Thu, 05 May 2016

New package norm2 with initial version 2.0.0
Package: norm2
Type: Package
Title: Analysis of Incomplete Multivariate Data under a Normal Model
Version: 2.0.0
Date: 2016-05-05
Author: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Maintainer: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Description: Functions for parameter estimation, Bayesian posterior simulation and multiple imputation from incomplete multivariate data under a normal model.
Depends: R (>= 3.1.0)
Imports: stats
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-05 16:44:14 UTC; schaf310
Repository: CRAN
Date/Publication: 2016-05-06 00:12:51

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New package lmem.qtler with initial version 0.1.0
Package: lmem.qtler
Type: Package
Title: Linear Mixed Effects Models for QTL Mapping for Multienvironment and Multitrait Analysis
Version: 0.1.0
Authors@R: c(person("Lucia", "Gutierrez", role = "aut", email = "gutierrezcha@wisc.edu"), person("Gaston", "Quero",role =c("aut","cre"), email = "gastonquero@gmail.com"), person("Schubert", "Fernandez",role ="aut", email = "sfernandez@inia.org.uy"), person("Sofia", "Brandariz",role ="aut", email = "brandarizsofia@gmail.com"), person("Sebastian", "Simondi",role ="ctb", email = "sebastian.simondi@gmail.com"))
Author: Lucia Gutierrez [aut], Gaston Quero [aut, cre], Schubert Fernandez [aut], Sofia Brandariz [aut], Sebastian Simondi [ctb]
Maintainer: Gaston Quero <gastonquero@gmail.com>
Description: Performs QTL mapping analysis for balanced and for multi-environment and multi-trait analysis using mixed models. Balanced population, single trait, single environment QTL mapping is performed through marker-regression (Haley and Knott (1992) <DOI:10.1038/hdy.1992.131>, Martinez and Curnow (1992) <DOI:10.1007/BF00222330>, while multi-environment and multi-trait QTL mapping is performed through linear mixed models. These functions could use any of the following populations: double haploid, F2, recombinant inbred lines, back-cross, and 4-way crosses. Performs a Single Marker Analysis, a Single Interval Mapping, or a Composite Interval Mapping analysis, and then constructs a final model with all of the relevant QTL.
License: GPL-3
Depends: R (>= 2.10)
LazyData: TRUE
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: qtl, lme4, lattice, pastecs, stringr, graphics, utils, grDevices, stats
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-05 15:16:20 UTC; GQ
Repository: CRAN
Date/Publication: 2016-05-06 00:09:50

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New package imputeMulti with initial version 0.4.5
Package: imputeMulti
Title: Imputation Methods for Multivariate Multinomial Data
Version: 0.4.5
Authors@R: person("Alex", "Whitworth", , "whitworth.alex@gmail.com", c("aut", "cre"))
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Depends: R (>= 3.2.1)
Imports: gtools (>= 3.3), methods, parallel, Rcpp
License: GPL-3
LazyData: true
Suggests: testthat
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-05 15:34:54 UTC; awhitworth
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-05 23:49:23

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New package PResiduals with initial version 0.2-2
Package: PResiduals
Type: Package
Title: Probability-Scale Residuals and Residual Correlations
Version: 0.2-2
Date: 2015-07-21
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont <charles.dupont@vanderbilt.edu>
Description: Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data.
Imports: MASS, Formula, rms,
Suggests: survival
License: GPL (>= 2)
Collate: 'GKGamma.R' 'PResiduals-package.R' 'pgumbel.R' 'newPolr.R' 'diagn.R' 'cobot.R' 'cocobot.R' 'cocobot_orm.R' 'condis.R' 'corTS.R' 'countbot.R' 'getCI.R' 'lm.scores.R' 'megabot.R' 'nb.scores.R' 'orm.scores.R' 'poisson.scores.R' 'presid.R' 'print.cobot.R' 'print.cocobot.R'
NeedsCompilation: no
Packaged: 2015-07-22 14:26:21 UTC; dupontct
Repository: CRAN
Date/Publication: 2015-07-23 04:45:55

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Wed, 04 May 2016

New package nortestARMA with initial version 1.0
Package: nortestARMA
Type: Package
Title: Neyman Smooth Tests of Normality for the Errors of ARMA Models
Version: 1.0
Date: 2016-05-04
License: GPL (> 2)
LazyLoad: yes
Author: Pierre Duchesne and Pierre Lafaye de Micheaux
Maintainer: Pierre Lafaye de Micheaux <lafaye@dms.umontreal.ca>
Description: Tests the goodness-of-fit to the Normal distribution for the errors of an ARMA model.
Depends: R (>= 2.10.0), astsa
Packaged: 2016-05-04 12:20:29 UTC; lafaye
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-05-04 18:04:22

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New package UNCLES with initial version 1.0
Package: UNCLES
Type: Package
Title: Unification of Clustering Results from Multiple Datasets using External Specifications
Version: 1.0
Date: 2016-04-29
Author: Basel Abu-Jamous
Maintainer: Basel Abu-Jamous <baselabujamous@gmail.com>
Description: Consensus clustering by the unification of clustering results from multiple datasets using external specifications.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-05-04 10:03:02 UTC; eepgbwa
Repository: CRAN
Date/Publication: 2016-05-04 13:16:23

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New package sparsevar with initial version 0.0.3
Package: sparsevar
Version: 0.0.3
Date: 2016-05-04
Title: A Package for Sparse VAR/VECM Estimation
Authors@R: c(person("Simone", "Vazzoler", role = c("aut", "cre"), email = "svazzole@gmail.com"), person("Lorenzo", "Frattarolo", role = "aut"))
Maintainer: Simone Vazzoler <svazzole@gmail.com>
Imports: Matrix, ncvreg, parallel, glmnet, MTS, ggplot2, reshape2, grid, caret
Suggests: knitr
Depends: R (>= 1.8.0)
Description: A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET, SCAD and MCP.
License: GPL-2
URL: http://github.com/svazzole/sparsevar
BugReports: http://github.com/svazzole/sparsevar
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 08:11:24 UTC; svazzole
Author: Simone Vazzoler [aut, cre], Lorenzo Frattarolo [aut]
Repository: CRAN
Date/Publication: 2016-05-04 12:47:00

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New package regspec with initial version 2.1
Package: regspec
Type: Package
Title: Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Version: 2.1
Date: 2016-04-12
Authors@R: c(person("Ben", "Powell", role=c("aut", "cre"), email="ben.powell@bristol.ac.uk"), person("Guy", "Nason", role=c("aut"), email="g.p.nason@bristol.ac.uk"))
Description: Computes linear Bayesian spectral estimates from multirate data for second-order stationary time series. Provides credible intervals and methods for plotting various spectral estimates.
License: GPL-2
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-04 08:41:45 UTC; bp13548
Author: Ben Powell [aut, cre], Guy Nason [aut]
Maintainer: Ben Powell <ben.powell@bristol.ac.uk>
Repository: CRAN
Date/Publication: 2016-05-04 12:46:58

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New package gepaf with initial version 0.1.0
Package: gepaf
Type: Package
Title: Google Encoded Polyline Algorithm Format
Version: 0.1.0
Date: 2016-05-03
Authors@R: c(person("Matthieu", "Viry", email = "matthieu.viry@ums-riate.fr",role = c("aut")),person("Timothée", "Giraud", email = "timothee.giraud@ums-riate.fr", role = c("ctb","cre")))
Description: Encode and decode the Google Encoded Polyline Algorithm Format (<https://developers.google.com/maps/documentation/utilities/polylinealgorithm>).
License: GPL-3
LazyData: TRUE
Imports: bitops
URL: https://github.com/mthh/gepaf
BugReports: https://github.com/mthh/gepaf/issues
RoxygenNote: 5.0.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-04 08:13:59 UTC; tg
Author: Matthieu Viry [aut], Timothée Giraud [ctb, cre]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Repository: CRAN
Date/Publication: 2016-05-04 12:46:38

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New package synergyfinder with initial version 0.1
Package: synergyfinder
Type: Package
Title: Calculate and Visualize Synergy Scores for Drug Combinations
Version: 0.1
Date: 2016-04-15
Author: Liye He <liye.he@helsinki.fi>, Jing Tang <jing.tang@helsinki.fi>
Maintainer: Liye He <liye.he@helsinki.fi>
Imports: drc (>= 2.5-12), reshape2 (>= 1.4.1), kriging (>= 1.1), ggplot2 (>= 2.1.0), gridBase (>= 0.4-7), grid (>= 3.2.4), lattice (>= 0.20-33), gplots (>= 3.0.0), nleqslv(>= 3.0)
Description: Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix.
License: Artistic License 2.0
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 06:49:24 UTC; admin
Repository: CRAN
Date/Publication: 2016-05-04 10:02:51

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New package gapfill with initial version 0.9.3
Package: gapfill
Type: Package
Title: Fill Missing Values in Satellite Data
Version: 0.9.3
Date: 2016-05-04
Author: Florian Gerber
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Description: Tools to fill missing values in satellite data and to develop new gap-fill algorithms. The methods are tailored to data (images) observed at equally-spaced points in time. The package is illustrated with MODIS NDVI data.
License: GPL (>= 2)
Depends: R (>= 3.1), ggplot2 (>= 2.0.0)
Imports: fields, foreach (>= 1.4), Rcpp (>= 0.12.1), quantreg (>= 5.0)
Suggests: roxygen2, spam, testthat
Enhances: raster, doParallel, doMPI
LinkingTo: Rcpp
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-04 07:54:46 UTC; flgerb
Repository: CRAN
Date/Publication: 2016-05-04 10:13:27

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New package addinslist with initial version 0.1
Package: addinslist
Title: Discover and Install Useful RStudio Addins
Version: 0.1
Authors@R: person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"))
Description: Browse through a continuously updated list of existing RStudio addins and install/uninstall their corresponding packages.
URL: https://github.com/daattali/addinslist
BugReports: https://github.com/daattali/addinslist/issues
Depends: R (>= 3.1.0)
Imports: curl, devtools, DT (>= 0.1), miniUI (>= 0.1), shiny (>= 0.13.2), shinyjs (>= 0.6), rappdirs (>= 0.3.1), rmarkdown, rvest (>= 0.3.1), utils, xml2 (>= 0.1.2)
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 07:33:49 UTC; Dean
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-04 10:02:46

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New package RSentiment with initial version 1.0.4
Package: RSentiment
Type: Package
Title: Analyse Sentiment of English Sentences
Version: 1.0.4
Imports: plyr,stringr
Date: 2016-04-20
Author: Subhasree Bose <subhasree10.7@gmail.com>
Maintainer: Subhasree Bose <subhasree10.7@gmail.com>
Description: Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative, Neutral or Sarcasm. For a vector of sentences, it counts the number of sentences in each category of sentiment.In calculating the score, negation and various degrees of adjectives are taken into consideration. It deals only with English sentences.
Depends: R (>= 2.1.0)
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-03 18:21:19 UTC; dodo
Repository: CRAN
Date/Publication: 2016-05-04 07:56:43

