Wed, 21 Feb 2018

New package rusk with initial version 0.1
Package: rusk
Title: Beautiful Graphical Representation of Multiplication Tables on a Modular Circle
Version: 0.1
Authors@R: person("Vincent", "Guyader", email = "vincent@thinkr.fr", role = c("aut", "cre"))
Description: By placing on a circle 10 points numbered from 1 to 10, and connecting them by a straight line to the point corresponding to its multiplication by 2. (1 must be connected to 1 * 2 = 2, point 2 must be set to 2 * 2 = 4, point 3 to 3 * 2 = 6 and so on). You will obtain an amazing geometric figure that complicates and beautifies itself by varying the number of points and the multiplication table you use.
License: GPL-3
URL: https://github.com/ThinkR-open/rusk
BugReports: https://github.com/ThinkR-open/rusk/issues
Depends: R (>= 3.4.0)
Imports: dplyr, ggforce, ggplot2, reshape2, shiny, tidyr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-21 10:15:13 UTC; vincent
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Repository: CRAN
Date/Publication: 2018-02-21 14:26:10 UTC

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New package sdm with initial version 1.0-46
Package: sdm
Type: Package
Title: Species Distribution Modelling
Version: 1.0-46
Date: 2018-02-20
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>
Depends: methods, sp (>= 1.2-0), R (>= 3.0.0)
Imports: raster
Suggests: R.rsp, shinyBS, shiny, dismo, rmarkdown
Description: An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
License: GPL (>= 3)
URL: http://biogeoinformatics.org
VignetteBuilder: R.rsp
Repository: CRAN
Repository/R-Forge/Project: sdm
Repository/R-Forge/Revision: 66
Repository/R-Forge/DateTimeStamp: 2018-02-20 22:19:19
Date/Publication: 2018-02-21 13:26:56 UTC
NeedsCompilation: no
Packaged: 2018-02-20 22:25:16 UTC; rforge

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Tue, 20 Feb 2018

New package reinsureR with initial version 0.1.0
Package: reinsureR
Type: Package
Title: Reinsurance Treaties Application
Version: 0.1.0
Author: Arnaud Buzzi
Maintainer: Arnaud Buzzi <arnaud.buzzi@sia-partners.com>
Description: Application of reinsurance treaties to claims portfolios. The package creates a class Claims whose objective is to store claims and premiums, on which different treaties can be applied. A statistical analysis can then be applied to measure the impact of reinsurance, producing a table or graphical output. This package can be used for estimating the impact of reinsurance on several portfolios or for pricing treaties through statistical analysis. Documentation for the implemented methods can be found in "Reinsurance: Actuarial and Statistical Aspects" by Hansjöerg Albrecher, Jan Beirlant, Jozef L. Teugels (2017, ISBN: 978-0-470-77268-3) and "REINSURANCE: A Basic Guide to Facultative and Treaty Reinsurance" by Munich Re (2010) <https://www.munichre.com/site/mram/get/documents_E96160999/mram/assetpool.mr_america/PDFs/3_Publications/reinsurance_basic_guide.pdf>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.2), data.table, dplyr, viridis, viridisLite, ggplot2, methods
RoxygenNote: 6.0.1
Collate: 'utils.R' 'SL-class.R' 'XL-class.R' 'QS-class.R' 'Claims-class.R'
NeedsCompilation: no
Packaged: 2018-02-20 16:10:35 UTC; abuzzi
Repository: CRAN
Date/Publication: 2018-02-20 19:07:33 UTC

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New package mixer with initial version 1.9
Package: mixer
Type: Package
Title: Random Graph Clustering
Version: 1.9
Date: 2019-02-20
Authors@R: c(person("Christophe", "Ambroise", role="aut"), person("Gilles", "Grasseau", role="aut"), person("Mark", "Hoebeke", role="aut"), person("Pierre", "Latouche", role=c("aut", "cre"), email="pierre.latouche@univ-paris1.fr"), person("Vincent", "Miele", role="aut"), person("Franck", "Picard", role="aut"), person("Alexander", "Smith", role="aut"), person("LAPACK authors", role = "aut", comment = "copyrights apply to src/*.f"), person("Laboratoire Statistique & Génome", role = "cph"), person("Carter T. Butts", role = "cph"))
Maintainer: Pierre Latouche <pierre.latouche@univ-paris1.fr>
URL: http://ssbgroup.fr/mixnet/mixer.html, http://ssbgroup.fr
License: GPL (>= 2)
Copyright: file inst/COPYRIGHTS for src/*.f obtained from LAPACK
Depends: R (>= 2.5.0), methods
Description: Estimates the parameters, the clusters, as well as the number of clusters of a (binary) stochastic block model (J.-J Daudin, F. Picard, S. Robin (2008) <doi:10.1007/s11222-007-9046-7>).
Encoding: UTF-8
Packaged: 2018-02-20 17:03:44 UTC; pierrelatouche
Repository: CRAN
Date/Publication: 2018-02-20 19:11:05 UTC
NeedsCompilation: yes
Author: Christophe Ambroise [aut], Gilles Grasseau [aut], Mark Hoebeke [aut], Pierre Latouche [aut, cre], Vincent Miele [aut], Franck Picard [aut], Alexander Smith [aut], LAPACK authors [aut] (copyrights apply to src/*.f), Laboratoire Statistique & Génome [cph], Carter T. Butts [cph]

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New package thinkr with initial version 0.11
Package: thinkr
Type: Package
Title: Tools for Cleaning Up Messy Files
Version: 0.11
Date: 2018-02-13
Authors@R: person("Vincent", "Guyader", email = "vincent@thinkr.fr", role = c("aut", "cre"))
Description: Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
License: GPL-3
LazyData: TRUE
Suggests: testthat
Imports: lazyeval, ggplot2, assertthat, ReporteRs, stringi, stringr, tidyr, magrittr, dplyr, lubridate, XLConnect, devtools
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-20 11:58:12 UTC; vincent
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Repository: CRAN
Date/Publication: 2018-02-20 18:52:58 UTC

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New package gvcR with initial version 0.1.0
Package: gvcR
Type: Package
Title: Genotypic Variance Components
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Sami", "Ullah"), email = "samiullahuos@@gmail.com", role = c("aut", "ctb")) )
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Functionalities to compute model based genetic components i.e. genotypic variance, phenotypic variance and heritability for given traits of different genotypes from replicated data using methodology explained by Burton, G. W. & Devane, E. H. (1953) (<doi:10.2134/agronj1953.00021962004500100005x>) and Allard, R.W. (2010, ISBN:8126524154).
Depends: R (>= 3.2.3)
Imports: dplyr, eda4treeR, lme4, magrittr, stats
License: GPL-3
URL: https://github.com/MYaseen208/gvcR
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-02-20 12:59:47 UTC; yaseen
Author: Muhammad Yaseen [aut, cre], Sami Ullah [aut, ctb]
Repository: CRAN
Date/Publication: 2018-02-20 18:56:27 UTC

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New package LLM with initial version 1.0.0
Package: LLM
Title: Logit Leaf Model Classifier for Binary Classification
Version: 1.0.0
Date: 2018-02-14
Authors@R: c(person("Arno", "De Caigny",role = c("aut", "cre"), email = "a.de-caigny@ieseg.fr"), person("Kristof", "Coussement", role = c("aut"), email = "k.coussement@ieseg.fr"), person("Koen W.", "De Bock", role = c("aut"), email = "kdebock@audencia.com"))
Author: Arno De Caigny [aut, cre], Kristof Coussement [aut], Koen W. De Bock [aut]
Maintainer: Arno De Caigny <a.de-caigny@ieseg.fr>
Description: Fits the Logit Leaf Model, makes predictions and visualizes the output. (De Caigny et al., (2018) <DOI:10.1016/j.ejor.2018.02.009>).
Depends: R (>= 3.4.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: mlbench
Imports: partykit, stats, stringr, RWeka
NeedsCompilation: no
Packaged: 2018-02-20 10:18:47 UTC; a.de-caigny
Repository: CRAN
Date/Publication: 2018-02-20 11:25:25 UTC

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New package fingerPro with initial version 1.0
Package: fingerPro
Type: Package
Title: Sediment Source Fingerprinting
Version: 1.0
Date: 2018-01-31
Authors@R: c( person("Ivan", "Lizaga", email = "lizaga.ivan10@gmail.com", role = c("aut", "cre")), person("Borja", "Latorre", role = "aut"), person("Leticia", "Gaspar", role = "aut"), person("Ana", "Navas", role = "aut"), person("Vince Q", "Vu", role = "ctb"))
Description: Quantifies the provenance of the sediments in a catchment or study area. Based on a comprehensive characterization of the sediment sources and the end sediment mixtures a mixing model algorithm is applied to the sediment mixtures in order to estimate the relative contribution of each potential source. The package includes several statistical methods such as Kruskal-Wallis test, discriminant function analysis ('DFA'), principal component plot ('PCA') to select the optimal subset of tracer properties. The variability within each sediment source is also considered to estimate the statistical distribution of the sources contribution.
License: GPL (>= 2)
URL: https://github.com/eead-csic-eesa
LazyData: true
Imports: Rcpp (>= 0.11.3), klaR (>= 0.6-12), ggplot2(>= 2.2.1), GGally(>= 1.3.2), MASS(>= 7.3.45), Rcmdr(>= 2.4-1), plyr (>= 1.8.4), reshape(>= 0.8.7), rgl(>= 0.99.9), grid(>= 3.1.1), gridExtra(>= 2.3), scales(>= 0.5.0), car(>= 2.1.6)
LinkingTo: Rcpp, RcppGSL
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-02-20 10:13:11 UTC; ilizaga
Author: Ivan Lizaga [aut, cre], Borja Latorre [aut], Leticia Gaspar [aut], Ana Navas [aut], Vince Q Vu [ctb]
Maintainer: Ivan Lizaga <lizaga.ivan10@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-20 11:30:30 UTC

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New package naivereg with initial version 1.0.1
Package: naivereg
Type: Package
Title: Nonparametric Additive Instrumental Variable Estimator: A Group Shrinkage Estimation Perspective
Version: 1.0.1
Author: Qingliang Fan, KongYu He, Wei Zhong
Maintainer: Qingliang Fan <michaelqfan@xmu.edu.cn>
Description: In empirical studies, instrumental variable (IV) regression is the signature method to solve the endogeneity problem. If we enforce the exogeneity condition of the IV, it is likely that we end up with a large set of IVs without knowing which ones are good. This package uses adaptive group lasso and B-spline methods to select the nonparametric components of the IV function, with the linear function being a special case. The package incorporates two stage least squares estimator (2SLS), generalized method of moment (GMM), generalized empirical likelihood (GEL) methods post instrument selection. It is nonparametric version of 'ivregress' in 'Stata' with IV selection and high dimensional features. The package is based on the paper "Nonparametric Additive Instrumental Variable Estimator: A Group Shrinkage Estimation Perspective" (2017) published online in Journal of Business & Economic Statistics <doi:10.1080/07350015.2016.1180991>.
Imports: grpreg,splines,gmm,stats
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-20 04:26:17 UTC; hky06
Repository: CRAN
Date/Publication: 2018-02-20 10:11:27 UTC

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New package meetupapi with initial version 0.1.0
Package: meetupapi
Type: Package
Title: Access 'Meetup' API
Version: 0.1.0
Author: Zac Davies <zaclavis@gmail.com>
Maintainer: Zac Davies <zaclavis@gmail.com>
Description: Allows management of 'Meetup' groups via the <https:www.meetup.com/meetup_api/>. Provided are a set of functions that enable fetching information of joined meetups, attendance, and members. This package requires the use of an API key.
License: GPL-3
URL: https://github.com/zacdav/meetupapi
BugReports: https://github.com/zacdav/meetupapi/issues
Imports: httr, purrr, dplyr, magrittr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 23:08:04 UTC; zdavies
Repository: CRAN
Date/Publication: 2018-02-20 10:04:28 UTC

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New package loggit with initial version 1.0.0
Package: loggit
Title: Effortless Exception Logging
Description: A very simple and easy-to-use set of suspiciously-familiar functions. 'loggit' provides a set of wrappings for base R's message(), warning(), and stop() functions that maintain identical functionality, but also log the handler message to a 'JSON' log file. While mostly automatic, powerful custom logging is available via these handlers' logging function, loggit(), which is also exported for use. No change in existing code is necessary to use this package.
Version: 1.0.0
Date: 2018-02-17
Authors@R: c(person("Ryan", "Price", email = "ryapric@gmail.com", role = c("cre", "aut")))
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
Imports: dplyr (>= 0.7.4), jsonlite (>= 1.5)
Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 23:21:54 UTC; Ryan
Author: Ryan Price [cre, aut]
Maintainer: Ryan Price <ryapric@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-20 10:08:33 UTC

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New package geogrid with initial version 0.1.0
Package: geogrid
Title: Turn Geospatial Polygons into Regular or Hexagonal Grids
Version: 0.1.0
Authors@R: c( person("Joseph", "Bailey", email = "jbailey@futurecities.catapult.org.uk", role = c("aut", "cre")), person("Ryan", "Hafen", email = "rhafen@gmail.com", role = "ctb"), person("Lars Simon Zehnder", role = "ctb", comment = "RcppArmadillo implmentation of Munkres' Assignment Algorithm" ))
Description: Turn irregular polygons (such as geographical regions) into regular or hexagonal grids. This package enables the generation of regular (square) and hexagonal grids through the package 'sp' and then assigns the content of the existing polygons to the new grid using the Hungarian algorithm, Kuhn (1955) (<doi:10.1007/978-3-540-68279-0_2>). This prevents the need for manual generation of hexagonal grids or regular grids that are supposed to reflect existing geography.
Imports: methods, sp, sf, rgeos, Rcpp
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, covr
RoxygenNote: 6.0.1
URL: https://github.com/jbaileyh/geogrid
BugReports: https://github.com/jbaileyh/geogrid/issues
NeedsCompilation: yes
Packaged: 2018-02-19 22:39:14 UTC; Joe
Author: Joseph Bailey [aut, cre], Ryan Hafen [ctb], Lars Simon Zehnder [ctb] (RcppArmadillo implmentation of Munkres' Assignment Algorithm)
Maintainer: Joseph Bailey <jbailey@futurecities.catapult.org.uk>
Repository: CRAN
Date/Publication: 2018-02-20 10:01:53 UTC

