Wed, 22 Mar 2017

New package ukds with initial version 0.1.0
Package: ukds
Type: Package
Title: Reproducible Data Retrieval from the UK Data Service
Version: 0.1.0
Date: 2017-03-22
Authors@R: c( person("Frederick", "Solt", email = "frederick-solt@uiowa.edu", role = c("aut", "cre")))
URL: https://github.com/fsolt/ukds
BugReports: https://github.com/fsolt/ukds/issues
Description: Reproducible, programmatic retrieval of datasets from the UK Data Service <https://www.ukdataservice.ac.uk>. The UKDS is "the UK's largest collection of social, economic and population data resources," but researchers taking advantage of these datasets are caught in a bind. The UKDS terms and conditions sharply limit redistribution of downloaded datasets, but to ensure that one's work can be reproduced, assessed, and built upon by others, one must provide access to the raw data one employed. The ukds package cuts this knot by providing programmatic, reproducible access to the UKDS datasets from within R.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: magrittr, rio, RSelenium (>= 1.7.1), stringr, tools, utils
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-22 17:11:05 UTC; fredsolt
Author: Frederick Solt [aut, cre]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Repository: CRAN
Date/Publication: 2017-03-22 19:20:58 UTC

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New package survutils with initial version 1.0.0
Package: survutils
Title: Utility Functions for Survival Analysis
Version: 1.0.0
Authors@R: person("Fong Chun", "Chan", , "fongchunchan@gmail.com", role = c("aut", "cre"))
Description: Functional programming principles to iteratively run Cox regression and plot its results. The results are reported in tidy data frames. Additional utility functions are available for working with other aspects of survival analysis such as survival curves, C-statistics, etc.
License: MIT + file LICENSE
LazyData: true
Depends: R (>= 3.1.2)
Imports: stats, dplyr (>= 0.4.3), survC1 (>= 1.0.2), survival (>= 2.38.3), ggplot2 (>= 1.0.0), purrr (>= 0.1.0), magrittr (>= 1.5), broom (>= 0.3.7), lazyeval (>= 0.2.0)
Suggests: tidyr (>= 0.4.1)
URL: https://github.com/tinyheero/survutils
BugReports: https://github.com/tinyheero/survutils/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-22 16:56:25 UTC; fongchun
Author: Fong Chun Chan [aut, cre]
Maintainer: Fong Chun Chan <fongchunchan@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-22 19:21:02 UTC

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New package mMPA with initial version 0.1.0
Package: mMPA
Type: Package
Title: Implementation of Marker-Assisted Mini-Pooling with Algorithm
Version: 0.1.0
Author: "Tao Liu <tliu@stat.brown.edu> [aut, cre]" "Yizhen Xu <yizhen_xu@brown.edu> [aut]"
Maintainer: Tao Liu <tliu@stat.brown.edu>
Description: To determine the number of quantitative assays needed for a sample of data using pooled testing methods, which include mini-pooling (MP), MP with algorithm (MPA), and marker-assisted MPA (mMPA). To estimate the number of assays needed, the package also provides a tool to conduct Monte Carlo (MC) to simulate different orders in which the sample would be collected to form pools. Using MC avoids the dependence of the estimated number of assays on any specific ordering of the samples to form pools.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-22 16:02:17 UTC; tliu
Repository: CRAN
Date/Publication: 2017-03-22 19:20:49 UTC

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New package margins with initial version 0.3.0
Package: margins
Type: Package
Title: Marginal Effects for Model Objects
Description: An R port of Stata's 'margins' command, which can be used to calculate marginal (or partial) effects from model objects.
License: MIT + file LICENSE
Version: 0.3.0
Date: 2017-03-21
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"), person("Jeffrey", "Arnold", role = c("ctb"), email = "jeffrey.arnold@gmail.com") )
URL: https://github.com/leeper/margins
BugReports: https://github.com/leeper/margins/issues
Imports: stats, prediction (>= 0.1.11), graphics, compiler, MASS
Suggests: sandwich, knitr, ggplot2, gapminder, stargazer, testthat
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-22 13:21:02 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre], Jeffrey Arnold [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-22 19:20:50 UTC

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New package focusedMDS with initial version 1.2.4
Package: focusedMDS
Title: Focused, Interactive Multidimensional Scaling
Version: 1.2.4
Authors@R: c(person("Lea", "Urpa", email = "lea.urpa@helsinki.fi", role = "cre"), person("Simon", "Anders", email = "simon.anders@helsinki.fi", role = "aut"))
Description: Takes a distance matrix and plots it as an interactive graph. Double click on any point to choose a new focus point, and hover over points to see their ID labels. In this graph, one point is focused on at the center of the graph. All other points are plotted around this central point at their exact distances to the point, as given in the distance matrix. In other words, the distance between each point and the focus point are the true distances given in the distance matrix. The non focus points are plotted with respect to each other as exactly as possible. For more details, see <https://lea-urpa.github.io/focusedMDS.html>.
Depends: R (>= 3.3.1)
Imports: htmlwidgets, grDevices
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-22 17:16:17 UTC; admin
Author: Lea Urpa [cre], Simon Anders [aut]
Maintainer: Lea Urpa <lea.urpa@helsinki.fi>
Repository: CRAN
Date/Publication: 2017-03-22 19:17:33 UTC

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New package alterryx with initial version 0.2.0
Package: alterryx
Type: Package
Title: An 'API' Client for the 'Alteryx' Gallery
Version: 0.2.0
Author: Michael Treadwell
Maintainer: Michael Treadwell <michael.treadwell@interworks.com>
Description: A tool to access each of the 'Alteryx' Gallery 'API' endpoints. Users can queue jobs, poll job status, and retrieve application output as a data frame. You will need an 'Alteryx' Server license and have 'Alteryx' Gallery running to utilize this package. The 'API' is accessed through the 'URL' that you setup for the server running 'Alteryx' Gallery and more information on the endpoints can be found at <https://gallery.alteryx.com/api-docs/>.
URL: https://github.com/mtreadwell/alterryx, https://gallery.alteryx.com/api-docs/
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: httr, utils, digest, base64enc, jsonlite
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-22 14:01:18 UTC; mtreadwell
Repository: CRAN
Date/Publication: 2017-03-22 19:23:52 UTC

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New package giphyr with initial version 0.1.0
Package: giphyr
Title: R Interface to the 'Giphy' 'API'
Version: 0.1.0
Authors@R: person("Hao", "Zhu", email = "haozhu233@gmail.com", role = c("aut", "cre"))
Description: An interface to the 'API' of 'Giphy', a popular index-based search engine for 'GIFs' and animated stickers (see <http://giphy.com/faq> and <https://github.com/Giphy/GiphyAPI> for more information about 'Giphy' and its 'API') . This package also provides a 'RStudio Addin', which can help users easily search and download 'GIFs' and insert them to a 'rmarkdown' presentation.
Depends: R (>= 3.2.2)
Imports: httr, shiny, miniUI, tibble, rstudioapi, utils, purrr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/haozhu233/giphyr
BugReports: https://github.com/haozhu233/giphyr/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-22 15:05:16 UTC; haozhu
Author: Hao Zhu [aut, cre]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-22 16:26:39 UTC