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New package cocoreg with initial version 0.1.0
Package: cocoreg
Type: Package
Title: Extracts Shared Variation in Collections of Datasets Using Regression Models
Version: 0.1.0
Description: The cocoreg algorithm extracts shared variation from a collection of datasets using regression models.
Authors@R: c( person("Jussi", "Korpela", role = c("aut", "cre"), email = "jussi.korpela@iki.fi"), person("Andreas", "Henelius", role = c("aut"), email = "andreas.henelius@iki.fi"), person("Finnish Institute of Occupational Health", role = "cph") )
Author: Jussi Korpela [aut, cre], Andreas Henelius [aut], Finnish Institute of Occupational Health [cph]
Maintainer: Jussi Korpela <jussi.korpela@iki.fi>
Depends: R (>= 3.2.0)
Imports: ggplot2, gridExtra, CCAGFA, RGCCA, combinat, abind, MASS, glmnet, pls, e1071, multiway, reshape
License: MIT + file LICENSE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-03 10:00:25 UTC; jkor
Repository: CRAN
Date/Publication: 2016-05-03 18:35:21

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New package beanz with initial version 1.0
Package: beanz
Title: Bayesian Analysis of Heterogeneous Treatment Effect
Version: 1.0
Author: Chenguang Wang [aut, cre], Ravi Varadhan [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>
Description: It is vital to assess the heterogeneity of treatment effects (HTE) when making health care decisions for an individual patient or a group of patients. Nevertheless, it remains challenging to evaluate HTE based on information collected from clinical studies that are often designed and conducted to evaluate the efficacy of a treatment for the overall population. The Bayesian framework offers a principled and flexible approach to estimate and compare treatment effects across subgroups of patients defined by their characteristics. This package allows users to explore a wide range of Bayesian HTE analysis models, and produce posterior inferences about HTE.
Depends: R (>= 3.0.2), Rcpp (>= 0.11.0)
License: GPL (>= 3)
LinkingTo: StanHeaders (>= 2.8.0), rstan (>= 2.8.1), BH (>= 1.58.0), Rcpp (>= 0.11.0), RcppEigen
RcppModules: stan_fit4nse_mod, stan_fit4fs_mod, stan_fit4sr_mod, stan_fit4bs_mod, stan_fit4srs_mod, stan_fit4ds_mod, stan_fit4eds_mod
LazyData: true
NeedsCompilation: yes
Imports: rstan (>= 2.8.1), methods, survival
Suggests: knitr, shiny, anoint, rmarkdown, pander
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Packaged: 2016-05-03 19:25:51 UTC; cwang68
Repository: CRAN
Date/Publication: 2016-05-04 09:00:44

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Tue, 03 May 2016

New package rankFD with initial version 0.0.0.2
Package: rankFD
Type: Package
Title: Rank-Based Tests for General Factorial Designs
Version: 0.0.0.2
Date: 2016-05-02
Author: Frank Konietschke, Sarah Friedrich, Edgar Brunner, Markus Pauly
Maintainer: Frank Konietschke <fxk141230@utdallas.edu>
Depends: R (>= 3.2.2)
Description: The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data in a crossed design with an arbitrary number of factors.
License: GPL-2 | GPL-3
Imports: lattice (>= 0.20-33), MASS (>= 7.3-43), Matrix (>= 1.2-2), coin (>= 1.1-2)
LazyData: TRUE
Suggests: RGtk2 (>= 2.20.31)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-02 14:39:27 UTC; sarah
Repository: CRAN
Date/Publication: 2016-05-02 17:50:37

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New package quhomology with initial version 1.1.0
Package: quhomology
Type: Package
Title: Calculation of Homology of Quandles, Racks, Biquandles and Biracks
Version: 1.1.0
Date: 2016-04-30
Authors@R: c(person("Ansgar", "Wenzel", email="ansgar.wenzel@gmail.com", role=c("aut", "cre")))
Description: This calculates the Quandle, Rack and Degenerate Homology groups of Racks and Biracks (as well as Quandles and Biquandles). In addition, a test is provided to ascertain if a given set with one or two given functions is indeed a biquandle or not.
License: GPL (>= 3)
Imports: MASS, numbers
Depends: R(>= 3.0.0)
ByteCompile: yes
Suggests: testthat
NeedsCompilation: no
Packaged: 2016-05-02 15:30:53 UTC; ansgar
Author: Ansgar Wenzel [aut, cre]
Maintainer: Ansgar Wenzel <ansgar.wenzel@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-02 17:59:48

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New package milonga with initial version 1.0
Package: milonga
Type: Package
Title: Multiple Imputation for Multivariate Binary Outcome
Version: 1.0
Date: 2016-01-26
Author: Dadong Zhang, Josyf C. Mychaleckyj
Maintainer: Dadong Zhang <ddzhangzz@gmail.com>
Description: Multiple imputation for multivariate binary outcome by using Gibbs' Sampler on all potential profiles.
License: GPL-3
Depends: R (>= 3.0.0), MCMCpack
LazyData: true
NeedsCompilation: no
Packaged: 2016-01-26 17:52:03 UTC; dz33
Repository: CRAN
Date/Publication: 2016-05-03 01:36:41

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New package kernscr with initial version 1.0.0
Package: kernscr
Type: Package
Title: Kernel Machine Score Test for Semi-Competing Risks
Version: 1.0.0
Date: 2016-05-02
Author: c(person("Boris P.", "Hejblum", role = c("aut", "cre"), email = "bhejblum@hsph.harvard.edu"), person("Matey", "Neykov", role = c("aut", "cre"), email = "mneykov@gmail.com")) person("Jennifer A.", "Sinnot", role = c("aut", "cre"), email = "jsinnott@stat.osu.edu"))
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>
Description: Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks.
Depends: R (>= 3.0)
Imports: graphics, MASS, mvtnorm, stats
Suggests: gdata, org.Hs.eg.db
License: GPL-2 | file LICENSE
LazyData: TRUE
BugReports: https://github.com/borishejblum/kernscr/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-02 17:32:34 UTC; bhejblum
Repository: CRAN
Date/Publication: 2016-05-03 08:20:43

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New package imputePSF with initial version 0.1.0
Package: imputePSF
Type: Package
Title: Impute Missing Data in Time Series Data with PSF Based Method
Version: 0.1.0
Author: Neeraj Bokde
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Description: Imputes the missing values in time series data with PSF algorithm based approach. The details about PSF algorithm are available at: <https://cran.r-project.org/package=PSF>.
License: GPL
Imports: PSF, graphics, stats
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-02 06:25:43 UTC; NEERAJ
Repository: CRAN
Date/Publication: 2016-05-02 09:08:42

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New package hms with initial version 0.1
Package: hms
Title: Pretty Time of Day
Date: 2016-04-30
Version: 0.1
Authors@R: person("Kirill", "Müller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org")
Description: Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.
Imports: methods
Suggests: testthat, lubridate
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/rstats-db/hms
BugReports: https://github.com/rstats-db/hms/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-30 14:47:59 UTC; muelleki
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Repository: CRAN
Date/Publication: 2016-05-02 13:21:12

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New package highSCREEN with initial version 0.1
Package: highSCREEN
Type: Package
Title: High Throughput Screening for Plate Based Essays
Version: 0.1
Date: 2016-04-28
Authors@R: c(person(c("Ivo", "D."), "Shterev", role = c("aut", "cre"), email = "i.shterev@duke.edu"), person("Cliburn", "Chan", role = "aut"), person(c("Gregory", "D."), "Sempowski", role = "aut"))
Description: Can be used to carry out extraction, normalization, quality control (QC), candidate hits identification and visualization for plate based essays, in drug discovery. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.
Depends: R (>= 3.2.3), gplots (>= 3.0.1)
VignetteBuilder: knitr
Suggests: knitr
License: GPL-3
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-05-02 13:59:25 UTC; is33
Author: Ivo D. Shterev [aut, cre], Cliburn Chan [aut], Gregory D. Sempowski [aut]
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Repository: CRAN
Date/Publication: 2016-05-02 17:28:34

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New package gutenbergr with initial version 0.1
Package: gutenbergr
Type: Package
Title: Download and Process Public Domain Works from Project Gutenberg
Version: 0.1
Date: 2016-05-02
Authors@R: person("David", "Robinson", email = "admiral.david@gmail.com", role = c("aut", "cre"))
Description: Download and process public domain works in the Project Gutenberg collection. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.
License: MIT + file LICENSE
LazyData: TRUE
Maintainer: David Robinson <admiral.david@gmail.com>
VignetteBuilder: knitr
Depends: R (>= 2.10)
Imports: dplyr, readr, purrr, urltools, rvest, xml2, stringr
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat, tidytext, ggplot2, tidyr
NeedsCompilation: no
Packaged: 2016-05-02 16:36:09 UTC; drobinson
Author: David Robinson [aut, cre]
Repository: CRAN
Date/Publication: 2016-05-03 08:20:41

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New package GHap with initial version 1.2.0
Package: GHap
Type: Package
Title: Genome-Wide Haplotyping
Version: 1.2.0
Date: 2016-04-29
Author: Yuri Tani Utsunomiya, Marco Milanesi
Maintainer: Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Description: Haplotype calling from phased SNP data.
License: GPL (>= 2)
Depends: bigmemory (>= 4.4.6), parallel (>= 3.0.0)
NeedsCompilation: no
Packaged: 2016-05-02 10:14:02 UTC; yuri
Repository: CRAN
Date/Publication: 2016-05-02 13:30:44

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New package BigQuic with initial version 1.1-5
Package: BigQuic
Type: Package
Title: Big Quadratic Inverse Covariance Estimation
Version: 1.1-5
Date: 2016-2-11
Author: Khalid B. Kunji [aut, cre], Cho-Jui Hsieh [ctb], Matyas A. Sustik [ctb], Inderjit S. Dhillon [ctb], Pradeep Ravikumar [ctb], Tuo Zhao [ctb], Xingguo Li [ctb], Han Liu [ctb], Kathryn Roeder [ctb], John Lafferty [ctb], Larry Wasserman [ctb], George Karypis [ctb], Melissa O'Neill [ctb], Richard Henderson [ctb]
Authors@R: c(person(given = "Khalid B.", family = "Kunji", role = c("aut", "cre"), email = "kkunji@qf.org.qa"), person(given = "Cho-Jui", family = "Hsieh", role = c("ctb")), person(given = "Matyas A.", family = "Sustik", role = c("ctb"), email = "sustik@cs.utexas.edu"), person(given = "Inderjit S.", family = "Dhillon", role = c("ctb")), person(given = "Pradeep", family = "Ravikumar", role = c("ctb")), person(given = "Tuo", family = "Zhao", role = c("ctb")), person(given = "Xingguo", family = "Li", role = c("ctb")), person(given = "Han", family = "Liu", role = c("ctb")), person(given = "Kathryn", family = "Roeder", role = c("ctb")), person(given = "John", family = "Lafferty", role = c("ctb")), person(given = "Larry", family = "Wasserman", role = c("ctb")), person(given = "George", family = "Karypis", role = c("ctb")), person(given = "Melissa", family = "O'Neill", role = c("ctb")), person(given = "Richard", family = "Henderson", role = c("ctb")))
Maintainer: Khalid B. Kunji <kkunji@qf.org.qa>
Repository: CRAN
Description: Use Newton's method, coordinate descent, and METIS clustering to solve the L1 regularized Gaussian MLE inverse covariance matrix estimation problem.
License: GPL (>= 3) | file LICENSE
Copyright: The included METIS library is Copyright 1997, Regents of the University of Minnesota
URL: http://www.r-project.org, http://www.cs.utexas.edu/users/sustik/QUIC http://glaros.dtc.umn.edu/gkhome/views/metis http://www.pcg-random.org/download.html https://gcc.gnu.org/projects/gomp/
Imports: Rcpp (>= 0.12.1), Matrix, scalreg
LinkingTo: Rcpp
Depends: R (>= 3.2.2), methods
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-02 12:43:07 UTC; kunji
Date/Publication: 2016-05-02 17:28:18