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New package trackr with initial version 0.7.4
Package: trackr
Type: Package
Title: Semantic Annotation and Discoverability System for R-Based Artifacts
Version: 0.7.4
Date: 2018-02-11
Authors@R: c( person("Gabriel", "Becker", role = c("aut", "cre"), email = "becker.gabriel@gene.com"), person("Sara", "Moore", role = c("aut"), email = "moore.sara@gene.com"))
Copyright: Genentech, Inc.
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Description: Automatically annotates R-based artifacts with relevant descriptive and provenance-related and provides a backend-agnostic storage and discoverability system for organizing, retrieving, and interrogating such artifacts.
License: Artistic-2.0
Depends: histry (>= 0.1.1)
Imports: fastdigest, ggplot2, lattice, gridGraphics, methods, CodeDepends, RJSONIO, rsolr, htmltools, miniUI, shiny, rmarkdown
Suggests: proto, png, httr, knitr, MASS, MEMSS, mlmRev, dplyr, gridExtra, RSelenium, rstudioapi
VignetteBuilder: knitr
Collate: 'Classes.R' 'DocCollectionRef-methods.R' 'Generics.R' 'PlotWrapper.R' 'ObjFeatureSet.R' 'Trackr-main-API.R' 'abbrev.R' 'accessor-methods.R' 'autotrack.R' 'backend-impls.R' 'coercerender.R' 'convenience_constructors.R' 'ggplotversions.R' 'knitr.R' 'makeRStudioExtras.R' 'parseCode.R' 'shiny.R' 'showMethods.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 19:22:42 UTC; beckerg4
Author: Gabriel Becker [aut, cre], Sara Moore [aut]
Repository: CRAN
Date/Publication: 2018-02-20 09:39:00 UTC

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New package tkRplotR with initial version 0.1.0
Package: tkRplotR
Type: Package
Title: Display Resizable Plots
Version: 0.1.0
Author: Filipe Campelo
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Description: Display a plot in a Tk canvas.
License: GPL (>= 2)
Depends: R (>= 3.3.0), tcltk, grDevices,
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 19:45:57 UTC; filipe
Repository: CRAN
Date/Publication: 2018-02-20 09:42:29 UTC

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New package RcppCWB with initial version 0.1.7
Package: RcppCWB
Type: Package
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Version: 0.1.7
Date: 2018-02-19
Author: Andreas Blaette [aut, cre], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stefan Evert [ctb], Arne Fitschen [ctb]
Authors@R: c( person("Andreas", "Blaette", role = c("aut", "cre"), email = "andreas.blaette@uni-due.de"), person("Oliver", "Christ", role = "ctb"), person("Bruno Maximilian", "Schulze", role = "ctb"), person("Stefan", "Evert", role = "ctb"), person("Arne", "Fitschen", role = "ctb") )
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre' (BSD license, see <https://www.pcre.org/licence.txt>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information.
License: GPL-3
Copyright: For the copyrights for the 'Corpus Workbench' (CWB) and acknowledgement of authorship, see file COPYRIGHTS.
NeedsCompilation: yes
SystemRequirements: On Unix-like operating systems, pcre (>= 7) and glib2 (>= 2) need to be present to compile 'RcppCWB'. See README.md for instructions how to install these dependencies. On Windows, no prior installations are necessary, as pre-built (i.e. cross-compiled) binaries of all required libraries are downloaded from a GitHub repository (<https://github.com/PolMine/libcl>) during installation.
Imports: Rcpp (>= 0.12.6)
Suggests: knitr, testthat
LinkingTo: Rcpp
Biarch: true
URL: https://www.github.com/PolMine/RcppCWB
BugReports: https://github.com/PolMine/RcppCWB/issues
RoxygenNote: 6.0.1
Collate: 'RcppCWB_package.R' 'RcppExports.R'
Packaged: 2018-02-19 21:10:31 UTC; blaette
Repository: CRAN
Date/Publication: 2018-02-20 09:38:40 UTC

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New package idx2r with initial version 1.0.0
Package: idx2r
Type: Package
Title: Convert Files to and from IDX Format to Vectors, Matrices and Arrays
Version: 1.0.0
Date: 2018-02-19
Author: Erik Doffagne
Maintainer: Erik Doffagne <erik.doffagne@gmail.com>
Description: Convert files to and from IDX format to vectors, matrices and arrays. IDX is a very simple file format designed for storing vectors and multidimensional matrices in binary format. The format is described on the website from Yann LeCun <http://yann.lecun.com/exdb/mnist/>.
License: MIT + file LICENSE
URL: https://github.com/edoffagne/idx2r
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 19:02:14 UTC; erik
Repository: CRAN
Date/Publication: 2018-02-20 09:35:13 UTC

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New package gdm with initial version 1.3.7
Package: gdm
Type: Package
Title: Generalized Dissimilarity Modeling
Version: 1.3.7
Date: 2018-02-19
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Karel Mokany, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@umces.edu>
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models (Ferrier et al. 2007, <doi:10.1111/j.1472-4642.2007.00341.x>).
License: GPL-2
Depends: R (>= 2.15.2), raster, foreach, doParallel, parallel
LinkingTo: Rcpp
Imports: Rcpp (>= 0.10.4), reshape2, vegan
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2018-02-19 21:48:11 UTC; mlisk
Repository: CRAN
Date/Publication: 2018-02-20 09:23:14 UTC

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New package cobalt with initial version 3.2.1
Package: cobalt
Title: Covariate Balance Tables and Plots
Version: 3.2.1
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', and 'WeightIt' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets. (Note that 'CBPS' and 'WeightIt' have been archived, but 'cobalt' is still compatible with older versions and development versions.)
Depends: R (>= 3.3.0)
Imports: ggplot2 (>= 2.2.0), ggstance
Suggests: MatchIt, twang, Matching, optmatch, ebal, mice, knitr, rmarkdown
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Date: 2018-02-18
VignetteBuilder: knitr
URL: https://github.com/ngreifer/cobalt
BugReports: https://github.com/ngreifer/cobalt/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-20 04:05:20 UTC; NoahGreifer
Repository: CRAN
Date/Publication: 2018-02-20 09:18:56 UTC

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New package BINCOR with initial version 0.1.0
Package: BINCOR
Type: Package
Title: Estimate the Correlation Between Two Irregular Climate Time Series
Version: 0.1.0
Authors@R: c(person("Josué M.", "Polanco-Martínez", role = c("aut", "cph", "cre"), email = "josue.m.polanco@gmail.com"), person("Mikko", "Korpela", role = c("ctb", "trl")), person("Aalto University", role = c("cph")), person("Manfred", "Mudelsee", role = "ctb"))
Author: Josué M. Polanco-Martínez [aut, cph, cre], Mikko Korpela [ctb, trl], Aalto University [cph], Manfred Mudelsee [ctb]
Copyright: Authors and file inst/COPYRIGHTS
Maintainer: Josué M. Polanco-Martínez <josue.m.polanco@gmail.com>
Imports: pracma
Description: Estimate the correlation between two irregular time series that are not necessarily sampled on identical time points. This program is also applicable to the situation of two evenly spaced time series that are not on the same time grid. 'BINCOR' is based on a novel estimation approach proposed by Mudelsee (2010, 2014) to estimate the correlation between two time series with different timescales. 'BINCOR' contains four functions: bin_cor() (the main function to build the binned time series), plot_ts() (to plot and compare the irregular and binned time series, cor_ts() (to estimate the correlation between the binned time series) and ccf_ts() (to estimate the cross-correlation between the binned time series).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Date/Publication: 2018-02-20 09:21:44 UTC
NeedsCompilation: no
Packaged: 2018-02-19 18:16:01 UTC; jomopo
Repository: CRAN

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Mon, 19 Feb 2018

New package WMWssp with initial version 0.3.2
Package: WMWssp
Type: Package
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Version: 0.3.2
Date: 2018-02-16
Authors@R: c( person("Arne C. Bathke", role = "aut"), person("Edgar Brunner", role = "aut"), person("Martin Happ", role = c("aut", "cre"), email = "martin.happ@aon.at"), person("Frank Konietschke", role = "aut") )
Author: Arne C. Bathke [aut], Edgar Brunner [aut], Martin Happ [aut, cre], Frank Konietschke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test that is needed for a given power and two sided type I error rate. The method works for metric data with and without ties, count data, ordered categorical data, and even dichotomous data. But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Imports: rankFD
Depends: R (>= 3.4.0)
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-19 09:56:57 UTC; b1011921
Repository: CRAN
Date/Publication: 2018-02-19 10:24:30 UTC

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New package projpred with initial version 0.7.0
Package: projpred
Title: Projection Predictive Feature Selection
Version: 0.7.0
Author: Markus Paasiniemi [aut], Juho Piironen [aut], Jonah Gabry [ctb], Aki Vehtari [ctb]
Maintainer: Juho Piironen <juho.piironen@aalto.fi>
Description: Performs projection predictive feature selection for generalized linear models (see, e.g., Piironen and Vehtari, 2017, <doi:10.1007/s11222-016-9649-y>). The package is compatible with 'rstanarm' package, but other reference models can also be used. See the package vignette for more information and examples.
Depends: R (>= 3.1.2)
Imports: rstan, rstanarm (>= 2.17.2), loo, ggplot2, Rcpp, utils
LinkingTo: Rcpp, RcppArmadillo
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, glmnet, bayesplot
VignetteBuilder: knitr
URL: https://github.com/stan-dev/projpred
BugReports: https://github.com/stan-dev/projpred/issues
NeedsCompilation: yes
Packaged: 2018-02-18 19:26:42 UTC; juho
Repository: CRAN
Date/Publication: 2018-02-19 10:10:41 UTC

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New package mfGARCH with initial version 0.1.2
Package: mfGARCH
Title: Mixed-Frequency GARCH Models
Version: 0.1.2
Authors@R: person("Onno", "Kleen", email = "r@onnokleen.de", role = c("aut", "cre"))
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: volatility forecasting using multiplicative component GARCH models" by Conrad, Kleen (2018, Working Paper). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: Rcpp, graphics, stats, numDeriv, zoo
LinkingTo: Rcpp
URL: https://github.com/onnokleen/mfGARCH/
BugReports: https://github.com/onnokleen/mfGARCH/issues
Suggests: testthat, dplyr, ggplot2, covr, rmarkdown
NeedsCompilation: yes
Packaged: 2018-02-19 10:02:58 UTC; Arbeit
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>
Repository: CRAN
Date/Publication: 2018-02-19 10:27:25 UTC

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New package GpGp with initial version 0.1.0
Package: GpGp
Type: Package
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Version: 0.1.0
Date: 2018-02-18
Authors@R: c( person("Joseph", "Guinness", email = "joeguinness@gmail.com", role = c("aut", "cre")), person("Matthias", "Katzfuss", email = "katzfuss@gmail.com", role = "aut" ) )
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Description: Functions for reordering input locations, finding ordered nearest neighbors (with help from 'FNN' package), grouping operations, approximate likelihood evaluations, profile likelihoods, Gaussian process predictions, and conditional simulations. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. The original approximation is due to Vecchia (1988) <http://www.jstor.org/stable/2345768>, and the reordering and grouping methods are from Guinness (2018) <doi:10.1080/00401706.2018.1437476>.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Imports: Rcpp (>= 0.12.13), FNN
Suggests: fields, knitr, rmarkdown, testthat
LinkingTo: Rcpp
RoxygenNote: 6.0.1
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2018-02-18 21:48:51 UTC; guinness
Author: Joseph Guinness [aut, cre], Matthias Katzfuss [aut]
Repository: CRAN
Date/Publication: 2018-02-19 10:14:03 UTC

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New package SPUTNIK with initial version 1.0.0
Package: SPUTNIK
Type: Package
Title: SPatially aUTomatic deNoising for Ims toolKit
Version: 1.0.0
Author: Paolo Inglese [aut, cre], Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Authors@R: c(person("Paolo", "Inglese", email = "p.inglese14@imperial.ac.uk", role = c("aut", "cre")), person("Goncalo", "Correia", role = c("aut", "ctb")))
Description: A set of tools for the peak filtering of mass spectrometry imaging data (MSI or IMS) based on spatial distribution of signal. Given a region-of-interest (ROI), representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimensionality and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimensionality and simplifying the chemical interpretation.
Depends: R (>= 3.4.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: no
Imports: spatstat, autothresholdr, viridis, viridisLite, SDMTools, ggplot2, reshape, imager, methods, infotheo
RoxygenNote: 6.0.1
URL: https://github.com/paoloinglese/SPUTNIK
BugReports: https://github.com/paoloinglese/SPUTNIK/issues
NeedsCompilation: no
Packaged: 2018-02-16 21:11:56 UTC; pi514
Repository: CRAN
Date/Publication: 2018-02-19 09:17:36 UTC