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New package xlsimple with initial version 0.0.1
Package: xlsimple
Type: Package
Title: 'XLConnect' Wrapper
Description: Provides a simple wrapper for some 'XLConnect' functions. 'XLConnect' is a package that allows for reading, writing, and manipulating Microsoft Excel files. This package, 'xlsimple', adds some documentation and pre-defined formatting to the outputted Excel file. Individual sheets can include a description on the first row to remind user what is in the data set. Auto filters and freeze rows are turned on. A brief readme file is created that provides a summary listing of the created sheets and, where provided, the description.
Author: Jon Harcum, Erik Leppo
Maintainer: Jon Harcum <jon.harcum@tetratech.com>
Version: 0.0.1
Date: 2017-03-15
Depends: R (>= 3.2.0),
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.0.1
Suggests: XLConnect, knitr
NeedsCompilation: no
Packaged: 2017-03-22 12:25:11 UTC; jon.harcum
Repository: CRAN
Date/Publication: 2017-03-22 14:20:58 UTC

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New package tensorflow with initial version 0.7
Package: tensorflow
Type: Package
Title: R Interface to TensorFlow
Version: 0.7
Date: 2017-03-21
Authors@R: c( person("JJ", "Allaire", role = c("aut", "cre"), comment = "R interface", email = "jj@rstudio.com"), person(family = "RStudio", role = "cph"), person("Dirk", "Eddelbuettel", role = c("ctb", "cph"), email = "edd@debian.org"), person("Nick", "Golding", role = c("ctb", "cph"), email = "nick.golding.research@gmail.com"), person("Yuan", "Tang", role = c("ctb", "cph"), email = "terrytangyuan@gmail.com"), person(family = "Google Inc.", role = c("ctb", "cph"), comment = "Examples and Tutorials") )
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
License: Apache License 2.0
URL: https://github.com/rstudio/tensorflow
BugReports: https://github.com/rstudio/tensorflow/issues
SystemRequirements: TensorFlow (https://www.tensorflow.org/)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: utils, reticulate (>= 0.7), yaml
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-03-22 14:01:58 UTC; jjallaire
Author: JJ Allaire [aut, cre] (R interface), RStudio [cph], Dirk Eddelbuettel [ctb, cph], Nick Golding [ctb, cph], Yuan Tang [ctb, cph], Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: JJ Allaire <jj@rstudio.com>
Repository: CRAN
Date/Publication: 2017-03-22 14:19:55 UTC

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New package frailtyEM with initial version 0.5.2
Package: frailtyEM
Type: Package
Title: Fitting Frailty Models with the EM Algorithm
Version: 0.5.2
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>
URL: https://github.com/teddybalan/frailtyEM
BugReports: https://github.com/teddybalan/frailtyEM/issues
Description: Contains functions for fitting shared frailty models with a semi-parametric baseline hazard with the Expectation-Maximization algorithm. Supported data formats include clustered failures with left truncation and recurrent events in gap-time or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable and the Power Variance Family are supported.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: survival
Imports: Rcpp (>= 0.12.8), magrittr, msm, optimx
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: ggplot2, dplyr, tidyr, statmod, plotly, frailtySurv, parfm
Collate: 'RcppExports.R' 'ca_test.R' 'em_fit.R' 'emfrail_aux.R' 'emfrail.R' 'emfrail_arguments.R' 'fast_Estep.R' 'plot_methods.R' 'predict.emfrail.R' 'print.emfrail.R' 'print.emfrail_summary.R' 'summary.emfrail.R'
NeedsCompilation: yes
Packaged: 2017-03-22 13:45:19 UTC; theodor
Repository: CRAN
Date/Publication: 2017-03-22 14:24:46 UTC

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New package CVR with initial version 0.1.1
Package: CVR
Type: Package
Title: Canonical Variate Regression
Version: 0.1.1
Date: 2017-03-17
Author: Chongliang Luo, Kun Chen.
Maintainer: Chongliang Luo <chongliang.luo@uconn.edu>
Description: Perform canonical variate regression (CVR) for two sets of covariates and a univariate response, with regularization and weight parameters tuned by cross validation.
License: GPL (>= 2)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
Depends: R (>= 3.2.1), PMA
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-03-22 03:15:52 UTC; chongliang
Repository: CRAN
Date/Publication: 2017-03-22 14:13:03 UTC

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New package rbcb with initial version 0.1.0
Package: rbcb
Type: Package
Title: R Interface to Brazilian Central Bank Web Services
Version: 0.1.0
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Description: The Brazilian Central Bank API delivers many datasets which regard economic activity, regional economy, international economy, public finances, credit indicators and many more. For more information please see <http://dadosabertos.bcb.gov.br/>. These datasets can be accessed through 'rbcb' functions and can be obtained in different data structures common to R ('tibble', 'data.frame', 'xts', ...).
URL: https://github.com/wilsonfreitas/rbcb
BugReports: https://github.com/wilsonfreitas/rbcb/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: httr, jsonlite, tibble, xts, xml2, utils
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-03-22 11:01:08 UTC; wilson
Repository: CRAN
Date/Publication: 2017-03-22 11:15:34 UTC

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New package bayesDP with initial version 1.0.0
Package: bayesDP
Type: Package
Title: Tools for the Bayesian Discount Prior Function
Version: 1.0.0
Date: 2017-03-20
Authors@R: c(person("Shawn", "Balcome", email = "sbalcome@mdic.org", role = c("cre")), person("Donnie", "Musgrove", email = "donald.r.musgrove@medtronic.com", role = c("aut")), person("Tarek", "Haddad", email = "tarek.d.haddad@medtronic.com", role = c("aut")), person("Christopher", "Jackson", email = "chris.jackson@mrc-bsu.cam.ac.uk", role = "ctb", comment="For the ppexp R code that was ported to C++."))
Depends: ggplot2, survival, methods
Description: Functions for augmenting data with historical controls using the Bayesian discount prior function for 1 arm and 2 arm clinical trials.
LazyLoad: yes
License: GPL-3
URL: https://github.com/balcomes/bayesDP
BugReports: https://github.com/balcomes/bayesDP/issues
NeedsCompilation: yes
Maintainer: Shawn Balcome <sbalcome@mdic.org>
Repository: CRAN
Imports: Rcpp
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
Suggests: testthat
Packaged: 2017-03-22 05:25:04 UTC; Shawn Balcome
Author: Shawn Balcome [cre], Donnie Musgrove [aut], Tarek Haddad [aut], Christopher Jackson [ctb] (For the ppexp R code that was ported to C++.)
Date/Publication: 2017-03-22 10:47:06 UTC