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New package BeviMed with initial version 1.2
Package: BeviMed
Type: Package
Title: Bayesian Evaluation of Variant Involvement in Mendelian Disorders
Version: 1.2
Date: 2016-05-01
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: Bayesian inference procedures for evaluating evidence of involvement of variants in Mendelian disorders based on intuitive models of dominant and recessive inheritance.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.3)
LinkingTo: Rcpp
Depends: R (>= 3.0.0)
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-02 17:38:23 UTC; dg333
Repository: CRAN
Date/Publication: 2016-05-03 08:20:38

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New package ASSISTant with initial version 1.2-3
Package: ASSISTant
Type: Package
Title: Adaptive Subgroup Selection in Group Sequential Trials
Version: 1.2-3
Date: 2016-05-02
VignetteBuilder: knitr
Authors@R: c(person("Tze Leung", "Lai", role=c("ctb"), email = "lavori@stanford.edu"), person("Philip", "Lavori", role=c("aut"), email = "lavori@stanford.edu"), person("Olivia", "Liao", role=c("aut"), email = "oliao@onyx.com"), person("Balasubramanian", "Narasimhan", role=c("aut", "cre"), email = "naras@stat.Stanford.EDU"), person("Ka Wai", "Tsang", role=c("aut"), email = "ktsang@stanford.edu"))
URL: https://github.com/bnaras/ASSISTant
BugReports: https://github.com/bnaras/ASSISTant/issues
Description: Clinical trial design for subgroup selection in three-stage group sequential trial. Includes facilities for design, exploration and analysis of such trials. An implementation of the initial DEFUSE-3 trial is also provided as a vignette.
License: GPL (>= 2)
RoxygenNote: 5.0.1
Imports: R6, mvtnorm
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2016-05-02 18:43:32 UTC; naras
Author: Tze Leung Lai [ctb], Philip Lavori [aut], Olivia Liao [aut], Balasubramanian Narasimhan [aut, cre], Ka Wai Tsang [aut]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Repository: CRAN
Date/Publication: 2016-05-03 01:35:52

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Mon, 02 May 2016

New package TippingPoint with initial version 1.0.0
Package: TippingPoint
Title: Enhanced Tipping Point Displays the Results of Sensitivity Analyses for Missing Data
Version: 1.0.0
Author: Shengjie Zhang <zhangshengjie@mrbc-nccd.com>, Xikun Han <hanxikun2014@163.com> and Victoria Liublinska <vliublin@g.harvard.edu>
Maintainer: Xikun Han <hanxikun2014@163.com>
Description: Using the idea of "tipping point" (proposed in Gregory Campbell, Gene Pennello and Lilly Yue(2011) <DOI:10.1080/10543406.2011.550094>) to visualize the results of sensitivity analysis for missing data, the package provides a set of functions to list out all the possible combinations of the values of missing data in two treatment arms, calculate corresponding estimated treatment effects and p values and draw a colored heat-map to visualize them. It could deal with randomized experiments with a binary outcome or a continuous outcome. In addition, the package provides a visualized method to compare various imputation methods by adding the rectangles or convex hulls on the basic plot.
Depends: R (>= 3.0.0)
Imports: ggplot2 (>= 2.0.0), RColorBrewer, bayesSurv, reshape2, Rcpp
Suggests: knitr, rmarkdown
License: GPL-2
LazyData: true
Date: 2016-05-01
RoxygenNote: 5.0.1
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-05-01 17:39:19 UTC; 1159225156
Repository: CRAN
Date/Publication: 2016-05-02 06:24:29

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New package surveybootstrap with initial version 0.0.1
Package: surveybootstrap
Title: Tools for the Bootstrap with Survey Data
Version: 0.0.1
Authors@R: c(person(given="Dennis", middle="M.", family="Feehan", email="feehan@berkeley.edu", role=c("aut", "cre")), person(given="Matthew", middle="J.", family="Salganik", email="mjs3@princeton.edu", role="ths"))
Description: Tools for using different kinds of bootstrap for estimating sampling variation using complex survey data.
License: MIT + file LICENSE
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
Depends: plyr, dplyr, functional, stringr
Suggests: knitr, testthat
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-01 18:59:13 UTC; dennis
Author: Dennis M. Feehan [aut, cre], Matthew J. Salganik [ths]
Maintainer: Dennis M. Feehan <feehan@berkeley.edu>
Repository: CRAN
Date/Publication: 2016-05-02 06:24:50

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New package recmap with initial version 0.2.1
Package: recmap
Type: Package
Title: Compute the Rectangular Statistical Cartogram
Version: 0.2.1
Author: Christian Panse
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Description: Provides an interface and a C++ implementation of the RecMap MP2 construction heuristic (see 'citation("recmap")' for details). This algorithm draws maps according to a given statistical value (e. g. election results, population or epidemiological data). The basic idea of the RecMap algorithm is that each map region (e. g. different countries) is represented by a rectangle. The area of each rectangle represents the statistical value given as input . Documentation about 'RecMap' is provided by a vignette included in this package and a 'RecMap gallery' site at <http://cartodraw.science/recmap/gallery>.
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.2), Rcpp (>= 0.12.4)
SystemRequirements: C++11
Suggests: knitr, testthat
LinkingTo: Rcpp (>= 0.12.4)
VignetteBuilder: knitr
NeedsCompilation: yes
URL: http://cartodraw.science/recmap/
Packaged: 2016-05-01 17:36:05 UTC; cp
Repository: CRAN
Date/Publication: 2016-05-02 06:24:49

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New package modellingTools with initial version 0.1.0
Package: modellingTools
Type: Package
Title: A Collection of Useful Custom Tools for D&A and Modelling
Version: 0.1.0
Date: 2016-04-07
Authors@R: person("Alex", "Stringer", email = "alex@alexstringer.ca", role = c("aut", "cre"))
URL: http://github.com/awstringer, http://alexstringer.ca
Description: Useful functions for performing common data analysis tasks that I could not find in other packages. For example, flexible functions for discretizing ("binning") continuous variables are included, since this is a common technique used in industry that is not well appreciated in academia. See the vignette for a more detailed high-level explanation, or the documentation for full details.
License: GPL-3
LazyData: TRUE
Imports: dplyr, ggplot2, stringr, foreach, magrittr, scales
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-01 22:12:51 UTC; Alex
Author: Alex Stringer [aut, cre]
Maintainer: Alex Stringer <alex@alexstringer.ca>
Repository: CRAN
Date/Publication: 2016-05-02 06:24:47

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New package generalCorr with initial version 1.0.0
Package: generalCorr
Type: Package
Title: Generalized Correlations and Initial Causal Path
Version: 1.0.0
Date: 2016-04-10
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Encoding: UTF-8
Depends: R (>= 3.0.0), np (>= 0.60), xtable (>= 1.8), meboot (>= 1.4), psych (>= 1.5)
Suggests: car
Description: Asymmetric generalized correlations r*(x|y) measure strength of the dependence of x on y. If |r*(x|y)|> |r*(y|x)| it suggests that y is more likely the "kernel cause" of x. There are at least two additional ways of comparing two kernel regressions helping identify the `cause'. In simultaneous equation models where endogeneity of regressors is feared, we can use Prof. Koopmans' method to ignore endogeneity problems when it kernel causes the dependent variable. The usual partial correlations can be generalized for the asymmetric matrix of r*'s. Partial correlations help asses effect of x on y after removing the effect of a set of variables. The package provides additional tools for causal assessment, for printing the causal detections in a clear, comprehensive compact summary form, for matrix algebra, for outlier detection, and for numerical integration by the trapezoidal rule, stochastic dominance, etc. The package has a function for bootstrap-based statistical inference and one for a heuristic t-test.
License: GPL (>= 2)
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-01 18:01:15 UTC; hdvinod
Repository: CRAN
Date/Publication: 2016-05-02 06:24:37

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New package description with initial version 1.0.0
Package: description
Title: Manipulate DESCRIPTION Files
Version: 1.0.0
Authors@R: c( person("Gabor", "Csardi",, "csardi.gabor@gmail.com", role = c("aut", "cre")), person("Kirill", "Müller", role = c("aut")))
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Description: Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/metacran/description
BugReports: https://github.com/metacran/description/issues
Depends: R (>= 3.2.0)
Suggests: testthat, whoami
Imports: utils, R6, crayon
Encoding: UTF-8
RoxygenNote: 5.0.1
Collate: 'assertions.R' 'authors-at-r.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'description.R' 'encoding.R' 'latex.R' 'non-oo-api.R' 'read.R' 'str.R' 'syntax_checks.R' 'utils.R' 'validate.R'
NeedsCompilation: no
Packaged: 2016-05-01 21:11:04 UTC; gaborcsardi
Author: Gabor Csardi [aut, cre], Kirill Müller [aut]
Repository: CRAN
Date/Publication: 2016-05-02 06:24:31

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Sun, 01 May 2016

New package lvplot with initial version 0.2.0
Package: lvplot
Version: 0.2.0
Title: Letter Value 'Boxplots'
Description: Implements the letter value 'boxplot' which extends the standard 'boxplot' to deal with both larger and smaller number of data points by dynamically selecting the appropriate number of letter values to display.
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre")), person("Heike", "Hofmann", , "hofmann@iastate.edu", "aut") )
License: GPL (>= 2)
Depends: R (>= 2.14)
Imports: ggplot2 (>= 2.0.0), grid, RColorBrewer
Suggests: depth
RoxygenNote: 5.0.1
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2016-05-01 16:20:54 UTC; hadley
Author: Hadley Wickham [aut, cre], Heike Hofmann [aut]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Repository: CRAN
Date/Publication: 2016-05-01 18:56:01

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New package ljr with initial version 1.4-0
Package: ljr
Version: 1.4-0
Date: 2016-4-30
Title: Logistic Joinpoint Regression
Author: Michal Czajkowski, Ryan Gill, Greg Rempala
Maintainer: Ryan Gill <ryan.gill@louisville.edu>
Description: Fits and tests logistic joinpoint models.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-05-01 00:09:41 UTC; vbrutac
Repository: CRAN
Date/Publication: 2016-05-01 18:55:59

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Sat, 30 Apr 2016

New package tcgsaseq with initial version 1.0.0
Package: tcgsaseq
Type: Package
Title: Time-Course Gene Set Analysis for RNA-Seq Data
Version: 1.0.0
Date: 2016-04-30
Authors@R: c(person("Denis", "Agniel", role = c("aut"), email = "denis.agniel@gmail.com"), person("Boris P.", "Hejblum", role = c("aut", "cre"), email = "bhejblum@hsph.harvard.edu"))
Depends: R (>= 3.0.2)
Imports: CompQuadForm, ggplot2, GSA, stats, utils
Suggests: limma
Description: Gene set analysis of longitudinal RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights.
LazyData: true
License: GPL-2 | file LICENSE
BugReports: https://github.com/denisagniel/tcgsaseq/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-30 15:25:26 UTC; borishejblum
Author: Denis Agniel [aut], Boris P. Hejblum [aut, cre]
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>
Repository: CRAN
Date/Publication: 2016-05-01 00:32:29

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New package hetmeta with initial version 0.1.0
Package: hetmeta
Type: Package
Title: Heterogeneity Measures in Meta-Analysis
Date: 2016-04-28
Version: 0.1.0
Author: Alessio Crippa
Maintainer: Alessio Crippa <alessio.crippa@ki.se>
Description: Assess the presence of statistical heterogeneity and quantify its impact in the context of meta-analysis. It includes test for heterogeneity as well as other statistical measures (R_b, I^2, R_I).
License: GPL-2
Depends: metafor
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-30 17:15:24 UTC; alecri
Repository: CRAN
Date/Publication: 2016-05-01 00:31:19