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New package riskyr with initial version 0.1.0
Package: riskyr
Type: Package
Title: Rendering Risk Literacy more Transparent
Version: 0.1.0
Date: 2018-02-16
Authors@R: c(person("Hansjoerg", "Neth", role = c("aut", "cre"), email = "h.neth@uni.kn"), person("Felix", "Gaisbauer", role = "aut"), person("Nico", "Gradwohl", role = "aut"), person("Wolfgang", "Gaissmaier", role = "aut"))
Author: Hansjoerg Neth [aut, cre], Felix Gaisbauer [aut], Nico Gradwohl [aut], Wolfgang Gaissmaier [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Description: Risk-related information can be expressed in terms of probabilities or frequencies. By providing a toolbox of methods and metrics, we compute, translate, and represent risk-related information in a variety of ways. By offering different, but complementary perspectives on the interplay between key parameters, 'riskyr' renders teaching and training of risk literacy more transparent.
Depends: R (>= 3.2)
Imports: diagram (>= 1.6.4), grid (>= 3.4.3), vcd (>= 1.4), utils (>= 3.4.3)
Suggests: devtools, rmarkdown, knitr, roxygen2
Collate: 'comp_util.R' 'init_txt.R' 'init_pal.R' 'init_prob.R' 'comp_prob_prob.R' 'init_freq.R' 'comp_freq_prob.R' 'init_num.R' 'init_prob_num.R' 'init_freq_num.R' 'comp_freq_freq.R' 'comp_prob_freq.R' 'comp_xxxx_prob.R' 'comp_popu.R' 'comp_accu.R' 'plot_mosaic.R' 'plot_icons.R' 'plot_tree.R' 'plot_fnet.R' 'plot_curve.R' 'plot_plane.R' 'data.R' 'read_data.R' 'riskyr_class.R' 'start_riskyr.R'
Encoding: UTF-8
LazyData: true
License: GPL-2 | GPL-3
BugReports: https://github.com/hneth/riskyr/issues
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 22:34:00 UTC; hneth
Repository: CRAN
Date/Publication: 2018-02-19 09:22:19 UTC

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New package forestControl with initial version 0.1.1
Package: forestControl
Type: Package
Title: Approximate False Positive Rate Control in Selection Frequency for Random Forest
Version: 0.1.1
Date: 2018-02-16
Authors@R: c( person("Tom", "Wilson", , "tpw2@aber.ac.uk", c("aut", "cre")), person("Jasen", "Finch", , "jsf9@aber.ac.uk", "aut"))
Description: Approximate false positive rate control in selection frequency for random forest using the methods described by Ender Konukoglu and Melanie Ganz (2015) <arXiv:1410.2838>. Methods for calculating the selection frequency threshold at false positive rates and selection frequency false positive rate feature selection.
Imports: Rcpp
Suggests: testthat, randomForest, ranger
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/aberHRML/forestControl
BugReports: https://github.com/aberHRML/forestControl/issues
RoxygenNote: 6.0.1
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-02-16 22:06:58 UTC; tom
Author: Tom Wilson [aut, cre], Jasen Finch [aut]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Repository: CRAN
Date/Publication: 2018-02-19 09:20:11 UTC

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Sun, 18 Feb 2018

New package agRee with initial version 0.5-1
Package: agRee
Title: Various Methods for Measuring Agreement
Version: 0.5-1
Author: Dai Feng
Description: Bland-Altman plot and scatter plot with identity line for visualization and point and interval estimates for different metrics related to reproducibility/repeatability/agreement including the concordance correlation coefficient, intraclass correlation coefficient, within-subject coefficient of variation, smallest detectable difference, and mean normalized smallest detectable difference.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), miscF (>= 0.1-4), lme4 (>= 1.0-4)
Imports: R2jags (>= 0.03-11), coda (>= 0.16-1)
License: GPL
NeedsCompilation: no
Packaged: 2018-02-18 21:34:49 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-18 21:55:41 UTC

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New package sim1000G with initial version 1.38
Package: sim1000G
Type: Package
Title: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Version: 1.38
Date: 2018-02-16
Author: Apostolos Dimitromanolakis <apostolis@live.ca>, Jingxiong Xu <jingxiong.xu@mail.utoronto.ca>, Agnieszka Krol <krol@lunenfeld.ca>, Laurent Briollais <laurent@lunenfeld.ca>
Maintainer: Apostolos Dimitromanolakis <apostolis@live.ca>
Description: Generates realistic simulated genetic data in families or unrelated individuals.
License: GPL (>= 2)
Depends: R (>= 2.15.2), stats, hapsim, MASS, stringr, readr
NeedsCompilation: no
VignetteBuilder: knitr, prettydoc
RoxygenNote: 6.0.1
Suggests: knitr, prettydoc, testthat, rmarkdown, gplots
Encoding: UTF-8
Repository: CRAN
Packaged: 2018-02-17 17:23:46 UTC; apo
Date/Publication: 2018-02-18 21:30:35 UTC

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New package PottsUtils with initial version 0.3-3
Package: PottsUtils
Title: Utility Functions of the Potts Models
Version: 0.3-3
Author: Dai Feng [aut, cre], Luke Tierney [ctb]
Description: There are three sets of functions. The first produces basic properties of a graph and generates samples from multinomial distributions to facilitate the simulation functions (they maybe used for other purposes as well). The second provides various simulation functions for a Potts model in Potts, R. B. (1952) <doi:10.1017/S0305004100027419>. The third currently includes only one function which computes the normalizing constant of a Potts model based on simulation results.
Maintainer: Dai Feng <daifeng.stat@gmail.com>
Depends: R (>= 3.0.2)
Imports: miscF (>= 0.1-4)
License: GPL-2
NeedsCompilation: yes
Packaged: 2018-02-18 20:53:32 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-18 21:04:47 UTC

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New package ecospace with initial version 1.2.3
Package: ecospace
Type: Package
Title: Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks
Version: 1.2.3
Date: 2018-01-17
Depends: R (>= 3.4.0)
Imports: FD (>= 1.0-12)
Authors@R: person("Phil", "Novack-Gottshall", email = "pnovack-gottshall@ben.edu", role = c("aut", "cre"))
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>
Description: Implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.
License: CC0
URL: https://github.com/pnovack-gottshall/ecospace, http://www.ben.edu/faculty/pnovack-gottshall/index.html
LazyData: TRUE
BugReports: https://github.com/pnovack-gottshall/ecospace/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, vegan
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-18 18:28:36 UTC; pnovack-gottshall
Author: Phil Novack-Gottshall [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-18 21:09:27 UTC

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New package codingMatrices with initial version 0.3.2
Package: codingMatrices
Type: Package
Title: Alternative Factor Coding Matrices for Linear Model Formulae
Version: 0.3.2
Author: Bill Venables
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Description: A collection of coding functions as alternatives to the standard functions in the stats package, which have names starting with 'contr.'. Their main advantage is that they provide a consistent method for defining marginal effects in factorial models. In a simple one-way ANOVA model the intercept term is always the simple average of the class means.
Depends: stats
Imports: Matrix, methods, fractional, utils
Suggests: knitr, MASS, dplyr, car, ggplot2, xtable
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-18 21:02:18 UTC; ven037
Repository: CRAN
Date/Publication: 2018-02-18 21:30:34 UTC

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Fri, 16 Feb 2018

New package miscF with initial version 0.1-4
Package: miscF
Title: Miscellaneous Functions
Version: 0.1-4
Author: Dai Feng
Description: Various functions for random number generation, density estimation, classification, curve fitting, and spatial data analysis.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), MASS (>= 7.3-45), R2jags (>= 0.5-7)
Imports: MCMCpack (>= 1.2-4), mvtnorm (>= 0.9-9992)
Suggests: mixAK (>= 2.6), BRugs (>= 0.8-6)
License: GPL
NeedsCompilation: yes
Packaged: 2018-02-16 21:41:16 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-16 22:59:53 UTC

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New package spider with initial version 1.5.0
Package: spider
Type: Package
Title: Species Identity and Evolution in R
Version: 1.5.0
Date: 2018-02-15
Author: Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Maintainer: Rupert A. Collins <rupertcollins@gmail.com>
Description: Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.
License: MIT + file LICENSE
LazyLoad: yes
Imports: ape, pegas, graphics, stats, utils
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-02-16 19:05:02 UTC; rc16041
Repository: CRAN
Date/Publication: 2018-02-16 19:33:47 UTC

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New package dub with initial version 0.1.0
Package: dub
Type: Package
Title: Unpacking Assignment for Lists via Pattern Matching
Version: 0.1.0
Authors@R: person("Eugene", "Ha", , "eha@posteo.de", c("aut", "cre"))
Description: Provides an operator for assigning nested components of a list to names via a concise, Haskell-like pattern matching syntax. This is especially convenient for assigning individual names to the multiple values that a function may return in the form of a list, and for extracting deeply nested list components.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
Suggests: covr, testthat
URL: https://github.com/egnha/dub
BugReports: https://github.com/egnha/dub/issues
Collate: 'util.R' 'assert.R' 'tree.R' 'names.R' 'assign.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 13:40:32 UTC; eha
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Repository: CRAN
Date/Publication: 2018-02-16 19:24:08 UTC

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New package adklakedata with initial version 0.6.1
Package: adklakedata
Type: Package
Title: Adirondack Long-Term Lake Data
Version: 0.6.1
Authors@R: c(person("Luke", "Winslow", role = c("aut", "cre"), email = "lawinslow@gmail.com"), person("Taylor", "Leach", role=c("aut")), person("Tobi", "Hahn", role=c("aut")))
Description: Package for the access and distribution of Long-term lake datasets from lakes in the Adirondack Park, northern New York state. Includes a wide variety of physical, chemical, and biological parameters from 28 lakes. Data are from multiple collection organizations and have been harmonized in both time and space for ease of reuse.
License: MIT + file LICENSE
Imports: rappdirs, httr, tools, utils
Suggests: ggplot2, maps, testthat, sf
Repository: CRAN
BugReports: https://github.com/lawinslow/adklakedata/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 15:34:27 UTC; lawinslow
Author: Luke Winslow [aut, cre], Taylor Leach [aut], Tobi Hahn [aut]
Maintainer: Luke Winslow <lawinslow@gmail.com>
Date/Publication: 2018-02-16 19:08:16 UTC

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New package IBCF.MTME with initial version 1.1-2
Package: IBCF.MTME
Title: Item Based Collaborative Filtering for Multi-Trait and Multi-Environment Data
Version: 1.1-2
Date: 2018-02-14
Authors@R: c(person("Francisco Javier", "Luna-Vazquez", email = "frahik@gmail.com", role = c("aut", "cre")), person("Osval Antonio", "Montesinos-Lopez", email= "oamontes1@ucol.mx", role = "aut"), person("Abelardo", "Montesinos-Lopez", role = "aut"), person("Jose", "Crossa", role = "aut"))
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Description: Implements the Item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.
Depends: R (>= 3.0.0)
License: LGPL-3
Encoding: UTF-8
LazyData: true
Type: Package
RoxygenNote: 6.0.1
URL: https://github.com/frahik/IBCF.MTME
BugReports: https://github.com/frahik/IBCF.MTME/issues/new
NeedsCompilation: no
Collate: CrossValidation.R IBCF.R IBCF.MTME.R IBCFYear.R methods.R Td2M.R Title.R Wheat_IBCF.R Year_IBCF.R
Imports: lsa, tidyr
Suggests: testthat, knitr, rmarkdown
Packaged: 2018-02-16 00:59:22 UTC; Francisco
Author: Francisco Javier Luna-Vazquez [aut, cre], Osval Antonio Montesinos-Lopez [aut], Abelardo Montesinos-Lopez [aut], Jose Crossa [aut]
Repository: CRAN
Date/Publication: 2018-02-16 18:29:26 UTC

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New package estudy2 with initial version 0.8.4
Package: estudy2
Type: Package
Title: An Implementation of Parametric and Nonparametric Event Study
Version: 0.8.4
Date: 2018-02-16
Authors@R: person("Iegor", "Rudnytskyi", , "iegor.rudnytskyi@gmail.com", c("aut", "cre"))
Description: An implementation of a most commonly used event study methodology, including both parametric and nonparametric tests. It contains variety aspects of the rate of return estimation (the core calculation is done in C++), as well as three classical for event study market models: mean adjusted returns, market adjusted returns and single-index market models. There are 6 parametric and 6 nonparametric tests provided, which examine cross-sectional daily abnormal return (see the documentation of the functions for more information). Parametric tests include tests proposed by Brown and Warner (1980) <DOI:10.1016/0304-405X(80)90002-1>, Brown and Warner (1985) <DOI:10.1016/0304-405X(85)90042-X>, Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Patell (1976) <DOI:10.2307/2490543>, and Lamb (1995) <DOI:10.2307/253695>. Nonparametric tests covered in estudy2 are tests described in Corrado and Zivney (1992) <DOI:10.2307/2331331>, McConnell and Muscarella (1985) <DOI:10.1016/0304-405X(85)90006-6>, Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Cowan (1992) <DOI:10.1007/BF00939016>, Corrado (1989) <DOI:10.1016/0304-405X(89)90064-0>, Campbell and Wasley (1993) <DOI:10.1016/0304-405X(93)90025-7>, Savickas (2003) <DOI:10.1111/1475-6803.00052>, Kolari and Pynnonen (2010) <DOI:10.1093/rfs/hhq072>. Furthermore, tests for the cumulative abnormal returns proposed by Brown and Warner (1985) <DOI:10.1016/0304-405X(85)90042-X> and Lamb (1995) <DOI:10.2307/253695> are included.
License: GPL-3
LazyData: TRUE
URL: http://github.com/irudnyts/estudy2
BugReports: http://github.com/irudnyts/estudy2/issues
Depends: R (>= 3.1)
Imports: tseries (>= 0.10-42), zoo (>= 1.8-0), matrixStats (>= 0.52.2), Rcpp (>= 0.12.13)
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, magrittr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-02-16 11:11:19 UTC; irudnyts
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-16 18:32:52 UTC

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New package ppcSpatial with initial version 0.1.0
Package: ppcSpatial
Type: Package
Title: Spatial Analysis of Pakistan Population Census
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Muhammad", "Arfan", "Dilber"), email = "pbsfsd041@gmail.com", role = c("aut", "ctb")) )
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Spatial Analysis for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>). It uses data from R package 'PakPC2017'.
Depends: R (>= 3.1)
Imports: dplyr, ggplot2, htmltools, htmlwidgets, leaflet, magrittr, PakPC2017, rgdal, scales, shiny, tidyr, tmap
Suggests: testthat
License: GPL-3
URL: https://github.com/MYaseen208/ppcSpatial
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-15 08:20:14 UTC; yaseen
Author: Muhammad Yaseen [aut, cre], Muhammad Arfan Dilber [aut, ctb]
Repository: CRAN
Date/Publication: 2018-02-16 16:52:31 UTC

