"))
Description: Create adjacency matrices of vocalisation graphs from dataframes containing sequences of speech and silence intervals, transforming these matrices into Markov diagrams, and generating datasets for classification of these diagrams by 'flattening' them and adding global properties (functionals) etc. Vocalisation diagrams date back to early work in psychiatry (Jaffe and Feldstein, 1970) and social psychology (Dabbs and Ruback, 1987) but have only recently been employed as a data representation method for machine learning tasks including meeting segmentation (Luz, 2012) <doi:10.1145/2328967.2328970> and classification (Luz, 2013) <doi:10.1145/2522848.2533788>.
Depends: R (>= 3.0.0)
Suggests: igraph, foreign
Imports: graphics
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2017-04-10 22:16:00 UTC; luzs
Author: Saturnino Luz [aut, cre]
Maintainer: Saturnino Luz <luzs@acm.org>
Repository: CRAN
Date/Publication: 2017-04-11 11:55:49 UTC

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New package RTransProb with initial version 0.1.0
Package: RTransProb
Type: Package
Title: Analyze and Forecast Credit Migrations
Version: 0.1.0
Date: 2017-03-17
Author: Ab NDiaye
Maintainer: Ab NDiaye <pabdndiaye@gmail.com>
Description: A set of functions used to automate commonly used methods in credit risk. This includes multiple methods for bootstrapping default rates and forecasting/stress testing credit exposures migrations, via Econometrics and Machine Learning algorithms.
License: GPL-2
LazyData: TRUE
RoxygenNote: 6.0.1
Depends: R (>= 2.2.0)
Imports: chron, e1071, expm, matrixStats, nnet, pracma, zoo
NeedsCompilation: no
Packaged: 2017-04-10 23:53:42 UTC; Jamdoulaye
Repository: CRAN
Date/Publication: 2017-04-11 12:00:27 UTC

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New package lpdensity with initial version 0.1
Package: lpdensity
Title: Local Polynomial Density Estimation and Inference
Version: 0.1
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <xinweima@umich.edu>
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric density estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density estimator based on local polynomial regression, documented in Cattaneo, Jansson and Ma (2017): lpdensity() to construct local polynomial based density (and derivatives) estimator; lpbwdensity() to perform data-driven bandwidth selection; and lpdensity.plot() for density plot with robust confidence interval.
Imports: ggplot2
Depends: R (>= 3.1)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-11 01:40:06 UTC; xinwei
Repository: CRAN
Date/Publication: 2017-04-11 11:55:51 UTC

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New package fastqcr with initial version 0.1.0
Package: fastqcr
Type: Package
Title: Quality Control of Sequencing Data
Version: 0.1.0
Date: 2017-04-12
Authors@R: c( person("Alboukadel", "Kassambara", role = c("aut", "cre"), email = "alboukadel.kassambara@gmail.com") )
Description: 'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data. It produces, for each sample, an html report and a compressed file containing the raw data. If you have hundreds of samples, you are not going to open up each 'HTML' page. You need some way of looking at these data in aggregate. 'fastqcr' Provides helper functions to easily parse, aggregate and analyze 'FastQC' reports for large numbers of samples. It provides a convenient solution for building a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.2)
Imports: dplyr, grid, gridExtra, ggplot2, magrittr, readr, rmarkdown(>= 1.4), rvest, tibble, tidyr, scales, stats, utils, xml2
Suggests: knitr
URL: http://www.sthda.com/english/rpkgs/fastqcr/
BugReports: https://github.com/kassambara/fastqcr/issues
RoxygenNote: 6.0.1
Collate: 'utilities.R' 'fastqc.R' 'fastqc_install.R' 'qc_aggregate.R' 'qc_plot.R' 'qc_problems.R' 'qc_read.R' 'qc_report.R' 'qc_unzip.R'
NeedsCompilation: no
Packaged: 2017-04-11 10:31:32 UTC; kassambara
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-11 10:43:29 UTC

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New package FactoInvestigate with initial version 1.0
Package: FactoInvestigate
Type: Package
Title: Automatic Description of Factorial Analysis
Version: 1.0
Date: 2017-04-10
Author: Simon THULEAU, Francois HUSSON
Maintainer: Simon THULEAU <factoinvestigate@gmail.com>
Description: Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Imports: FactoMineR (>= 1.33), stats, methods, graphics, rrcov, rmarkdown, parallel
License: GPL (>= 2)
Encoding: latin1
LazyLoad: yes
NeedsCompilation: no
Packaged: 2017-04-11 07:25:55 UTC; husson
Repository: CRAN
Date/Publication: 2017-04-11 10:49:41 UTC

