Tue, 31 May 2016

New package R6Frame with initial version 0.1.0
Package: R6Frame
Type: Package
Title: R6 Wrapper for Data Frames
Version: 0.1.0
Authors@R: person("Kristian D.", "Olsen", , "kristian@doingit.no", c("aut", "cre"))
Description: Provides a R6 "frame" around data which allows one to create more complex objects/operations based on the underlying data.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.2)
Imports: data.table (>= 1.9.6), lazyeval, R6
Suggests: dplyr, knitr, reshape2, rmarkdown, testthat, tidyr
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-31 11:57:42 UTC; Kristian
Author: Kristian D. Olsen [aut, cre]
Maintainer: Kristian D. Olsen <kristian@doingit.no>
Repository: CRAN
Date/Publication: 2016-05-31 15:18:12

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New package simLife with initial version 0.2
Package: simLife
Title: Simulation of Fatigue Lifetimes
Version: 0.2
Date: 2016-05-31
Authors@R: c(person("Markus Baaske", role = c("aut", "cre"), email = "markus.baaske@math.tu-freiberg.de"), person("Felix", "Ballani", role = c("aut","ctb"), email = "ballani@math.tu-freiberg.de"))
Author: Markus Baaske [aut, cre], Felix Ballani [aut, ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Description: Provides methods for simulation and analysis of a very general fatigue lifetime model for (metal matrix) composite materials.
Depends: R (>= 3.1.0), unfoldr
Imports: grDevices, graphics, stats, rgl, splancs, GenSA, Hmisc, lattice, parallel
License: GPL-2
Repository: CRAN
LazyData: no
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-31 08:35:33 UTC; root
Date/Publication: 2016-05-31 11:36:38

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New package rvsel with initial version 0.2.1
Package: rvsel
Type: Package
Title: Rare Variant Selection Procedure
Version: 0.2.1
Date: 2016-05-31
Author: Chunghui Lee and Hokeun Sun
Maintainer: Hokeun Sun <hsun@pusan.ac.kr>
Depends: R (>= 3.1.0)
Description: When a gene or a genetic region is significantly associated with a disease or a trait, the rare variant selection procedure is able to distinguish causal (risk or protective) rare variants from noncausal rare variants located within the same gene or the same genetic region.
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
Packaged: 2016-05-31 01:45:58 UTC; root
Date/Publication: 2016-05-31 11:22:47

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Mon, 30 May 2016

New package googleway with initial version 0.2.0
Package: googleway
Type: Package
Title: Retrieve Routes from Google Directions API and Decode Encoded Polylines
Version: 0.2.0
Date: 2016-05-20
Authors@R: c( person("David", "Cooley", ,"dcooley@symbolix.com.au", role = c("aut", "cre")), person("Paulo", "Barcelos", role = "ctb", comment = "Author of c++ decode_pl") )
Description: Retrieves routes and decodes polylines generated from Google's directions API (https://developers.google.com/maps/documentation/directions/).
License: Apache License 2.0
LazyData: TRUE
Depends: R (>= 3.0.0)
Imports: Rcpp (>= 0.12.5), jsonlite (>= 0.9.20), curl
LinkingTo: Rcpp
RoxygenNote: 5.0.1
BugReports: https://github.com/SymbolixAU/googleway/issues
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-30 06:50:22 UTC; dave
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_pl)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Repository: CRAN
Date/Publication: 2016-05-30 15:56:43

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New package DODR with initial version 0.99.2
Package: DODR
Type: Package
Title: Detection of Differential Rhythmicity
Version: 0.99.2
Date: 2016-05-30
Author: Paul Thaben, Pål O. Westermark
Maintainer: Paul Thaben <paul.thaben@charite.de>
Description: Detect Differences in rhythmic time series. Using linear least squares and the robust semi-parametric rfit() method. Differences in harmonic fitting could be detected as well as differences in scale of the noise distribution.
License: GPL-2
Depends: Matrix, Rfit, npsm, parallel
Imports: methods, stats
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-30 14:12:22 UTC; thaben
Repository: CRAN
Date/Publication: 2016-05-30 16:36:36

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New package blendedLink with initial version 0.1
Package: blendedLink
Type: Package
Title: A New Link Function that Blends Two Specified Link Functions
Version: 0.1
Date: 2016-05-30
Author: Robert Clark
Maintainer: "Robert Clark" <rclark@uow.edu.au>
Imports: stats
Description: A new link function that equals one specified link function up to a cutover then a linear rescaling of another specified link function. For use in glm() or glm2(). The intended use is in binary regression, in which case the first link should be set to "log" and the second to "logit". This ensures that fitted probabilities are between 0 and 1 and that exponentiated coefficients can be interpreted as relative risks for probabilities up to the cutoff.
License: GPL-2 | GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-30 10:26:04 UTC; rclark
Repository: CRAN
Date/Publication: 2016-05-30 16:38:53

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Sun, 29 May 2016

New package rcss with initial version 1.0
Package: rcss
Type: Package
Title: Convex Switching Systems
Version: 1.0
Date: 2016-05-26
Author: Juri Hinz and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Description: The numerical treatment of optimal switching problems in a finite time setting when the state evolves as a controlled Markov chain consisting of a uncontrolled continuous component following linear dynamics and a controlled Markov chain taking values in a finite set. The reward functions are assumed to be convex and Lipschitz continuous in the continuous state. The action set is finite.
License: GPL
Depends: rflann (>= 1.0)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppArmadillo
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2016-05-29 15:41:10 UTC; jeremyyee
Repository: CRAN
Date/Publication: 2016-05-29 21:14:04

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New package waterfalls with initial version 0.1.0
Package: waterfalls
Type: Package
Title: Create Waterfall Charts
Version: 0.1.0
Author: Hugh Parsonage
Maintainer: Hugh Parsonage <hugh.parsonage+waterfall@gmail.com>
Description: There seems to be no simple way to create 'waterfall charts' in 'ggplot2' currently. This package contains a single function (waterfall) that draws simply a waterfall chart as a 'ggplot2' object. Some flexibility in the appearance is available.
License: MIT + file LICENSE
Imports: ggplot2 (>= 2.0.0),
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-29 07:45:35 UTC; hughGrattan
Repository: CRAN
Date/Publication: 2016-05-29 15:21:34

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New package rflann with initial version 1.0
Package: rflann
Type: Package
Title: Basic R Interface to the FLANN C++ Library
Version: 1.0
Date: 2016-05-28
Author: Marius Muja, David Lowe and Jeremy Yee
Maintainer: Jeremy Yee <jeremyyee@outlook.com.au>
Description: Basic R interface for the FLANN C++ library written by Marius Muja and David Lowe. This package was written primarily for another package, 'rcss'. This packages utilises a few features from the FLANN C++ library. When I have time (and if there is sufficient demand), I will add more functions.
License: GPL
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2016-05-29 07:41:50 UTC; jeremyyee
Repository: CRAN
Date/Publication: 2016-05-29 15:20:18

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New package qrmdata with initial version 2016-01-03-1
Package: qrmdata
Version: 2016-01-03-1
Encoding: UTF-8
Title: Data Sets for Quantitative Risk Management Practice
Description: Various data sets (stocks, stock indices, constituent data, FX, zero-coupon bond yield curves, volatility, commodities) for Quantitative Risk Management practice.
Authors@R: c(person(given = "Marius", family = "Hofert", role = c("aut", "cre"), email = "marius.hofert@uwaterloo.ca"), person(given = "Kurt", family = "Hornik", role = "aut", email = "Kurt.Hornik@R-project.org"))
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Depends: R (>= 3.0.0)
Imports: xts
Suggests: knitr, qrmtools
Enhances:
License: GPL-2 | GPL-3
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-05-29 16:54:37
Packaged: 2016-05-29 12:56:37 UTC; mhofert

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Sat, 28 May 2016

New package cocor with initial version 1.1-3
Package: cocor
Type: Package
Title: Comparing Correlations
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen <mail@birkdiedenhofen.de>
Depends: methods
Suggests: testthat
Enhances: rkward
Imports: stats
Description: Statistical tests for the comparison between two correlations based on either independent or dependent groups. Dependent correlations can either be overlapping or nonoverlapping. A web interface is available on the website http://comparingcorrelations.org. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from https://rkward.kde.org to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
URL: http://comparingcorrelations.org
Authors@R: c(person(given="Birk", family="Diedenhofen", email="mail@birkdiedenhofen.de", role=c("aut", "cre")))
Version: 1.1-3
Date: 2016-05-28
RoxygenNote: 5.0.1
Collate: '0helper.r' 'as.htest.r' 'cocor-package.R' 'cocor.dep.groups.nonoverlap.r' 'cocor.dep.groups.overlap.r' 'cocor.indep.groups.r' 'cocor.r' 'get.cocor.input.r' 'get.cocor.results.r'
NeedsCompilation: no
Packaged: 2016-05-28 16:24:29 UTC; birk
Repository: CRAN
Date/Publication: 2016-05-28 20:30:27

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New package riem with initial version 0.1.0
Package: riem
Type: Package
Title: Accesses Weather Data from the Iowa Environment Mesonet
Version: 0.1.0
Authors@R: c(person("Maëlle", "Salmon", email = "maelle.salmon@yahoo.se", role = c("aut", "cre")), person("Brooke", "Anderson", role = c("rev"), comment = "Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/39."))
Description: Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.
License: GPL (>= 2)
LazyData: TRUE
Imports: httr (>= 1.1.0), lubridate (>= 1.5.6), dplyr (>= 0.4.3), jsonlite (>= 0.9.19), readr (>= 0.2.2), lazyeval (>= 0.1.10)
RoxygenNote: 5.0.1
URL: http://github.com/ropenscilabs/riem
BugReports: http://github.com/ropenscilabs/riem/issues
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-28 13:36:04 UTC; Maelle
Author: Maëlle Salmon [aut, cre], Brooke Anderson [rev] (Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/39.)
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>
Repository: CRAN
Date/Publication: 2016-05-28 15:52:50

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New package ZeligEI with initial version 0.1-0
Package: ZeligEI
Maintainer: James Honaker <zelig.zee@gmail.com>
License: GPL (>= 2)
Title: Zelig Ecological Inference Models
Author: James Honaker
Description: Add-on package for Zelig 5. Enables the use of a variety of ecological inference models.
Version: 0.1-0
Date: 2016-05-27
Imports: methods, Zelig (>= 5.0-11), MASS, jsonlite, dplyr, eiPack, ei, MCMCpack
Suggests: testthat, knitr
Collate: 'create-json.R' 'model-ei.R' 'model-dynamic-ei.R' 'model-hier-ei.R' 'model-ml-ei.R' 'model-rxc-ei.R'
NeedsCompilation: no
Packaged: 2016-05-28 03:41:40 UTC; tercer
Repository: CRAN
Date/Publication: 2016-05-28 08:18:30

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New package preprosim with initial version 0.1.0
Package: preprosim
Type: Package
Title: Lightweight Data Quality Simulation for Classification
Version: 0.1.0
Date: 2016-05-28
Authors@R: person("Markus", "Vattulainen", email = "markus.vattulainen@gmail.com", role = c("aut", "cre"))
Description: Data quality simulation can be used to check the robustness of data analysis findings and learn about the impact of data quality contaminations on classification. This package helps to add contaminations (noise, missing values, outliers, low variance, irrelevant features, class swap (inconsistency), class imbalance and decrease in data volume) to data and then evaluate the simulated data sets for classification accuracy. As a lightweight solution simulation runs can be set up with no or minimal up-front effort.
License: GPL-2
LazyData: TRUE
Imports: DMwR, reshape2, ggplot2, methods, stats, caret, doParallel, foreach
Suggests: gbm, testthat, preprocomb, preproviz, knitr, rmarkdown
URL: https://github.com/mvattulainen/preprosim
BugReports: https://github.com/mvattulainen/preprosim/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-28 04:39:33 UTC; Markus
Author: Markus Vattulainen [aut, cre]
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-28 08:18:24