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New package phenoCDM with initial version 0.0.2
Package: phenoCDM
Title: Continuous Development Models for Incremental Time-Series Analysis
Version: 0.0.2
Date: 2018-02-14
Authors@R: person("Bijan", "Seyednasrollah", email = "bijan.s.nasr@gmail.com", role = c("aut", "cre"))
Author: Bijan Seyednasrollah [aut, cre]
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Description: Using the Bayesian state-space approach, we developed a continuous development model to quantify dynamic incremental changes in the response variable. While the model was originally developed for daily changes in forest green-up, the model can be used to predict any similar process. The CDM can capture both timing and rate of nonlinear processes. Unlike statics methods, which aggregate variations into a single metric, our dynamic model tracks the changing impacts over time. The CDM accommodates nonlinear responses to variation in predictors, which changes throughout development.
Depends: rjags
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
BugReports: https://github.com/bnasr/phenoCDM/issues
NeedsCompilation: no
Packaged: 2018-02-14 22:35:19 UTC; bijan
Repository: CRAN
Date/Publication: 2018-02-16 16:48:17 UTC

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New package genBart with initial version 1.0.0
Package: genBart
Type: Package
Title: Generate 'BART' File
Version: 1.0.0
Authors@R: c( person("Jacob", "Cardenas", email = "jacob.cardenas@bswhealth.org", role = c("aut", "cre")), person("Jacob", "Turner", role = "aut"), person("Derek", "Blankenship", role = "aut") )
Description: A set of functions to generate and format results from statistical analyses of a wide range of high throughput experiments that can then be uploaded into the 'BART' (Bio-Statistical Analysis Reporting Tool) 'shiny' app <https://github.com/jcardenas14/BART>. The app provides users with tools to visualize and efficiently sift through large amounts of data and results.
Depends: R (>= 3.4.0)
Imports: clValid (>= 0.6-6), data.table (>= 1.10.4), fastcluster (>= 1.1.22), ggplot2 (>= 2.2.1), grid (>= 3.3.3), gtools (>= 3.5.0), limma (>= 3.30.13), NMF (>= 0.20.6), pca3d (>= 0.10), psych (>= 1.7.3.21), qusage (>= 2.6.1), RColorBrewer (>= 1.1-2), reshape2 (>= 1.4.2), rmarkdown (>= 1.5), scales (>= 0.4.1), shiny (>= 1.0.3), shinydashboard (>= 0.5.3), shinyjs (>= 0.9), statmod (>= 1.2.2), stats (>= 3.3.3), stringr (>= 1.2.0), tools (>= 3.3.3), VennDiagram (>= 1.6.17)
Suggests: DESeq2 (>= 1.14.1), edgeR (>= 3.16.5), knitr (>= 1.15.1), SummarizedExperiment (>= 1.1.6), testthat
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews: Microarray, RNASeq, AnnotationData
NeedsCompilation: no
Packaged: 2018-02-14 20:56:10 UTC; e89628
Author: Jacob Cardenas [aut, cre], Jacob Turner [aut], Derek Blankenship [aut]
Maintainer: Jacob Cardenas <jacob.cardenas@bswhealth.org>
Repository: CRAN
Date/Publication: 2018-02-16 16:36:31 UTC

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Thu, 15 Feb 2018

New package madness with initial version 0.2.3
Package: madness
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Authors@R: c(person(c("Steven", "E."), "Pav", role=c("aut","cre"), email="shabbychef@gmail.com"))
Version: 0.2.3
Date: 2018-02-14
License: LGPL-3
Title: Automatic Differentiation of Multivariate Operations
BugReports: https://github.com/shabbychef/madness/issues
Description: An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.
Depends: R (>= 3.2.0)
Imports: Matrix, matrixcalc, expm, methods
Suggests: testthat, R.rsp, knitr
URL: https://github.com/shabbychef/madness
VignetteBuilder: R.rsp
Collate: 'AllClass.r' 'utils.r' 'Ops.r' 'bind.r' 'blockrep.r' 'coerce.r' 'det.r' 'diag.r' 'eigen.r' 'elwise.r' 'madness_pkg.r' 'matwise.r' 'max.r' 'norm.r' 'numderiv.r' 'reshape.r' 'solve.r' 'sum.r' 'sums.r' 'theta.r' 'to_objective.r' 'trace.r' 'twomoments.r' 'vcov.r' 'vec.r'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-15 05:31:39 UTC; spav
Author: Steven E. Pav [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-15 23:15:22 UTC

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New package crmPack with initial version 0.2.6
Package: crmPack
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
License: GPL (>= 2)
Title: Object-Oriented Implementation of CRM Designs
LazyLoad: yes
Author: Daniel Sabanes Bove <sabanesd@roche.com>, Wai Yin Yeung <winnie.yeung@roche.com>, Giuseppe Palermo <giuseppe.palermo@roche.com>, Thomas Jaki <jaki.thomas@gmail.com>
Description: Implements a wide range of model-based dose escalation designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. The focus is on Bayesian inference, making it very easy to setup a new design with its own JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules.
Version: 0.2.6
Date: 2018-02-15
Copyright: F. Hoffmann-La Roche Ltd
Depends: R (>= 3.0.0), ggplot2 (>= 2.0.0), graphics
Imports: methods, grid, gridExtra, GenSA, mvtnorm, parallel, rjags, utils, tools, MASS
Suggests: ggmcmc, R2WinBUGS, Rcpp, RcppArmadillo
Collate: 'helpers.R' 'Data-class.R' 'Data-methods.R' 'Rules-class.R' 'Model-class.R' 'Design-class.R' 'writeModel.R' 'McmcOptions-methods.R' 'McmcOptions-class.R' 'Samples-class.R' 'mcmc.R' 'Simulations-class.R' 'Model-methods.R' 'Rules-methods.R' 'Design-methods.R' 'fromQuantiles.R' 'Samples-methods.R' 'Simulations-methods.R' 'crmPack-package.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-15 10:49:19 UTC; sabanesd
Repository: CRAN
Date/Publication: 2018-02-15 23:04:23 UTC

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Wed, 14 Feb 2018

New package RSDA with initial version 2.0.3
Package: RSDA
Type: Package
Title: R to Symbolic Data Analysis
Version: 2.0.3
Date: 2018-02-14
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.4)
Imports: RJSONIO, glmnet, abind, scatterplot3d, graphics, stats, utils, FactoMineR (>= 1.36), XML, scales, ggplot2, princurve, sqldf, dplyr (>= 0.7.1), tidyr, stringr, lazyeval, nloptr (>= 1.0.4) ,xtable,pander, rlang(>= 0.1.1), RColorBrewer
URL: http://www.oldemarrodriguez.com
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-14 19:51:42 UTC; promidat04
Repository: CRAN
Date/Publication: 2018-02-14 21:08:33 UTC

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New package tidyLPA with initial version 0.1.1
Type: Package
Package: tidyLPA
Title: Easily Carry Out Latent Profile Analysis
Version: 0.1.1
Authors@R: c( person(c("Joshua", "M"), "Rosenberg", role = c("aut", "cre"), email = "jmichaelrosenberg@gmail.com"), person(c("Jennifer", "A"), "Schmidt", role = "ctb", email = "jaschmid@msu.edu"), person(c("Patrick", "N"), "Beymer", role = "ctb", email = "beymerpa@msu.edu"), person(c("Rebecca", "R"), "Steingut", role = "ctb", email = "rebeccarosesteingut@gmail.com") )
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: dplyr, forcats, ggplot2, magrittr, mclust, purrr, readr, rlang, stringr, tibble, tidyr
Suggests: covr, devtools, knitr, MplusAutomation, rmarkdown, roxygen2, testthat,
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-14 17:23:05 UTC; joshuarosenberg
Author: Joshua M Rosenberg [aut, cre], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Rebecca R Steingut [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-14 19:07:56 UTC

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New package stpp with initial version 2.0-3
Package: stpp
Version: 2.0-3
Title: Space-Time Point Pattern Simulation, Visualisation and Analysis
Date: 2018-01-14
Authors@R: c(person("Edith", "Gabriel", role=c("aut","cre"),email="edith.gabriel@univ-avignon.fr"), person("Peter J","Diggle",role="aut",email="p.diggle@lancaster.ac.uk"), person("Barry","Rowlingson",role="aut",email="b.rowlingson@lancaster.ac.uk"), person("Francisco J","Rodriguez-Cortes",role="aut", email="cortesf@uji.es"))
Maintainer: Edith Gabriel <edith.gabriel@univ-avignon.fr>
Depends: R (>= 3.3.0), grDevices, graphics, rpanel, splancs
Imports: KernSmooth, ggplot2, gridExtra, plot3D, rgl, spatstat
Suggests: knitr(>= 1.11), rmarkdown(>= 0.8.1)
Description: Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
RoxygenNote: 6.0.1
BuildVignettes: True
VignetteBuilder: knitr
BugReports: https://github.com/stpp-GitHub-community
Packaged: 2018-02-14 01:43:24 UTC; frajaroco
Author: Edith Gabriel [aut, cre], Peter J Diggle [aut], Barry Rowlingson [aut], Francisco J Rodriguez-Cortes [aut]
Repository: CRAN
Date/Publication: 2018-02-14 19:02:33 UTC

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New package ssrm.logmer with initial version 0.1
Package: ssrm.logmer
Title: Sample Size Determination for Longitudinal Designs with Binary Outcome
Version: 0.1
Authors@R: person("Kush", "Kapur", email = "kush.kapur@childrens.harvard.edu", role = c("aut", "cre"))
Description: Provides the necessary sample size for a longitudinal study with binary outcome in order to attain a pre-specified power while strictly maintaining the Type I error rate. Kapur K, Bhaumik R, Tang XC, Hur K, Reda DJ, Bhaumik D (2014) <doi:10.1002/sim.6203>.
Depends: R (>= 3.4.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
Maintainer: Kush Kapur <kush.kapur@childrens.harvard.edu>
Imports: statmod, stats, sfsmisc
Suggests: knitr, rmarkdown
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-14 17:48:22 UTC; CH164375
Author: Kush Kapur [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-14 19:18:30 UTC

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New package serrsBayes with initial version 0.3-10
Package: serrsBayes
Type: Package
Title: Bayesian Modelling of Raman Spectroscopy
Version: 0.3-10
Date: 2018-02-14
Authors@R: c( person("Matt", "Moores", role = c("aut", "cre"), email = "M.T.Moores@warwick.ac.uk", comment = c(ORCID = "0000-0003-4531-3572")), person("Jake", "Carson", role="aut", email="Jake.Carson@warwick.ac.uk"), person("Mark", "Girolami", role="aut", email="M.Girolami@warwick.ac.uk"), person("Engineering and Physical Sciences Research Council", role="fnd", comment="EPSRC programme grant ref: EP/L014165/1"), person("University of Warwick", role="cph"))
Description: Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS), using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate observations of SERRS are highly collinear and lend themselves to a reduced-rank representation. The GAMM separates the SERRS signal into three components: a sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline; and additive white noise. The parameters of each component of the model are estimated iteratively using SMC. The posterior distributions of the parameters given the observed spectra are represented as a population of weighted particles.
License: GPL (>= 2) | file LICENSE
URL: https://github.com/mooresm/serrsBayes
BugReports: https://github.com/mooresm/serrsBayes/issues
Depends: R (>= 3.1.0), Matrix, truncnorm, splines, MASS
Imports: Rcpp (>= 0.11.3), methods
LinkingTo: Rcpp, RcppEigen
Suggests: hyperSpec, testthat
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-02-14 12:03:27 UTC; matt
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>), Jake Carson [aut], Mark Girolami [aut], Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1), University of Warwick [cph]
Maintainer: Matt Moores <M.T.Moores@warwick.ac.uk>
Repository: CRAN
Date/Publication: 2018-02-14 18:46:02 UTC

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New package cgmanalysis with initial version 1.3
Package: cgmanalysis
Title: Clean and Analyze Continuous Glucose Monitor Data
Version: 1.3
Authors@R: person("Tim", "Vigers", email = "tim.b.vigers@gmail.com", role = c("aut", "cre"))
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>) or 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>) data. The makecsv() function can convert files to CSV if they have been saved as 'Excel' documents. The cleaniprodata() and cleandexcomdata() functions take a directory of CGM data files and clean them for analysis. Finally, cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file. This spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry).
Depends: R (>= 3.4.0), gdata, zoo, pracma
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports:
NeedsCompilation: no
Packaged: 2018-02-14 15:40:01 UTC; timvigers
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-14 18:58:37 UTC

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New package hR with initial version 0.1.1
Package: hR
Type: Package
Title: An HR Analytics Toolkit
Version: 0.1.1
Author: Dale Kube [aut, cre]
Authors@R: person("Dale","Kube",email="dkube@uwalumni.com",role=c("aut","cre"))
Maintainer: Dale Kube <dkube@uwalumni.com>
Description: Manipulate and visualize people data in meaningful and common ways. This package is meant for Human Resources analytics (often referred to as talent analytics or people analytics).
Encoding: UTF-8
License: GPL
LazyData: true
RoxygenNote: 6.0.1
Imports: data.tree, reshape2, visNetwork
NeedsCompilation: no
Packaged: 2018-02-14 03:14:05 UTC; Dale
Repository: CRAN
Date/Publication: 2018-02-14 16:59:01 UTC