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Mon, 10 Apr 2017

New package SeerMapperRegs with initial version 1.2.0
Package: SeerMapperRegs
Type: Package
Version: 1.2.0
Date: 2017-04-10
Title: Supplemental U. S. 2000 Census Tract Boundary for 15 States with Seer Registries for 'SeerMapper'
Author: "Jim Pearson" <jpearson@statnetconsulting.com> and "U. S. Census Bureau" <geo.tiger@census.gov>
Maintainer: "Jim Pearson" <jpearson@statnetconsulting.com>
Depends: R (>= 3.2.0)
Imports: sp
Suggests:
Description: Provides supplemental 2000 census tract boundaries for the 15 states containing Seer Registries for use with the 'SeerMapper' package. The data contained in this package is derived from U. S. Census data and is in the public domain.
License: GPL (>= 2)
LazyData: no
LazyLoad: no
BuildResaveData: yes
ByteCompile: yes
NeedsCompilation: no
Packaged: 2017-04-10 13:18:53 UTC; jpearson
Repository: CRAN
Date/Publication: 2017-04-10 22:34:48 UTC

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New package D3GB with initial version 1.1
Package: D3GB
Type: Package
Version: 1.1
Date: 2017-04-10
Title: Interactive Genome Browser with R
Description: Creates interactive genome browser with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.
URL: http://d3gb.usal.es
License: CC BY-NC-SA 4.0
Depends: R (>= 3.0.0)
Imports: RSQLite (>= 1.0.0), DBI (>= 0.3.1), stats, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Author: Carlos Prieto <cprietos@usal.es>, David Barrios <metal@usal.es>
Maintainer: Carlos Prieto <cprietos@usal.es>
Packaged: 2017-04-10 15:07:36 UTC; cprieto
Repository: CRAN
Date/Publication: 2017-04-10 22:29:14 UTC

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New package lspline with initial version 1.0-0
Package: lspline
Type: Package
Title: Linear Splines with Convenient Parametrisations
Version: 1.0-0
Description: Linear splines with convenient parametrisations such that (1) coefficients are slopes of consecutive segments or (2) coefficients are slope changes at consecutive knots. Knots can be set manually or at break points of equal-frequency or equal-width intervals covering the range of 'x'. The implementation follows Greene (2003), chapter 7.2.5.
Suggests: testthat, knitr, rmarkdown, scales, ggplot2, broom
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Authors@R: c(person("Michal", "Bojanowski", role=c("aut", "cre"), email="michal2992@gmail.com"))
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-10 20:49:24 UTC; mbojan
Author: Michal Bojanowski [aut, cre]
Maintainer: Michal Bojanowski <michal2992@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-10 21:15:06 UTC

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New package rsolr with initial version 0.0.4
Package: rsolr
Type: Package
Title: R to Solr Interface
Version: 0.0.4
Author: Michael Lawrence, Gabe Becker, Jan Vogel
Maintainer: Michael Lawrence <michafla@gene.com>
Description: A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
License: Apache License (== 2.0)
Imports: restfulr (>= 0.0.2), graph, S4Vectors (>= 0.7.18), rjson, XML, RCurl
Depends: R (>= 3.2.0), BiocGenerics (>= 0.15.1), methods
Suggests: nycflights13, RUnit, MASS
Collate: utils.R pminmax.R Context-class.R DocCollection-class.R Expression-class.R Facets-class.R FieldInfo-class.R FieldType-class.R Promise-class.R SolrExpression-class.R SolrQuery-class.R SolrSchema-class.R SolrCore-class.R SolrResult-class.R SolrSummary-class.R Solr-class.R SolrList-class.R SolrFrame-class.R SolrPromise-class.R GroupedSolrFrame-class.R test.R zzz.R
NeedsCompilation: yes
Packaged: 2017-04-10 09:36:09 UTC; michafla
Repository: CRAN
Date/Publication: 2017-04-10 12:50:49 UTC

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New package CausalImpact with initial version 1.2.0
Package: CausalImpact
Title: Inferring Causal Effects using Bayesian Structural Time-Series Models
Date: 2017-04-06
Author: Kay H. Brodersen <kbrodersen@google.com>, Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
URL: https://google.github.io/CausalImpact/
Description: Implements a Bayesian approach to causal impact estimation in time series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>. See the package documentation on GitHub <https://google.github.io/CausalImpact/> to get started.
Copyright: Copyright (C) 2014-2017 Google, Inc.
Version: 1.2.0
VignetteBuilder: knitr
License: Apache License 2.0 | file LICENSE
Imports: assertthat, Boom, dplyr, ggplot2, zoo
Depends: bsts
Suggests: knitr, testthat
NeedsCompilation: no
Packaged: 2017-04-10 08:32:06 UTC; husi
Repository: CRAN
Date/Publication: 2017-04-10 12:59:47 UTC