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New package rGoodData with initial version 0.1.0
Package: rGoodData
Type: Package
Title: GoodData API Client Package
Description: Export raw reports from 'GoodData' business intelligence platform (see <http://www.gooddata.com> for more information).
Version: 0.1.0
Author: Bulat Yapparov [aut, cre]
Maintainer: Bulat Yapparov <byapparov@gmail.com>
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: data.table, httr, jsonlite
Suggests: testthat, httptest, mockery
Collate: 'request.R' 'login.R' 'report.R'
NeedsCompilation: no
Packaged: 2017-03-21 22:09:20 UTC; byapparov
Repository: CRAN
Date/Publication: 2017-03-22 08:55:39 UTC

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New package qboxplot with initial version 0.1
Package: qboxplot
Title: Quantile-Based Boxplot
Version: 0.1
Date: 2017-03-21
Author: Tom Pike
Maintainer: Tom Pike <tpike@lincoln.ac.uk>
Description: Produce quantile-based box-and-whisker plot(s).
Depends: stats
Imports: methods
License: GPL-2
NeedsCompilation: no
Packaged: 2017-03-21 21:02:07 UTC; Tom Pike
Repository: CRAN
Date/Publication: 2017-03-22 08:55:38 UTC

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New package collapsibleTree with initial version 0.1.4
Package: collapsibleTree
Type: Package
Title: Interactive Collapsible Tree Diagrams using 'D3.js'
Version: 0.1.4
Author: Adeel Khan [aut, cre], Michael Bostock [ctb, cph] (D3.js library)
Maintainer: Adeel Khan <AdeelK@gwu.edu>
Description: Interactive Reingold-Tilford tree diagrams created using 'D3.js', where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame. See 'collapsibleTree' website for more information and examples.
License: GPL (>= 3)
URL: https://github.com/AdeelK93/collapsibleTree, https://AdeelK93.github.io/collapsibleTree/
BugReports: https://github.com/AdeelK93/collapsibleTree/issues
Encoding: UTF-8
Depends: R (>= 3.0.0)
Imports: htmlwidgets, data.tree, stats
Enhances: knitr, shiny
LazyData: true
RoxygenNote: 6.0.1
Suggests: colorspace, RColorBrewer, dplyr, testthat
NeedsCompilation: no
Packaged: 2017-03-22 02:25:29 UTC; Adeel
Repository: CRAN
Date/Publication: 2017-03-22 06:13:12 UTC

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Tue, 21 Mar 2017

New package rnaturalearth with initial version 0.1.0
Package: rnaturalearth
Title: World Map Data from Natural Earth
Version: 0.1.0
Authors@R: c( person("Andy", "South", email = "southandy@gmail.com", role = c("aut", "cre")) )
Description: Facilitates mapping by making natural earth map data from <http://www.naturalearthdata.com/> more easily available to R users.
License: MIT + file LICENSE
LazyData: true
LazyDataCompression: xz
URL: https://github.com/ropenscilabs/rnaturalearth
BugReports: https://github.com/ropenscilabs/rnaturalearth/issues
Additional_repositories: http://packages.ropensci.org
Depends: R (>= 3.1.1)
Imports: sp (>= 1.0.15), utils (>= 3.2.3), sf (>= 0.3-4)
Suggests: rgdal, knitr (>= 1.12.3), testthat (>= 0.9.1), httr (>= 1.1.0), devtools (>= 1.10.0), rnaturalearthdata (>= 0.1.0), rnaturalearthhires (>= 0.1.0), raster (>= 2.5-2), rgeos
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-20 10:12:26 UTC; andy
Author: Andy South [aut, cre]
Maintainer: Andy South <southandy@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-21 21:58:11 UTC

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New package orgutils with initial version 0.4-1
Package: orgutils
Type: Package
Title: Helper Functions for Org Files
Version: 0.4-1
Date: 2017-03-21
Author: Enrico Schumann
Maintainer: Enrico Schumann <es@enricoschumann.net>
Description: Helper functions for Org files (<http://orgmode.org/>): a generic function 'toOrg' for transforming R objects into Org markup (most useful for data frames; there are also methods for Dates/POSIXt) and a function to read Org tables into data frames.
License: GPL (>= 2)
Imports: textutils
Suggests: RUnit
NeedsCompilation: no
Packaged: 2017-03-21 21:22:06 UTC; es19
Repository: CRAN
Date/Publication: 2017-03-21 21:28:17 UTC

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New package KENDL with initial version 1.0
Package: KENDL
Type: Package
Title: Kernel-Smoothed Nonparametric Methods for Environmental Exposure Data Subject to Detection Limits
Version: 1.0
Date: 2017-03-13
Author: Yuchen Yang <yuchen.y@uky.edu>, Li Chen <lichenuky@uky.edu>
Maintainer: Yuchen Yang <yuchen.y@uky.edu>
Description: Calculate the kernel-smoothed nonparametric estimator for the exposure distribution in presence of detection limits.
License: GPL-2
NeedsCompilation: no
Packaged: 2017-03-21 16:44:01 UTC; yyang02
Repository: CRAN
Date/Publication: 2017-03-21 21:09:13 UTC

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New package FMC with initial version 1.0.0
Package: FMC
Type: Package
Title: Factorial Experiments with Minimum Level Changes
Version: 1.0.0
Authors@R: c( person("Shwetank", "Lall", email = "shwetanklall@gmail.com", role = c("aut", "cre")), person("Arpan", "Bhowmik", email = "arpan.stat@gmail.com ", role = "ctb"), person("Eldho", "Varghese", email = "eldhoiasri@gmail.com", role = "aut"), person("Seema", "Jaggi", email = "seema@iasri.res.in ", role = "ctb"), person("Cini", "Varghese", email = "cini_v@iasri.res.in ", role = "ctb") )
Maintainer: Shwetank Lall <shwetanklall@gmail.com>
Description: Generate cost effective minimally changed run sequences for symmetrical as well as asymmetrical factorial designs.
Imports: utils, minimalRSD, stats
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-21 15:33:49 UTC; Design
Author: Shwetank Lall [aut, cre], Arpan Bhowmik [ctb], Eldho Varghese [aut], Seema Jaggi [ctb], Cini Varghese [ctb]
Repository: CRAN
Date/Publication: 2017-03-21 20:59:08 UTC

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New package RchivalTag with initial version 0.0.1
Package: RchivalTag
Type: Package
Title: Analyzing Archival Tagging Data
Version: 0.0.1
Date: 2017-03-20
Author: Robert Bauer
Maintainer: Robert Bauer <robert.bauer@ird.fr>
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Depends: R (>= 3.0.1)
Imports: plyr, akima, maptools, graphics, stats, raster, rgeos, ncdf4, maps, mapdata, grDevices, oceanmap, sp, methods, PBSmapping
License: CC BY-NC-SA 4.0
LazyLoad: yes
Packaged: 2017-03-21 09:28:11 UTC; robert
Repository: CRAN
Date/Publication: 2017-03-21 15:20:26 UTC
NeedsCompilation: no