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Fri, 29 Apr 2016

New package prodigenr with initial version 0.2.6
Package: prodigenr
Title: Research Project Directory Generator
Version: 0.2.6
Authors@R: person("Luke", "Johnston", , "lwjohnst@gmail.com", c("aut", "cre"))
Description: Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
Depends: R (>= 3.1.2)
License: MIT + file LICENSE
LazyData: true
Suggests: rmarkdown, git2r, packrat, knitr, testthat
RoxygenNote: 5.0.1
VignetteBuilder: knitr
URL: https://github.com/lwjohnst86/prodigenr
BugReports: https://github.com/lwjohnst86/prodigenr/issues
NeedsCompilation: no
Packaged: 2016-04-29 17:00:58 UTC; luke
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-30 00:16:00

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New package plac with initial version 0.1.1
Package: plac
Type: Package
Title: A Pairwise Likelihood Augmented Cox Estimator for Left-Truncated Data
Version: 0.1.1
Date: 2016-04-29
Authors@R: person("Fan", "Wu", email = "fannwu@umich.edu", role = c("aut", "cre"))
Description: A semi-parametric estimation method for the Cox model with left-truncated data using augmented information from the marginal of truncation times.
Depends: R (>= 3.2.0), survival (>= 2.38-3)
License: GPL-3
LazyData: TRUE
Imports: Rcpp (>= 0.12.1),
URL: https://github.com/942kid/plac
BugReports: https://github.com/942kid/plac/issues
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2016-04-29 11:25:40 UTC; fan
Author: Fan Wu [aut, cre]
Maintainer: Fan Wu <fannwu@umich.edu>
Repository: CRAN
Date/Publication: 2016-04-30 00:15:59

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New package sparsebnUtils with initial version 0.0.1
Package: sparsebnUtils
Title: Utilities for Learning Sparse Bayesian Networks
Version: 0.0.1
Date: 2016-04-28
Authors@R: person("Bryon", "Aragam", email = "sparsebn@gmail.com", role = c("aut", "cre"))
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Description: A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data.
Depends: R (>= 3.2.3)
Imports: Matrix, stats, utils
Suggests: graph, igraph, network, testthat
URL: https://github.com/itsrainingdata/sparsebnUtils
BugReports: https://github.com/itsrainingdata/sparsebnUtils/issues
License: GPL (>= 2)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-28 19:25:10 UTC; Zigmund-2
Author: Bryon Aragam [aut, cre]
Repository: CRAN
Date/Publication: 2016-04-29 12:11:58

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New package irtDemo with initial version 0.1.0
Package: irtDemo
Type: Package
Title: Item Response Theory Demo Collection
Version: 0.1.0
Date: 2016-04-27
Author: Metin Bulus [aut,cre]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Description: Includes a collection of shiny applications to demonstrate or to explore fundamental item response theory (IRT) concepts such as estimation, scoring, and multidimensional IRT models.
Imports: shiny (>= 0.13.2), shinydashboard (>= 0.5.1), fGarch (>= 3010.82)
Depends: R (>= 3.2.4)
License: GPL (>= 2)
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-04-28 13:18:30 UTC; METIN
Repository: CRAN
Date/Publication: 2016-04-29 07:31:38

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New package ClusteredMutations with initial version 1.0.1
Package: ClusteredMutations
Version: 1.0.1
Date: 2016-04-28
Title: Location and Visualization of Clustered Somatic Mutations
Authors@R: person("David", "Lora", email = "david@h12o.es", role = c("aut", "cre"))
Depends: seriation
Description: Identification and visualization of groups of closely spaced mutations in the DNA sequence of cancer genome. The extremely mutated zones are searched in the symmetric dissimilarity matrix using the anti-Robinson matrix properties. Different data sets are obtained to describe and plot the clustered mutations information.
License: GPL-3
Packaged: 2016-04-28 15:54:35 UTC; david
Author: David Lora [aut, cre]
Maintainer: David Lora <david@h12o.es>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-04-29 07:44:36

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Thu, 28 Apr 2016

New package CalibrateSSB with initial version 1.0
Package: CalibrateSSB
Type: Package
Title: Weighting and Estimation for Panel Data with Non-Response
Version: 1.0
Date: 2016-04-28
Author: Oyvind Langsrud
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Depends: R (>= 3.0.0), survey
Description: Function to calculate weights and estimates for panel data with non-response.
License: GPL-2
NeedsCompilation: no
Packaged: 2016-04-28 10:45:59 UTC; oyl
Repository: CRAN
Date/Publication: 2016-04-28 15:55:19

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New package tidytext with initial version 0.1.0
Package: tidytext
Type: Package
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Version: 0.1.0
Date: 2016-04-27
Authors@R: c(person("Gabriela", "De Queiroz", email = "gabidequeiroz@gmail.com", role = c("ctb")), person("David", "Robinson", email = "admiral.david@gmail.com", role = c("aut")), person("Julia", "Silge", email = "julia.silge@gmail.com", role = c("aut", "cre")))
Description: Text mining for word processing and sentiment analysis using 'dplyr', 'ggplot2', and other tidy tools.
License: MIT + file LICENSE
LazyData: TRUE
URL: http://github.com/juliasilge/tidytext
BugReports: http://github.com/juliasilge/tidytext/issues
RoxygenNote: 5.0.1
Depends: R (>= 2.10)
Imports: dplyr, stringr, tidyr, plyr, broom, Matrix, tokenizers, janeaustenr, purrr, methods
Suggests: readr, XML, tm, wordcloud, knitr, rmarkdown, ggplot2, reshape2, topicmodels, quanteda, NLP, scales, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-28 00:32:40 UTC; juliasilge
Author: Gabriela De Queiroz [ctb], David Robinson [aut], Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-28 11:50:08

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New package EpiWeek with initial version 1.1
Package: EpiWeek
Type: Package
Title: Conversion Between Epidemiological Weeks and Calendar Dates
Version: 1.1
Date: 2016-04-28
Author: Xiahong Zhao
Maintainer: Xiahong Zhao <zxiahong@gmail.com>
Description: Users can easily derive the calendar dates from epidemiological weeks, and vice versa.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-28 01:38:50 UTC; ephzhao
Repository: CRAN
Date/Publication: 2016-04-28 11:50:00

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New package ClusterRankTest with initial version 1.0
Package: ClusterRankTest
Type: Package
Title: Rank Tests for Clustered Data
Version: 1.0
Date: 2016-04-21
Author: Sandipan Dutta, Somnath Datta
Maintainer: Sandipan Dutta <sandipan.dutta07@gmail.com>
Description: Nonparametric rank based tests (rank-sum tests and signed-rank tests) for clustered data, especially useful for clusters having informative cluster size and intra-cluster group size.
License: GPL-2 | GPL-3
Depends: graphics, stats, utils
Packaged: 2016-04-27 05:43:24 UTC; sandy
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-04-28 11:49:57

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Wed, 27 Apr 2016

New package ParallelTree with initial version 0.1.0
Package: ParallelTree
Type: Package
Title: Parallel Tree
Version: 0.1.0
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>
Description: Provides two functions: Group_function() and Parallel_Tree(). Group_function() applies a given function (e.g.,mean()) to input variable(s) by group across levels. Has additional data management options. Parallel_Tree() uses 'ggplot2' to create a parallel coordinate plots (technically a facsimile of parallel coordinate plots in a Cartesian coordinate system). Used in combination these functions can create parallel tree plots, a variant of parallel coordinate plots, which are useful for visualizing multilevel data.
Depends: ggplot2
Imports: stats
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-27 19:09:06 UTC; Patrick
Repository: CRAN
Date/Publication: 2016-04-28 00:27:46

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New package ShapePattern with initial version 1.0
Package: ShapePattern
Type: Package
Title: Tools for Analyzing Planar Shape and Associated Patterns
Version: 1.0
Date: 2016-04-25
Author: Tarmo K. Remmel
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Description: An evolving and growing collection of tools for the quantification, assessment, and comparison of planar shape and pattern. The current flagship functionality is in the spatial decomposition of planar shapes using 'ShrinkShape' to incrementally shrink shapes to extinction while computing area, perimeter, and number of parts at each iteration of shrinking. The spectra of results are returned in graphic and tabular formats. Additional utility tools for handling data are provided and this package will be added to as more tools are created, cleaned-up, and documented.
License: GPL-2
LazyData: yes
LazyDataCompression: xz
Depends: R (>= 2.14), rgdal, sp, rgeos
NeedsCompilation: no
Packaged: 2016-04-27 17:02:29 UTC; remmelt
Repository: CRAN
Date/Publication: 2016-04-27 19:51:54

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New package pandocfilters with initial version 0.1-1
Package: pandocfilters
Title: Pandoc Filters for R
Version: 0.1-1
Authors@R: c(person("Florian", "Schwendinger", role = c("aut", "cre"), email = "FlorianSchwendinger@gmx.at"), person("Kurt", "Hornik", role = "aut"))
Description: The document converter 'pandoc' <http://pandoc.org/> is widely used in the R community. One feature of 'pandoc' is that it can produce and consume JSON-formatted abstract syntax trees (AST). This allows to transform a given source document into JSON-formatted AST, alter it by so called filters and pass the altered JSON-formatted AST back to 'pandoc'. This package provides functions which allow to write such filters in native R code. Although this package is inspired by the Python package 'pandocfilters' <https://github.com/jgm/pandocfilters/>, it provides additional convenience functions which make it simple to use the 'pandocfilters' package as a report generator. Since 'pandocfilters' inherits most of it's functionality from 'pandoc' it can create documents in many formats (for more information see <http://pandoc.org/>) but is also bound to the same limitations as 'pandoc'.
URL: http://pandoc.org/, https://github.com/jgm/pandocfilters/
Depends: R (>= 2.15)
Imports: jsonlite, base
SystemRequirements: pandoc (> 1.12)
License: GPL-3
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-26 13:44:49 UTC; florian
Author: Florian Schwendinger [aut, cre], Kurt Hornik [aut]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Repository: CRAN
Date/Publication: 2016-04-27 19:51:55

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New package NAEPprimer with initial version 1.0.1
Package: NAEPprimer
Version: 1.0.1
Date: 2016-04-04
Title: The NAEP Primer
Author: NAEP Primer data by Emmanuel Sikali. Creation of R package by Paul Bailey and Michael Lee.
Maintainer: Emmanuel Sikali <Emmanuel.Sikali@ed.gov>
Description: Contains a sample of the 2005 Grade 8 Mathematics data from the National Assessment of Educational Progress (NAEP). This data set is called the NAEP Primer.
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-07 18:10:13 UTC; mlee
Repository: CRAN
Date/Publication: 2016-04-27 19:51:52

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New package REAT with initial version 1.0.0
Package: REAT
Type: Package
Title: Regional Economic Analysis Tools
Version: 1.0.0
Date: 2016-03-27
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Description: Collection of analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and regional specialization.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-04-26 19:13:23 UTC; Thomas
Repository: CRAN
Date/Publication: 2016-04-27 13:30:50