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New package partools with initial version 1.1.6
Package: partools
Version: 1.1.6
Author: Norm Matloff <normmatloff@gmail.com> [cre,aut], Clark Fitzgerald <clarkfitzg@gmail.com> [aut], with contributions by Alex Rumbaugh <aprumbaugh@ucdavis.edu> and Hadley Wickham <h.wickham@gmail.com>
Maintainer: Norm Matloff <normmatloff@gmail.com>
Title: Tools for the 'Parallel' Package
Description: Miscellaneous utilities for parallelizing large computations. Alternative to MapReduce. File splitting and distributed operations such as sort and aggregate. "Software Alchemy" method for parallelizing most statistical methods, presented in N. Matloff, Parallel Computation for Data Science, Chapman and Hall, 2015. Includes a debugging aid.
Depends: regtools,parallel,stats,utils,data.table,pdist,methods
Suggests: rpart,e1071,testthat
ByteCompile: yes
NeedsCompilation: no
License: GPL (>= 2)
URL: https://github.com/matloff/partools
BugReports: https://github.com/matloff/partools/issues
Packaged: 2017-04-10 05:17:39 UTC; nm
Repository: CRAN
Date/Publication: 2017-04-10 09:16:20 UTC

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Sun, 09 Apr 2017

New package RLT with initial version 3.1.0
Package: RLT
Version: 3.1.0
Date: 2017-04-08
Title: Reinforcement Learning Trees
Author: Ruoqing Zhu <teazrq@gmail.com>
Maintainer: Ruoqing Zhu <teazrq@gmail.com>
Depends: R (>= 3.0.0)
Suggests: randomForest, parallel, survival, randomForestSRC, glmnet
Description: Random forest with a variety of additional features for regression, classification and survival analysis. The features include: parallel computing with OpenMP, embedded model for selecting the splitting variable (based on Zhu, Zeng & Kosorok, 2015), subject weight, variable weight, tracking subjects used in each tree, etc.
License: GPL (>= 2)
URL: https://sites.google.com/site/teazrq/
NeedsCompilation: yes
Repository: CRAN
RoxygenNote: 6.0.1
Packaged: 2017-04-09 17:22:48 UTC; Ruoqing Zhu
Date/Publication: 2017-04-09 21:25:51 UTC

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New package TeXCheckR with initial version 0.1.1
Package: TeXCheckR
Type: Package
Title: Parses LaTeX Documents for Errors
Date: 2017-04-10
Version: 0.1.1
Author: Hugh Parsonage
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
URL: https://github.com/HughParsonage/TeXCheckR
BugReports: https://github.com/HughParsonage/TeXCheckR/issues
Description: Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.
License: GPL-2
Depends: R (>= 2.10)
Imports: magrittr, dplyr, data.table, stringi, hunspell, clisymbols, crayon, gmailr, twitteR, readr, zoo
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-04-09 15:27:33 UTC; hughp
Repository: CRAN
Date/Publication: 2017-04-09 15:59:56 UTC

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New package vennplot with initial version 0.9
Package: vennplot
Type: Package
Title: Venn Diagrams in 2D and 3D
Version: 0.9
Date: 2017-03-16
Authors@R: c(person("Zehao", "Xu", email = "z267xu@uwaterloo.ca", role = c("aut", "cre")), person("R. Wayne", "Oldford", role = "ctb"), person("Martin", "Lysy", role = "ctb"))
Description: Calculate and plot Venn diagrams in 2D and 3D.
License: GPL (>= 3)
Imports: Rcpp (>= 0.12.7), stringr, rgl
LinkingTo: Rcpp
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-04-09 04:03:19 UTC; bigzi
Author: Zehao Xu [aut, cre], R. Wayne Oldford [ctb], Martin Lysy [ctb]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>
Repository: CRAN
Date/Publication: 2017-04-09 13:57:07 UTC

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New package mRchmadness with initial version 1.0.0
Package: mRchmadness
Title: Numerical Tools for Filling Out an NCAA Basketball Tournament Bracket
Version: 1.0.0
Authors@R: c( person("Eli", "Shayer", email = "eshayer@stanford.edu", role = c("aut", "cre")), person("Scott", "Powers", email = "sspowers@stanford.edu", role = "aut"))
URL: https://github.com/elishayer/mRchmadness
Imports: dplyr, glmnet, Matrix, rvest, shiny, xml2
Description: Scrape season results, estimate win probabilities, and find a competitive bracket for your office pool. Additional utilities include: scraping population picks; simulating tournament results; and testing your bracket in simulation.
Depends: R (>= 3.3.0)
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-09 05:13:38 UTC; elishayer
Author: Eli Shayer [aut, cre], Scott Powers [aut]
Maintainer: Eli Shayer <eshayer@stanford.edu>
Repository: CRAN
Date/Publication: 2017-04-09 13:56:07 UTC