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New package stmgp with initial version 1.0
Package: stmgp
Type: Package
Title: Rapid and Accurate Genetic Prediction Modeling for Genome-Wide Association or Whole-Genome Sequencing Study Data
Version: 1.0
Date: 2017-03-13
Author: Masao Ueki
Maintainer: Masao Ueki <uekimrsd@nifty.com>
Description: Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
SystemRequirements: PLINK must be installed
License: GPL (>= 2)
Depends: MASS
NeedsCompilation: no
Packaged: 2017-03-21 07:00:51 UTC; uekim
Repository: CRAN
Date/Publication: 2017-03-21 08:26:01 UTC

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New package VarReg with initial version 1.0
Package: VarReg
Type: Package
Title: Semi-Parametric Variance Regression
Version: 1.0
Authors@R: c(person("Kristy","Robledo", email = "robledo.kristy@gmail.com", role = c("aut", "cre")),person("Ian", "Marschner", role = c("ths")))
Maintainer: Kristy Robledo <robledo.kristy@gmail.com>
Description: Methods for fitting semi-parametric mean and variance models, with normal or censored data. Also extended to allow a regression in the location, scale and shape parameters.
License: GPL-3
Depends: R (>= 2.10)
LazyData: TRUE
Suggests: testthat
Imports: splines, stats, graphics, sn, survival, utils
RoxygenNote: 6.0.0
NeedsCompilation: no
Packaged: 2017-03-21 00:27:23 UTC; 43486037
Author: Kristy Robledo [aut, cre], Ian Marschner [ths]
Repository: CRAN
Date/Publication: 2017-03-21 06:50:28 UTC

More information about VarReg at CRAN
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New package rolr with initial version 1.0.0
Package: rolr
Type: Package
Title: Finding Optimal Three-Group Splits Based on a Survival Outcome
Version: 1.0.0
Author: Pingping Qu and John Crowley
Maintainer: Pingping Qu <quping14@gmail.com>
Description: Provides fast procedures for exploring all pairs of cutpoints of a single covariate with respect to survival and determining optimal cutpoints using a hierarchical method and various ordered logrank tests.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats, survival
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2017-03-20 19:21:31 UTC; pingpingq
Repository: CRAN
Date/Publication: 2017-03-21 06:51:14 UTC

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Mon, 20 Mar 2017

New package kerasR with initial version 0.4.1
Package: kerasR
Type: Package
Title: R Interface to the Keras Deep Learning Library
Version: 0.4.1
Date: 2017-03-16
Authors@R: c(person("Taylor", "Arnold", email = "taylor.arnold@acm.org", role = c("aut", "cre")))
Author: Taylor Arnold [aut, cre]
Maintainer: Taylor Arnold <taylor.arnold@acm.org>
Description: Provides a consistent interface to the 'Keras' Deep Learning Library directly from within R. 'Keras' (see <https://keras.io/> for more information) provides specifications for describing dense neural networks, convolution neural networks (CNN) and recurrent neural networks (RNN) running on top of either 'TensorFlow' (<https://www.tensorflow.org/>) or 'Theano' (<http://deeplearning.net/software/theano/>). Type conversions between Python and R are automatically handled correctly, even when the default choices would otherwise lead to errors. Includes complete R documentation and many working examples.
Depends: R (>= 3.3.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: reticulate
URL: https://github.com/statsmaths/kerasR
Encoding: UTF-8
SystemRequirements: Python (>= 2.7); keras <https://keras.io/> (>= 2.0.1)
License: LGPL-2
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-20 13:22:00 UTC; taylor
Repository: CRAN
Date/Publication: 2017-03-20 17:34:39 UTC

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New package anomalyDetection with initial version 0.1.0
Package: anomalyDetection
Type: Package
Title: Implementation of Augmented Network Log Anomaly Detection Procedures
Version: 0.1.0
Author: Authors@R: c( person("Bradley", "Boehmke", email = "bradleyboehmke@gmail.com", role = c("aut", "cre")), person("Robert", "Gutierrez", email = "rjgutierrez2015@gmail.com", role = c("aut", "cre"), person("Kenneth", "Bauer", email = "kenneth.bauer@afit.edu", role = c("ctb"), person("Trevor", "Bihl", email = "trevor.bihl.2@us.af.mil", role = c("ctb"), person("Cade", "Saie", email = "cade.saie@gmail.com", role = c("ctb")) )
Maintainer: Bradley Boehmke <bradleyboehmke@gmail.com>
Date: 2017-03-19
Description: Implements procedures to aid in detecting network log anomalies. By combining various multivariate analytic approaches relevant to network anomaly detection, it provides cyber analysts efficient means to detect suspected anomalies requiring further evaluation.
URL: https://github.com/bradleyboehmke/anomalyDetection
BugReports: https://github.com/bradleyboehmke/anomalyDetection/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: stats, MASS, magrittr, plyr, gmp, caret, matrixStats, qdapTools, dplyr, purrr, tibble, RColorBrewer, tidyverse, gplots
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-20 11:05:25 UTC; bradboehmke
Repository: CRAN
Date/Publication: 2017-03-20 12:49:15 UTC

More information about anomalyDetection at CRAN
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New package sdmpredictors with initial version 0.2.5
Package: sdmpredictors
Type: Package
Title: Species Distribution Modelling Predictor Datasets
Version: 0.2.5
Date: 2017-03-20
Depends: R (>= 3.2.5), raster (>= 2.5-8), rgdal (>= 1.1-10)
Imports: R.utils (>= 2.4.0), stats, utils
Authors@R: c( person("Samuel", "Bosch", email = "mail@samuelbosch.com", role = c("aut", "cre")), person("Lennert", "Tyberghein", email = "lennert.tyberghein@vliz.be", role = c("ctb")), person("Olivier", "De Clerck", email = "olivier.declerck@ugent.be", role = c("ctb")))
Description: Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <http://www.worldclim.org/>,, ENVIREM <http://envirem.github.io/>, Bio-ORACLE <http://www.oracle.ugent.be/> and MARSPEC <http://www.marspec.org/>.
License: MIT + file LICENSE
URL: http://www.samuelbosch.com/p/sdmpredictors.html
BugReports: https://github.com/lifewatch/sdmpredictors/issues
LazyData: true
Suggests: ggplot2, reshape2, testthat, knitr, rmarkdown
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-20 09:51:28 UTC; swbosch
Author: Samuel Bosch [aut, cre], Lennert Tyberghein [ctb], Olivier De Clerck [ctb]
Maintainer: Samuel Bosch <mail@samuelbosch.com>
Repository: CRAN
Date/Publication: 2017-03-20 11:52:08

More information about sdmpredictors at CRAN
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New package Rvoterdistance with initial version 1.1
Package: Rvoterdistance
Type: Package
Title: Calculates the Distance Between Voter and Multiple Polling Locations
Version: 1.1
Date: 2017-03-17
Author: Loren Collingwood
Maintainer: Loren Collingwood <loren.collingwood@ucr.edu>
Description: Designed to calculate the distance between each voter in a voter file -- given lat/long coordinates -- and many potential (early) polling or vote by mail drop box locations, then return the minimum distance.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.9)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2017-03-20 07:40:33 UTC; lorencollingwood
Repository: CRAN
Date/Publication: 2017-03-20 08:38:54 UTC