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New package NPflow with initial version 0.9.0
Package: NPflow
Type: Package
Title: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data
Version: 0.9.0
Date: 2016-04-26
Authors@R: c(person("Boris P.", "Hejblum", role = c("aut", "cre"), email = "bhejblum@hsph.harvard.edu"), person("Chariff", "Alkhassim", role = c("aut"), email = "chariff.alkhassim@isped.fr"), person("Francois", "Caron", role = c("aut"), email = "francois.caron@stats.ox.ac.uk") )
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.1), Rcpp (>= 0.12.4), truncnorm
Imports: graphics, stats, grDevices, ellipse, fastcluster, gplots, ggplot2, pheatmap, reshape2
Suggests: foreach, parallel, doParallel, microbenchmark
Description: Dirichlet process mixture of multivariate normal, skew-normal or skew t-distributions modeling oriented towards flow-cytometry data preprocessing applications.
License: LGPL-3 | file LICENSE
BugReports: https://github.com/borishejblum/NPflow/issues
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-26 23:55:28 UTC; bhejblum
Author: Boris P. Hejblum [aut, cre], Chariff Alkhassim [aut], Francois Caron [aut]
Repository: CRAN
Date/Publication: 2016-04-27 13:30:45

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New package nmfgpu4R with initial version 0.2.4
Package: nmfgpu4R
Type: Package
Title: Non-Negative Matrix Factorization (NMF) using CUDA
Version: 0.2.4
Date: 2016-04-27
Author: Sven Koitka [aut, cre, cph], Christoph M. Friedrich [ctb]
Maintainer: Sven Koitka <sven.koitka@fh-dortmund.de>
Description: Wrapper package for the nmfgpu library, which implements several Non-negative Matrix Factorization (NMF) algorithms for CUDA platforms. By using the acceleration of GPGPU computing, the NMF can be used for real-world problems inside the R environment. All CUDA devices starting with Kepler architecture are supported by the library.
License: GPL-3 | file LICENSE
URL: https://github.com/razorx89/nmfgpu4R
BugReports: https://github.com/razorx89/nmfgpu4R/issues
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.4), Matrix, SparseM, stats, stringr, tools, utils
Suggests: gdata
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-27 09:27:37 UTC; Sven Koitka
Repository: CRAN
Date/Publication: 2016-04-27 18:28:35

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New package face with initial version 0.1-1
Package: face
Title: Fast Covariance Estimation for Sparse Functional Data
Version: 0.1-1
Author: Luo Xiao [aut,cre], Cai Li [aut], Will Checkley [aut], Ciprian Crainiceanu [aut]
Maintainer: Luo Xiao <lxiao5@ncsu.edu>
Description: Fast covariance estimation for sparse functional data.
Depends: R (>= 2.1.4)
Imports: stats, splines, Matrix, matrixcalc
License: GPL-3
LazyLoad: yes
LazyData: true
Repository: CRAN
NeedsCompilation: no
Packaged: 2016-04-27 13:15:24 UTC; lxiao5
Date/Publication: 2016-04-27 18:56:48

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Tue, 26 Apr 2016

New package REREFACT with initial version 1.0
Package: REREFACT
Version: 1.0
Date: 2016-04-15
Title: Reordering and/or Reflecting Factors for Simulation Studies with Exploratory Factor Analysis
Author: Soyeon Ahn, Cengiz Zopluoglu, Seniz Celimli, Min Lu, & Nicholas D. Myers
Maintainer: Soyeon Ahn <s.ahn@miami.edu>
Depends: psych, combinat, Matrix, gdata, methods
Description: Executes a post-rotation algorithm that REorders and/or REflects FACTors (REREFACT) for each replication of a simulation study with exploratory factor analysis.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-04-26 14:53:08 UTC; c.zopluoglu1
Repository: CRAN
Date/Publication: 2016-04-26 19:32:02

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New package flexrsurv with initial version 1.3.3
Package: flexrsurv
Type: Package
Title: Flexible Relative Survival
Version: 1.3.3
Date: 2016-04-22
Authors@R: c( person("Isabelle", "Clerc-Urms", role="aut"), person("Michel", "Grzebyk", role = c("aut", "cre"), email = "michel.grzebyk@inrs.fr"), person("Guy", "Hdelin", role="ctb"), person("CENSUR working survival group", role = "ctb") )
Author: Isabelle Clerc-Urms [aut], Michel Grzebyk [aut, cre], Guy Hdelin [ctb], CENSUR working survival group [ctb]
Maintainer: Michel Grzebyk <michel.grzebyk@inrs.fr>
Description: Perform relative survival analyses using approaches described in Remontet et al. (2007) <DOI:10.1002/sim.2656> and Mahboubi et al. (2011) <DOI:10.1002/sim.4208>. It implements non-linear, non-proportional effects and both non proportional and non linear effects using splines (B-spline and truncated power basis).
License: GPL (>= 2.0)
Depends: methods, splines, survival, stats, matrixcalc, Epi
Suggests: relsurv
Imports: utils, orthogonalsplinebasis
Encoding: latin1
NeedsCompilation: yes
Packaged: 2016-04-25 16:11:06 UTC; michel.grzebyk
Repository: CRAN
Date/Publication: 2016-04-26 19:32:05

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New package asymmetry with initial version 1.0
Package: asymmetry
Type: Package
Title: The Slide-Vector Model for Multidimensional Scaling of Asymmetric Data
Version: 1.0
Date: 2016-04-22
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Description: The slide-vector model is provided in this package together with functions for the analysis and graphical display of asymmetry. The slide vector model is a scaling model for asymmetric data. A distance model is fitted to the symmetric part of the data whereas the asymmetric part of the data is represented by projections of the coordinates onto the slide-vector. The slide-vector points in the direction of large asymmetries in the data. The distance is modified in such a way that the distance between two points that are parallel to the slide-vector is larger in the direction of this vector. The distance is smaller in the opposite direction. If the line connecting two points is perpendicular to the slide-vector the difference between the two projections is zero. In this case the distance between the two points is symmetric. The algorithm for fitting this model is derived from the majorization approach to multidimensional scaling.
License: GPL (>= 2)
Imports: rJava
NeedsCompilation: yes
SystemRequirements: Java JDK 1.2 or higher (for JRI/REngine JDK 1.4 or higher), GNU make
Packaged: 2016-04-26 17:13:57 UTC; berrie
Repository: CRAN
Date/Publication: 2016-04-26 20:52:24

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New package factoextra with initial version 1.0.3
Package: factoextra
Type: Package
Title: Extract and Visualize the Results of Multivariate Data Analyses
Version: 1.0.3
Date: 2016-03-31
Authors@R: c( person("Alboukadel", "Kassambara", role = c("aut", "cre"), email = "alboukadel.kassambara@gmail.com"), person("Fabian", "Mundt", role = c("aut"), email = "f.mundt@inventionate.de") )
Description: Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization.
License: GPL-2
LazyData: true
Depends: R (>= 3.1.0), ggplot2
Imports: cluster, dendextend, grid, stats, reshape2, ggrepel, abind
Suggests: ade4, ca, FactoMineR, MASS, knitr
URL: http://www.sthda.com/english/rpkgs/factoextra
BugReports: https://github.com/kassambara/factoextra/issues
Collate: 'cluster_utilities.R' 'decathlon2.R' 'eigenvalue.R' 'utilities.R' 'dist.R' 'fviz_dend.R' 'hcut.R' 'print.factoextra.R' 'get_pca.R' 'fviz_cluster.R' 'eclust.R' 'facto_summarize.R' 'fviz_add.R' 'fviz_ca.R' 'fviz_contrib.R' 'fviz_cos2.R' 'get_hmfa.R' 'fviz_hmfa.R' 'get_mca.R' 'fviz_mca.R' 'get_mfa.R' 'fviz_mfa.R' 'fviz_nbclust.R' 'fviz_pca.R' 'fviz_silhouette.R' 'get_ca.R' 'get_clust_tendency.R' 'hkmeans.R' 'housetasks.R' 'multishapes.R' 'poison.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-26 13:11:54 UTC; alboukadel
Author: Alboukadel Kassambara [aut, cre], Fabian Mundt [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-26 16:50:39

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New package msmtools with initial version 1.0
Package: msmtools
Type: Package
Title: Building Augmented Data to Run Multi-State Models with 'msm' Package
Version: 1.0
Date: 2016-04-26
Authors@R: person("Francesco", "Grossetti", email = "francesco.grossetti@polimi.it", role = c("aut", "cre"))
Description: A fast and general method for restructuring classical longitudinal data into augmented ones. The reason for this is to facilitate the modeling of longitudinal data under a multi-state framework using the 'msm' package.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Depends: R (>= 3.2.0)
Imports: data.table (>= 1.9.6), msm (>= 1.6), survival (>= 2.38.0)
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-26 07:47:15 UTC; franz
Author: Francesco Grossetti [aut, cre]
Maintainer: Francesco Grossetti <francesco.grossetti@polimi.it>
Repository: CRAN
Date/Publication: 2016-04-26 11:20:20

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New package RZabbix with initial version 0.1.0
Package: RZabbix
Version: 0.1.0
Type: Package
Title: R Module for Working with the 'Zabbix API'
Authors@R: c( person("Marcin", "Kosinski", role = c("aut", "cre"), email = "m.p.kosinski@gmail.com") )
Description: R interface to the 'Zabbix API' data <https://www.zabbix.com/documentation/3.0/manual/api/reference>. Enables easy and direct communication with 'Zabbix API' from 'R'.
Repository: CRAN
License: GPL-2
LazyLoad: yes
LazyData: yes
Depends: R (>= 3.2.0)
Imports: httr (>= 1.1.0), jsonlite (>= 0.9.19)
BugReports: https://github.com/MarcinKosinski/RZabbix/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-25 17:40:23 UTC; mkosinski
Author: Marcin Kosinski [aut, cre]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
Date/Publication: 2016-04-26 08:44:09

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New package CovSelHigh with initial version 1.0.0
Package: CovSelHigh
Version: 1.0.0
Author: Jenny Häggström
Maintainer: Jenny Häggström <jenny.haggstrom@umu.se>
Depends: R (>= 2.14.0)
Imports: bnlearn,MASS, bindata, Matching, doRNG, glmnet, randomForest,foreach,xtable, doParallel
Title: Model-Free Covariate Selection in High Dimensions
Description: Model-free selection of covariates in high dimensions under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011) <DOI:10.1093/biomet/asr041> and VanderWeele and Shpitser (2011) <DOI:10.1111/j.1541-0420.2011.01619.x>. Confounder selection can be performed via either Markov/Bayesian networks, random forests or LASSO.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-04-25 17:51:10 UTC; jennyhaggstrom
Repository: CRAN
Date/Publication: 2016-04-26 08:44:06

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Mon, 25 Apr 2016

New package UBL with initial version 0.0.3
Package: UBL
Type: Package
Title: An Implementation of Several Approaches to Utility-Based Learning for Both Classification and Regression Tasks
Description: Provides a set of functions that can be used to obtain better predictive performance on cost-sensitive and cost/benefits tasks (for both regression and classification). This includes re-sampling approaches, cost-based methods, special purpose evaluation metrics as well as specific learning systems.
Version: 0.0.3
Depends: R(>= 3.0), methods, grDevices, stats
Suggests: MASS, rpart, testthat, DMwR
Date: 2016-04-22
Authors@R: c(person("Paula", "Branco", email = "paobranco@gmail.com", role = c("aut", "cre")), person("Rita", "Ribeiro", email = "rpribeiro@dcc.fc.up.pt", role = c("aut", "ctb")), person("Luis", "Torgo", email = "ltorgo@dcc.fc.up.pt", role = c("aut", "ctb")))
URL: https://github.com/paobranco/UBL
BugReports: https://github.com/paobranco/UBL/issues
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
Packaged: 2016-04-25 22:12:23 UTC; pbranco
Author: Paula Branco [aut, cre], Rita Ribeiro [aut, ctb], Luis Torgo [aut, ctb]
Maintainer: Paula Branco <paobranco@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-26 01:28:01