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New package evclust with initial version 1.0.1
Package: evclust
Type: Package
Title: Evidential Clustering
Version: 1.0.1
Date: 2016-05-15
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Description: Various clustering algorithms that produce a credal partition, i.e., a set of Dempster-Shafer mass functions representing the membership of objects to clusters. The mass functions quantify the cluster-membership uncertainty of the objects. The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM), Constrained Evidential c-Means (CECM), EVCLUS and EK-NNclus.
Depends: R (>= 3.1.0),
Imports: FNN, R.utils, limSolve, Matrix
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Suggests: knitr,rmarkdown
NeedsCompilation: no
Packaged: 2016-05-28 03:27:49 UTC; Thierry
Repository: CRAN
Date/Publication: 2016-05-28 08:18:28

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Fri, 27 May 2016

New package rslurm with initial version 0.3.0
Package: rslurm
Type: Package
Title: Submit R Calculations to a 'SLURM' Cluster
Description: Functions that simplify the R interface the 'SLURM' cluster workload manager, and automate the process of dividing a parallel calculation across cluster nodes.
Version: 0.3.0
License: GPL-3
URL: https://github.com/SESYNC-ci/rslurm
BugReports: https://github.com/SESYNC-ci/rslurm/issues
Authors@R: c(person('Philippe', 'Marchand', email = 'pmarchand@sesync.org', role = c('aut', 'cre')), person('Mike', 'Smorul', role = 'ctb'))
Depends: R (>= 3.2.0)
Imports: parallel, whisker (>= 0.3)
RoxygenNote: 5.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-27 23:17:32 UTC; pmarchand
Author: Philippe Marchand [aut, cre], Mike Smorul [ctb]
Maintainer: Philippe Marchand <pmarchand@sesync.org>
Repository: CRAN
Date/Publication: 2016-05-28 01:55:25

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New package dataone with initial version 2.0.0
Package: dataone
Version: 2.0.0
Date: 2016-05-24
Title: R Interface to the DataONE REST API
Authors@R: c( person("Matthew B.", "Jones", role = c("aut", "cre"), email = "jones@nceas.ucsb.edu"), person("Peter", "Slaughter", role = "aut", email = "slaughter@nceas.ucsb.edu"), person("Rob", "Nahf", role = "aut", email = "rnahf@unm.edu"), person("Carl", "Boettiger", role = "aut", email = "cboettig@gmail.com"), person("Chris", "Jones", role = "aut", email = "cjones@nceas.ucsb.edu"), person("Jordan", "Read", role = "aut", email = "jread@usgs.gov"), person("Lauren", "Walker", role = "aut", email = "walker@nceas.ucsb.edu"), person("Edmund", "Hart", role = "aut", email = "edmund.m.hart@gmail.com"), person("Scott", "Chamberlain", role = "aut", email = "myrmecocystus@gmail.com"), person("Regents of the University of California", role = c("cph")))
VignetteBuilder: knitr
Description: Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.
Depends: R (>= 3.1.1),
Suggests: knitr, testthat, digest, openssl (>= 0.9.3)
Imports: XML (>= 3.95-0.1), hash, httr, methods, stringr, datapack, plyr, parsedate, uuid, base64enc, jsonlite
License: Apache License 2.0
URL: https://github.com/DataONEorg/rdataone
BugReports: https://github.com/DataONEorg/rdataone/issues
Collate: 'AbstractTableDescriber.R' 'auth_request.R' 'D1Node.R' 'AuthenticationManager.R' 'CNode.R' 'CertificateManager.R' 'D1Object.R' 'MNode.R' 'D1Client.R' 'EMLParser.R' 'dataone-package.R' 'yyy.R' 'zzz.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-27 18:24:44 UTC; jones
Author: Matthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Jordan Read [aut], Lauren Walker [aut], Edmund Hart [aut], Scott Chamberlain [aut], Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
X-CRAN-Comment: Archived on 2014-08-29 as dataonelibs was.
Repository: CRAN
Date/Publication: 2016-05-28 01:52:05

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New package vembedr with initial version 0.1.0
Package: vembedr
Title: Functions to Embed Video in HTML
Version: 0.1.0
Authors@R: c( person("Ian", "Lyttle", email = "ian.lyttle@schneider-electric.com", role = c("aut", "cre", "cph")) )
Description: A set of functions for generating HTML to embed hosted video in your R Markdown documents or Shiny apps.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: htmltools, httr, stringr
RoxygenNote: 5.0.1
URL: https://github.com/ijlyttle/vembedr
BugReports: https://github.com/ijlyttle/vembedr/issues
Suggests: testthat, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-27 16:20:09 UTC; ijlyttle
Author: Ian Lyttle [aut, cre, cph]
Maintainer: Ian Lyttle <ian.lyttle@schneider-electric.com>
Repository: CRAN
Date/Publication: 2016-05-27 18:38:56

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New package rsq with initial version 0.3
Package: rsq
Title: Coefficient of Determination
Version: 0.3
Date: 2016-05-27
Author: Dabao Zhang
Maintainer: Dabao Zhang <zhangdb@stat.purdue.edu>
Description: Calculates a newly defined coefficient of determination, aka R^2, and coefficient of partial determination, aka partial R^2 by Zhang (2016) for generalized linear models (including quasi models with well defined variance functions). It also avoids overstatement of variation proportion explained by the model or a group of covariates.
Imports: methods
Suggests: stats, MASS
License: GPL-2
NeedsCompilation: no
Packaged: 2016-05-27 14:32:34 UTC; zhangdb
Repository: CRAN
Date/Publication: 2016-05-27 18:48:53

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New package plotfunctions with initial version 1.0
Package: plotfunctions
Title: Various Functions to Facilitate Visualization of Data and Analysis
Version: 1.0
Date: 2016-05-26
Author: Jacolien van Rij [aut, cre]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Description: When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.
License: GPL (>= 2)
LazyData: true
Depends: R (>= 2.10)
Suggests: knitr, sp
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-27 16:08:42 UTC; jacolien
Repository: CRAN
Date/Publication: 2016-05-27 18:15:05

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New package QFASA with initial version 1.0.0
Package: QFASA
Title: Quantitative Fatty Acid Signature Analysis
Version: 1.0.0
Authors@R: c( person("Sara", "Iverson", email = "Sara.Iverson@dal.ca", role = c("aut")), person("Chris", "Field", email = "field@mathstat.dal.ca", role = c("aut")), person("Don", "Bowen", email = "Don.Bowen@dfo-mpo.gc.ca", role = c("aut")), person("Wade", "Blanchard", email = "wade.blanchard@anu.edu.au", role = c("aut")), person("Connie", "Stewart", email = "connie.stewart@unb.ca", role = c("aut", "cph")), person("Shelly", "Lang", email = "shelley.lang@dfo-mpo.gc.ca", role = c("aut")), person("Justin", "Kamerman", email = "justin.kamerman@unb.ca", role = c("cre", "cph")))
Description: Accurate estimates of the diets of predators are required in many areas of ecology, but for many species current methods are imprecise, limited to the last meal, and often biased. The diversity of fatty acids and their patterns in organisms, coupled with the narrow limitations on their biosynthesis, properties of digestion in monogastric animals, and the prevalence of large storage reservoirs of lipid in many predators, led us to propose the use of quantitative fatty acid signature analysis (QFASA) to study predator diets.
Depends: R (>= 3.2)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: Rsolnp, grid
RoxygenNote: 5.0.1
VignetteBuilder: rmarkdown, knitr
Suggests: knitr, rmarkdown, testthat, plyr, gtools
NeedsCompilation: no
Packaged: 2016-05-27 13:12:00 UTC; ec2-user
Author: Sara Iverson [aut], Chris Field [aut], Don Bowen [aut], Wade Blanchard [aut], Connie Stewart [aut, cph], Shelly Lang [aut], Justin Kamerman [cre, cph]
Maintainer: Justin Kamerman <justin.kamerman@unb.ca>
Repository: CRAN
Date/Publication: 2016-05-27 15:46:28

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New package jose with initial version 0.1
Package: jose
Type: Package
Title: Javascript Object Signing and Encryption
Version: 0.1
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Description: A collection of specifications to securely transfer claims such as authorization information between parties. A JSON Web Token (JWT) contains claims used by systems to apply access control rules to its resources. One potential use case of the JWT is authentication and authorization for a system that exposes resources through OAuth 2.0.
License: MIT + file LICENSE
URL: https://datatracker.ietf.org/wg/jose/documents/ https://github.com/jeroenooms/jose
BugReports: https://github.com/jeroenooms/jose/issues
Depends: openssl (>= 0.9.4)
Imports: jsonlite
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Suggests: testthat, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2016-05-27 11:33:37 UTC; jeroen
Repository: CRAN
Date/Publication: 2016-05-27 15:50:53

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New package elpatron with initial version 0.0.1
Package: elpatron
Title: Bicycling Data Analysis with R
Version: 0.0.1
Authors@R: person("Jordan", "Mackie", email = "jmackie@protonmail.com", role = c("aut", "cre"))
Description: Functions to facilitate cycling analysis within the R environment.
Depends: R (>= 3.2.5)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, dplyr, purrr, lazyeval
Suggests: readr, raster, magrittr
URL: https://github.com/jmackie4/elpatron
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-25 16:01:41 UTC; jmach
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Repository: CRAN
Date/Publication: 2016-05-27 15:58:48

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New package GK2011 with initial version 0.1.3
Package: GK2011
Type: Package
Title: Gaines and Kuklinski (2011) Estimators for Hybrid Experiments
Version: 0.1.3
Date: 2016-05-26
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"))
Description: Implementations of the treatment effect estimators for hybrid (self-selection) experiments, as developed by Brian J. Gaines and James H. Kuklinski, (2011), "Experimental Estimation of Heterogeneous Treatment Effects Related to Self-Selection," American Journal of Political Science 55(3): 724-736.
License: GPL (>= 2)
URL: https://github.com/leeper/GK2011
BugReports: https://github.com/leeper/GK2011/issues
LazyData: TRUE
Imports: stats
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 16:42:11 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-27 10:59:07

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Thu, 26 May 2016

New package CHFF with initial version 0.1.0
Package: CHFF
Type: Package
Title: Closest History Flow Field Forecasting for Bivariate Time Series
Version: 0.1.0
Author: Patrick Fleming
Maintainer: Kyle A. Caudle <kyle.caudle@sdsmt.edu>
Description: The software matches the current history to the closest history in a time series to build a forecast.
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-26 17:06:11 UTC; kcaudle
Repository: CRAN
Date/Publication: 2016-05-26 23:10:00