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New package CorrectedFDR with initial version 1.0
Package: CorrectedFDR
Type: Package
Title: Correcting False Discovery Rates
Version: 1.0
Date: 2018-02-08
Author: Abbas Rahal, Anna Akpawu, Justin Chitpin and David R. Bickel
Maintainer: Abbas Rahal <arahal@uOttawa.ca>
Description: There are many estimators of false discovery rate. In this package we compute the Nonlocal False Discovery Rate (NFDR) and the estimators of local false discovery rate: Corrected False discovery Rate (CFDR), Re-ranked False Discovery rate (RFDR) and the blended estimator. Bickel, D. R. (2016) <http://hdl.handle.net/10393/34277>.
Depends: R(>= 2.14.2)
Suggests: LFDR.MLE, LFDREmpiricalBayes, ProData
biocViews: Bayesian Statistics, MathematicalBiology
URL: https://davidbickel.com
License: LGPL-3
NeedsCompilation: no
Packaged: 2018-02-14 03:02:42 UTC; Rahal
Repository: CRAN
Date/Publication: 2018-02-14 16:56:05 UTC

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Tue, 13 Feb 2018

New package umx with initial version 2.0.2
Package: umx
Version: 2.0.2
Date: 2018-01-29
Title: Structural Equation and Twin Modeling in R
Authors@R: c(person("Timothy C", "Bates", role = c("aut", "cre"), email = "timothy.c.bates@gmail.com"))
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
License: GPL-3
Encoding: UTF-8
URL: http://github.com/tbates/umx
Description: Quickly create, run, and report structural equation and twin models. See '?umx' to learn more.
Depends: R (>= 3.2.0), OpenMx (>= 2.7.9)
Imports: cowplot, ggplot2, DiagrammeR, knitr, MASS, Matrix, mvtnorm, nlme, numDeriv, polycor, R2HTML, RCurl, sfsmisc, xtable, methods, utils
Suggests: cocor, devtools, gdata, Hmisc, testthat, rmarkdown
BugReports: http://github.com/tbates/umx/issues
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-13 22:25:03 UTC; tim
Author: Timothy C Bates [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-13 23:40:21 UTC

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New package RGF with initial version 1.0.0
Package: RGF
Type: Package
Title: Regularized Greedy Forest
Version: 1.0.0
Date: 2018-02-12
Authors@R: c( person("Lampros", "Mouselimis", email = "mouselimislampros@gmail.com", role = c("aut", "cre")), person("Ryosuke", "Fukatani", role = "cph", comment = "Author of the python wrapper of the 'Regularized Greedy Forest' machine learning algorithm"), person("Tong", "Zhang", role = "cph", comment = "Author of the 'Regularized Greedy Forest' and of the Multi-core implementation of Regularized Greedy Forest machine learning algorithm"), person("Rie", "Johnson", role = "cph", comment = "Author of the 'Regularized Greedy Forest' machine learning algorithm") )
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Description: Regularized Greedy Forest wrapper of the 'Regularized Greedy Forest' <https://github.com/fukatani/rgf_python> 'python' package, which also includes a Multi-core implementation (FastRGF) <https://github.com/baidu/fast_rgf>.
License: GPL-3
Copyright: inst/COPYRIGHTS
SystemRequirements: Python (>= 2.7), rgf_python, fast_rgf, scikit-learn (>= 0.19.0), scipy ( >= 1.0.0), numpy ( >= 1.14.0). Detailed installation instructions for each operating system can be found in the README file.
Depends: R(>= 3.2.3)
Imports: reticulate, R6, Matrix
Suggests: testthat, covr, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-12 18:48:02 UTC; lampros
Author: Lampros Mouselimis [aut, cre], Ryosuke Fukatani [cph] (Author of the python wrapper of the 'Regularized Greedy Forest' machine learning algorithm), Tong Zhang [cph] (Author of the 'Regularized Greedy Forest' and of the Multi-core implementation of Regularized Greedy Forest machine learning algorithm), Rie Johnson [cph] (Author of the 'Regularized Greedy Forest' machine learning algorithm)
Repository: CRAN
Date/Publication: 2018-02-13 16:37:32 UTC

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New package future.callr with initial version 0.2.0
Package: future.callr
Version: 0.2.0
Depends: R (>= 3.2.0), future (>= 1.7.0)
Imports: callr (>= 2.0.2)
Suggests: future.apply, listenv, markdown, R.rsp
VignetteBuilder: R.rsp
Title: A Future API for Parallel Processing using 'callr'
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Implementation of the Future API on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession'), the 'callr' backend provided here can run more than 125 parallel R processes.
License: LGPL (>= 2.1)
LazyLoad: TRUE
URL: https://github.com/HenrikBengtsson/future.callr
BugReports: https://github.com/HenrikBengtsson/future.callr/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-13 04:09:23 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2018-02-13 12:56:10 UTC

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New package huxtable with initial version 2.0.2
Package: huxtable
Type: Package
Title: Simply Create LaTeX and HTML Tables
Version: 2.0.2
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Description: Creates HTML and LaTeX tables. Provides similar functionality to 'xtable', but does more, with a simpler interface. Allows export to Microsoft Word or PowerPoint using the 'officer' package. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liner commands to print data as Word, PDF or HTML.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, devtools, broom, ggplot2, officer, flextable, psych, nnet, covr, lme4, crayon
RoxygenNote: 6.0.1
URL: https://hughjonesd.github.io/huxtable
BugReports: https://github.com/hughjonesd/huxtable/issues
Imports: knitr, rmarkdown, htmltools, lazyeval, utils, dplyr, tibble, glue, assertthat, stringr
VignetteBuilder: knitr
Authors@R: person(given = "David", family = "Hugh-Jones", role = c("aut", "cre"), email = "davidhughjones@gmail.com")
NeedsCompilation: no
Packaged: 2018-02-08 21:19:34 UTC; david
Repository: CRAN
Date/Publication: 2018-02-08 22:36:35

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New package fishdata with initial version 0.1.3
Package: fishdata
Type: Package
Title: A Small Collection of Fish Population Datasets
Version: 0.1.3
Authors@R: person("Conor", "Neilson", email = "condwanaland@gmail.com", role = c("aut", "cre"))
Maintainer: Conor Neilson <condwanaland@gmail.com>
Description: A collection of four datasets based around the population dynamics of migratory fish. Datasets contain both basic size information on a per fish basis, as well as otolith data that contains a per day record of fish growth history. All data in this package was collected by the author, from 2015-2016, in the Wellington region of New Zealand.
License: GPL-3
Depends: R (>= 2.10)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, dplyr, magrittr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-13 04:16:26 UTC; apple
Author: Conor Neilson [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-13 10:09:12 UTC

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New package MLML2R with initial version 0.1.0
Package: MLML2R
Type: Package
Title: Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Levels
Version: 0.1.0
Author: Samara Kiihl [aut, cre], Maria Jose Martinez-Garrido [aut], Arce Domingo-Relloso [aut], Jose Bermudez [aut], Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>
Description: Maximum likelihood estimates (MLE) of the levels of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2018, to appear).
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
biocViews: Software, MethylationArray, Epigenetics, DNAMethylation, Microarray, TwoChannel, OneChannel
RoxygenNote: 6.0.1
Suggests: minfi, BiocStyle, microbenchmark, GEOquery, knitr, rmarkdown
BugReports: https://github.com/samarafk/MLML2R/issues
NeedsCompilation: no
Packaged: 2018-02-13 02:55:09 UTC; samara
Repository: CRAN
Date/Publication: 2018-02-13 09:40:10 UTC

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New package librarysnapshot with initial version 0.1.2
Package: librarysnapshot
Date: 2018-02-12
Version: 0.1.2
Type: Package
Title: Library Snapshot for Packages and Dependencies in Use by Current Session
Authors@R: c( person( "Peter", "Meissner", role = c("aut", "cre"), email = "retep.meissner@gmail.com" ) )
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Description: Generate a local library copy with relevant packages. All packages currently found within the search path - except base packages - will be copied to the directory provided and can be used later on with the .libPaths() function.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: utils
URL: https://github.com/petermeissner/librarysnapshot
BugReports: https://github.com/petermeissner/librarysnapshot/issues
Suggests: covr, testthat
NeedsCompilation: no
Packaged: 2018-02-12 20:43:54 UTC; peter
Author: Peter Meissner [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-13 09:34:24 UTC

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New package cRegulome with initial version 0.1.0
Package: cRegulome
Type: Package
Version: 0.1.0
Title: Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Description: Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
License: GPL-3
Authors@R: person("Mahmoud", "Ahmed", email = "mahmoud.s.fahmy@students.kasralainy.edu.eg", role = c("aut", "cre"))
URL: https://github.com/MahShaaban/cRegulome
BugReports: https://github.com/MahShaaban/cRegulome/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R(>= 2.10.0)
Imports: DBI, graphics, httr, RSQLite, UpSetR, VennDiagram, magrittr, dplyr, ggplot2, ggridges, tidyr, reshape2, purrr, grid, R.utils
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat, covr, dbplyr, clusterProfiler, igraph, org.Hs.eg.db, readxl, AnnotationDbi, BiocInstaller
NeedsCompilation: no
Packaged: 2018-02-13 02:07:08 UTC; rstudio
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Repository: CRAN
Date/Publication: 2018-02-13 09:44:49 UTC

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New package clusteredinterference with initial version 1.0.0
Package: clusteredinterference
Type: Package
Date: 2018-02-12
Title: Causal Effects from Observational Studies with Clustered Interference
Version: 1.0.0
Authors@R: c(person("Brian G.", "Barkley", email = "BarkleyBG@outlook.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1787-4735")), person("Bradley", "Saul", role = c("ctb")))
Author: Brian G. Barkley [aut, cre] (<https://orcid.org/0000-0003-1787-4735>), Bradley Saul [ctb]
Maintainer: Brian G. Barkley <BarkleyBG@outlook.com>
Description: Estimating causal effects from observational studies assuming clustered (or partial) interference. These inverse probability-weighted estimators target new estimands arising from population-level treatment policies. The estimands and estimators are introduced in Barkley et al. (2017) <arXiv:1711.04834>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 3.2)
Imports: Formula (>= 1.1-2), cubature (>= 1.1-2), lme4 (>= 1.1-10), numDeriv (>= 2014.2-1), rootSolve (>= 1.6.6)
Suggests: testthat, rprojroot, knitr, rmarkdown, covr
VignetteBuilder: knitr
URL: http://github.com/BarkleyBG/clusteredinterference
BugReports: http://github.com/BarkleyBG/clusteredinterference/issues
NeedsCompilation: no
Packaged: 2018-02-12 20:07:21 UTC; Brian G. Barkley
Repository: CRAN
Date/Publication: 2018-02-13 09:24:28 UTC

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Mon, 12 Feb 2018

New package RNOmni with initial version 0.1.5
Package: RNOmni
Title: Omnibus Test for Genetic Association Analysis using the Rank Normal Transformation
Version: 0.1.5
Date: 2018-02-12
Authors@R: person("Zachary","McCaw",email="zmccaw@g.harvard.edu",role=c("aut","cre"))
Description: Implementation of genetic association tests that utilize the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two INT-based approaches, termed direct INT (DINT) and partially indirect INT (PIINT). In genome scale simulations, the omnibus test routinely provided valid inference against continuous phenotypes with skewed and heavy tailed residual distributions. Association testing against these same phenotypes via standard linear regression led to an excess of false positive associations. In addition to controlling the type I error, the omnibus approach provided power comparable to the more powerful of the component methods.
Depends: R (>= 3.2.2)
Imports: abind, foreach, mvtnorm, RcppEigen
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: cowplot, ggplot2, knitr, reshape2, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-12 20:28:50 UTC; zmccaw
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Repository: CRAN
Date/Publication: 2018-02-12 23:30:29 UTC

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New package basicspace with initial version 0.20
Package: basicspace
Version: 0.20
Date: 2018-02-12
Title: Recovering a Basic Space from Issue Scales
Author: Keith Poole <ktpoole@uga.edu>, Howard Rosenthal <hr31@nyu.edu>, Jeffrey Lewis <jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce Carroll <rcarroll@rice.edu>
Maintainer: James Lo <lojames@usc.edu>
Depends: R (>= 3.0.0), tools (>= 2.0.0)
Description: Conducts Aldrich-McKelvey and Blackbox Scaling (Poole et al 2016) <doi:10.18637/jss.v069.i07> to recover latent dimensions of judgment.
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
Packaged: 2018-02-12 22:32:58 UTC; jameslo
Date/Publication: 2018-02-12 23:30:33 UTC

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New package na.tools with initial version 0.2.1
Package: na.tools
Title: Comprehensive Library for Working with Missing (NA) Values in Vectors
Version: 0.2.1
Date: 2018-02-12
Authors@R: c( person("Christopher", "Brown", , "chris.brown@decisionpatterns.com", c("aut", "cre") ), person("Decision Patterns", role = "cph") )
URL: https://github.com/decisionpatterns/na.tools
Description: This comprehensive toolkit provide a consistent and extensible framework for working with missing values in vectors. The companion package 'tidyimpute' provides similar functionality for list-like and table-like structures). Functions exist for detection, removal, replacement, imputation, recollection, etc. of 'NAs'.
BugReports: https://github.com/decisionpatterns/na.actions/issues
Depends: R (>= 3.1.0)
Imports: stats, methods
Suggests: testthat (>= 1.0.2)
License: GPL-3 | file LICENSE
LazyData: true
RoxygenNote: 6.0.1.9000
Repository: CRAN
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-02-12 18:11:31 UTC; cbrown
Author: Christopher Brown [aut, cre], Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Date/Publication: 2018-02-12 19:12:33 UTC

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New package BlockFeST with initial version 1.3
Package: BlockFeST
Type: Package
Title: Bayesian Calculation of Region-Specific Fixation Index to Detect Local Adaptation
Version: 1.3
Date: 2018-02-8
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>
Depends: R (>= 2.14.2), BASIX
Imports: methods
Suggests: PopGenome
Description: An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
License: GPL-2
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2018-02-12 18:33:57 UTC; user
Repository: CRAN
Date/Publication: 2018-02-12 19:14:25 UTC