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New package RGoogleFit with initial version 0.1.0
Package: RGoogleFit
Type: Package
Title: R Interface to Google Fit API
Version: 0.1.0
Author: Marcin Szymanski
Maintainer: Marcin Szymanski <ms32035@gmail.com>
Description: Provides interface to Google Fit REST API v1 (see <https://developers.google.com/fit/rest/v1/reference/>).
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.0), RCurl, jsonlite, bit64
Imports: utils
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-25 17:19:06 UTC; ms32035
Repository: CRAN
Date/Publication: 2016-04-26 01:28:03

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New package RobAStRDA with initial version 1.0.2
Package: RobAStRDA
Version: 1.0.2
Date: 2016-04-25
Title: Interpolation Grids for Packages of the 'RobASt' - Family of Packages
Description: Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is currently used by package 'RobExtremes' only.
Depends: R (>= 2.14.0)
Authors@R: c(person("Matthias", "Kohl", role=c("aut", "cph")), person("Bernhard", "Spangl", role="ctb", comment="contributed smoothed grid values of the Lagrange multipliers"), person("Sascha", "Desmettre", role="ctb", comment="contributed smoothed grid values of the Lagrange multipliers"), person("Eugen", "Massini", role="ctb", comment="contributed an interactive smoothing routine for smoothing the Lagrange multipliers and smoothed grid values of the Lagrange multipliers"), person("Mykhailo", "Pupashenko", role="ctb", comment="helped with manual smoothing of the interpolators"), person("Daria", "Pupashenko", role="ctb", comment="helped with manual smoothing of the interpolators"), person("Gerald", "Kroisandt", role="ctb", comment="helped with manual smoothing of the interpolators"), person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="peter.ruckdeschel@uni-oldenburg.de"))
LazyData: yes
ByteCompile: yes
License: LGPL-3
URL: http://robast.r-forge.r-project.org/
LastChangedDate: {$LastChangedDate: 2011-09-30 11:10:33 +0200 (Fr, 30 Sep 2011) $}
LastChangedRevision: {$LastChangedRevision: 453 $}
SVNRevision: 874
NeedsCompilation: no
Packaged: 2016-04-25 15:42:20 UTC; ruckdesc
Author: Matthias Kohl [aut, cph], Bernhard Spangl [ctb] (contributed smoothed grid values of the Lagrange multipliers), Sascha Desmettre [ctb] (contributed smoothed grid values of the Lagrange multipliers), Eugen Massini [ctb] (contributed an interactive smoothing routine for smoothing the Lagrange multipliers and smoothed grid values of the Lagrange multipliers), Mykhailo Pupashenko [ctb] (helped with manual smoothing of the interpolators), Daria Pupashenko [ctb] (helped with manual smoothing of the interpolators), Gerald Kroisandt [ctb] (helped with manual smoothing of the interpolators), Peter Ruckdeschel [cre, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Repository: CRAN
Date/Publication: 2016-04-25 18:51:59

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New package subcopem2D with initial version 1.0-0
Package: subcopem2D
Type: Package
Title: Bivariate Empirical Subcopula
Version: 1.0-0
Date: 2016-04-24
Author: Arturo Erdely
Maintainer: Arturo Erdely <arturo.erdely@comunidad.unam.mx>
Description: Calculate empirical subcopula and dependence measures from a given bivariate sample.
License: GPL-3
NeedsCompilation: no
Packaged: 2016-04-25 13:51:57 UTC; aerde
Repository: CRAN
Date/Publication: 2016-04-25 16:52:15

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New package sigmoid with initial version 0.1.0
Package: sigmoid
Title: Sigmoid Functions for Machine Learning
Version: 0.1.0
Authors@R: person("Bastiaan", "Quast", email = "bquast@gmail.com", role = c("aut", "cre"))
Description: Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
Depends: R (>= 3.2.2)
License: GPL-3
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-25 13:38:26 UTC; quast
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-25 16:52:14

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New package genomeplot with initial version 1.0
Package: genomeplot
Type: Package
Title: 'Plot genome wide values for all chromosomes'
Version: 1.0
Date: 2016-04-20
Author: Jing Xu and Yongshuai Jiang
Maintainer: Jing Xu<xujingaddressee@foxmail.com>
Description: Plot values of markers(SNPs, expression, genes, RNA,...) for all chromosomes.
License: GPL (>= 3)
Depends: ggplot2
NeedsCompilation: no
Packaged: 2016-04-25 08:04:48 UTC; Administrator
Repository: CRAN
Date/Publication: 2016-04-25 15:32:14

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Sun, 24 Apr 2016

New package word.alignment with initial version 1.0.2
Package: word.alignment
Type: Package
Title: Computing Word Alignment Using IBM Model 1 (and Symmetrization) for a Given Parallel Corpus and Evaluation
Version: 1.0.2
Date: 2016-04-16
Author: Neda Daneshagr and Majid Sarmad.
Maintainer: Neda Daneshgar<ne_da978@stu-mail.um.ac.ir>
Description: For a given Sentence-Aligned Parallel Corpus, it aligns words for each sentence pair. It considers many-to-one and symmetrization alignments. Moreover, it evaluates word alignment based on this package and some other software or method. It also builds an automatic dictionary of two languages based on given parallel corpus.
Depends: R(>= 3.2.2), data.table, openxlsx, quanteda,
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-04-24 17:35:11 UTC; Asus
Repository: CRAN
Date/Publication: 2016-04-24 23:15:02

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New package weightr with initial version 1.0.0
Package: weightr
Title: Estimating Weight-Function Models for Publication Bias in R
Version: 1.0.0
Authors@R: c( person(c("Kathleen", "M."), "Coburn", email = "kcoburn@ucmerced.edu", role = c("aut", "cre")), person(c("Jack", "L."), "Vevea", email = "jvevea@ucmerced.edu", role = c("aut")))
Description: Set of functions for estimating the Vevea and Hedges (1995) weight-function model in R. By specifying arguments, users can also estimate the modified model described in Vevea and Woods (2005), which may be more practical with small datasets. Users can also specify moderators to estimate a linear model. The package functionality allows users to easily extract the results of these analyses as R objects for other uses. In addition, the package includes a function to launch both models as a Shiny application. Although the Shiny application is also available online, this function allows users to launch it locally if they choose.
URL: http://faculty.ucmerced.edu/jvevea/, https://vevealab.shinyapps.io/WeightFunctionModel/, http://bayes-1.ucmerced.edu/jvevea/pdfs/Vevea%20&%20Hedges%201995.pdf, http://bayes-1.ucmerced.edu/jvevea/pdfs/vevea%20and%20woods.pdf
Depends: R (>= 3.2.3)
License: GPL-2 | GPL-3
LazyData: true
Suggests: shiny (>= 0.12.2), shinyBS (>= 0.61)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-24 19:13:24 UTC; kathleencoburn
Author: Kathleen M. Coburn [aut, cre], Jack L. Vevea [aut]
Maintainer: Kathleen M. Coburn <kcoburn@ucmerced.edu>
Repository: CRAN
Date/Publication: 2016-04-24 23:12:56

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New package mlmc with initial version 1.0.0
Package: mlmc
Type: Package
Title: Multi-Level Monte Carlo
Version: 1.0.0
Authors@R: c( person("Louis", "Aslett", email = "aslett@stats.ox.ac.uk", role = c("cre", "aut", "trl")), person("Mike", "Giles", email = "Mike.Giles@maths.ox.ac.uk", role = "ctb"), person("Tigran", "Nagapetyan", email = "nagapetyan@stats.ox.ac.uk", role = "ctb"), person("Sebastian", "Vollmer", email = "vollmer@stats.ox.ac.uk", role = "ctb"))
Maintainer: Louis Aslett <aslett@stats.ox.ac.uk>
Description: An implementation of Multi-level Monte Carlo for R. This package builds on the original 'Matlab' and C++ implementations by Mike Giles to provide a full MLMC driver and example level samplers. Multi-core parallel sampling of levels is provided built-in.
Imports: ggplot2, grid, parallel, Rcpp
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-04-24 20:47:03 UTC; louis
Author: Louis Aslett [cre, aut, trl], Mike Giles [ctb], Tigran Nagapetyan [ctb], Sebastian Vollmer [ctb]
Repository: CRAN
Date/Publication: 2016-04-24 23:19:03

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New package grpSLOPE with initial version 0.1.0
Package: grpSLOPE
Type: Package
Title: Group Sorted L1 Penalized Estimation
Version: 0.1.0
Authors@R: c(person("Alexej", "Gossmann", email = "alexej.go@googlemail.com", role = c("aut", "cre")), person("Damian", "Brzyski", role = "aut"), person("Weijie", "Su", role = "aut"), person("Malgorzata", "Bogdan", role = "aut"), person("Ewout", "van den Berg", role = "ctb", comment = "A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3"), person("Emmanuel", "Candes", role = "ctb", comment = "A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3"))
Description: Group SLOPE is a penalized linear regression method that is used for adaptive selection of groups of significant predictors in a high-dimensional linear model. The Group SLOPE method can control the (group) false discovery rate at a user-specified level (i.e., control the expected proportion of irrelevant among all selected groups of predictors).
License: GPL-3
URL: https://github.com/agisga/grpSLOPE.git
BugReports: https://github.com/agisga/grpSLOPE/issues
LazyData: TRUE
Imports: Rcpp (>= 0.12.1), SLOPE (>= 0.1.1)
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 5.0.0
Suggests: testthat, knitr, rmarkdown, pander
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-04-24 17:57:55 UTC; alexej
Author: Alexej Gossmann [aut, cre], Damian Brzyski [aut], Weijie Su [aut], Malgorzata Bogdan [aut], Ewout van den Berg [ctb] (A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3), Emmanuel Candes [ctb] (A part of the optimization code was obtained from http://statweb.stanford.edu/~candes/SortedL1/software.html under GNU GPL-3)
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>
Repository: CRAN
Date/Publication: 2016-04-24 23:23:46

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New package TELP with initial version 1.0
Package: TELP
Type: Package
Title: Social Representation Theory Application: The Free Evocation of Words Technique
Version: 1.0
Date: 2016-04-21
LazyData: true
Author: Gabriel Henrique Oliveira Assuncao
Maintainer: Gabriel Henrique Oliveira Assuncao <gabrielhenryoliver@hotmail.com>
Description: Using The Free Evocation of Words Technique method with some functions, this package will make a social representation and other analysis. The Free Evocation of Words Technique consists of collecting a number of words evoked by a subject facing exposure to an inducer term. The purpose of this technique is to understand the relationships created between words evoked by the individual and the inducer term. This technique is included in the theory of social representations, therefore, on the information transmitted by an individual, seeks to create a profile that define a social group.
License: GPL (> 2)
Depends: tcltk2
Imports: tm,wordcloud,RColorBrewer,arules,arulesViz,ggplot2,gridExtra
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-24 04:26:09 UTC; Meu Computador
Repository: CRAN
Date/Publication: 2016-04-24 17:04:43