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New package BetaBit with initial version 1.2.1
Package: BetaBit
Title: Mini Games from Adventures of Beta and Bit
Version: 1.2.1
Authors@R: c( person("Przemysław", "Biecek", email = "przemyslaw.biecek@gmail.com", role = c("aut", "cre")), person("Witold", "Chodor", email = "witoldchodor@gmail.com", role = c("trl")), person("Katarzyna", "Fak", role = c("aut")), person("Foundation", "SmarterPoland.pl", email = "smarterpoland@gmail.com", role = c("cph")))
Description: Two games: proton and frequon. Both are console-based data-crunching games for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. You have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. The knowledge of 'dplyr' package is not required but may be very helpful. This game is linked with the ,,Pietraszko's Cave'' story available at <http://biecek.pl/BetaBit/Warsaw>. It's a part of Beta and Bit series. You will find more about the Beta and Bit series at <http://betabit.wiki>.
Depends: R (>= 3.0.0)
Imports: digest
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 17:14:41 UTC; pbiecek
Author: Przemysław Biecek [aut, cre], Witold Chodor [trl], Katarzyna Fak [aut], Foundation SmarterPoland.pl [cph]
Maintainer: Przemysław Biecek <przemyslaw.biecek@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 23:09:59

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New package heatmaply with initial version 0.3.2
Package: heatmaply
Type: Package
Title: Interactive Heat Maps Using 'plotly'
Version: 0.3.2
Date: 2016-05-25
Authors@R: c(person("Tal", "Galili", role = c("aut", "cre", "cph"), email = "tal.galili@gmail.com", comment = "http://www.r-statistics.com"))
Description: Create interactive heatmaps that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms. Heatmaps are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive heatmaps allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the heatmap by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar heatmaps as 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), and the ability to zoom from the dendrogram panes.
Depends: R (>= 3.0.0), plotly (>= 3.6.0), viridis
Imports: ggplot2, dendextend, magrittr (>= 1.0.1), reshape2, scales, utils, stats
Suggests: knitr, rmarkdown, gplots
VignetteBuilder: knitr
License: GPL-2 | GPL-3
URL: https://cran.r-project.org/package=heatmaply, https://github.com/talgalili/heatmaply/, http://www.r-statistics.com/tag/heatmaply/
BugReports: https://github.com/talgalili/heatmaply/issues
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-26 07:40:04 UTC; junior
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com)
Maintainer: Tal Galili <tal.galili@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:50:25

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New package fakeR with initial version 1.0
Package: fakeR
Type: Package
Title: Simulates Data from a Data Frame of Different Variable Types
Version: 1.0
Date: 2016-05-25
Authors@R: c(person("Lily", "Zhang", email = "lilyhzhang1029@gmail.com", role = c("aut", "cre")), person("Dustin","Tingley", email = "dtingley@gov.harvard.edu", role = c("aut")))
Description: Generates fake data from a dataset of different variable types. The package contains the functions simulate_dataset and simulate_dataset_ts to simulate time-independent and time-dependent data. It randomly samples character and factor variables from contingency tables and numeric and ordered factors from a multivariate normal distribution. It currently supports the simulation of stationary and zero-inflated count time series.
License: CC0
Imports: mvtnorm, polycor, pscl, VGAM, stats
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-26 06:59:29 UTC; lilyzhang
Author: Lily Zhang [aut, cre], Dustin Tingley [aut]
Maintainer: Lily Zhang <lilyhzhang1029@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-26 17:54:23

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Wed, 25 May 2016

New package mvtboost with initial version 0.5.0
Package: mvtboost
Type: Package
Title: Tree Boosting for Multivariate Outcomes
Version: 0.5.0
Date: 2016-05-25
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Description: Fits a multivariate model of decision trees for multiple, continuous outcome variables. A model for each outcome variable is fit separately, selecting predictors that explain covariance in the outcomes. Built on top of 'gbm', which fits an ensemble of decision trees to univariate outcomes.
License: GPL (>= 2) | file LICENSE
URL: https://github.com/patr1ckm/mvtboost
BugReports: https://github.com/patr1ckm/mvtboost/issues
Depends: R (>= 3.0.0)
Suggests: testthat, plyr, MASS, parallel, lars, ggplot2, knitr, rmarkdown
Imports: gbm, RColorBrewer, stats, graphics, grDevices, utils,
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-25 14:41:06 UTC; pmille13
Repository: CRAN
Date/Publication: 2016-05-25 18:08:26

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New package condSURV with initial version 0.1.0
Package: condSURV
Type: Package
Title: Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Version: 0.1.0
Date: 2016-05-25
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Luis Meira-Machado <lmachado@math.uminho.pt>
Description: Method to implement some newly developed methods for the estimation of the conditional survival function.
Depends: R (>= 3.0.1)
License: GPL (>= 2)
LazyData: TRUE
Imports: KernSmooth, doParallel, parallel, doRNG, foreach
NeedsCompilation: yes
Packaged: 2016-05-25 09:43:25 UTC; Sestelo
Repository: CRAN
Date/Publication: 2016-05-25 11:56:42

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New package rSARP with initial version 1.0.0
Package: rSARP
Title: Functions to Create and Evaluate Search and Rescue Plans
Version: 1.0.0
Author: John Hutcheson [aut, cre]
Maintainer: John Hutcheson <jacknx8a@gmail.com>
Description: Tools to create, evaluate, critique, revise, track progress, and communicate a detailed wilderness or urban search plan to management. This package uses and creates csv files in the R working directory to document inputs and results. It also creates a series of PDF and PNG files to accomplish communication of the plan. The program creates and revises search plans using Bayesian models. The package includes functions bestsearch(), searchstatus() and searchme() to model the number of searchers and hours required to search an area, calculate the probability of detection, probability of success, and project the best plan given limited resources.
Depends: R (>= 3.2.4)
Imports: ggplot2, lattice, qcc, grid, methods, grDevices, graphics, stats
License: GPL (>= 3)
LazyData: TRUE
BuildVignettes: TRUE
Packaged: 2016-05-24 16:10:22 UTC; NX8A
Suggests: R.rsp
VignetteBuilder: R.rsp
RoxygenNote: 5.0.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-05-25 06:09:17

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Tue, 24 May 2016

New package bitrugs with initial version 0.1
Package: bitrugs
Type: Package
Title: Bayesian Inference of Transmission Routes Using Genome Sequences
Version: 0.1
Date: 2016-05-24
Author: Colin Worby
Maintainer: Colin Worby <cworby@hsph.harvard.edu>
Description: MCMC methods to estimate transmission dynamics and infection routes in hospitals using genomic sampling data.
License: GPL-3
NeedsCompilation: yes
Packaged: 2016-05-24 17:38:46 UTC; colin
Repository: CRAN
Date/Publication: 2016-05-24 23:30:13

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New package QCEWAS with initial version 1.0-6
Package: QCEWAS
Type: Package
Title: Fast & Easy Quality Control of EWAS Results Files
Version: 1.0-6
Date: 2016-05-24
Author: Peter J. van der Most, Leanne K. Kupers, Ilja M. Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Depends: R (>= 3.0.0)
Description: Tools for (automated and manual) quality control of the results of Epigenome-Wide Association Studies.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2016-05-24 12:50:15 UTC; mostPJ
Repository: CRAN
Date/Publication: 2016-05-24 16:32:45

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New package bayesbio with initial version 1.0.0
Package: bayesbio
Title: Miscellaneous Functions for Bioinformatics and Bayesian Statistics
Version: 1.0.0
Authors@R: person("Andrew", "McKenzie", email = "amckenz@gmail.com", role = c("aut", "cre"))
Description: A hodgepodge of hopefully helpful functions. Two of these perform shrinkage estimation: one using a simple weighted method where the user can specify the degree of shrinkage required, and one using James-Stein shrinkage estimation for the case of unequal variances.
Depends: R (>= 3.2.0)
Suggests: ggplot2, RISmed, testthat
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-24 13:50:20 UTC; amckenz
Author: Andrew McKenzie [aut, cre]
Maintainer: Andrew McKenzie <amckenz@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-24 16:32:42

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New package DBItest with initial version 1.2
Package: DBItest
Title: Testing 'DBI' Back Ends
Version: 1.2
Date: 2016-05-21
Authors@R: c( person(given = "Kirill", family = "Müller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org"), person("RStudio", role = "cph") )
Description: A helper that tests 'DBI' back ends for conformity to the interface, currently work in progress.
Depends: R (>= 3.0.0)
Imports: methods, testthat (>= 1.0.2), withr, DBI (>= 0.4-1)
Suggests: devtools, lintr, knitr, rmarkdown
License: LGPL (>= 2)
LazyData: true
Encoding: UTF-8
BugReports: https://github.com/rstats-db/DBItest/issues
Collate: 'DBItest.R' 'context.R' 'expectations.R' 'import-dbi.R' 'import-testthat.R' 'run.R' 'test_all.R' 'test_getting_started.R' 'test_driver.R' 'test_connection.R' 'test_result.R' 'test_sql.R' 'test_meta.R' 'test_compliance.R' 'tweaks.R' 'utf8.R' 'utils.R'
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-24 12:15:07 UTC; muelleki
Author: Kirill Müller [aut, cre], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Repository: CRAN
Date/Publication: 2016-05-24 14:49:34

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New package adespatial with initial version 0.0-2
Package: adespatial
Title: Multivariate Multiscale Spatial Analysis
Version: 0.0-2
Date: 2016-05-24
Author: Stéphane Dray, Guillaume Blanchet, Guillaume Guenard, Thibaut Jombart, Pierre Legendre, Helene H Wagner
Description: Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Imports: ade4 (>= 1.7-1), adegraphics, sp, spdep, lattice, methods, grDevices, graphics, stats, utils, vegan
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2016-05-24 11:55:17 UTC; stephane
Repository: CRAN
Date/Publication: 2016-05-24 14:49:37

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New package photobiologyInOut with initial version 0.4.4
Package: photobiologyInOut
Type: Package
Title: Read Spectral Data from Foreign Files
Version: 0.4.4
Date: 2016-05-22
Author: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Description: Functions for reading and writing foreign files containing spectral data from spectrometers and their associated software, and output from simulation models in common use.
License: GPL (>= 3)
VignetteBuilder: knitr
Depends: R (>= 3.2.0)
Imports: lubridate (>= 1.5.6), tibble (>= 1.0), dplyr (>= 0.4.3), readr (>= 0.2.2), photobiology (>= 0.9.8), reshape2 (>= 1.4.1), hyperSpec (>= 0.98), pavo (>= 0.5-5), lazyeval (>= 0.1.10), methods
Suggests: knitr (>= 1.13), ggspectra (>= 0.1.7), photobiologyWavebands (>= 0.4.0), ggplot2 (>= 2.1.0), ggmap (>= 2.6.1), testthat (>= 1.0.2)
LazyLoad: yes
LazyData: yes
ByteCompile: true
Encoding: UTF-8
URL: http://www.r4photobiology.info
BugReports: https://bitbucket.org/aphalo/photobiologyinout/
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 11:39:18 UTC; aphalo
Repository: CRAN
Date/Publication: 2016-05-24 11:02:23

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New package ChangepointTesting with initial version 1.0
Package: ChangepointTesting
Type: Package
Title: Change Point Estimation for Clustered Signals
Version: 1.0
Date: 2016-02-01
Author: Hongyuan Cao, Wei Biao Wu, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Description: A multiple testing procedure for clustered alternative hypotheses. It is assumed that the p-values under the null hypotheses follow U(0,1) and that the distributions of p-values from the alternative hypotheses are stochastically smaller than U(0,1). By aggregating information, this method is more sensitive to detecting signals of low magnitude than standard methods. Additionally, sporadic small p-values appearing within a null hypotheses sequence are avoided by averaging on the neighboring p-values.
License: GPL-2
Depends: graphics, methods, stats
NeedsCompilation: no
Packaged: 2016-05-23 22:36:17 UTC; sthollow
Repository: CRAN
Date/Publication: 2016-05-24 05:38:52