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New package shinyalert with initial version 1.0
Package: shinyalert
Title: Easily Create Pretty Popup Messages (Modals) in 'Shiny'
Version: 1.0
Authors@R: c( person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"), comment = "R interface"), person("Tristan", "Edwards", role = c("aut"), comment = "sweetalert library") )
Description: Easily create pretty popup messages (modals) in 'Shiny'. A modal can contain text, images, OK/Cancel buttons, an input to get a response from the user, and many more customizable options.
URL: https://github.com/daattali/shinyalert https://daattali.com/shiny/shinyalert-demo/
BugReports: https://github.com/daattali/shinyalert/issues
Depends: R (>= 3.0.2)
Imports: digest, shiny (>= 1.0.4), stats
Suggests: colourpicker, knitr, rmarkdown
License: MIT + file LICENSE
SystemRequirements: pandoc with https support
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-12 16:41:07 UTC; Dean
Author: Dean Attali [aut, cre] (R interface), Tristan Edwards [aut] (sweetalert library)
Maintainer: Dean Attali <daattali@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-12 18:20:44 UTC

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New package GPCMlasso with initial version 0.1-1
Package: GPCMlasso
Type: Package
Title: Differential Item Functioning in Generalized Partial Credit Models
Version: 0.1-1
Date: 2018-02-06
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Description: Provides a function to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.4), wordcloud, TeachingDemos, cubature, car, caret, statmod, mvtnorm, mirt, methods
Depends: ltm
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-02-12 16:59:27 UTC; schaubergerg
Repository: CRAN
Date/Publication: 2018-02-12 18:23:52 UTC

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New package elementR with initial version 1.3.5
Package: elementR
Type: Package
Title: An Framework for Reducing Elemental LAICPMS Data from Solid Structures
Version: 1.3.5
Date: 2018-02-07
Author: Charlotte Sirot, Francois Guilhaumon
Maintainer: Charlotte Sirot <charlott.sirot@gmail.com>
Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LAICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The 'elementR' package provides a reactive and user friendly interface (based on a 'shiny' application) and a set of 'R6' classes for conducting all steps needed for an optimal data reduction while leaving maximum control for user.
Repository: CRAN
Depends: R (>= 3.2.3)
Imports: gdata, shiny,devtools, shinyjs, gnumeric, R6, shinydashboard, abind, stringr, lmtest, tcltk,tcltk2, reader, readODS, readxl, EnvStats, outliers, zoo, colourpicker, stats, graphics, utils
License: GPL (>= 2)
Suggests: testthat
URL: https://github.com/charlottesirot/elementR
BugReports: https://github.com/charlottesirot/elementR/issues
NeedsCompilation: no
Packaged: 2018-02-12 16:15:57 UTC; cha
Date/Publication: 2018-02-12 18:18:26 UTC

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New package EDMeasure with initial version 1.0.0
Package: EDMeasure
Title: Dependence Measures via Energy Statistics
Version: 1.0.0
Date: 2018-01-30
Authors@R: c( person("Ze", "Jin", email = "zj58@cornell.edu", role = c("aut", "cre")), person("Shun", "Yao", email = "shunyao2@illinois.edu", role = c("aut")), person("David S.", "Matteson", email = "matteson@cornell.edu", role = c("aut")), person("Xiaofeng", "Shao", email = "xshao@illinois.edu", role = c("aut")) )
Description: Implementations of (1) mutual dependence measures and mutual independence tests in Jin, Z., and Matteson, D. S. (2017) <arXiv:1709.0253>; (2) independent component analysis methods based on mutual dependence measures in Jin, Z., and Matteson, D. S. (2017) <arXiv:1709.0253> and Pfister, N., et al. (2018) <doi:10.1111/rssb.12235>; (3) conditional mean dependence measures and conditional mean independence tests in Shao, X., and Zhang, J. (2014) <doi:10.1080/01621459.2014.887012> and Park, T., et al. (2015) <doi:10.1214/15-EJS1047>.
Depends: R (>= 3.4.0)
Imports: energy (>= 1.7-0), dHSIC (>= 2.0), rBayesianOptimization (>= 1.1.0)
Suggests: testthat (>= 2.0.0)
License: GPL (>= 2)
LazyData: true
RoxygenNote: 6.0.1
Collate: 'EDMeasure-package.R' 'cmdm_functions.R' 'pmdd.R' 'mdd.R' 'cmdm_test.R' 'mdc.R' 'mdm.R' 'mdm_ica_functions.R' 'mdm_ica.R' 'mdm_test.R' 'pmdc.R'
NeedsCompilation: yes
Packaged: 2018-02-12 17:50:38 UTC; btluck
Author: Ze Jin [aut, cre], Shun Yao [aut], David S. Matteson [aut], Xiaofeng Shao [aut]
Maintainer: Ze Jin <zj58@cornell.edu>
Repository: CRAN
Date/Publication: 2018-02-12 18:26:17 UTC

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New package Rlinsolve with initial version 0.2.0
Package: Rlinsolve
Type: Package
Title: Iterative Solvers for (Sparse) Linear System of Equations
Version: 0.2.0
Authors@R: person("Kisung", "You", email = "kyou@nd.edu", role = c("aut", "cre"),comment=c(ORCID="0000-0002-8584-459X"))
Description: Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. We provide basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using 'Matrix' package along with 'RcppArmadillo'. For a more detailed description, see a book by Saad (2003) <doi:10.1137/1.9780898718003>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.4), Matrix, Rdpack
LinkingTo: bigmemory, BH, Rcpp, RcppArmadillo
Depends: R (>= 3.3.0), bigmemory
RoxygenNote: 6.0.1
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2018-02-05 09:27:53 UTC; kisung
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Repository: CRAN
Date/Publication: 2018-02-12 16:12:49 UTC

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New package stability with initial version 0.1.0
Package: stability
Type: Package
Title: Stability Analysis of Genotype by Environment Interaction (GEI)
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Kent", "M.", "Eskridge"), email = "keskridge1@unl.edu ", role = c("aut", "ctb")) )
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Functionalities to perform Stability Analysis of Genotype by Environment Interaction (GEI) to identify superior and stable genotypes under diverse environments. It performs Eberhart & Russel's ANOVA (1966) (<doi:10.2135/cropsci1966.0011183X000600010011x>), Finlay and Wilkinson (1963) Joint Linear Regression (<doi:10.1071/AR9630742>), Wricke (1962, 1964) Ecovalence, Shukla's stability variance parameter (1972) (<doi:10.1038/hdy.1972.87>) and Kang's (1991) (<doi:10.2134/agronj1991.00021962008300010037x>) simultaneous selection for high yielding and stable parameter.
Depends: R (>= 3.1)
Imports: dplyr, lme4, magrittr, matrixStats, reshape2, stats
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-12 13:39:34 UTC; yaseen
Author: Muhammad Yaseen [aut, cre], Kent M. Eskridge [aut, ctb]
Repository: CRAN
Date/Publication: 2018-02-12 15:06:51 UTC

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New package npmlda with initial version 1.0.0
Package: npmlda
Type: Package
Title: Nonparametric Models for Longitudinal Data
Version: 1.0.0
Date: 2018-02-12
Author: Xin Tian, Colin Wu
Maintainer: Xin Tian <tianxtt@gmail.com>
Description: Support the book: Wu CO and Tian X (2018). Nonparametric Models for Longitudinal Data. Chapman & Hall/CRC (to appear); and provide fit for using global and local smoothing methods for the conditional-mean and conditional-distribution based models with longitudinal Data.
License: GPL (>= 2)
BugReports: https://github.com/npmldabook/npmlda/issues
URL: https://github.com/npmldabook/npmlda/
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: splines
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-12 05:26:15 UTC; tianx
Repository: CRAN
Date/Publication: 2018-02-12 12:34:47 UTC

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New package Cluster.OBeu with initial version 1.2.1
Package: Cluster.OBeu
Type: Package
Title: Cluster Analysis 'OpenBudgets'
Version: 1.2.1
Date: 2018-01-31
Description: Estimate and return the needed parameters for visualisations designed for 'OpenBudgets' <http://openbudgets.eu/> data. Calculate cluster analysis measures in budget data of municipalities across Europe, according to the 'OpenBudgets' data model. It involves a set of techniques and algorithms used to find and divide the data into groups of similar observations. Also, can be used generally to extract visualisation parameters convert them to 'JSON' format and use them as input in a different graphical interface.
Authors@R: c( person("Kleanthis", "Koupidis", , "koupidis@okfn.gr", role = c("aut", "cre")), person("Charalampos", "Bratsas", , "charalampos.bratsas@okfn.org", role = "aut"), person("Jaroslav", "Kuchar", , "jaroslav.kuchar@gmail.com", role = "ctb") )
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
URL: https://github.com/okgreece/Cluster.OBeu
BugReports: https://github.com/okgreece/Cluster.OBeu/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: TRUE
Imports: car, cluster, clValid, data.tree, dendextend, graphics, jsonlite, mclust, methods, RCurl, reshape, reshape2, stringr, tibble, utils
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-11 16:15:46 UTC; Kleanthis-Okf
Author: Kleanthis Koupidis [aut, cre], Charalampos Bratsas [aut], Jaroslav Kuchar [ctb]
Repository: CRAN
Date/Publication: 2018-02-12 11:56:09 UTC

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New package Bivariate.Pareto with initial version 1.0.0
Package: Bivariate.Pareto
Type: Package
Title: Bivariate Pareto Models
Version: 1.0.0
Date: 2018-02-10
Author: Jia-Han Shih, Wei Lee
Maintainer: Jia-Han Shih <tommy355097@gmail.com>
Description: Perform competing risks analysis under bivariate Pareto models. See Shih et al. (2018, to appear).
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Repository: CRAN
NeedsCompilation: no
Packaged: 2018-02-11 07:22:29 UTC; Tommy
Date/Publication: 2018-02-12 11:44:54 UTC

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New package telegram.bot with initial version 1.0.0
Package: telegram.bot
Type: Package
Title: Develop a 'Telegram Bot' with R
Version: 1.0.0
Authors@R: person("Ernest", "Benedito", email = "ebeneditos@gmail.com", role = c("aut", "cre"))
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Description: Features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer. It is built on top of the pure API implementation, being an extension of the 'telegram' package, an R wrapper around the 'Telegram Bot API' <http://core.telegram.org/bots/api>.
URL: http://github.com/ebeneditos/telegram.bot
BugReports: http://github.com/ebeneditos/telegram.bot/issues
Imports: R6, httr
Depends: R (>= 3.2.3), telegram (>= 0.6.0)
Suggests: covr, testthat
License: LGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-10 19:08:31 UTC; Ernest
Author: Ernest Benedito [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-12 10:29:51 UTC

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New package SolveLS with initial version 1.0
Package: SolveLS
Type: Package
Title: Iterative Methods for Solving Linear System of Equations
Version: 1.0
Authors@R: person("Kisung", "You", email = "kyou@nd.edu", role = c("aut", "cre"),comment=c(ORCID="0000-0002-8584-459X"))
Description: Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. We provide basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using 'Matrix' package along with 'RcppArmadillo'. For a more detailed description, see a book by Saad (2003) <doi:10.1137/1.9780898718003>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.4), Matrix, Rdpack
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2018-02-11 05:05:12 UTC; kisung
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Repository: CRAN
Date/Publication: 2018-02-12 10:32:53 UTC

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New package RNentropy with initial version 1.1.2
Package: RNentropy
Type: Package
Title: Entropy Based Method for the Detection of Significant Variation in Gene Expression Data
Version: 1.1.2
Date: 2018-02-08
Authors@R: c( person("Federico", "Zambelli", email = "federico.zambelli@unimi.it", role = "cre", comment = c(ORCID = "0000-0003-3487-4331")), person("Giulio", "Pavesi", email = "giulio.pavesi@unimi.it", role = "aut", comment = c(ORCID = "0000-0001-5705-6249")))
Description: An implementation of a method based on information theory devised for the identification of genes showing a significant variation of expression across multiple conditions. Given expression estimates from any number of RNA-Seq samples and conditions it identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed. Zambelli et al. (2018) <doi:10.1093/nar/gky055>.
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 18:44:51 UTC; federicozambelli
Author: Federico Zambelli [cre] (<https://orcid.org/0000-0003-3487-4331>), Giulio Pavesi [aut] (<https://orcid.org/0000-0001-5705-6249>)
Maintainer: Federico Zambelli <federico.zambelli@unimi.it>
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-02-12 10:15:16 UTC

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New package kmed with initial version 0.0.1
Package: kmed
Type: Package
Title: Distance-Based k-Medoids
Version: 0.0.1
Date: 2018-02-09
Author: Weksi Budiaji
Maintainer: Weksi Budiaji <budiaji@untirta.ac.id>
Description: A simple and fast distance-based k-medoids clustering algorithm from Park and Jun (2009) <doi:10.1016/j.eswa.2008.01.039>. Calculate distances for mixed variable data such as Gower (1971) <doi:10.2307/2528823>, Wishart (2003) <doi:10.1007/978-3-642-55721-7_23>, Podani (1999) <doi:10.2307/1224438>, Huang (1997) <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.9984&rep=rep1&type=pdf>, and Harikumar and PV (2015) <doi:10.1016/j.procs.2015.10.077>. Cluster validation applies bootstrap procedure producing a heatmap with a flexible reordering matrix algorithm such as complete, ward, or average linkages.
Depends: R (>= 2.10)
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: ggplot2
NeedsCompilation: no
Packaged: 2018-02-09 19:51:10 UTC; Weksi
Repository: CRAN
Date/Publication: 2018-02-12 10:12:53 UTC