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New package EstimateGroupNetwork with initial version 0.1.2
Package: EstimateGroupNetwork
Type: Package
Title: Perform the Joint Graphical Lasso and Selects Tuning Parameters
Version: 0.1.2
Author: Giulio Costantini, Sacha Epskamp
Maintainer: Giulio Costantini <giulio.costantini@unimib.it>
Description: Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / eBIC) or crossvalidation.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: parallel, igraph, qgraph
Suggests: mvtnorm, JGL, psych
NeedsCompilation: no
Packaged: 2017-03-20 08:24:36 UTC; Giulio
Repository: CRAN
Date/Publication: 2017-03-20 08:38:51 UTC

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New package pathmapping with initial version 1.0.1
Package: pathmapping
Type: Package
Title: Compute Deviation and Correspondence Between Spatial Paths
Version: 1.0.1
Date: 2017-03-19
Author: Shane T. Mueller & Brandon S. Perelman
Maintainer: Shane T. Mueller <shanem@mtu.edu>
Description: Functions to compute and display the area-based deviation between spatial paths and to compute a mapping based on minimizing area and distance-based cost. For details, see: Mueller, S. T., Perelman, B. S., & Veinott, E. S. (2016) <DOI:10.3758/s13428-015-0562-7>.
License: GPL-2
URL: https://sites.google.com/a/mtu.edu/mapping/, https://github.com/stmueller/pathmapping/
NeedsCompilation: yes
Packaged: 2017-03-20 05:45:34 UTC; smueller
Repository: CRAN
Date/Publication: 2017-03-20 06:13:09 UTC

More information about pathmapping at CRAN
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New package rjmcmc with initial version 0.2.2
Package: rjmcmc
Type: Package
Title: Reversible-Jump MCMC Using Post-Processing
Version: 0.2.2
Date: 2017-03-16
Authors@R: c(person("Nick", "Gelling", email="ngelling@maths.otago.ac.nz", role=c("aut","cre")), person(c("Matthew", "R."), "Schofield", email="mschofield@maths.otago.ac.nz", role="aut"), person(c("Richard", "J."), "Barker", email="rbarker@maths.otago.ac.nz", role="aut"))
Description: Performs reversible-jump MCMC (Green, 1995) <doi:10.2307/2337340>, specifically the restriction introduced by Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling problem. Previously-calculated posterior distributions are used to quickly estimate posterior model probabilities. Jacobian matrices are found using automatic differentiation.
License: GPL-3
Depends: madness, R (>= 3.2.0)
Imports: utils, R2jags, coda
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
LazyData: TRUE
NeedsCompilation: no
Packaged: 2017-03-19 20:27:19 UTC; rachaelyoung
Author: Nick Gelling [aut, cre], Matthew R. Schofield [aut], Richard J. Barker [aut]
Maintainer: Nick Gelling <ngelling@maths.otago.ac.nz>
Repository: CRAN
Date/Publication: 2017-03-20 05:22:26 UTC

More information about rjmcmc at CRAN
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New package CSeqpat with initial version 0.1.0
Package: CSeqpat
Type: Package
Title: Frequent Contiguous Sequential Pattern Mining of Text
Version: 0.1.0
Author: Anantha Janakiraman
Maintainer: Anantha Janakiraman <anantharaman.j@gmail.com>
Description: Mines contiguous sequential patterns in text.
Depends: R (>= 3.1.0)
Imports: NLP, tm, utils
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-19 20:08:03 UTC; anantharamanjanakiraman
Repository: CRAN
Date/Publication: 2017-03-20 05:22:11 UTC

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Sun, 19 Mar 2017

New package supc with initial version 0.1
Package: supc
Type: Package
Title: The Self-Updating Process Clustering Algorithms
Version: 0.1
Authors@R: c( person("Wush", "Wu", email = "wush978@gmail.com", role = c("aut", "cre")), person("Shang-Ying", "Shiu", email = "", role = c("aut", "ctb")))
Maintainer: Wush Wu <wush978@gmail.com>
Description: Implements the self-updating process clustering algorithms proposed in Shiu and Chen (2016) <doi:10.1080/00949655.2015.1049605>.
License: GPL (>= 3)
LazyData: TRUE
Depends: R (>= 3.0.2)
Imports: stats, Rcpp
Suggests: amap, knitr, rmarkdown
Enhances: gputools
LinkingTo: Rcpp(>= 0.12), BH(>= 1.62)
VignetteBuilder: knitr
RoxygenNote: 6.0.1
SystemRequirements: C++11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2017-03-19 18:14:10 UTC; wush
Author: Wush Wu [aut, cre], Shang-Ying Shiu [aut, ctb]
Repository: CRAN
Date/Publication: 2017-03-19 18:19:02 UTC

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New package shinyShortcut with initial version 0.1.0
Package: shinyShortcut
Title: Creates an Executable Shortcut for Shiny Applications
Version: 0.1.0
Authors@R: person("Ewan", "Keith", email = "ewan.keith100@gmail.com", role = c("aut", "cre"))
Description: Provides function shinyShortcut() that, when given the base directory of a shiny application, will produce an executable file that runs the shiny app directly in the user's default browser. Tested on both windows and unix machines. Inspired by and borrowing from <http://www.mango-solutions.com/wp/2017/03/shiny-based-tablet-or-desktop-app/>.
Depends: R (>= 3.2.3)
License: GPL (>= 3) | file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-19 13:53:46 UTC; ewan
Author: Ewan Keith [aut, cre]
Maintainer: Ewan Keith <ewan.keith100@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-19 18:13:08 UTC

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New package sicegar with initial version 0.1
Package: sicegar
Type: Package
Title: Analysis of Single-Cell Viral Growth Curves
Version: 0.1
Date: 2017-03-17
Authors@R: c( person("M. Umut", "Caglar", role = c("aut", "cre"), email = "umut.caglar@gmail.com"), person("Claus O.", "Wilke", role = c("aut"), email = "wilke@austin.utexas.edu") )
Description: Classifies time course fluorescence data of viral growth. The package categorize time course data into one of four categories, "ambiguous", "no signal", "sigmoidal", and "double sigmoidal" by fitting a series of mathematical models to the data. The origin of the package name came from "SIngle CEll Growth Analysis in R".
URL: https://github.com/wilkelab/sicegar
Imports: dplyr, minpack.lm, fBasics, ggplot2, stats
License: GPL-2 | GPL-3
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
BugReports: https://github.com/wilkelab/sicegar/issues
Collate: 'categorize.R' 'mainFunctions.R' 'lineFitFunctions.R' 'sigmoidalFitFunctions.R' 'doublesigmoidalFitFunctions.R' 'normalizationFunction.R' 'sicegar.R' 'dataInputCheck.R' 'numericalReCalculation.R' 'generateFigures.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-19 04:59:38 UTC; umut
Author: M. Umut Caglar [aut, cre], Claus O. Wilke [aut]
Maintainer: M. Umut Caglar <umut.caglar@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-19 11:39:19 UTC