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Mon, 23 May 2016

New package sjstats with initial version 0.1.0
Package: sjstats
Type: Package
Encoding: UTF-8
Title: Collection of Convenient Functions for Common Statistical Computations
Version: 0.1.0
Date: 2016-05-23
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Description: Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like standard errors or root mean squared errors). Second, these shortcut functions are generic (if appropriate), and can be applied not only to vectors, but also to other objects as well (e.g., the Coefficient of Variation can be computed for vectors, linear models, or linear mixed models; the r2()-function returns the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects). The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models and mixed effects models. However, some of the functions also deal with other statistical measures, like Cronbach's Alpha, Cramer's V, Phi etc.
License: GPL-3
Depends: R (>= 3.2), stats, utils
Imports: coin, lme4, MASS, Matrix, nlme, sjmisc
Suggests: AER, arm, pwr
URL: https://github.com/sjPlot/sjstats
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 16:52:26 UTC; Standardbenutzer
Repository: CRAN
Date/Publication: 2016-05-23 23:37:22

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New package SafeBayes with initial version 1.0
Package: SafeBayes
Type: Package
Title: Generalized and Safe-Bayesian Ridge and Lasso Regression
Version: 1.0
Date: 2016-05-21
Authors@R: c(person("Rianne", "de Heide", role = c("aut", "cre"), email = "r.de.heide@cwi.nl"), person("Gustavo", "de los Campos", role = "ctb"), person("Paulino", "Perez Rodriguez", role = "ctb"), person("Bob", "Wheeler", role = "ctb"))
Depends: R (>= 3.1.2), stats
Description: Functions for Generalized and Safe-Bayesian Ridge and Lasso Regression models with both fixed and varying variance.
License: GPL-2
NeedsCompilation: yes
LazyLoad: true
Packaged: 2016-05-23 14:48:19 UTC; Rianne
Author: Rianne de Heide [aut, cre], Gustavo de los Campos [ctb], Paulino Perez Rodriguez [ctb], Bob Wheeler [ctb]
Maintainer: Rianne de Heide <r.de.heide@cwi.nl>
Repository: CRAN
Date/Publication: 2016-05-23 17:05:40

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New package extremefit with initial version 0.1
Package: extremefit
Type: Package
Title: Estimation of Extreme Conditional Quantiles and Probabilities
Version: 0.1
Date: 2016-05-23
Author: Gilles Durrieu, Ion Grama, Kevin Jaunatre, Quang-Khoai Pham, Jean-Marie Tricot
Depends: R (>= 2.10)
Maintainer: Kevin Jaunatre <kevin.jaunatre@univ-ubs.fr>
Description: Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 13:56:08 UTC; kevin
Repository: CRAN
Date/Publication: 2016-05-23 16:28:14

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New package ILS with initial version 0.1.0
Package: ILS
Type: Package
Title: Interlaboratory Study
Version: 0.1.0
Date: 2016-05-22
Authors@R: c( person("Miguel","Flores",role=c("aut","cre"), email="ma.flores@outlook.com"), person("Salvador","Naya",role="ctb"), person("Javier","Tarrio-Saavedra",role="ctb"), person("Ruben","Fernandez",role="ctb"), person("Rubi","Arias",role="ctb") )
Depends: R (>= 3.1.0), multcomp, depthTools, fda.usc, MASS
Description: It performs interlaboratory studies (ILS) to detect those laboratories that provide non-consistent results when comparing to others. It permits to work simultaneously with various testing materials, from standard univariate, and functional data analysis (FDA) perspectives. The univariate approach based on ASTM E691-08 consist of estimating the Mandel's h and k statistics to identify those laboratories that provide more significant different results, testing also the presence of outliers by Cochran and Grubbs tests, Analysis of variance (ANOVA) techniques are provided (F and Tuckey tests) to test differences in means corresponding to different laboratories per each material. Taking into account the functional nature of data retrieved in analytical chemistry, applied physics and engineering (spectra, thermograms, etc.). ILS package provides a FDA approach for finding the Mandel's k and h statistics distribution by smoothing bootstrap resampling.
License: GPL (>= 2)
LazyData: yes
Author: Miguel Flores [aut, cre], Salvador Naya [ctb], Javier Tarrio-Saavedra [ctb], Ruben Fernandez [ctb], Rubi Arias [ctb]
Maintainer: Miguel Flores <ma.flores@outlook.com>
Repository: CRAN
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 10:48:30 UTC; MiguelA
Date/Publication: 2016-05-23 13:04:51

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New package eechidna with initial version 0.1
Package: eechidna
Version: 0.1
Title: Exploring Election and Census Highly Informative Data Nationally for Australia
Description: Data from the 2013 Australian Federal Election (House of Representatives) and the 2011 Australian Census. Includes tools for visualizing and analysing the data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission) 2016.
Depends: R (>= 3.2.3)
Imports: dplyr, ggplot2 (>= 2.0.0), tidyr, shiny, plotly (>= 3.5.2), ggthemes, shinyjs, methods
Suggests: testthat, knitr, rmarkdown, maptools, purrr, sp, GGally, corrplot, broom, plyr, scales, readr, gridExtra
Authors@R: c(person("Di", "Cook", role = c("aut")), person("Heike", "Hofmann", role = c("aut")), person("Rob", "Hyndman", role = c("aut")), person("Thomas", "Lumley", role = c("aut")), person("Ben", "Marwick", role = c("aut", "cre"), email = "benmarwick@gmail.com"), person("Carson", "Sievert", role = c("aut")), person("Nicholas", "Tierney", role = c("aut")), person("Nathaniel", "Tomasetti", role = c("aut")), person("Fang", "Zhou", role = c("aut")), person("Commonwealth of Australia", "AEC", role = c("cph")))
Maintainer: Ben Marwick <benmarwick@gmail.com>
LazyData: true
ByteCompile: TRUE
License: GPL (>= 2)
URL: https://github.com/ropenscilabs/eechidna
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 23:28:11 UTC; marwick
Author: Di Cook [aut], Heike Hofmann [aut], Rob Hyndman [aut], Thomas Lumley [aut], Ben Marwick [aut, cre], Carson Sievert [aut], Nicholas Tierney [aut], Nathaniel Tomasetti [aut], Fang Zhou [aut], Commonwealth of Australia AEC [cph]
Repository: CRAN
Date/Publication: 2016-05-23 06:01:37

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Sun, 22 May 2016

New package VDAP with initial version 2.0.0
Package: VDAP
Type: Package
Title: Peptide Array Analysis Tools
Version: 2.0.0
Date: 2016-04-26
Author: Cody Moore
Maintainer: Cody Moore <Jumper9400@gmail.com>
Description: Analyze Peptide Array Data and characterize peptide sequence space. Allows for high level visualization of global signal, Quality control based on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters, Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU signal weighting. Basic signal trends can be used to generate peptides that follow the observed compositional trends.
License: GPL-2
Imports: stringr, drc, ggplot2, reshape2
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-22 19:13:48 UTC; Draguru
Repository: CRAN
Date/Publication: 2016-05-22 22:54:19

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New package LindleyR with initial version 1.0.0
Package: LindleyR
Type: Package
Title: The Lindley Distribution and Its Modifications
Version: 1.0.0
License: GPL (>= 2)
Date: 2016-05-22
Author: Josmar Mazucheli and Larissa B. Fernandes
Maintainer: Josmar Mazucheli <jmazucheli@gmail.com>
Description: Implements the probability density function, quantile function, cumulative distribution function, random number generation and the hazard rate function for the continuous one-parameter Lindley distribution as well as for 15 of its modifications. Also is it possible to draw censored random samples, with a desired censoring rate, when the event times are any continuous lifetime distribution supported by R.
Depends: R (>= 3.0.2), actuar, LambertW, VGAM, zipfR
Imports: stats
Suggests: fitdistrplus
RoxygenNote: 5.0.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-22 18:30:17 UTC; josmar
Repository: CRAN
Date/Publication: 2016-05-22 22:54:21

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New package GRANBase with initial version 1.1.14
Package: GRANBase
Type: Package
Title: Creating Continuously Integrated Package Repositories from Manifests
Version: 1.1.14
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Copyright: Genentech Inc
Description: Repository based tools for department and analysis level reproducibility. 'GRANBase' allows creation of custom branched, continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.
License: Artistic-2.0
Imports: tools, hwriter
Depends: switchr (>= 0.9.28), methods
Suggests: parallel, BiocStyle, RUnit
SystemRequirements: svn, git
URL: https://github.com/gmbecker/gRAN
BugReports: https://github.com/gmbecker/gRAN/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 17:15:05 UTC; beckerg4
Repository: CRAN
Date/Publication: 2016-05-22 20:34:42

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New package prof.tree with initial version 0.1.0
Package: prof.tree
Type: Package
Title: An Alternative Display Profiling Data as Tree Structure
Description: An alternative data structure for the profiling information generated by Rprof().
Version: 0.1.0
Author: Artem Kelvtsov [aut, cre]
Maintainer: Artem Kelvtsov <a.a.klevtsov@gmail.com>
URL: https://github.com/artemklevtsov/prof.tree
BugReports: https://github.com/artemklevtsov/prof.tree/issues
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports: data.tree
RoxygenNote: 5.0.1
Collate: 'env.R' 'parse.R' 'prof-tree.R'
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2016-05-22 14:56:53 UTC; xxx
Repository: CRAN
Date/Publication: 2016-05-22 17:23:47

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New package kinn with initial version 0.1
Package: kinn
Type: Package
Title: An Implementation of 'kinn' Algorithm, a Graph Based Regression Model
Version: 0.1
Date: 2016-05-22
Author: Yossi Keshet
Maintainer: Yossi Keshet <jossiekat@icloud.com>
Description: A graph based regression model from flat unstructured dataset. Each line in the input data set is treated as a node from which an edge to another line (node) can be formed. In the training process, a model is created which contains sparse graph adjacency matrix. This model is then used for prediction by taking a predictor and the model as inputs and outputs a prediction which is an average of the most similar node and its neighbours in the model graph.
Depends: R (>= 3.2.4)
Imports: stringr,igraph,KRLS,caTools,mclust,caret,stats,graphics
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 15:32:02 UTC; josephkeshet
Repository: CRAN
Date/Publication: 2016-05-22 17:40:26

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New package landscapeR with initial version 1.0.0
Package: landscapeR
Type: Package
Title: Categorical Landscape Simulation Facility
Version: 1.0.0
Date: 2016-05-22
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dmasan@ceh.ac.uk>
URL: https://github.com/dariomasante/landscapeR
Imports: raster, fastmatch
Description: This set of functions allows the simulation of categorical maps from scratch in a geographically referenced landscape or the manipulation of existing ones. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion), therefore expands more or less circularly picking cells at the edges randomly.
License: GPL (>= 3)
LazyLoad: yes
LazyData: TRUE
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-22 11:31:43 UTC; dmasan
Repository: CRAN
Date/Publication: 2016-05-22 16:02:06

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New package rosetteApi with initial version 1.0
Package: rosetteApi
Type: Package
Title: Rosette API
Version: 1.0
Date: 2016-04-26
Author: Sam Hausmann
Maintainer: Sam Hausmann <shausmann@basistech.com>
Description: Rosette is an API for multilingual text analysis and information extraction. More information can be found at https://developer.rosette.com.
License: Apache License
Depends: R (>= 3.1.0), httr, rjson
URL: https://developer.rosette.com
BugReports: https://developer.rosette.com/support-ticket
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 16:03:41 UTC; shausmann
Repository: CRAN
Date/Publication: 2016-05-22 09:21:04