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New package gglorenz with initial version 0.0.1
Package: gglorenz
Title: Plotting Lorenz Curve with the Blessing of 'ggplot2'
Version: 0.0.1
Authors@R: c( person("JJ", "Chen", email = "jiajia.chern@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8482-8398")) )
Description: Provides statistical transformations for plotting empirical ordinary Lorenz curve (Lorenz 1905) <doi:10.2307/2276207> and generalized Lorenz curve (Shorrocks 1983) <doi:10.2307/2554117>.
Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/jjchern/gglorenz
BugReports: https://github.com/jjchern/gglorenz/issues
RoxygenNote: 6.0.1
Imports: ineq
NeedsCompilation: no
Packaged: 2018-02-09 20:06:30 UTC; chan
Author: JJ Chen [aut, cre] (<https://orcid.org/0000-0001-8482-8398>)
Maintainer: JJ Chen <jiajia.chern@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-12 10:05:40 UTC

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New package gamm4.test with initial version 0.1.0
Package: gamm4.test
Type: Package
Title: Comparing Nonlinear Curves and Surface Estimations by Semiparametric Methods
Version: 0.1.0
Author: Shi Zhao <shizhao@iu.edu>
Maintainer: Shi Zhao <shizhao@iu.edu>
Description: To compare nonlinear curves and surface estimations between groups using semiparametric methods for cross-sectional and longitudinal dataset.
Date: 2018-02-09
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 2.14.0)
Imports: gamm4, mgcv, doParallel, foreach, parallel, plotly, Matrix, RColorBrewer
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-02-09 20:35:07 UTC; shizhao
Repository: CRAN
Date/Publication: 2018-02-12 10:10:48 UTC

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New package Lavash with initial version 1.0
Package: Lavash
Type: Package
Title: Lava Estimation for the Sum of Sparse and Dense Signals
Version: 1.0
Date: 2018-02-09
Author: Victor Chernozhukov [aut, cre], Christian Hansen [aut, cre], Yuan Liao [aut, cre], Jaeheon Jung [ctb, cre]
Maintainer: Jaeheon Jung <jaeheonj81@gmail.com>
Description: The lava estimation is a new technique to recover signals that is the sum of a sparse and dense signals. The post-lava method corrects the shrinkage bias of lava. For more information on the lava estimation, see Chernozhukov, Hansen, and Liao (2017) <doi:10.1214/16-AOS1434>.
Depends: MASS, glmnet, pracma
License: GPL-2
Repository: CRAN
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 19:45:14 UTC; Jung
Date/Publication: 2018-02-12 09:25:12 UTC

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Sun, 11 Feb 2018

New package Rraven with initial version 1.0.1
Type: Package
Package: Rraven
Title: Connecting R and 'Raven' Sound Analysis Software
Version: 1.0.1
Date: 2018-02-11
Author: Marcelo Araya-Salas
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Description: A tool to exchange data between R and 'Raven' sound analysis software <http://www.birds.cornell.edu/brp/raven/RavenOverview.html> (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
License: GPL (>= 2)
Imports: pbapply, warbleR, utils, stats, vegan, dplyr,kableExtra
Depends: R (>= 3.2.1)
LazyData: TRUE
URL: https://github.com/maRce10/Rraven
BugReports: https://github.com/maRce10/Rraven/issues
NeedsCompilation: no
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Packaged: 2018-02-11 19:07:42 UTC; m
Repository: CRAN
Date/Publication: 2018-02-11 21:01:17 UTC

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New package histry with initial version 0.1.1
Package: histry
Type: Package
Title: Enhanced Command History Tracking for R Sessions and Dynamic Documents
Version: 0.1.1
Date: 2018-02-08
Authors@R: person("Gabriel", "Becker", role = c("aut", "cre"), email = "becker.gabriel@gene.com")
Copyright: Genentech Inc
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Description: Automatically tracks and makes programmatically available code evaluation history in R sessions and dynamic documents.
License: Artistic-2.0
Depends: methods
Suggests: CodeDepends, rmarkdown, knitr, trackr
Imports: fastdigest, evaluate
VignetteBuilder: knitr
Collate: '00first.R' 'allClasses.R' 'history.R' 'tracking.R' 'zzz.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 16:44:57 UTC; beckerg4
Author: Gabriel Becker [aut, cre]
Repository: CRAN
Date/Publication: 2018-02-11 21:10:37 UTC

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New package ggfortify with initial version 0.4.2
Package: ggfortify
Type: Package
Title: Data Visualization Tools for Statistical Analysis Results
Version: 0.4.2
Date: 2018-02-10
Authors@R: c( person("Masaaki", "Horikoshi", role = c("aut"), email = "sinhrks@gmail.com"), person("Yuan", "Tang", role = c("aut", "cre"), email = "terrytangyuan@gmail.com"), person("Austin", "Dickey", role = c("ctb")), person("Matthias", "Grenié", role = c("ctb")), person("Ryan", "Thompson", role = c("ctb")), person("Luciano", "Selzer", role = c("ctb")), person("Dario", "Strbenac", role = c("ctb")), person("Kirill", "Voronin", role = c("ctb")) )
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
URL: https://github.com/sinhrks/ggfortify
BugReports: https://github.com/sinhrks/ggfortify/issues
Encoding: UTF-8
Description: Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.
License: GPL-2
VignetteBuilder: knitr
Depends: methods, ggplot2 (>= 2.0.0)
Imports: dplyr (>= 0.3), tidyr, gridExtra, grid, scales, stringr, tibble
Suggests: testthat, cluster, changepoint, dlm, fGarch, forecast, ggrepel, glmnet, grDevices, KFAS, knitr, lintr, mapdata, MASS, MSwM, nlme, raster, ROCR, sp, stats, strucchange, survival, timeSeries, tseries, utils, vars, xts, zoo, lfda
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-11 16:58:29 UTC; terrytangyuan
Author: Masaaki Horikoshi [aut], Yuan Tang [aut, cre], Austin Dickey [ctb], Matthias Grenié [ctb], Ryan Thompson [ctb], Luciano Selzer [ctb], Dario Strbenac [ctb], Kirill Voronin [ctb]
Repository: CRAN
Date/Publication: 2018-02-11 17:16:23 UTC

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New package autoplotly with initial version 0.1.1
Package: autoplotly
Type: Package
Title: Automatic Generation of Interactive Visualizations for Popular Statistical Results
Version: 0.1.1
Authors@R: person("Yuan", "Tang", role = c("aut", "cre"), email = "terrytangyuan@gmail.com")
Description: Functionalities to automatically generate interactive visualizations for popular statistical results supported by 'ggfortify', such as time series, PCA, clustering and survival analysis, with 'plotly.js' <https://plot.ly/> and 'ggplot2' style. The generated visualizations can also be easily extended using 'ggplot2' and 'plotly' syntax while staying interactive.
License: Apache License 2.0
URL: https://github.com/terrytangyuan/autoplotly
BugReports: https://github.com/terrytangyuan/autoplotly/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1)
Imports: methods, ggplot2, plotly, ggfortify
RoxygenNote: 6.0.1
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2018-02-11 17:18:22 UTC; terrytangyuan
Author: Yuan Tang [aut, cre]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-11 17:36:06 UTC

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New package warbleR with initial version 1.1.10
Package: warbleR
Type: Package
Title: Streamline Bioacoustic Analysis
Version: 1.1.10
Date: 2018-01-28
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository 'Xeno-Canto' <http://xeno-canto.org/>, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
License: GPL (>= 2)
Imports: bitops, doParallel, dtw, fftw, foreach, graphics, grDevices, iterators, jpeg, monitoR, parallel, pbapply, pbmcapply, proxy, RCurl, rjson, stats, signal, utils, methods
Depends: R (>= 3.2.1), maps, tuneR, seewave (>= 2.0.1), NatureSounds
LazyData: TRUE
URL: https://github.com/maRce10/warbleR
BugReports: https://github.com/maRce10/warbleR/issues
NeedsCompilation: no
Suggests: knitr, ggplot2, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Packaged: 2018-02-10 15:53:13 UTC; m
Repository: CRAN
Date/Publication: 2018-02-11 15:37:12 UTC

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New package snappier with initial version 0.1.0
Package: snappier
Title: Compress and Decompress 'Snappy' Encoded Data
Version: 0.1.0
Authors@R: c( person("Huw", "Campbell", email = "huw.campbell@gmail.com", role = c("aut", "cre")) , person("Jeff", "Dean", role = "ctb") , person("Sanjay", "Ghemawat", role = "ctb") , person("Steinar", "Gunderson", role = "ctb") , person("Martin", "Gieseking", email = "martin.gieseking@uos.de", role = "ctb") , person("Google Inc.", role = "cph") )
Description: Compression and decompression with 'Snappy'.
Depends: R (>= 3.3.0)
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2018-02-08 09:50:59 UTC; hcampbell
Author: Huw Campbell [aut, cre], Jeff Dean [ctb], Sanjay Ghemawat [ctb], Steinar Gunderson [ctb], Martin Gieseking [ctb], Google Inc. [cph]
Maintainer: Huw Campbell <huw.campbell@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-11 15:27:41 UTC

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New package lakemorpho with initial version 1.1.1
Package: lakemorpho
Type: Package
Title: Lake Morphometry Metrics
Version: 1.1.1
Authors@R: c( person(given = "Jeffrey W.", family = "Hollister", role = c("aut","cre"), email = "hollister.jeff@epa.gov"), person(given = "Joseph", family = "Stachelek", role = "ctb") )
URL: http://www.github.com/jhollist/lakemorpho
BugReports: https://www.github.com/jhollist/lakemorpho/issues
Maintainer: Jeffrey W. Hollister <hollister.jeff@epa.gov>
License: CC0
Description: Lake morphometry metrics are used by limnologists to understand, among other things, the ecological processes in a lake. Traditionally, these metrics are calculated by hand, with planimeters, and increasingly with commercial GIS products. All of these methods work; however, they are either outdated, difficult to reproduce, or require expensive licenses to use. The 'lakemorpho' package provides the tools to calculate a typical suite of these metrics from an input elevation model and lake polygon. The metrics currently supported are: fetch, major axis, minor axis, major/minor axis ratio, maximum length, maximum width, mean width, maximum depth, mean depth, shoreline development, shoreline length, surface area, and volume.
Depends: R (>= 3.0.0)
Imports: methods, stats, grDevices, rgdal, raster, rgeos, sp, geosphere, cluster
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 22:03:17 UTC; jhollist
Author: Jeffrey W. Hollister [aut, cre], Joseph Stachelek [ctb]
Repository: CRAN
Date/Publication: 2018-02-11 14:45:57 UTC

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Fri, 09 Feb 2018

New package srp with initial version 1.0.0
Package: srp
Title: Smooth-Rough Partitioning of the Regression Coefficients
Version: 1.0.0
Authors@R: c(person("Hyeyoung", "Maeng", email = "h.maeng@lse.ac.uk", role = c("aut", "cre")), person("Piotr", "Fryzlewicz", email = "p.fryzlewicz@lse.ac.uk", role="aut"))
Description: Performs the change-point detection in regression coefficients of linear model by partitioning the regression coefficients into two classes of smoothness. The change-point and the regression coefficients are jointly estimated.
Depends: R (>= 3.4.0)
License: GPL
LazyData: true
Imports: fda, mgcv
NeedsCompilation: no
RoxygenNote: 6.0.1
Packaged: 2018-02-09 16:57:05 UTC; maengh
Author: Hyeyoung Maeng [aut, cre], Piotr Fryzlewicz [aut]
Maintainer: Hyeyoung Maeng <h.maeng@lse.ac.uk>
Repository: CRAN
Date/Publication: 2018-02-09 18:29:54 UTC

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New package SoilHyP with initial version 0.1.0
Package: SoilHyP
Type: Package
Title: Soil Hydraulic Properties
Version: 0.1.0
Date: 2018-01-12
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Authors@R: c(person('Ullrich', 'Dettmann', email = 'ullrich.dettmann@thuenen.de', role = c('aut', 'cre')), person('Felix', 'Andrews', role = 'ctb', comment = 'For the code copied from the hydromad::SCEoptim function (Version: 0.9-15) which is not on r-cran (https://github.com/floybix/hydromad). The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code'), person('Brecht', 'Donckels', role = 'ctb', comment = 'For the Matlab code which was adapted and reviesed in the hydromad::SCEoptim function.'), person('Qingyun', 'Duan', role = 'ctb', comment = 'For the MATLAB code adapted from Brecht Donkels.'))
Description: Provides functions for (1) soil water retention and unsaturated hydraulic conductivity (van Genuchten-Mualem (vGM/vG) (van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>; Mualem (1976) <doi:10.1029/WR012i003p00513>), Peters-Durner-Iden (PDI) (Peters (2013) <doi:10.1002/wrcr.20548>; Iden and Durner (2013) <doi:10.1002/2014WR015937>; Peters (2014) <doi:10.1002/2014WR015937>)), (2) fitting of parameter for soil water retention (SWC) and/or unsaturated hydraulic conductivity function (Ku) using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (unsaturated hydraulic conductivities and soil water contents) based on the simplfied evaporation method (SEM) (Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016>).
Encoding: UTF-8
License: GPL (>= 2)
Depends: R (>= 3.4.0)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 16:24:16 UTC; ulli
Author: Ullrich Dettmann [aut, cre], Felix Andrews [ctb] (For the code copied from the hydromad::SCEoptim function (Version: 0.9-15) which is not on r-cran (https://github.com/floybix/hydromad). The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code), Brecht Donckels [ctb] (For the Matlab code which was adapted and reviesed in the hydromad::SCEoptim function.), Qingyun Duan [ctb] (For the MATLAB code adapted from Brecht Donkels.)
Repository: CRAN
Date/Publication: 2018-02-09 18:42:24 UTC