More information about sicegar at CRAN
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New package RIA with initial version 1.0.0
Package: RIA
Type: Package
Title: Radiomics Image Analysis Toolbox for Grayscale Images
Version: 1.0.0
Date: 2017-03-17
Authors@R: person("Marton", "Kolossvary", role = c("aut", "cre"), email = "marton.kolossvary@cirg.hu")
Maintainer: Marton Kolossvary <marton.kolossvary@cirg.hu>
Description: Radiomics image analysis toolbox for grayscale 2D and 3D images. RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics. Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters only takes minutes on a single core of a conventional PC.
License: AGPL-3
Depends: R (>= 3.3.0)
Imports: oro.dicom (>= 0.5.0)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-18 23:22:57 UTC; Marci
Author: Marton Kolossvary [aut, cre]
Repository: CRAN
Date/Publication: 2017-03-19 11:41:05 UTC

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Sat, 18 Mar 2017

New package OSCV with initial version 1.0
Package: OSCV
Title: One-Sided Cross-Validation
Version: 1.0
Author: Olga Savchuk
Maintainer: Olga Savchuk <olga.y.savchuk@gmail.com>
Description: Functions for implementing different versions of the OSCV method in the kernel regression and density estimation frameworks. The package mainly supports the following articles: (1) Savchuk, O.Y., Hart, J.D. (2017). Fully robust one-sided cross-validation for regression functions. Computational Statistics, <doi:10.1007/s00180-017-0713-7> and (2) Savchuk, O.Y. (2017). One-sided cross-validation for nonsmooth density functions, <arXiv:1703.05157>.
Depends: R (>= 3.1.1), mc2d
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-18 13:52:43 UTC; olgay
Repository: CRAN
Date/Publication: 2017-03-18 17:51:59 UTC

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New package FuzzyNumbers.Ext.2 with initial version 1.0
Package: FuzzyNumbers.Ext.2
Type: Package
Title: Apply Two Fuzzy Numbers on a Monotone Function
Version: 1.0
Date: 2017-03-16
Author: Abbas Parchami (Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran)
Maintainer: Abbas Parchami <parchami@uk.ac.ir>
Description: One can easily draw the membership function of f(x,y) by package 'FuzzyNumbers.Ext.2' in which f(.,.) is supposed monotone and x and y are two fuzzy numbers. This work is possible using function f2apply() which is an extension of function fapply() from Package 'FuzzyNumbers' for two-variable monotone functions.
License: LGPL (>= 3)
Imports: FuzzyNumbers
NeedsCompilation: no
Packaged: 2017-03-17 13:48:15 UTC; parchami
Repository: CRAN
Date/Publication: 2017-03-18 17:51:58 UTC

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New package exampletestr with initial version 0.3.0
Package: exampletestr
Type: Package
Title: Help for Writing Tests Based on Function Examples
Version: 0.3.0
Authors@R: c(person("Rory", "Nolan", email = "rorynoolan@gmail.com", role = c("aut", "cre")), person("Sergi", "Padilla-Parra", email = "spadilla@well.ox.ac.uk", role = c("ths")))
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Description: Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package. Documentation must be done with 'roxygen2'.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: filesstrings, magrittr, stringr, BBmisc, devtools
RoxygenNote: 6.0.1
Suggests: testthat, covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-18 17:12:34 UTC; rnolan
Author: Rory Nolan [aut, cre], Sergi Padilla-Parra [ths]
Repository: CRAN
Date/Publication: 2017-03-18 17:52:04 UTC

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New package brant with initial version 0.1-0
Package: brant
Type: Package
Title: Test for Parallel Regression Assumption
Version: 0.1-0
Date: 2017-03-16
Author: Benjamin Schlegel [aut,cre], Marco Steenbergen [aut]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Description: Tests the parallel regression assumption for ordinal logit models generated with the function polr() from the package MASS.
License: GPL (>= 2)
Depends: R (>= 3.1.0)
Imports: MASS
URL: https://benjaminschlegel.ch/r/glm.predict/
NeedsCompilation: no
Packaged: 2017-03-18 08:47:22 UTC; schlegel
Repository: CRAN
Date/Publication: 2017-03-18 17:52:01 UTC

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New package iMediate with initial version 0.2
Package: iMediate
Type: Package
Title: Methods for Mediation Analysis
Version: 0.2
Date: 2017-03-15
Author: Dr. Kai Wang
Maintainer: Kai Wang <kai-wang@uiowa.edu>
Depends:
Imports: mediation
Description: Implements likelihood based methods for mediation analysis proposed in Wang (2016) and Wang (2017).
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2017-03-18 01:03:55 UTC; kaiwang
Repository: CRAN
Date/Publication: 2017-03-18 08:34:35 UTC

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Fri, 17 Mar 2017

New package MonteCarlo with initial version 1.0.0
Package: MonteCarlo
Type: Package
Title: Automatic Parallelized Monte Carlo Simulations
Version: 1.0.0
Date: 2017-03-10
Author: Christian Hendrik Leschinski
Maintainer: Christian Hendrik Leschinski <leschinski@statistik.uni-hannover.de>
Description: Simplifies Monte Carlo simulation studies by automatically setting up loops to run over parameter grids and parallelising the Monte Carlo repetitions. It also generates LaTeX tables.
URL: http://github.com/FunWithR/MonteCarlo
BugReports: http://github.com/FunWithR/MonteCarlo/issues
License: GPL-2
Depends: R (>= 3.0.2)
Imports: abind(>= 1.4-0), codetools(>= 0.2-8), rlecuyer(>= 0.3-4), snow(>= 0.4-1), snowfall(>= 1.84-4), stats(>= 3.0.2), utils(>= 3.0.2)
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-11 11:32:33 UTC; Christian
Repository: CRAN
Date/Publication: 2017-03-17 13:01:20 UTC

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New package AcousticNDLCodeR with initial version 1.0.0
Package: AcousticNDLCodeR
Type: Package
Title: Coding Sound Files for Use with NDL
Version: 1.0.0
Date: 2017-03-17
Authors@R: person("Denis", "Arnold", email="denis.arnold@uni-tuebingen.de", role = c("aut","dtc","cre"))
Maintainer: Denis Arnold <denis.arnold@uni-tuebingen.de>
Depends: R (>= 3.0.0)
Description: Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used in the PLOS ONE paper: Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (accepted). Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit. PLOS ONE More details can be found in the paper and the supplement. 'ndl' is available on CRAN. 'ndl2' is available by request from <konstantin.sering@uni-tuebingen.de>.
Imports: tuneR, zoo, seewave, parallel
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-17 12:16:10 UTC; darnold
Author: Denis Arnold [aut, dtc, cre]
Repository: CRAN
Date/Publication: 2017-03-17 13:01:17 UTC