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New package pETM with initial version 0.1.5
Package: pETM
Type: Package
Title: Penalized Exponential Tilt Model
Version: 0.1.5
Date: 2016-05-21
Author: Hokeun Sun
Depends: Matrix (>= 1.0-6), utils
Maintainer: Hokeun Sun <hsun@pusan.ac.kr>
Description: In analysis of high-dimensional DNA methylation data, a penalized exponential tilt model can identify differentially methylated loci between cases and controls, using network based regularization. It is able to detect any differences in means only, in variances only or in both means and variances.
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
Packaged: 2016-05-21 12:40:08 UTC; root
Date/Publication: 2016-05-22 09:21:01

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New package linear.tools with initial version 1.2.0
Package: linear.tools
Type: Package
Title: Manipulate Formulas and Evaluate Marginal Effects
Version: 1.2.0
Author: Fan Yang
Maintainer: Fan Yang <yfno1@msn.com>
Description: Provides tools to manipulate formulas, such as getting x, y or contrasts from the model/formula, and functions to evaluate and check the marginal effects of a linear model.
License: GPL-3
LazyData: True
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: ggplot2, plyr, pryr, stringr, stats, utils, magrittr, scales
NeedsCompilation: no
Packaged: 2016-05-22 02:43:08 UTC; yangguodaxia
Repository: CRAN
Date/Publication: 2016-05-22 09:20:57

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New package Branching with initial version 0.9.2
Package: Branching
Version: 0.9.2
Date: 2016-05-21
Title: Simulation and Estimation for Branching Processes
Author: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Maintainer: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Description: Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.
License: GPL (>= 2)
Encoding: latin1
NeedsCompilation: yes
Packaged: 2016-05-22 05:27:46 UTC; cjtorresj
Repository: CRAN
Date/Publication: 2016-05-22 09:20:46

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New package autoSEM with initial version 0.1.0
Package: autoSEM
Type: Package
Title: Performs Specification Search in Structural Equation Models
Version: 0.1.0
Author: Ross Jacobucci
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Description: Implements multiple heuristic search algorithms for automatically creating structural equation models.
License: GPL (>= 2)
LazyData: TRUE
Depends: lavaan, snowfall
Imports: GA
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-21 15:35:13 UTC; RJacobucci
Repository: CRAN
Date/Publication: 2016-05-22 09:20:51

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Sat, 21 May 2016

New package Ramble with initial version 0.1.0
Package: Ramble
Type: Package
Title: Combinatory Parser Implementation
Version: 0.1.0
Date: 2016-05-21
Author: Chapman Siu
Maintainer: Chapman Siu <chpmn.siu@gmail.com>
Description: Parser generator for R using combinatory parsers. It is inspired by combinatory parsers developed in Haskell.
License: MIT + file LICENSE
Imports: methods
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 5.0.1
URL: https://github.com/chappers/Ramble
NeedsCompilation: no
Packaged: 2016-05-21 03:07:12 UTC; chapm
Repository: CRAN
Date/Publication: 2016-05-21 12:04:35

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New package iqspr with initial version 1.0
Package: iqspr
Type: Package
Title: Generate Chemical Strings (SMILES) with the Inverse QSPR Model
Version: 1.0
Date: 2016-5-21
Author: Hisaki Ikebata
Maintainer: Hisaki Ikebata <ikebata.hisaki@ism.ac.jp>
Description: Generate chemical structures possibly satisfying desired properties using the inverse QSPR model. It has three reference classes. ENgram is a class for learning the grammar structure of existing chemical strings using an extended N-gram model. QSPRpred contains a simple Bayes regression model to predict properties from structures. SmcChem is a class of the generator of chemical strings from the Inverse-QSPR model. This class has ENgram and QSPRpred class objects inside. The generator is implemented by the Sequential Monte Carlo sampler.
License: Artistic-2.0
SystemRequirements: OpenBabel (>= 2.3.1) with headers. http://openbabel.org
Suggests: testthat
Depends: R (>= 2.10), rcdk
Imports: methods
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-21 09:36:32 UTC; hisaki
Repository: CRAN
Date/Publication: 2016-05-21 12:07:40

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Fri, 20 May 2016

New package icpsrdata with initial version 0.1.0
Package: icpsrdata
Type: Package
Title: Reproducible Retrieval from the ICPSR Data Archive
Version: 0.1.0
Date: 2016-05-16
Authors@R: c( person("Frederick", "Solt", email = "frederick-solt@uiowa.edu", role = c("aut", "cre")), person("Kellen", "Gracey", email = "kellen-gracey@uiowa.edu", role = c("aut")), person("Eric", "Persson", email = "expersso5@gmail.com", role = c("ctb")))
Description: Reproducible, programmatic retrieval of datasets from the Inter-university Consortium for Political and Social Research archive.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: RSelenium
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-20 21:20:58 UTC; fredsolt
Author: Frederick Solt [aut, cre], Kellen Gracey [aut], Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Repository: CRAN
Date/Publication: 2016-05-21 01:12:53

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New package statar with initial version 0.6.1
Package: statar
Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Version: 0.6.1
Authors@R: person("Matthieu","Gomez", email = "mattg@princeton.edu", role = c("aut", "cre"))
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize', 'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
License: GPL-2
URL: https://github.com/matthieugomez/statar
BugReports: https://github.com/matthieugomez/statar/issues
Depends: R (>= 3.2.0)
Imports: data.table, dplyr (>= 0.4.3), ggplot2 (>= 2.0.0), lazyeval, matrixStats, methods, stringr, tidyr
Suggests: knitr, lubridate, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-20 19:05:20 UTC; Matthieu
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Repository: CRAN
Date/Publication: 2016-05-21 00:05:31

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New package xmlparsedata with initial version 1.0.0
Package: xmlparsedata
Title: Parse Data of 'R' Code as an 'XML' Tree
Version: 1.0.0
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <gcsardi@mango-solutions.com>
Description: Convert the output of 'utils::getParseData()' to an 'XML' tree, that is searchable and easier to manipulate in general.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/MangoTheCat/xmlparsedata#readme
BugReports: https://github.com/MangoTheCat/xmlparsedata/issues
RoxygenNote: 5.0.1.9000
Suggests: covr, testthat, xml2
Depends: R (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-20 14:24:27 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2016-05-20 22:37:10

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New package MonoInc with initial version 1.1
Package: MonoInc
Type: Package
Title: Monotonic Increasing
Version: 1.1
Date: 2016-05-19
Author: Melyssa Minto, Michele Josey, and ClarLynda Williams-DeVane
Maintainer: Michele Josey <mjosey@nccu.edu>
Description: Various imputation methods are utilized in this package, where one can flag and impute non-monotonic data that is outside of a prespecified range.
License: GPL-3
Encoding: UTF-8
Depends: compare, doParallel, foreach, iterators, parallel
Imports: sitar
NeedsCompilation: no
Packaged: 2016-05-20 16:57:57 UTC; michelejosey
Repository: CRAN
Date/Publication: 2016-05-20 22:36:53

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New package decoder with initial version 1.1.0
Package: decoder
Type: Package
Title: Decode Coded Variables to Plain Text (and Vice Versa)
Version: 1.1.0
Date: 2016-05-20
Authors@R: person("Erik", "Bulow", email = "erik.bulow@rccvast.se", role = c("aut", "cre"))
Description: Main function "decode" is used to decode coded key values to plain text. Function "code"" can be used to code plain text to code if there is a 1:1 relation between the two. The concept relies on "keyvalue" objects used for translation. There are several "keyvalue"" objects included in the areas of geographical regional codes, administrative health care unit codes, diagnosis codes et cetera but it is also easy to extend the use by arbitrary code sets.
License: GPL-2
Depends: R (>= 2.10)
Suggests: testthat, knitr
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://www.bitbucket.com/cancercentrum/decoder
BugReports: https://www.bitbucket.com/cancercentrum/decoder/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-20 12:09:34 UTC; erikbulow
Author: Erik Bulow [aut, cre]
Maintainer: Erik Bulow <erik.bulow@rccvast.se>
Repository: CRAN
Date/Publication: 2016-05-20 22:36:59

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New package crtests with initial version 0.2.1
Package: crtests
Type: Package
Title: Classification and Regression Tests
Version: 0.2.1
Date: 2016-05-13
Authors@R: person("Sjoerd", "van der Spoel", , "R@sjoerdvanderspoel.nl", role = c("aut", "cre"))
Description: Provides wrapper functions for running classification and regression tests using different machine learning techniques, such as Random Forests and decision trees. The package provides standardized methods for preparing data to suit the algorithm's needs, training a model, making predictions, and evaluating results. Also, some functions are provided to run multiple instances of a test.
License: GPL-3 | file LICENSE
Imports: caret (>= 6.0.41), plyr (>= 1.8.1), stringr (>= 0.6.2)
Suggests: testthat, knitr, e1071, randomForest, rpart, adabag, rmarkdown
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-20 12:29:50 UTC; sjoerd
Author: Sjoerd van der Spoel [aut, cre]
Maintainer: Sjoerd van der Spoel <R@sjoerdvanderspoel.nl>
Repository: CRAN
Date/Publication: 2016-05-20 22:36:56

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Thu, 19 May 2016

New package PathSelectMP with initial version 1.0
Package: PathSelectMP
Type: Package
Title: Backwards Variable Selection for Paths using M Plus
Version: 1.0
Date: 2016-05-19
Author: William Terry, Meredith Ray, Hongmei Zhang
Maintainer: William Terry <wterryj6a214@gmail.com>
Description: Primarily for use with datasets containing only categorical variables, although continuous variables may be included as independent variables in paths. Using M Plus, backward variable selection is performed on all Total, Total Indirect, and then Direct effects until none of these effects have p-values greater than the specified target p-value. If there are missing values in the data, imputations are performed using the Mice package. Then selection is performed with the imputed data sets, and results are averaged.
License: GPL (>= 2)
Depends: R (>= 3.1.2)
Imports: mice, MplusAutomation
Packaged: 2016-05-19 21:40:23 UTC; wterr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-05-20 01:16:03

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New package binst with initial version 0.1.0
Package: binst
Type: Package
Title: Data Preprocessing, Binning for Classification and Regression
Version: 0.1.0
Date: 2016-05-19
Author: Chapman Siu
Maintainer: Chapman Siu <chpmn.siu@gmail.com>
Description: Various supervised and unsupervised binning tools including using entropy, recursive partition methods and clustering.
LazyData: TRUE
Imports: stats
Suggests: discretization, partykit, Formula, testthat
RoxygenNote: 5.0.1
License: MIT + file LICENSE
URL: https://github.com/chappers/binst
NeedsCompilation: no
Packaged: 2016-05-19 21:46:04 UTC; chapm
Repository: CRAN
Date/Publication: 2016-05-20 01:16:01

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New package fourierin with initial version 0.1.1
Package: fourierin
Type: Package
Title: Computes Numeric Fourier Integrals
Version: 0.1.1
Date: 2016-05-18
Author: Guillermo Basulto-Elias
Maintainer: Guillermo Basulto-Elias <guillermobasulto@gmail.com>
Description: Computes Fourier integrals of functions of one and two variables using the Fast Fourier transform. The Fourier transforms must be evaluated on a regular grid.
License: MIT + file LICENSE
LazyData: TRUE
LinkingTo: RcppArmadillo, Rcpp
Imports: Rcpp
Suggests: MASS, knitr, rmarkdown, microbenchmark
RoxygenNote: 5.0.1
URL: http://github.com/gbasulto/fourierin
BugReports: https://github.com/gbasulto/fourierin/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-19 17:46:01 UTC; guillermo
Repository: CRAN
Date/Publication: 2016-05-19 20:02:07