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New package NCutYX with initial version 0.1.0
Package: NCutYX
Type: Package
Title: Clustering of Omics Data of Multiple Types with a Multilayer Network Representation
Version: 0.1.0
Author: Sebastian J. Teran Hidalgo, Shuangge Ma, Ruofan Bie
Maintainer: Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>
Description: Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>).
License: GPL-3
Depends: R (>= 3.4)
Imports: Rcpp (>= 0.12.2), glmnet (>= 2.0-5), MASS (>= 7.3-47), mvtnorm (>= 1.0-6), fields (>= 9.0)
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 6.0.1
URL: https://github.com/Seborinos/NCutYX
BugReports: https://github.com/Seborinos/NCutYX/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-02-09 16:43:40 UTC; sebastianteranhidalgo
Repository: CRAN
Date/Publication: 2018-02-09 18:27:31 UTC

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New package facilitation with initial version 0.5.2
Package: facilitation
Title: A C++ Framework for Plant-Plant Interaction IBMs
Version: 0.5.2
Authors@R: c(person("Mali", "Salles", email = "marinacs@gmail.com", role = c("aut", "cre")), person("Andre", "Chalom", email="andrechalom@gmail.com", role=c("aut")), person("Alexandre", "Adalardo", email="aleadalardo@gmail.com", role="aut"), person("Camila", "Castanho", role="ctb"))
Description: A tool for simulating a variety of spatial individual-based models of plant-plant interactions. User-created models can include any number of species, each of which can be structured in any number of life-stages, where each life-stage has specific death, growth and reproduction rates, as well as specific interaction radius, dispersal radius, and interaction effects over each other species/life-stage. Life stages were modeled so as to be a stochastic, individual-based version of differential Matrix Population Models (Caswell 2001, ISBN:0-87893-096-5). Interactions can be positive (facilitation) or negative (competition) and can affect death rates, growth rates or reproduction rates. Interactions from multiple numbers are additive, so as to best approximate classic population dynamics models such as the logistic model and Lotka-Volterra model (Britton 2004, ISBN:9781852335366). All models work in continuous time, implemented as an optimized version of the Gillespie algorithm (Gillespie 1976 <doi:10.1016/0021-9991(76)90041-3>) for independent exponential times, and continuous space.
Imports: Rcpp (>= 0.12.14), Matrix, grid, animation
LinkingTo: Rcpp
Suggests: knitr, rmarkdown
Depends: R (>= 3.1.0)
SystemRequirements: C++11
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1
URL: https://github.com/Lobz/facilitation
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-02-09 16:37:36 UTC; oz
Author: Mali Salles [aut, cre], Andre Chalom [aut], Alexandre Adalardo [aut], Camila Castanho [ctb]
Maintainer: Mali Salles <marinacs@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-09 18:25:21 UTC

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New package Dykstra with initial version 1.0-0
Package: Dykstra
Type: Package
Title: Quadratic Programming using Cyclic Projections
Version: 1.0-0
Date: 2018-02-09
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Description: Solves quadratic programming problems using Richard L. Dykstra's cyclic projection algorithm. Routine allows for a combination of equality and inequality constraints. See Dykstra (1983) <doi:10.1080/01621459.1983.10477029> for details.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-02-09 16:52:11 UTC; Nate
Repository: CRAN
Date/Publication: 2018-02-09 18:34:56 UTC

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New package oxcAAR with initial version 1.0.0
Package: oxcAAR
Type: Package
Title: Interface to 'OxCal' Radiocarbon Calibration
Version: 1.0.0
Date: 2018-02-08
Authors@R: c( person("Hinz", "Martin", email = "martin.hinz@ufg.uni-kiel.de", role = c("aut", "cre")), person("Clemens", "Schmid", email = "clemens@nevrome.de", role = c("aut")), person("Daniel", "Knitter", email = "knitter@geographie.uni-kiel.de", role = c("aut")), person("Carolin", "Tietze", email = "Carolin Tietze <ctietze1991@gmail.com>", role = c("aut")) )
Description: A set of tools that enables using 'OxCal' from within R. 'OxCal' (<https://c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to provide 14C calibration and analysis of archaeological and environmental chronological information. 'OxcAAR' allows simple calibration with 'Oxcal' and plotting of the results as well as the execution of sophisticated ('OxCal') code and the import of the results of bulk analysis and complex Bayesian sequential calibration.
License: GPL-2 | file LICENSE
LazyData: TRUE
Imports: stringr, jsonlite
Suggests: knitr, testthat
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-09 12:49:55 UTC; martin
Author: Hinz Martin [aut, cre], Clemens Schmid [aut], Daniel Knitter [aut], Carolin Tietze [aut]
Maintainer: Hinz Martin <martin.hinz@ufg.uni-kiel.de>
Repository: CRAN
Date/Publication: 2018-02-09 13:05:11 UTC

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New package NatureSounds with initial version 1.0.0
Package: NatureSounds
Type: Package
Title: Animal Sounds for Bioacustic Analysis
Version: 1.0.0
Date: 2018-08-28
Author: Marcelo Araya-Salas
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Description: Collection of example animal sounds for bioacoustic analysis.
License: GPL (>= 2)
Imports:
Depends: R (>= 3.2.1)
LazyData: TRUE
URL: https://github.com/maRce10/NatureSounds
BugReports: https://github.com/maRce10/NatureSounds/issues
NeedsCompilation: no
Suggests:
RoxygenNote: 6.0.1
Repository: CRAN
Packaged: 2018-02-08 23:33:55 UTC; m
Date/Publication: 2018-02-09 13:31:48 UTC

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New package odkr with initial version 0.1.3
Package: odkr
Type: Package
Title: 'Open Data Kit' ('ODK') R API
Version: 0.1.3
Authors@R: c( person("Ernest", "Guevarra", email = "ernestgmd@gmail.com", role = c("aut", "cre")), person("Laura", "Bramley", email = "laura@validinternational.org", role = "aut"), person("Valid", "International", email = "office@validinternational", role = "cph"))
Description: Utility functions for working with datasets gathered using 'Open Data Kit' ('ODK') <https://opendatakit.org/>. These include an API to interface with 'ODK Briefcase', a 'Java' application for fetching and pushing 'ODK' forms and their contents, that allows pulling of data from either a remote 'ODK Aggregate Server' or a local 'ODK' folder, a rename function to give more human readable variable names for 'ODK' datasets, a merge function to create a single dataframe from a nested 'ODK' dataset and an expand function to disaggregate multiple choice answers that have been collapsed into single code by 'ODK'.
Imports: stringr, Hmisc
Depends: R (>= 2.10)
Suggests: testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
SystemRequirements: Java
RoxygenNote: 6.0.1
URL: https://github.com/validmeasures/odkr
BugReports: https://github.com/validmeasures/odkr/issues
NeedsCompilation: no
Packaged: 2018-02-09 11:19:33 UTC; ernest
Author: Ernest Guevarra [aut, cre], Laura Bramley [aut], Valid International [cph]
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-09 12:26:02 UTC

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New package BSPADATA with initial version 1.0
Package: BSPADATA
Type: Package
Title: Bayesian Proposal to Fit Spatial Econometric Models
Version: 1.0
Date: 2018-02-09
Author: Jorge Sicacha-Parada and Edilberto Cepeda-Cuervo
Maintainer: Jorge Sicacha-Parada <jasicachap@unal.edu.co>
Depends: R (>= 3.1.1), mvtnorm, spdep, pscl
Description: The purpose of this package is to fit the three Spatial Econometric Models proposed in Anselin (1988, ISBN:9024737354) in the homoscedastic and the heteroscedatic case. The fit is made through MCMC algorithms and observational working variables approach.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-02-09 10:23:26 UTC; USER
Repository: CRAN
Date/Publication: 2018-02-09 12:21:13 UTC

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New package miceExt with initial version 1.0.0
Package: miceExt
Title: Extension Package to 'mice'
Version: 1.0.0
Authors@R: c( person("Tobias", "Schumacher", email = "tobias.schumacher1@rwth-aachen.de", role = c("aut", "cre")), person("Philipp", "Gaffert", email = "philipp.gaffert@gfk.com", role = "aut"), person("Stef", "van Buuren", email = "stef.vanbuuren at tno.nl", role = "ctb"), person("Karin", "Groothuis-Oudshoorn", role = "ctb", email = "c.g.m.oudshoorn@utwente.nl"))
Maintainer: Tobias Schumacher <tobias.schumacher1@rwth-aachen.de>
Description: Extends and builds on the 'mice' package by adding a functionality to perform multivariate predictive mean matching on imputed data as well as new functionalities to perform predictive mean matching on factor variables.
Depends: R (>= 3.3), mice (>= 2.46.0)
Imports: RANN (>= 2.5.1), RANN.L1 (>= 2.5)
License: GPL-2
Author: Tobias Schumacher [aut, cre], Philipp Gaffert [aut], Stef van Buuren [ctb], Karin Groothuis-Oudshoorn [ctb]
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-02-08 18:49:16 UTC; tobi_
Repository: CRAN
Date/Publication: 2018-02-09 11:12:24 UTC

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New package knitrProgressBar with initial version 1.0.0
Package: knitrProgressBar
Type: Package
Title: Provides Progress Bars in 'knitr'
Version: 1.0.0
Authors@R: c(person(given = c("Robert", "M"), family = "Flight", email = "rflight79@gmail.com", role = c("aut", "cre")), person("Hadley", "Wickham", role = "ctb", comment = "Author of included dplyr fragments"), person("Romain", "Francois", role = "ctb", comment = "Author of included dplyr fragments"), person("Lionel", "Henry", role = "ctb", comment = "Author of included dplyr fragments"), person("Kirill", "Müller", role = "ctb", comment = "Author of included dplyr fragments"), person("RStudio", role = "cph", comment = "Copyright holder of included dplyr fragments"))
Description: Provides a progress bar similar to 'dplyr' that can write progress out to a variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown', and you still want to see progress of calculations in the terminal.
BugReports: https://github.com/rmflight/knitrProgressBar/issues
URL: https://rmflight.github.io/knitrProgressBar
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: R6, R.oo
Suggests: knitr, rmarkdown, purrr, testthat, covr, mockr, withr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-08 20:45:55 UTC; rmflight
Author: Robert M Flight [aut, cre], Hadley Wickham [ctb] (Author of included dplyr fragments), Romain Francois [ctb] (Author of included dplyr fragments), Lionel Henry [ctb] (Author of included dplyr fragments), Kirill Müller [ctb] (Author of included dplyr fragments), RStudio [cph] (Copyright holder of included dplyr fragments)
Maintainer: Robert M Flight <rflight79@gmail.com>
Repository: CRAN
Date/Publication: 2018-02-09 11:32:54 UTC

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New package idealstan with initial version 0.2.7
Package: idealstan
Type: Package
Title: Bayesian IRT Ideal Point Models with 'Stan'
Version: 0.2.7
Date: 2018-02-07
Authors@R: c(person("Robert","Kubinec", role = c("aut","cre"), email = "rmk7xy@virginia.edu"), person("Jonah", "Gabry", role = "ctb"), person("Ben", "Goodrich", role = "ctb"), person("Trustees of Columbia University",role='cph'))
BugReports: https://github.com/saudiwin/idealstan/issues
Description: Offers item-response theory (IRT) ideal-point scaling/dimension reduction methods that incorporate additional response categories and missing/censored values, including absences and abstentions, for roll call voting data (or any other kind of binary or ordinal item-response theory data). Full and approximate Bayesian inference is done via the 'Stan' engine (www.mc-stan.org).
License: GPL
Depends: R (>= 3.1), Rcpp (>= 0.12.7)
Imports: rstan (>= 2.13.2), rstantools (>= 1.1.0), methods (>= 3.3.1), dplyr, tidyr, stringr, bayesplot, ggplot2, lazyeval, rlang, shinystan
Suggests: pscl, loo, knitr, rmarkdown
LinkingTo: StanHeaders (>= 2.13.1), rstan (>= 2.13.2), BH (>= 1.62.0.1), Rcpp (>= 0.12.7), RcppEigen (>= 0.3.2.9.0)
RoxygenNote: 6.0.1
LazyData: false
VignetteBuilder: knitr
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2018-02-08 18:35:01 UTC; bobku
Author: Robert Kubinec [aut, cre], Jonah Gabry [ctb], Ben Goodrich [ctb], Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7xy@virginia.edu>
Repository: CRAN
Date/Publication: 2018-02-09 11:16:51 UTC

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Thu, 08 Feb 2018

New package specklestar with initial version 0.0.1.7
Package: specklestar
Version: 0.0.1.7
Title: Reduction of Speckle Data from BTA 6-m Telescope
Description: A set of functions for obtaining positional parameters and magnitude difference between components of binary and multiple stellar systems from series of speckle images.
Author: Denis Rastegaev
Maintainer: Denis Rastegaev <drastega@gmail.com>
URL: https://drastega.github.io/docs/specklestar_vignette.html
BugReports: https://github.com/drastega/specklestar/issues
Depends: R (>= 3.0.0)
Imports: Rcpp
Suggests: imager, tidyverse, rgl, fftw, mrbsizeR, knitr, rmarkdown
License: GPL-2
NeedsCompilation: yes
SystemRequirements: fftw3 (>= 3.1.2)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Packaged: 2018-02-08 13:50:57 UTC; leda
Repository: CRAN
Date/Publication: 2018-02-08 18:14:49 UTC

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New package qcQpcr with initial version 1.5
Package: qcQpcr
Type: Package
Title: Histone ChIP-Seq qPCR Analyzer
Version: 1.5
Date: 2018-02-02
Author: Alireza Lorzadeh
Maintainer: Alireza Lorzadeh <alorzadeh@bcgsc.ca>
Description: Quality control of chromatin immunoprecipitation libraries (ChIP-seq) by quantitative polymerase chain reaction (qPCR). This function calculates Enrichment value with respect to reference for each histone modification (specific to 'Vii7' software <http://www.thermofisher.com/ca/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system/viia-7-software.html>). This function is applicable to full panel of histone modifications described by International Human Epigenomic Consortium (IHEC).
Imports: ggplot2
License: MIT + file LICENSE
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2018-02-08 18:09:49 UTC; epigenomics_lab_01
Repository: CRAN
Date/Publication: 2018-02-08 18:44:50 UTC

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