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New package ropercenter with initial version 0.1.0
Package: ropercenter
Type: Package
Title: Reproducible Data Retrieval from the Roper Center Data Archive
Version: 0.1.0
Date: 2017-03-01
Authors@R: c( person("Frederick", "Solt", email = "frederick-solt@uiowa.edu", role = c("aut", "cre")))
URL: https://github.com/fsolt/ropercenter
BugReports: https://github.com/fsolt/ropercenter/issues
Description: Reproducible, programmatic retrieval of datasets from the Roper Center data archive. The Roper Center for Public Opinion Research <https://ropercenter.cornell.edu> maintains the largest archive of public opinion data in existence, but researchers using these datasets are caught in a bind. The Center's terms and conditions bar redistribution of downloaded datasets, but to ensure that one's work can be reproduced, assessed, and built upon by others, one must provide access to the raw data one employed. The `ropercenter` package cuts this knot by providing registered users with programmatic, reproducible access to Roper Center datasets from within R.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: rvest, httr, xml2, dplyr, stringr, haven, foreign
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-16 12:50:20 UTC; fredsolt
Author: Frederick Solt [aut, cre]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Repository: CRAN
Date/Publication: 2017-03-17 11:16:32 UTC

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New package denseFLMM with initial version 0.1.0
Package: denseFLMM
Type: Package
Title: Functional Linear Mixed Models for Densely Sampled Data
Version: 0.1.0
Author: Sonja Greven, Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@stat.uni-muenchen.de>
Description: Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
License: GPL-2
LazyData: TRUE
Depends: R (>= 3.3.1), mgcv (>= 1.8-12)
Imports: methods, parallel, MASS, Matrix, mvtnorm
Suggests:
Collate: 'denseFLMM.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-17 09:41:55 UTC; Jona
Repository: CRAN
Date/Publication: 2017-03-17 11:16:29 UTC

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New package treespace with initial version 1.0.0
Package: treespace
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Version: 1.0.0
Date: 2017-03-15
Authors@R: c(TJ = person("Thibaut", "Jombart", email="thibautjombart@gmail.com", role = c("aut", "cre")), MK = person("Michelle", "Kendall", email="m.kendall@imperial.ac.uk", role = "aut"), JAG = person("Jacob", "Almagro-Garcia", role = "aut"), CC = person("Caroline", "Colijn", role = "aut"))
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treespaceServer()'.
Depends: R (>= 3.1.2), ape, ade4
Imports: adegenet, adegraphics, adephylo, combinat, compiler, distory, fields, htmlwidgets, MASS, phangorn, Rcpp, RLumShiny, scatterD3, shiny, shinyBS, utils
LinkingTo: Rcpp
Suggests: igraph, RColorBrewer, ggplot2, testthat, knitr, rmarkdown, rgl
License: MIT + file LICENSE
LazyData: true
Collate: RcppExports.R metrics.R medTree.R treespace.R findGroves.R plotGroves.R plotTreeDiff.R servers.R transmissionTrees.R data.R
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-03-16 17:00:55 UTC; thibaut
Author: Thibaut Jombart [aut, cre], Michelle Kendall [aut], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Repository: CRAN
Date/Publication: 2017-03-17 07:24:30 UTC

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New package Polychrome with initial version 0.8.2
Package: Polychrome
Title: Qualitative Palettes with Many Colors
Version: 0.8.2
Date: 2017-03-16
Author: Kevin R. Coombes, Guy Brock
Description: Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors.
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Depends: R (>= 3.0)
Imports: colorspace, rgl, methods, graphics, grDevices, stats, utils
Suggests: RColorBrewer, knitr, rmarkdown
License: Apache License (== 2.0)
LazyLoad: yes
LazyData: no
URL: http://oompa.r-forge.r-project.org/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-16 19:07:11 UTC; Kevin
Repository: CRAN
Date/Publication: 2017-03-17 07:24:10 UTC

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Thu, 16 Mar 2017

New package Rlda with initial version 0.1.0
Package: Rlda
Type: Package
Title: Bayesian LDA for Mixed-Membership Clustering Analysis
Version: 0.1.0
Author: Pedro Albuquerque and Denis Valle and Daijiang Li
Maintainer: Pedro Albuquerque <pedroa@unb.br>
Description: Describes the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries).
License: GPL-2
LazyData: TRUE
Depends: R (>= 2.10), Rcpp (>= 0.9.4), RcppProgress (>= 0.1)
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Imports: gtools
SystemRequirements: GNU make
Suggests: knitr, rmarkdown
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-03-16 14:01:05 UTC; p.albuquerque
Repository: CRAN
Date/Publication: 2017-03-16 16:16:17 UTC

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New package graphkernels with initial version 1.0
Package: graphkernels
Type: Package
Title: Graph Kernels
Version: 1.0
Date: 2017-03-10
Author: Mahito Sugiyama
Maintainer: Mahito Sugiyama <mahito@ar.sanken.osaka-u.ac.jp>
Description: A fast C++ implementation of various graph kernels.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.9)
Depends: igraph (>= 1.0.1)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2017-03-16 13:31:11 UTC; mahito
Repository: CRAN
Date/Publication: 2017-03-16 16:16:18 UTC

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New package RankingProject with initial version 0.1.1
Package: RankingProject
Type: Package
Title: The Ranking Project: Visualizations for Comparing Populations
Version: 0.1.1
Date: 2017-03-16
Authors@R: c( person("Jerzy", "Wieczorek", email = "jerzywieczorek@gmail.com", role = c("cre", "aut")), person("Joel", "Beard", role = "ctb"), person("Andy", "Liaw", role = "ctb"), person("Robert", "Gentleman", role = "ctb"), person("Martin", "Maechler", role = "ctb"))
Description: Functions to generate plots and tables for comparing independently- sampled populations. Companion package to "A Primer on Visualizations for Comparing Populations, Including the Issue of Overlapping Confidence Intervals" by Wright, Klein, and Wieczorek (2017, in press).
License: GPL-2
LazyData: TRUE
Depends: R (>= 2.10)
Suggests: knitr (>= 1.15.1), rmarkdown (>= 0.9.6), tikzDevice (>= 0.10-1)
VignetteBuilder: knitr
URL: http://github.com/civilstat/RankingProject
BugReports: http://github.com/civilstat/RankingProject/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-16 11:49:31 UTC; jerzy
Author: Jerzy Wieczorek [cre, aut], Joel Beard [ctb], Andy Liaw [ctb], Robert Gentleman [ctb], Martin Maechler [ctb]
Maintainer: Jerzy Wieczorek <jerzywieczorek@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-16 13:35:05

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New package prioritylasso with initial version 0.1.0
Package: prioritylasso
Type: Package
Title: Analyzing Multiple Omics Data with an Offset Approach
Version: 0.1.0
Author: Simon Klau, Anne-Laure Boulesteix
Maintainer: Simon Klau <simonklau@ibe.med.uni-muenchen.de>
Description: Fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block.
Depends: R (>= 2.10.0)
License: GPL-2
LazyData: TRUE
Imports: survival, glmnet
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, pROC
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-16 09:06:51 UTC; simonklau
Repository: CRAN
Date/Publication: 2017-03-16 13:35:07