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New package dlsem with initial version 1.0
Package: dlsem
Type: Package
Title: Distributed-Lag Structural Equation Modelling
Version: 1.0
Date: 2016-05-19
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Description: Fit distributed-lag structural equation models and perform path analysis at different time lags.
Depends: graph, gRbase, Rgraphviz, tseries
License: GPL-2
NeedsCompilation: no
Packaged: 2016-05-19 15:16:34 UTC; ASUS
Repository: CRAN
Date/Publication: 2016-05-19 17:55:16

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New package LSPFP with initial version 1.0.0
Package: LSPFP
Type: Package
Title: Lysate and Secretome Peptide Feature Plotter
Version: 1.0.0
Date: 2016-05-13
Author: Rafael Dellen, with contributions of Fabian Kruse
Maintainer: Rafael Dellen <Rafael.Dellen@uni-duesseldorf.de>
Description: Creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.
License: GPL-3
Depends: seqinr, RCurl, data.table, bit64
Imports: tcltk2, R.utils, graphics, grDevices, stats, utils
NeedsCompilation: no
Packaged: 2016-05-19 10:46:48 UTC; dellen
Repository: CRAN
Date/Publication: 2016-05-19 16:35:29

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New package SpatMCA with initial version 1.0.0.0
Package: SpatMCA
Type: Package
Title: Regularized Spatial Maximum Covariance Analysis
Version: 1.0.0.0
Date: 2016-05-19
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Description: Provide regularized maximum covariance analysis incorporating smoothness, sparseness and orthogonality of couple patterns by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
License: GPL-2
Imports: Rcpp, RcppParallel (>= 0.11.2), fields
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2016-05-19 06:27:31 UTC; egpivo
Repository: CRAN
Date/Publication: 2016-05-19 12:02:38

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New package profvis with initial version 0.3.2
Package: profvis
Title: Interactive Visualizations for Profiling R Code
Version: 0.3.2
Authors@R: c( person("Winston", "Chang", email = "winston@rstudio.com", role = c("aut", "cre")), person("Javier", "Luraschi", email = "javier@rstudio.com", role = "aut"), person(family = "RStudio", role = "cph"), person(family = "jQuery Foundation", role = "cph", comment = "jQuery library"), person(family = "jQuery contributors", role = c("ctb", "cph"), comment = "jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt"), person("Mike", "Bostock", role = c("ctb", "cph"), comment = "D3 library"), person(family = "D3 contributors", role = "ctb", comment = "D3 library"), person("Ivan", "Sagalaev", role = c("ctb", "cph"), comment = "highlight.js library") )
Description: Interactive visualizations for profiling R code.
Depends: R (>= 3.0)
Imports: htmlwidgets (>= 0.3.2), stringr
License: GPL-3 | file LICENSE
Suggests: knitr, ggplot2, rmarkdown, testthat
RoxygenNote: 5.0.1
URL: https://rstudio.github.io/profvis/
NeedsCompilation: no
Packaged: 2016-05-18 20:41:58 UTC; winston
Author: Winston Chang [aut, cre], Javier Luraschi [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mike Bostock [ctb, cph] (D3 library), D3 contributors [ctb] (D3 library), Ivan Sagalaev [ctb, cph] (highlight.js library)
Maintainer: Winston Chang <winston@rstudio.com>
Repository: CRAN
Date/Publication: 2016-05-19 05:46:47

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New package MetProc with initial version 1.0.1
Package: MetProc
Type: Package
Title: Separate Metabolites into Likely Measurement Artifacts and True Metabolites
Version: 1.0.1
Date: 2016-05-18
Author: Mark Chaffin
Maintainer: Mark Chaffin <mac8278@mail.harvard.edu>
Description: Split an untargeted metabolomics data set into a set of likely true metabolites and a set of likely measurement artifacts. This process involves comparing missing rates of pooled plasma samples and biological samples. The functions assume a fixed injection order of samples where biological samples are randomized and processed between intermittent pooled plasma samples. By comparing patterns of missing data across injection order, metabolites that appear in blocks and are likely artifacts can be separated from metabolites that seem to have random dispersion of missing data. The two main metrics used are: 1. the number of consecutive blocks of samples with present data and 2. the correlation of missing rates between biological samples and flanking pooled plasma samples.
Depends: R (>= 3.1.0)
Imports: gplots, fastcluster
License: GPL (>= 2)
LazyLoad: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-18 17:39:01 UTC; Mark
Repository: CRAN
Date/Publication: 2016-05-19 05:46:39

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Wed, 18 May 2016

New package inctools with initial version 1.0.3
Encoding: UTF-8
Package: inctools
Type: Package
Title: Incidence Estimation Tools
Version: 1.0.3
Date: 2016-05-18
Authors@R: c( person("Alex","Welte", email="alexwelte@sun.ac.za", role="aut"), person("Eduard","Grebe",email="eduardgrebe@sun.ac.za",role=c("cre","aut")), person("Avery","McIntosh",email="avery.i.mcintosh@gmail.com",role="aut"), person("Petra","Bäumler",email="petra.baeumler@med.uni-muenich.de",role="aut"), person("Reshma","Kassanjee", role="ctb"), person("Hilmarie","Brand", role="ctb"), person("Yuruo","Li",email="yul123@pitt.edu", role="ctb"), person("Simon","Daniel",email="skjdaniel@gmail.com", role="ctb"), person("Stefano","Ongarello", email="stefano.ongarello@finddx.org", role="ctb"), person("Yusuke","Asai", email="yusuke.asai@yahoo.de", role="ctb") )
Description: Tools for estimating incidence from biomarker data in cross- sectional surveys and for calibrating tests for recent infection.
Depends: R (>= 3.2.1)
License: GPL-3
LazyData: True
Imports: stats, utils, cubature, ggplot2, glm2, MASS, plyr, pracma, foreach
Suggests: doMC, knitr, survey
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-18 11:05:01 UTC; eduardgrebe
Author: Alex Welte [aut], Eduard Grebe [cre, aut], Avery McIntosh [aut], Petra Bäumler [aut], Reshma Kassanjee [ctb], Hilmarie Brand [ctb], Yuruo Li [ctb], Simon Daniel [ctb], Stefano Ongarello [ctb], Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>
Repository: CRAN
Date/Publication: 2016-05-18 18:22:44

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New package icesAdvice with initial version 1.1-0
Package: icesAdvice
Version: 1.1-0
Date: 2016-05-18
Title: Functions Related to ICES Advice
Authors@R: c(person("Arni", "Magnusson", role=c("aut","cre"), email="arni.magnusson@ices.dk"), person("Colin", "Millar", role="ctb"))
Author: Arni Magnusson [aut, cre], Colin Millar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Imports: stats
Description: Functions that are related to the advisory work of ICES (International Council for the Exploration of the Sea).
License: GPL (>= 2)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-18 16:39:17 UTC; arnima
Repository: CRAN
Date/Publication: 2016-05-18 19:02:50

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New package gensphere with initial version 1.0
Package: gensphere
Type: Package
Title: Generalized Spherical Distributions
Version: 1.0
Date: 2016-05-18
Author: John P Nolan
Maintainer: John P Nolan <jpnolan@american.edu>
Depends: R (>= 3.0), mvmesh, geometry, SphericalCubature, rgl, utils, grDevices, graphics
Description: Define and compute with generalized spherical distributions - multivariate probability laws that are specified by a star shaped contour (directional behavior) and a radial component.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2016-05-18 14:03:50 UTC; John
Repository: CRAN
Date/Publication: 2016-05-18 17:28:22

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New package DrBats with initial version 0.1.3
Package: DrBats
Type: Package
Title: Data Representation: Bayesian Approach That's Sparse
Version: 0.1.3
Date: 2016-05-18
Authors@R: c(person("Gabrielle", "Weinrott", email = "gabrielle.weinrott@supagro.inra.fr", role = c("aut", "cre")), person("Brigitte", "Charnomordic", email = "bch@supagro.inra.fr", role = "aut"), person("Benedicte", "Fontez", email = "benedicte.fontez@supagro.fr", role = "aut"), person("Nadine", "Hilgert", email = "nadine.hilgert@supagro.inra.fr", role = "aut"), person("Susan", "Holmes", email = "susan@stat.stanford.edu", role = "aut"))
Maintainer: Gabrielle Weinrott <gabrielle.weinrott@supagro.inra.fr>
Description: Feed longitudinal data into a Bayesian Latent Factor Model to obtain a low-rank representation. Parameters are estimated using a Hamiltonian Monte Carlo algorithm with STAN. See G. Weinrott, B. Fontez, N. Hilgert and S. Holmes, "Bayesian Latent Factor Model for Functional Data Analysis", Actes des JdS 2016.
Depends: R (>= 3.1.0)
Imports: ade4, coda, MASS, Matrix, rstan, sde
License: GPL-3
LazyData: TRUE
Suggests: fda, ggplot2, knitr, parallel, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-18 14:36:29 UTC; weinrott
Author: Gabrielle Weinrott [aut, cre], Brigitte Charnomordic [aut], Benedicte Fontez [aut], Nadine Hilgert [aut], Susan Holmes [aut]
Repository: CRAN
Date/Publication: 2016-05-18 17:26:34

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New package mscsweblm4r with initial version 0.1.0
Package: mscsweblm4r
Type: Package
Title: R Client for the Microsoft Cognitive Services Web Language Model REST API
Version: 0.1.0
Author: person("Phil", "Ferriere", email="pferriere@hotmail.com", role = c("aut", "cre"))
Maintainer: Phil Ferriere <pferriere@hotmail.com>
Description: R Client for the Microsoft Cognitive Services Web Language Model REST API, including Break Into Words, Calculate Conditional Probability, Calculate Joint Probability, Generate Next Words, and List Available Models. A valid account MUST be registered at the Microsoft Cognitive Services website (https://www.microsoft.com/cognitive-services/) in order to obtain a (free) API key. Without an API key, this package will not work properly.
License: MIT + file LICENSE
URL: https://github.com/philferriere/mscsweblm4r
BugReports: http://www.github.com/philferriere/mscsweblm4r/issues
VignetteBuilder: knitr
Imports: methods, httr, jsonlite, pander
Suggests: knitr, rmarkdown, testthat
SystemRequirements: A valid account MUST be registered with Microsoft's Cognitive Services website (https://www.microsoft.com/cognitive-services/) in order to obtain a (free) API key. Without an API key, this package will not work properly.
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-18 05:43:44 UTC; Phil
Repository: CRAN
Date/Publication: 2016-05-18 11:50:34

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New package wCorr with initial version 1.8.0
Package: wCorr
Type: Package
Title: Weighted Correlations
Version: 1.8.0
Date: 2016-05-03
Author: Ahmad Emad & Paul Bailey
Maintainer: Paul Bailey <pbailey@air.org>
Description: Calculates Pearson, Spearman, polychoric, and polyserial correlation coefficients, in weighted or unweighted form. The package implements tetrachoric correlation as a special case of the polychoric and biserial correlation as a specific case of the polyserial.
License: GPL-2
BugReports: https://github.com/ahmademad/wCorr/issues
Imports: minqa, mnormt, Rcpp, stats, doBy
Depends: R (>= 3.0.0)
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, lattice, captioner
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2016-05-18 03:48:55 UTC; pbailey
Repository: CRAN
Date/Publication: 2016-05-18 06:53:53