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New package rodeo with initial version 0.3
Package: rodeo
Type: Package
Title: A Code Generator for ODE-Based Models
Version: 0.3
Date: 2016-04-21
Author: David Kneis <david.kneis@tu-dresden.de>
Maintainer: David Kneis <david.kneis@tu-dresden.de>
Description: Provides a reference class and several utility methods to facilitate the implementation of models based on ordinary differential equations. The heart of the package is a code generator that creates compiled 'Fortran' (or 'R') code which can be passed to a numerical solver. There is direct support for solvers contained in packages 'deSolve' and 'rootSolve'.
License: GPL (>= 2)
Imports: methods, deSolve
NeedsCompilation: no
Packaged: 2016-04-23 20:29:47 UTC; dkneis
Repository: CRAN
Date/Publication: 2016-04-24 16:37:40

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Sat, 23 Apr 2016

New package RcppNumerical with initial version 0.2-0
Package: RcppNumerical
Type: Package
Title: 'Rcpp' Integration for Numerical Computing Libraries
Version: 0.2-0
Date: 2016-04-23
Authors@R: c( person("Yixuan", "Qiu", , "yixuan.qiu@cos.name", c("aut", "cre")), person("Sreekumar", "Balan", role = "aut", comment = "Numerical integration library"), person("Matt", "Beall", role = "aut", comment = "Numerical integration library"), person("Mark", "Sauder", role = "aut", comment = "Numerical integration library"), person("Naoaki", "Okazaki", role = "aut", comment = "libLBFGS library"), person("Thomas", "Hahn", role = "aut", comment = "Cuba library") )
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Description: A collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with 'Rcpp'.
License: GPL (>= 2)
Copyright: See file COPYRIGHTS
LazyData: TRUE
Imports: Rcpp
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-23 17:44:10 UTC; qyx
Author: Yixuan Qiu [aut, cre], Sreekumar Balan [aut] (Numerical integration library), Matt Beall [aut] (Numerical integration library), Mark Sauder [aut] (Numerical integration library), Naoaki Okazaki [aut] (libLBFGS library), Thomas Hahn [aut] (Cuba library)
Repository: CRAN
Date/Publication: 2016-04-23 21:43:43

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New package protolite with initial version 1.0
Package: protolite
Type: Package
Title: Fast and Simple Object Serialization to Protocol Buffers
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Description: High-performance C++ re-implementation of the object serialization functionality from the 'RProtoBuf' package. Permissively licensed, fully compatible, no bloat.
Version: 1.0
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/protolite#readme
BugReports: https://github.com/jeroenooms/protolite/issues
SystemRequirements: libprotobuf and protobuf-compiler
LinkingTo: Rcpp
Imports: Rcpp
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-23 12:18:57 UTC; jeroen
Repository: CRAN
Date/Publication: 2016-04-23 14:24:07

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New package IntNMF with initial version 1.0
Package: IntNMF
Type: Package
Title: Integrative Clustering of Multiple Genomic Dataset
Version: 1.0
Date: 2016-04-10
Author: Prabhakar Chalise, Rama Raghavan, Brooke Fridley
Maintainer: Rama Raghavan <rraghavan@kumc.edu>
Description: Carries out integrative clustering analysis using multiple types of genomic dataset.
License: GPL-2
Depends: R (>= 2.14), MASS, NMF, mclust, cluster, InterSIM
NeedsCompilation: no
Packaged: 2016-04-22 21:22:40 UTC; rama
Repository: CRAN
Date/Publication: 2016-04-23 13:47:58

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New package IncucyteDRC with initial version 0.5.4
Package: IncucyteDRC
Type: Package
Title: Dose Response Curves from Incucyte Proliferation Assays
Version: 0.5.4
Date: 2016-04-23
Author: Phil Chapman <phil.chapman@cruk.manchester.ac.uk>
Maintainer: Phil Chapman <phil.chapman@cruk.manchester.ac.uk>
Description: Package to import data generated by the Incucyte Zoom from Essen Biosciences and use this to fit dose response curves using the drc package.
URL: https://github.com/chapmandu2/IncucyteDRC
BugReports: https://github.com/chapmandu2/IncucyteDRC/issues
License: GPL-2
LazyData: TRUE
Imports: cowplot, dplyr, drc, DT, ggplot2, magrittr, shiny, tidyr, XML
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-23 07:40:43 UTC; pchapman
Repository: CRAN
Date/Publication: 2016-04-23 14:21:03

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New package vaersvax with initial version 1.0.0
Package: vaersvax
Title: US Vaccine Adverse Event Reporting System (VAERS) Vaccine Data for Present
Version: 1.0.0
Depends: R (>= 2.14.0)
Suggests: data.table, dplyr, rpivotTable
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Description: US VAERS vaccine data for 01/01/2016 - 03/14/2016. If you want to explore the full VAERS data for 1990 - Present (data, symptoms, and vaccines), then check out the 'vaers' package from the URL below. The URL and BugReports below correspond to the 'vaers' package, of which 'vaersvax' is a small subset (2016 only). 'vaers' is not hosted on CRAN due to the large size of the data set. "VAERS is a national vaccine safety surveillance program co-sponsored by the US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." For more information about the data, visit https://vaers.hhs.gov/index. For information about vaccination/immunization hazards, visit http://www.questionuniverse.com/rethink.html/#vaccine.
URL: https://gitlab.com/iembry/vaers
BugReports: https://gitlab.com/iembry/vaers/issues
License: CC0
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-23 02:53:14 UTC; uoxyh
Repository: CRAN
Date/Publication: 2016-04-23 09:02:38

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New package vaersNDvax with initial version 1.0.0
Package: vaersNDvax
Title: Non-Domestic Vaccine Adverse Event Reporting System (VAERS) Vaccine Data for Present
Version: 1.0.0
Depends: R (>= 2.14.0)
Suggests: data.table, dplyr, rpivotTable
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Description: Non-Domestic VAERS vaccine data for 01/01/2016 - 03/14/2016. If you want to explore the full VAERS data for 1990 - Present (data, symptoms, and vaccines), then check out the 'vaersND' package from the URL below. The URL and BugReports below correspond to the 'vaersND' package, of which 'vaersNDvax' is a small subset (2016 only). 'vaersND' is not hosted on CRAN due to the large size of the data set. "VAERS is a national vaccine safety surveillance program co-sponsored by the US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." For more information about the data, visit https://vaers.hhs.gov/index. For information about vaccination/immunization hazards, visit http://www.questionuniverse.com/rethink.html/#vaccine.
URL: https://gitlab.com/iembry/vaersND
BugReports: https://gitlab.com/iembry/vaersND/issues
License: CC0
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-23 02:54:25 UTC; uoxyh
Repository: CRAN
Date/Publication: 2016-04-23 09:02:47

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Fri, 22 Apr 2016

New package uHMM with initial version 1.0
Package: uHMM
Type: Package
Title: Construct an Unsupervised Hidden Markov Model
Version: 1.0
Date: 2016-03-18
Authors@R: c(person(given="Emilie", family="POISSON-CAILLAULT", role = c("aut"), email = "emilie.caillault@lisic.univ-littoral.fr" ), person(given="Paul", family="TERNYNCK", role = c("aut", "cre"), email = "ternynck@lisic.univ-littoral.fr" ) )
Author: Emilie POISSON-CAILLAULT [aut], Paul TERNYNCK [aut, cre]
Maintainer: Paul TERNYNCK <ternynck@lisic.univ-littoral.fr>
Description: Construct a Hidden Markov Model with states learnt by unsupervised classification.
License: GPL (>= 2)
RoxygenNote: 5.0.1
LazyData: TRUE
Depends: R (>= 3.0.0), stats, grDevices
Imports: tcltk, tcltk2, tkrplot, HMM, clValid, class, cluster, FactoMineR, corrplot, chron
NeedsCompilation: no
Packaged: 2016-04-22 13:03:49 UTC; ternynck
Repository: CRAN
Date/Publication: 2016-04-22 16:25:47

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New package bridgedist with initial version 0.1.0
Package: bridgedist
Title: An Implementation of the Bridge Distribution with Logit-Link as in Wang and Louis (2003)
Version: 0.1.0
Authors@R: person("Bruce", "Swihart", email = "bruce.swihart@gmail.com", role = c("aut", "cre"))
Description: An implementation of the bridge distribution with logit-link in R. In Wang and Louis (2003) <DOI:10.1093/biomet/90.4.765>, such a univariate bridge distribution was derived as the distribution of the random intercept that 'bridged' a marginal logistic regression and a conditional logistic regression. The conditional and marginal regression coefficients are a scalar multiple of each other. Such is not the case if the random intercept distribution was Gaussian.
Depends: R (>= 3.0.0)
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, reshape2, ggplot2, testthat
Imports: stats
VignetteBuilder: knitr
URL: http://github.com/swihart/bridgedist
BugReports: http://github.com/swihart/bridgedist/issues
NeedsCompilation: no
Packaged: 2016-04-22 13:17:23 UTC; swihartbj
Author: Bruce Swihart [aut, cre]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-22 15:30:23

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New package wbstats with initial version 0.1
Package: wbstats
Type: Package
Title: Programmatic Access to Data and Statistics from the World Bank API
Description: Tools for searching and downloading data and statistics from the World Bank Data API (<http://data.worldbank.org/developers/api-overview>) and the World Bank Data Catalog API (<http://data.worldbank.org/developers/data-catalog-api>).
Version: 0.1
Date: 2016-04-21
Authors@R: c( person("Jesse", "Piburn", email = "piburnjo@ornl.gov", role = c("aut", "cre")), person("UT-Battelle, LLC", role = "cph") )
Maintainer: Jesse Piburn <piburnjo@ornl.gov>
URL: https://github.com/GIST-ORNL/wbstats
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 2.10)
Imports: httr, jsonlite
Suggests: ggplot2, knitr, lubridate (>= 1.5.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-22 10:13:19 UTC; pij
Author: Jesse Piburn [aut, cre], UT-Battelle, LLC [cph]
Repository: CRAN
Date/Publication: 2016-04-22 13:10:19

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New package subspaceMOA with initial version 0.5.1
Package: subspaceMOA
Type: Package
Title: Interface to 'subspaceMOA'
Version: 0.5.1
Date: 2016-04-21
Author: c(person("Marwan","Hassani",role=c("aut","cre"),email="rsubspace@cs.rwth- aachen.de") person("Matthias","Hansen",role="aut"), person("Yunsu","Kim",role="ctb"), person("Thomas","Seidl",role="ctb"), person("University of","Waikato",role=c("ctb","cph")))
Maintainer: Marwan Hassani <rsubspace@cs.rwth-aachen.de>
Description: An interface to 'subspaceMOA', a Framework for the Evaluation of subspace stream clustering algorithms. (see <http://dme.rwth-aachen.de/de/subspacemoa> for more information.)
License: GPL-2
Imports: rJava(>= 0.9), ggplot2 (>= 1.0.1), gridExtra (>= 2.0.0), grid (>= 3.2.2), fields (>= 8.3), magrittr (>= 1.5), shiny (>= 0.12), methods, stats (>= 3.2.2)
Depends: stream(>= 1.2), streamMOA(>= 1.1)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-22 09:49:16 UTC; mth
Repository: CRAN
Date/Publication: 2016-04-22 13:10:12

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New package mixedsde with initial version 1.0
Package: mixedsde
Version: 1.0
Date: 2016-01-19
Title: Estimation Methods for Stochastic Differential Mixed Effects Models
Author: Charlotte Dion [aut, cre], Adeline Sansom [aut], Simone Hermann [aut]
Maintainer: Charlotte Dion <charlotte.dion@imag.fr>
Depends: R (>= 3.0.2), sde, moments, MASS, stats, graphics, methods
Imports: plot3D, grDevices
Description: Inference on stochastic differential models Ornstein-Uhlenbeck or Cox-Ingersoll-Ross, with one or two random effects in the drift function.
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2016-04-22 09:08:56 UTC; hermann
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-04-22 13:09:58