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New package GMAC with initial version 1.0
Package: GMAC
Type: Package
Title: Genomic Mediation Analysis with Adaptive Confounding Adjustment
Version: 1.0
Date: 2017-04-08
Author: Fan Yang, Jiebiao Wang and Lin Chen
Maintainer: Fan Yang <yfcarolyn@gmail.com>
Description: Performs genomic mediation analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/078683>. It implements large scale mediation analysis and adaptively selects potential confounding variables to adjust for each mediation test from a pool of candidate confounders. The package is tailored for but not limited to genomic mediation analysis (e.g., cis-gene mediating trans-gene regulation pattern where an eQTL, its cis-linking gene transcript, and its trans-gene transcript play the roles as treatment, mediator and the outcome, respectively), restricting to scenarios with the presence of cis-association (i.e., treatment-mediator association) and random eQTL (i.e., treatment).
License: GPL
Depends: parallel, qvalue
LazyData: TRUE
NeedsCompilation: no
Packaged: 2017-04-08 22:20:33 UTC; JWang
Repository: CRAN
Date/Publication: 2017-04-09 14:18:23 UTC

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New package eLNNpaired with initial version 0.2.3
Package: eLNNpaired
Type: Package
Title: Model-Based Gene Clustering for Genomics Data from Paired/Matched Designs
Version: 0.2.3
Date: 2017-04-03
Author: Yunfeng Li <colinlee1999@gmail.com> and Weiliang Qiu <stwxq@channing.harvard.edu>
Maintainer: Yunfeng Li <colinlee1999@gmail.com>
Description: Perform model based gene clustering for genomics data generated from paired/matched design based on mixture of extended lognormal normal Bayesian hierarchical models (See Li Y, Morrow J, Raby B, Tantisira K, Weiss ST, Huang W, Qiu W. (2017), <doi:10.1371/journal.pone.0174602>).
License: GPL (>= 2)
Depends: R (>= 3.3.0), Biobase, stats
Imports: graphics, methods, utils, iCheck, samr, GSEAlm, globaltest
biocViews: Bioinformatics, DifferentialExpression
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-03 14:06:45 UTC; stwxq
Repository: CRAN
Date/Publication: 2017-04-09 14:21:04 UTC

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Fri, 07 Apr 2017

New package easyNCDF with initial version 0.0.1
Package: easyNCDF
Title: Tools to Easily Read/Write NetCDF Files into/from Multidimensional R Arrays
Version: 0.0.1
Authors@R: c( person("BSC-CNS", role = c("aut", "cph")), person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")))
Description: Set of wrappers for the 'ncdf4' package to simplify and extend its reading/writing capabilities into/from multidimensional R arrays.
Depends: R (>= 2.14.1)
Imports: ncdf4, abind
License: LGPL-3
URL: https://earth.bsc.es/gitlab/es/easyNCDF/wikis/home
BugReports: https://earth.bsc.es/gitlab/es/easyNCDF/issues
LazyData: true
SystemRequirements: netcdf development libraries
NeedsCompilation: no
Packaged: 2017-04-07 23:07:32 UTC; nmanubens
Author: BSC-CNS [aut, cph], Nicolau Manubens [aut, cre]
Maintainer: Nicolau Manubens <nicolau.manubens@bsc.es>
Repository: CRAN
Date/Publication: 2017-04-07 23:22:53 UTC

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New package reghelper with initial version 0.3.3
Package: reghelper
Type: Package
Title: Helper Functions for Regression Analysis
Version: 0.3.3
Date: 2017-04-07
Authors@R: person("Jeffrey", "Hughes", email="jeff.hughes@gmail.com", role=c("aut", "cre"))
Description: A set of functions used to automate commonly used methods in regression analysis. This includes plotting interactions, calculating simple slopes, calculating standardized coefficients, etc. See the reghelper documentation for more information, documentation, and examples.
License: GPL-3
URL:
Depends: R (>= 3.1.0)
LazyData: true
Imports: ggplot2 (>= 1.0.0), stats, nlme, lme4, utils
Suggests: testthat (>= 0.8.1)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-07 21:19:06 UTC; jeffh
Author: Jeffrey Hughes [aut, cre]
Maintainer: Jeffrey Hughes <jeff.hughes@gmail.com>
Repository: CRAN
Date/Publication: 2017-04-07 22:53:04 UTC

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