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New package multiplyr with initial version 0.1.0
Package: multiplyr
Type: Package
Title: Data Manipulation with Parallelism and Shared Memory Matrices
Description: Provides a new form of data frame backed by shared memory matrices and a way to manipulate them. Upon creation these data frames are shared across multiple local nodes to allow for simple parallel processing.
Version: 0.1.0
Date: 2016-05-15
Maintainer: Jim Blundell <james.blundell@keble.ox.ac.uk>
Authors@R: c(person(given="Jim", family="Blundell", role = c("aut", "cre", "cph"), email = "james.blundell@keble.ox.ac.uk"))
License: GPL-3
Imports: bigmemory (>= 4.5.19), bigmemory.sri (>= 0.1.3), lazyeval (>= 0.1.10), parallel, methods
Depends: magrittr (>= 1.5)
LazyData: TRUE
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-17 15:46:46 UTC; jim
Author: Jim Blundell [aut, cre, cph]
Repository: CRAN
Date/Publication: 2016-05-18 06:52:59

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Tue, 17 May 2016

New package tmod with initial version 0.26
Package: tmod
Type: Package
Title: Transcriptional Module Analysis
Version: 0.26
Date: 2016-05-13
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Description: Gene set enrichment analysis tools and definitions of human blood transcriptional modules.
License: GPL (>= 2.0)
LazyData: false
VignetteBuilder: knitr
URL: http://bioinfo.mpiib-berlin.mpg.de/tmod
Imports: beeswarm,pca3d,tagcloud,XML,methods
Suggests: limma,org.Hs.eg.db, testthat,knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-14 21:17:37.216 UTC; january
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2016-05-18 01:41:10

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New package saasCNV with initial version 0.3.4
Package: saasCNV
Version: 0.3.4
Date: 2016-05-10
Title: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data
Author: Zhongyang Zhang [aut, cre], Ke Hao [aut], Nancy R. Zhang [ctb]
Maintainer: Zhongyang Zhang <zhongyang.zhang@mssm.edu>
Depends: R (>= 2.10), RANN, DNAcopy
Description: Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.
License: GPL (>= 2)
URL: https://zhangz05.u.hpc.mssm.edu/saasCNV/
NeedsCompilation: no
Packaged: 2016-05-17 14:58:22 UTC; zhangz05
Repository: CRAN
Date/Publication: 2016-05-18 02:04:56

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New package pvar with initial version 2.2.2
Package: pvar
Version: 2.2.2
Title: Calculation and Application of p-Variation
Date: 2016-05-17
Author: Vygantas Butkus
Maintainer: Vygantas Butkus <Vygantas.Butkus@gmail.com>
Description: The calculation of p-variation of the finite sample data.
LazyData: yes
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp
Suggests: e1071, testthat, knitr, formatR,
VignetteBuilder: knitr
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-17 18:48:31 UTC; vygantas
Repository: CRAN
Date/Publication: 2016-05-18 01:29:16

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New package genemodel with initial version 1.0.0.0
Package: genemodel
Title: Gene Model Plotting in R
Date: 2016-05-17
Version: 1.0.0.0
Authors@R: person("J Grey", "Monroe", email = "greymonroe@gmail.com", role = c("aut", "cre"))
Description: Using simple input, this package creates publication worthy plots of gene models. Users can create plots of alternatively spliced gene variants and the positions of mutations and other gene features.
Depends: R (>= 3.2.5)
Imports: stringr
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
URL: https://bitbucket.org/greymonroe/genemodel
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-17 20:38:23 UTC; greymonroe
Author: J Grey Monroe [aut, cre]
Maintainer: J Grey Monroe <greymonroe@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-18 01:20:11

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New package flexdashboard with initial version 0.2.0
Package: flexdashboard
Type: Package
Title: R Markdown Format for Flexible Dashboards
Version: 0.2.0
Description: Format for converting an R Markdown document to a grid oriented dashboard. The dashboard flexibly adapts the size of it's components to the containing web page.
Authors@R: c( person("JJ", "Allaire", role = c("aut", "cre"), email = "jj@rstudio.com"), person(family = "RStudio", role = "cph"), person(family = "Keen IO", role = c("ctb", "cph"), comment = "Dashboard CSS"), person("Abdullah", "Almsaeed", role = c("ctb", "cph"), comment = "Dashboard CSS"), person("Jonas", "Mosbech", role = c("ctb", "cph"), comment = "StickyTableHeaders"), person("Noel", "Bossart", role = c("ctb", "cph"), comment = "Featherlight"), person("Lea", "Verou", role = c("ctb", "cph"), comment = "Prism"), person("Dmitry", "Baranovskiy", role = c("ctb", "cph"), comment = "Raphael.js"), person(family = "Sencha Labs", role = c("ctb", "cph"), comment = "Raphael.js"), person("Bojan", "Djuricic", role = c("ctb", "cph"), comment = "JustGage"), person("Tomas", "Sardyha", role = c("ctb", "cph"), comment = "Sly"), person("Bryan", "Lewis", role = c("ctb", "cph"), comment = "Examples"), person("Carson", "Sievert", role = c("ctb", "cph"), comment = "Examples"), person("Joshua", "Kunst", role = c("ctb", "cph"), comment = "Examples"), person("Ryan", "Hafen", role = c("ctb", "cph"), comment = "Examples"), person("Bob", "Rudis", role = c("ctb", "cph"), comment = "Examples"), person("Joe", "Cheng", role = c("ctb"), comment = "Examples") )
URL: http://rmarkdown.rstudio.com/flexdashboard
BugReports: https://github.com/rstudio/flexdashboard/issues
Depends: R (>= 3.0.2)
Imports: tools, jsonlite, htmltools, knitr (>= 1.13), htmlwidgets (>= 0.6), rmarkdown (>= 0.9.6), shiny (>= 0.13)
Suggests: testthat
LazyData: TRUE
License: MIT + file LICENSE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-17 13:21:20 UTC; jjallaire
Author: JJ Allaire [aut, cre], RStudio [cph], Keen IO [ctb, cph] (Dashboard CSS), Abdullah Almsaeed [ctb, cph] (Dashboard CSS), Jonas Mosbech [ctb, cph] (StickyTableHeaders), Noel Bossart [ctb, cph] (Featherlight), Lea Verou [ctb, cph] (Prism), Dmitry Baranovskiy [ctb, cph] (Raphael.js), Sencha Labs [ctb, cph] (Raphael.js), Bojan Djuricic [ctb, cph] (JustGage), Tomas Sardyha [ctb, cph] (Sly), Bryan Lewis [ctb, cph] (Examples), Carson Sievert [ctb, cph] (Examples), Joshua Kunst [ctb, cph] (Examples), Ryan Hafen [ctb, cph] (Examples), Bob Rudis [ctb, cph] (Examples), Joe Cheng [ctb] (Examples)
Maintainer: JJ Allaire <jj@rstudio.com>
Repository: CRAN
Date/Publication: 2016-05-18 01:57:45

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New package feather with initial version 0.0.1
Package: feather
Title: R Bindings to the Feather 'API'
Version: 0.0.1
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph"), person("Feather developers", role = "ctb", comment = "Bundled feather library"), person("Google", role = "ctb", comment = "Bundled flatbuffers code"), person("LevelDB Authors", role = "ctb") )
Description: Read and write feather files, a lightweight binary columnar data store designed for maximum speed.
Encoding: UTF-8
License: Apache License 2.0
LazyData: true
URL: https://github.com/wesm/feather
BugReports: https://github.com/wesm/feather/issues
LinkingTo: Rcpp
Imports: Rcpp, tibble
Suggests: testthat, dplyr
SystemRequirements: C++11
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-17 02:38:49 UTC; hadley
Author: Hadley Wickham [aut, cre], RStudio [cph], Feather developers [ctb] (Bundled feather library), Google [ctb] (Bundled flatbuffers code), LevelDB Authors [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Repository: CRAN
Date/Publication: 2016-05-18 01:38:48

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New package BigVAR with initial version 1.0
Package: BigVAR
Type: Package
Title: Dimension Reduction Methods for Multivariate Time Series
Version: 1.0
Authors@R: c( person("Will", "Nicholson", email = "wbn8@cornell.edu", role = c("cre","aut")), person("David", "Matteson", email = "matteson@cornell.edu", role = "aut"), person("Jacob", "Bien", email = "bien@cornell.edu", role = "aut"))
Date: 2016-05-13
Description: Estimates VAR and VARX models with structured Lasso Penalties.
Depends: R (>= 3.1.0), methods
Imports: MASS, zoo, lattice, Rcpp, stats, utils, grDevices, graphics
License: GPL (>= 2)
LazyLoad: yes
SystemRequirements: C++11
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
Packaged: 2016-05-17 23:07:44 UTC; will
URL: http://www.github.com/wbnicholson/BigVAR
RoxygenNote: 5.0.1
NeedsCompilation: yes
Author: Will Nicholson [cre, aut], David Matteson [aut], Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>
Repository: CRAN
Date/Publication: 2016-05-18 01:34:21

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Mon, 16 May 2016

New package datarobot with initial version 2.2.32
Package: datarobot
Title: DataRobot Predictive Modeling API
Version: 2.2.32
Description: For working with the DataRobot predictive modeling platform's API.
Depends: R (>= 3.1.1), methods (>= 3.2.3)
Imports: httr (>= 1.0), jsonlite (>= 0.9.19), yaml (>= 2.1.13),
License: MIT + file LICENSE
LazyData: true
Author: Ron Pearson [aut], Zachary Meyer [aut], David Chudzicki [aut], Dallin Akagi [aut]
Maintainer: David Chudzicki <api-maintainer@datarobot.com>
Suggests: knitr, MASS, testthat, beanplot, mlbench, car, rmarkdown, insuranceData, doBy, lintr, stubthat
VignetteBuilder: rmarkdown, knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 20:31:18 UTC; david
Repository: CRAN
Date/Publication: 2016-05-17 01:06:50

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New package saeRobust with initial version 0.1.0
Package: saeRobust
Title: Robust Small Area Estimation
Version: 0.1.0
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <Sebastian.Warnholz@fu-berlin.de>
Description: Methods to fit robust alternatives to commonly used models used in Small Area Estimation. The methods here used are based on best linear unbiased predictions and linear mixed models. At this time available models include area level models incorporating spatial and temporal correlation in the random effects.
BugReports: https://github.com/wahani/saeRobust/issues
Depends: R (>= 3.3), methods, aoos
Imports: assertthat, ggplot2, Matrix, magrittr, MASS, modules, memoise, Rcpp, spdep
License: MIT + file LICENSE
LazyData: true
Suggests: knitr, rmarkdown, sae, saeSim, testthat
VignetteBuilder: knitr
Encoding: UTF-8
ByteCompile: true
RoxygenNote: 5.0.1
LinkingTo: Rcpp, RcppArmadillo
Collate: 'NAMESPACE.R' 'RcppExports.R' 'bootstrap.R' 'correlation.R' 'fit.R' 'fixedPoint.R' 'helper.R' 'makeXY.R' 'mat.R' 'matModels.R' 'mse.R' 'plot.R' 'print.R' 'psiFunctions.R' 'rfh.R' 'robustEstimationEquations.R' 'robustObjectiveFunctions.R' 'testData.R' 'update.R' 'variance.R'
NeedsCompilation: yes
Packaged: 2016-05-16 15:57:48 UTC; sebastian
Repository: CRAN
Date/Publication: 2016-05-16 19:47:53

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New package imageData with initial version 0.1-21
Package: imageData
Version: 0.1-21
Date: 2016-05-16
Title: Aids in Processing and Plotting Data from a Lemna-Tec Scananalyzer
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Depends: R (>= 2.10.0)
Imports: dae, ggplot2, stats, XLConnect, Hmisc, GGally, RColorBrewer, reshape, grid
Description: Extracts traits from imaging data produced using a Lemna-Tec Scananalyzer. Growth rates are between successive imagings are obtained and those for a nominated set of intervals can also be calculated. Profile or longitudinal plots of the traits and growth rates can be produced.
License: GPL (>= 2)
URL: http://chris.brien.name
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 13:20:38 UTC; briencj
Repository: CRAN
Date/Publication: 2016-05-16 15:43:47