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New package edf with initial version 1.0.0
Package: edf
Type: Package
Title: Read Data from European Data Format (EDF and EDF+) Files
Version: 1.0.0
Description: Import physiologic data stored in the European Data Format (EDF and EDF+) into R. Both EDF and EDF+ files are supported. Discontinuous EDF+ files are not yet supported.
Author: Andreas Henelius <andreas.henelius@iki.fi>
Maintainer: Andreas Henelius <andreas.henelius@iki.fi>
URL: https://github.com/bwrc/edf
Depends: R (>= 3.0.2)
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-22 06:58:47 UTC; anhe
Repository: CRAN
Date/Publication: 2016-04-22 13:09:51

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New package aimPlot with initial version 1.0.0
Package: aimPlot
Title: Create Pie Like Plot for Completeness
Version: 1.0.0
Authors@R: person("Yusman", "Kamaleri", email = "ybkamaleri@gmail.com", role = c("aut", "cre"))
Description: Create a pie like plot to visualise if the aim or several aims of a project is achieved or close to be achieved i.e the aim is achieved when the point is at the center of the pie plot. Imagine it's like a dartboard and the center means 100% completeness/achievement. Achievement can also be understood as 100% coverage. The standard distribution of completeness allocated in the pie plot is 50%, 80% and 100% completeness.
Depends: R (>= 3.2.0), utils
Imports: ggplot2 (>= 2.1.0)
Suggests: grid, gridExtra
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-22 07:54:42 UTC; yuskam
Author: Yusman Kamaleri [aut, cre]
Maintainer: Yusman Kamaleri <ybkamaleri@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-22 13:09:49

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New package xkcdcolors with initial version 1.0
Package: xkcdcolors
Type: Package
Title: Color Names from the XKCD Color Survey
Version: 1.0
Author: Thomas Lumley, using data from Randall Munroe and about 2.2e5 survey participants
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Description: The XKCD color survey asked participants to name colours. Randall Munroe published the top thousand(roughly) names and their sRGB hex values. This package lets you use them.
Imports: grDevices, FNN
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2016-04-22 01:31:51 UTC; tlumley
Repository: CRAN
Date/Publication: 2016-04-22 08:40:12

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New package hextri with initial version 0.6
Package: hextri
Type: Package
Title: Hexbin Plots with Triangles
Version: 0.6
Author: Thomas Lumley (Jie Fu Yu made a prototype)
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Description: Display hexagonally binned scatterplots for multi-class data, using coloured triangles to show class proportions.
License: MIT + file LICENSE
Imports: hexbin, graphics, FNN, grid, grDevices
Suggests: lattice, knitr, datasets
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-22 04:17:05 UTC; tlumley
Repository: CRAN
Date/Publication: 2016-04-22 08:40:09

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Thu, 21 Apr 2016

New package discgolf with initial version 0.1.0
Package: discgolf
Title: Discourse 'API' Client
Description: Client for the Discourse 'API'. Discourse is a open source discussion forum platform (<http://www.discourse.org/>). It comes with 'RESTful' API access to an installation. This client requires that you are authorized to access a Discourse installation, either yours or another.
Version: 0.1.0
License: MIT + file LICENSE
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")
URL: https://github.com/sckott/discgolf
BugReports: https://github.com/sckott/discgolf/issues
LazyData: true
Imports: httr (>= 1.1.0), jsonlite, xml2
Suggests: testthat, covr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-21 21:57:20 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-22 01:16:52

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New package sourceR with initial version 0.1.0
Package: sourceR
Type: Package
Title: Fits a Non-Parametric Bayesian Source Attribution Model
Version: 0.1.0
Date: 2016-03-29
Authors@R: person("Poppy", "Miller", email = "p.miller@lancaster.ac.uk", role = c("aut", "cre"))
Description: Implements a non-parametric source attribution model to attribute cases of disease to sources in Bayesian framework with source and type effects. Type effects are clustered using a Dirichlet Process. Multiple times and locations are supported.
License: GPL-3
Imports: gtools (>= 3.4.1), Rlab (>= 2.15.1), SPIn (>= 1.1), inline (>= 0.3.13), Rcpp (>= 0.11.3), methods
Depends: R (>= 3.1.2)
Suggests: cluster (>= 1.15.3), ggplot2 (>= 1.1.0), gplots (>= 2.16.0)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: yes
Packaged: 2016-04-21 21:38:11 UTC; millerp
Author: Poppy Miller [aut, cre]
Maintainer: Poppy Miller <p.miller@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2016-04-22 01:12:06

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New package sdat with initial version 1.0
Package: sdat
Type: Package
Title: Signal Detection via Adaptive Test
Version: 1.0
Date: 2016-04-21
Authors@R: c(person("Yichi", "Zhang", role = c("aut", "cre"), email = "yzhang52@ncsu.edu"))
Author: Yichi Zhang [aut, cre]
Maintainer: Yichi Zhang <yzhang52@ncsu.edu>
Description: Test the global null in linear models using marginal approach.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-04-21 16:46:35 UTC; Yichi
Repository: CRAN
Date/Publication: 2016-04-21 22:13:08

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New package pcrsim with initial version 1.0.0
Package: pcrsim
Type: Package
Title: Simulation of the Forensic DNA Process
Version: 1.0.0
Date: 2016-04-20
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
URL: https://github.com/OskarHansson/pcrsim
BugReports: https://github.com/OskarHansson/pcrsim/issues
Imports: ggplot2, data.table, gWidgets, mc2d, plyr
Depends: strvalidator (>= 1.6)
Description: Simulate the forensic DNA process: generate random or fixed DNA profiles, create forensic samples including mixtures of diploid and haploid cells, simulate DNA extraction, normalization, degradation, amplification including stutters and inter-locus balance, and capillary electrophoresis. DNA profiles are visualized as electropherograms and saved in tables. The command pcrsim() opens up a graphical user interface which allow the user to create projects, to enter, load, and save parameters required for the simulation. The simulation is transparent and the parameters used in each step of the simulation can be viewed in the result tables.
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-20 10:59:56 UTC; nioh
Repository: CRAN
Date/Publication: 2016-04-21 21:43:57

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New package neat with initial version 0.0
Package: neat
Type: Package
Title: Network Enrichment Analysis Test (NEAT)
Version: 0.0
Date: 2016-04-21
Depends: R (>= 3.2.0)
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Description: Includes functions and examples to compute NEAT, a network-based test for gene enrichment analysis.
Suggests: igraph, Matrix
License: GPL-3
NeedsCompilation: no
Packaged: 2016-04-21 11:51:39 UTC; Mirko
Repository: CRAN
Date/Publication: 2016-04-21 22:13:05

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New package minimaxdesign with initial version 0.1.0
Package: minimaxdesign
Type: Package
Title: Minimax and Minimax Projection Designs
Version: 0.1.0
Author: Simon Mak
Maintainer: Simon Mak <smak6@gatech.edu>
Description: The 'minimaxdesign' package provides two main functions: mMcPSO() and miniMaxPro(), which generates minimax designs and minimax projection designs using clustering and particle swarm optimization (PSO) techniques. These designs can be used in a variety of settings, e.g., as space-filling designs for computer experiments or sensor allocation designs. A detailed description of the two designs and the employed algorithms can be found in Mak and Joseph (2016).
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.12.4), randtoolbox, DiceDesign, MaxPro, doParallel, gtools, nloptr, foreach
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-04-21 17:14:08 UTC; SimonLenovo
Repository: CRAN
Date/Publication: 2016-04-21 22:13:03

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New package IsoplotR with initial version 0.1
Package: IsoplotR
Title: Statistical Toolbox for Radiometric Geochronology
Version: 0.1
Authors@R: person("Pieter", "Vermeesch", , "p.vermeesch@ucl.ac.uk", role = c("aut", "cre"))
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams, taking into account error correlations. Future versions will include functionality for the Ar-Ar, Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, including isochrons, age spectra, ternary diagrams, kernel density estimates, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Depends: R (>= 3.0.0)
Imports:
License: GPL-2
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-21 19:21:52 UTC; pvermees
Repository: CRAN
Date/Publication: 2016-04-21 22:12:54

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New package falconx with initial version 0.1
Package: falconx
Version: 0.1
Date: 2016-04-21
Title: Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Depends: R (>= 3.0.1)
Description: This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-04-21 16:10:26 UTC; haochen
Repository: CRAN
Date/Publication: 2016-04-21 22:13:02

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New package eyelinker with initial version 0.1
Package: eyelinker
Type: Package
Title: Load Raw Data from Eyelink Eye Trackers
Version: 0.1
Date: 2016-04-20
Author: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Description: Eyelink eye trackers output a horrible mess, typically under the form of a '.asc' file. The file in question is an assorted collection of messages, events and raw data. This R package will attempt to make sense of it.
Depends: R (>= 3.1.1)
Imports: plyr, stringi, stringr, readr, magrittr, intervals
License: GPL-3
RoxygenNote: 5.0.1
Suggests: testthat, knitr, rmarkdown, dplyr, ggplot2, tidyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-21 08:40:30 UTC; simon
Repository: CRAN
Date/Publication: 2016-04-21 13:46:06

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New package rematch with initial version 1.0.1
Package: rematch
Title: Match Regular Expressions with a Nicer 'API'
Version: 1.0.1
Author: Gabor Csardi
Maintainer: Gabor Csardi <gcsardi@mango-solutions.com>
Description: A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/MangoTheCat/rematch
BugReports: https://github.com/MangoTheCat/rematch/issues
RoxygenNote: 5.0.1.9000
Suggests: covr, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-04-20 19:54:37 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2016-04-21 08:20:46

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New package postGIStools with initial version 0.1.0
Package: postGIStools
Type: Package
Title: Tools for Interacting with 'PostgreSQL' / 'PostGIS' Databases
Description: Functions to convert geometry and 'hstore' data types from 'PostgreSQL' into standard R objects, as well as to simplify the import of R data frames (including spatial data frames) into 'PostgreSQL'.
Version: 0.1.0
License: GPL-3
URL: https://github.com/SESYNC-ci/postGIStools
BugReports: https://github.com/SESYNC-ci/postGIStools/issues
Authors@R: person('Philippe', 'Marchand', email = 'pmarchand@sesync.org', role = c('aut', 'cre'))
Depends: R (>= 3.2.3), sp (>= 1.2)
Imports: DBI (>= 0.3), jsonlite (>= 0.9), methods, rgdal (>= 0.8), rgeos (>= 0.3), RPostgreSQL (>= 0.4), stringr (>= 1.0)
Suggests: testthat, knitr, rmarkdown
LazyData: TRUE
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-20 19:21:56 UTC; pmarchand
Author: Philippe Marchand [aut, cre]
Maintainer: Philippe Marchand <pmarchand@sesync.org>
Repository: CRAN
Date/Publication: 2016-04-21 08:20:45

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Wed, 20 Apr 2016

New package rnpn with initial version 0.1.0
Package: rnpn
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
Version: 0.1.0
License: MIT + file LICENSE
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"), person("Lee", "Marsh", role = "aut", email = "npnlee85@gmail.com") )
LazyData: yes
Imports: stats, httr (>= 1.1.0), jsonlite (>= 0.9.19), plyr, data.table (>= 1.9.6)
Suggests: ggplot2, testthat, covr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-20 17:53:42 UTC; sacmac
Author: Scott Chamberlain [aut, cre], Lee Marsh [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-20 21:20:13

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