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New package LncPath with initial version 1.0
Package: LncPath
Type: Package
Title: Identifying the Pathways Regulated by LncRNA Sets of Interest
Version: 1.0
Date: 2016-04-27
Author: Junwei Han, Zeguo Sun
Maintainer: Junwei Han <hanjunwei1981@163.com>
Description: Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.
Imports: stats, graphics, utils, grDevices
Depends: R (>= 3.2.2), igraph, samr
Suggests: Matrix,graph
License: GPL (>= 2)
LazyData: Yes
NeedsCompilation: no
Packaged: 2016-05-16 02:22:47 UTC; sunyao
Repository: CRAN
Date/Publication: 2016-05-16 14:45:44

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New package clusterhap with initial version 0.1
Package: clusterhap
Type: Package
Title: Clustering Genotypes in Haplotypes
Version: 0.1
Date: 2016-05-13
Author: Gaston Quero <gastonquero@gmail.com> and Sebastian Simondi <sebastian.simondi@gmail.com> , with contributions from Victoria Bonnecarrere and Lucia Gutierrez
Maintainer: Gaston Quero <gastonquero@gmail.com>
Description: One haplotype is a combination of SNP (Single Nucleotide Polymorphisms) within the QTL (Quantitative Trait Loci). clusterhap groups together all individuals of a population with the same haplotype. Each group contains individual with the same allele in each SNP, whether or not missing data. Thus, clusterhap groups individuals, that to be imputed, have a non-zero probability of having the same alleles in the entire sequence of SNP's. Moreover, clusterhap calculates such probability from relative frequencies.
Depends: R (>= 2.10)
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: graphics, utils
NeedsCompilation: no
Packaged: 2016-05-15 21:35:40 UTC; GQ
Repository: CRAN
Date/Publication: 2016-05-16 14:37:36

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New package ARCensReg with initial version 1.0
Package: ARCensReg
Type: Package
Title: Fitting Univariate Censored Linear Regression Model with Autoregressive Errors
Version: 1.0
Date: 2016-05-14
Author: Fernanda L. Schumacher, Victor H. Lachos and Christian E. Galarza
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Imports: mvtnorm, tmvtnorm, msm, numDeriv, utils, graphics, stats
Suggests: SMNCensReg
Description: It fits an univariate left or right censored linear regression model with autoregressive errors under the normal distribution. It provides estimates and standard errors of the parameters, prediction of future observations and it supports missing values on the dependent variable. It also provides convergence plots when exists at least one censored observation.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-05-16 01:56:01 UTC; ra143711
Repository: CRAN
Date/Publication: 2016-05-16 14:37:35

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Sun, 15 May 2016

New package rmsfact with initial version 0.0.1
Package: rmsfact
Type: Package
Title: Amazing Random Facts About the World's Greatest Hacker
Version: 0.0.1
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Description: Display a randomly selected quote about Richard M. Stallman based on the collection in the 'GNU Octave' function 'fact()' which was aggregated by Jordi Gutiérrez Hermoso based on the (now defunct) site <http://www.stallmanfacts.com>.
License: GPL-3
LazyData: TRUE
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-15 14:56:34.749015 UTC; edd
Repository: CRAN
Date/Publication: 2016-05-15 21:46:35

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New package LEAP with initial version 0.1
Package: LEAP
Type: Package
Title: Constructing Gene Co-Expression Networks for Single-Cell RNA-Sequencing Data Using Pseudotime Ordering
Version: 0.1
Date: 2016-05-12
Author: Alicia T. Specht and Jun Li
Maintainer: Alicia T. Specht <aspecht2@nd.edu>
Suggests: ggplot2
Description: Advances in sequencing technology now allow researchers to capture the expression profiles of individual cells. Several algorithms have been developed to attempt to account for these effects by determining a cell's so-called `pseudotime', or relative biological state of transition. By applying these algorithms to single-cell sequencing data, we can sort cells into their pseudotemporal ordering based on gene expression. LEAP (Lag-based Expression Association for Pseudotime-series) then applies a time-series inspired lag-based correlation analysis to reveal linearly dependent genetic associations.
License: GPL-2
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-15 13:08:46 UTC; aspecht2
Repository: CRAN
Date/Publication: 2016-05-15 22:01:52

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New package cystiSim with initial version 0.1.0
Package: cystiSim
Title: Agent-Based Model for Taenia_solium Transmission and Control
Version: 0.1.0
Date: 2016-05-15
Authors@R: c(person("Brecht", "Devleesschauwer", role = c("aut", "cre"), email = "brechtdv@gmail.com"), person("Uffe Christian", "Braae", role = "aut"))
Author: Brecht Devleesschauwer [aut, cre], Uffe Christian Braae [aut]
Maintainer: Brecht Devleesschauwer <brechtdv@gmail.com>
Description: The cystiSim package provides an agent-based model for Taenia solium transmission and control. cystiSim was developed within the framework of CYSTINET, the European Network on taeniosis/cysticercosis, COST ACTION TD1302.
URL: https://github.com/brechtdv/cystiSim
BugReports: https://github.com/brechtdv/cystiSim/issues
Depends: R (>= 3.3.0), ggplot2
Imports: magrittr, knitr, graphics, grDevices, stats, utils
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2016-05-15 13:00:04 UTC; UGent
Repository: CRAN
Date/Publication: 2016-05-15 21:46:33

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New package colorSpec with initial version 0.5-2
Package: colorSpec
Type: Package
Title: Color Calculations with Emphasis on Spectral Data
Version: 0.5-2
Encoding: UTF-8
Date: 2016-05-15
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners. Build complex systems from simpler parts using a spectral product algebra. For light sources, compute CCT and CRI. For object colors, compute optimal colors and Logvinenko coordinates. Work with the standard CIE illuminants and color matching functions, and read spectra from text files, including CGATS files. Sample text files, and 4 vignettes are included.
License: GPL (>= 3)
LazyLoad: yes
LazyData: yes
Depends: R (>= 2.15)
Imports: MASS
Suggests: rgl, knitr
NeedsCompilation: no
Repository: CRAN
VignetteBuilder: knitr
BuildVignettes: yes
Packaged: 2016-05-15 14:18:36 UTC; Glenn
Date/Publication: 2016-05-15 21:50:29

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Sat, 14 May 2016

New package rr with initial version 1.3.1
Package: rr
Version: 1.3.1
Date: 2016-5-13
Title: Statistical Methods for the Randomized Response Technique
Author: Graeme Blair <graeme.blair@columbia.edu>, Yang-Yang Zhou <yz3@princeton.edu>, Kosuke Imai <kimai@princeton.edu>
Maintainer: Graeme Blair <graeme.blair@columbia.edu>
Depends: R (>= 3.0.0), utils
Imports: MASS, arm, coda
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at <http://graemeblair.com/papers/randresp.pdf>.
LazyLoad: yes
LazyData: yes
License: GPL (>= 3)
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-14 18:52:38 UTC; gblair
X-CRAN-Comment: Archived on 2016-05-02 as check problems were not corrected despite reminders.
Repository: CRAN
Date/Publication: 2016-05-14 23:31:33

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New package dnc with initial version 1.1
Package: dnc
Type: Package
Title: Dynamic Network Clustering
Version: 1.1
Date: 2016-05-06
Author: Daniel K. Sewell
Maintainer: Dan Sewell <daniel-sewell@uiowa.edu>
Description: Community detection for dynamic networks, i.e., networks measured repeatedly over a sequence of discrete time points, using a latent space approach.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.4), igraph, MCMCpack, vegan, skmeans, plot3D, plot3Drgl, BayesLogit, movMF, tcltk, stats, grDevices, graphics
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.2.3)
LazyData: true
NeedsCompilation: yes
Packaged: 2016-05-14 19:51:39 UTC; daniel-admin
Repository: CRAN
Date/Publication: 2016-05-14 23:36:56

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New package SSL with initial version 0.1
Package: SSL
Type: Package
Title: Semi-Supervised Learning
Version: 0.1
Date: 2016-05-01
Author: Junxiang Wang
Maintainer: Junxiang Wang <xianggebenben@163.com>
Description: Semi-supervised learning has attracted the attention of machine learning community because of its high accuracy with less annotating effort compared with supervised learning.The question that semi-supervised learning wants to address is: given a relatively small labeled dataset and a large unlabeled dataset, how to design classification algorithms learning from both ? This package is a collection of some classical semi-supervised learning algorithms in the last few decades.
License: GPL (>= 3)
LazyData: TRUE
RoxygenNote: 5.0.1
Depends: R (>= 3.2)
Imports: NetPreProc (>= 1.1), Rcpp (>= 0.12.2), caret (>= 6.0-52), proxy (>= 0.4-15), xgboost (>= 0.4), klaR (>= 0.6-12), e1071 (>= 1.6-7), stats (>= 3.2)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-05-14 13:26:18 UTC; Wangjunxiang
Repository: CRAN
Date/Publication: 2016-05-14 23:12:09

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New package mcPAFit with initial version 0.1.1
Package: mcPAFit
Type: Package
Title: Estimating Node Fitness from a Single Network Snapshot by Markov Chain Monte Carlo
Version: 0.1.1
Date: 2016-05-14
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Description: A Markov chain Monte Carlo method is provided to estimate fitness from a single network snapshot. Conventional methods require the complete information about the appearance order of nodes and edges in the network. This package performs inference on the timeline space, and so does not require such information.
License: GPL-3
Depends: R(>= 2.10.0)
Imports: Rcpp (>= 0.11.3) , grDevices, graphics, stats, RColorBrewer, PAFit
LinkingTo: Rcpp
LazyData: True
NeedsCompilation: yes
Suggests: R.rsp
Packaged: 2016-05-14 07:25:06 UTC; pham
Repository: CRAN
Date/Publication: 2016-05-14 22:42:22

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New package rollbar with initial version 0.1.0
Package: rollbar
Type: Package
Title: Error Tracking and Logging
Version: 0.1.0
Date: 2016-05-12
Authors@R: person("Andrew", "Kane", email = "andrew@chartkick.com", role = c("aut", "cre"))
Description: Reports errors and messages to Rollbar, the error tracking platform <https://rollbar.com>.
License: MIT + file LICENSE
LazyData: TRUE
Imports: httr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-14 02:40:29 UTC; andrew
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Repository: CRAN
Date/Publication: 2016-05-14 09:18:57

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Fri, 13 May 2016

New package dtables with initial version 0.0.1
Package: dtables
Title: Simplifying Descriptive Frequencies and Statistics
Version: 0.0.1
Authors@R: person(c("Ronald", "E."), "Robertson",, "rrobertson@aibrt.org", c("cre", "aut"))
Description: Towards automation of descriptive frequencies and statistics tables.
Depends: R (>= 3.2.2)
License: GPL-3
LazyData: true
URL: https://github.com/gitronald/dtables
BugReports: https://github.com/gitronald/dtables/issues
RoxygenNote: 5.0.1
Imports: psych
NeedsCompilation: no
Packaged: 2016-05-13 02:30:19 UTC; aibrt
Author: Ronald E. Robertson [cre, aut]
Maintainer: Ronald E. Robertson <rrobertson@aibrt.org>
Repository: CRAN
Date/Publication: 2016-05-14 00:06:21

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