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New package FlexDir with initial version 1.0
Package: FlexDir
Version: 1.0
Title: Tools to Work with the Flexible Dirichlet Distribution
Authors@R: c( person(given="Sonia", family="Migliorati",role = "aut"), person(given=c("Agnese","Maria"), family=c("Di","Brisco"), email="agnese.dibrisco@unimib.it", role = c("aut", "cre")), person(given="Matteo", family="Vestrucci", role = "aut") )
Author: Sonia Migliorati [aut], Agnese Maria Di Brisco [aut, cre], Matteo Vestrucci [aut]
Maintainer: Agnese Maria Di Brisco <agnese.dibrisco@unimib.it>
Description: Provides tools to work with the Flexible Dirichlet distribution. The main features are an E-M algorithm for computing the maximum likelihood estimate of the parameter vector and a function based on conditional bootstrap to estimate its asymptotic variance-covariance matrix. It contains also functions to plot graphs, to generate random observations and to handle compositional data.
Depends: R (>= 3.0.0)
Imports: stats, graphics, utils, grDevices
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2015-08-07 08:47:02 UTC; everett
RoxygenNote: 6.0.0
Suggests: testthat
Repository: CRAN
Date/Publication: 2017-03-16 13:35:03

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New package rolypoly with initial version 0.1.0
Package: rolypoly
Type: Package
Title: Identifying Trait-Relevant Functional Annotations
Version: 0.1.0
Date: 2017-3-15
Author: Diego Calderon
Maintainer: Diego Calderon <dcal@stanford.edu>
Description: Using enrichment of genome-wide association summary statistics to identify trait-relevant cellular functional annotations.
Depends: R (>= 3.1.3),
Imports: data.table (>= 1.9.6), dplyr (>= 0.4.3), foreach (>= 1.4.3), ggplot2 (>= 1.0.1), glmnet (>= 2.0-5), MASS (>= 7.3-45), Matrix (>= 1.2-6), matrixcalc (>= 1.0-3),
LinkingTo:
Suggests: CompQuadForm (>= 1.4.1), knitr, testthat, rmarkdown
License: GPL-3
VignetteBuilder: knitr
LazyData: TRUE
URL: https://github.com/dcalderon/rolypoly
BugReports: https://github.com/dcalderon/rolypoly/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-16 05:03:47 UTC; dcal
Repository: CRAN
Date/Publication: 2017-03-16 08:44:35

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New package rif with initial version 0.1.0
Package: rif
Title: Client for 'Neuroscience' Information Framework 'APIs'
Description: Client for 'Neuroscience' Information Framework ('NIF') 'APIs' (<https://neuinfo.org/>; <http://nif-services.neuinfo.org/servicesv1/>). Package includes functions for each 'API' route, and gives back data in tidy data.frame format.
Version: 0.1.0
License: MIT + file LICENSE
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus+r@gmail.com")
URL: https://github.com/ropensci/rif
BugReports: https://github.com/ropensci/rif/issues
VignetteBuilder: knitr
Imports: jsonlite, crul (>= 0.3.0), data.table, tibble
Suggests: roxygen2 (>= 6.0.1), testthat, rmarkdown, knitr, covr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-15 21:02:56 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-16 08:44:30

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New package rddensity with initial version 0.1
Package: rddensity
Type: Package
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity test (a.k.a. manipulation test) is commonly employed in regression discontinuity designs and other treatment effect settings to detect whether there is evidence suggesting perfect self-selection (manipulation) around a cutoff where a treatment/policy assignment changes. This package provides tools for conducting the aforementioned statistical test: rddensity() to construct local polynomial based density discontinuity test given a prespecified cutoff, and rdbwdensity() to perform bandwidth selection.
Version: 0.1
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <xinweima@umich.edu>
Depends: R (>= 3.1.0)
License: GPL-2
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-15 17:42:45 UTC; xinwei
Repository: CRAN
Date/Publication: 2017-03-16 08:44:29

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New package MOEADr with initial version 0.2.0
Package: MOEADr
Type: Package
Title: Component-Wise MOEA/D Implementation
Version: 0.2.0
Date: 2017-3-16
Imports: FNN, assertthat, R.utils
Suggests: smoof, testthat, knitr, rmarkdown, irace
Depends: R (>= 3.3.0)
Author: c(person("Felipe", "Campelo", email = "fcampelo@ufmg.br", role = c("aut", "cre"), comment = "Original concept; organization; coding"), person("Lucas", "Batista", email = "lusoba@ufmg.br", role = "com", comment = "Literature review; initial formalization of operators"), person("Claus", "Aranha", email = "caranha@cs.tsukuba.ac.jp", role = "aut", comment = "Coding; testing"))
Maintainer: Felipe Campelo <fcampelo@ufmg.br>
Description: Modular implementation of MOEA/D approaches for multiobjective optimization.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-16 04:06:03 UTC; fcampelo
Repository: CRAN
Date/Publication: 2017-03-16 08:43:58

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New package fetchR with initial version 2.0-0
Package: fetchR
Type: Package
Title: Calculate Wind Fetch in R
Version: 2.0-0
Date: 2017-03-16
Authors@R: person("Blake", "Seers", role = c("aut", "cre"), email = "blake.seers@gmail.com")
Imports: rgdal, sp, methods, rgeos, plotKML
Suggests: knitr, ggplot2, maps, rmarkdown
URL: https://github.com/blasee/fetchR
BugReports: https://github.com/blasee/fetchR/issues
Description: Wind fetch is the unobstructed length of water over which wind can blow from a certain direction. Averaging the wind fetch for numerous directions at the same location is therefore a reasonable measure of the overall wind exposure for a specific marine location. However, this process of calculating wind fetch can be extremely time-consuming and tedious, particularly if a large number of fetch vectors are required at many locations. The fetchR package calculates wind fetch with ease and summarises the information efficiently. There are also plot methods to help visualise the wind exposure at the various locations, and methods to output the fetch vectors to a KML file for further investigation.
License: GPL-2
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-16 03:16:48 UTC; blake
Author: Blake Seers [aut, cre]
Maintainer: Blake Seers <blake.seers@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-16 08:44:13

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New package DisHet with initial version 0.1.0
Package: DisHet
Type: Package
Title: Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples
Version: 0.1.0
Date: 2017-3-6
Author: Tao Wang
Maintainer: Tao Wang <tao.wang@utsouthwestern.edu>
Depends: R (>= 2.15.0), gtools, matrixStats
Description: Model cell type heterogeneity of bulk renal cell carcinoma. The observed gene expression in bulk tumor sample is modeled by a log-normal distribution with the location parameter structured as a linear combination of the component-specific gene expressions.
License: GPL-2
NeedsCompilation: no
Packaged: 2017-03-15 15:36:18 UTC; s168319
Repository: CRAN
Date/Publication: 2017-03-16 08:43:54

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New package CNull with initial version 1.0
Package: CNull
Type: Package
Title: Fast Algorithms for Frequency-Preserving Null Models in Ecology
Version: 1.0
Date: 2017-3-14
Authors@R: c(person("Constantinos", "Tsirogiannis", role = c("aut", "cre"), email = "tsirogiannis.c@gmail.com"), person("Adrija", "Kalvisa", role = "aut"))
Author: Constantinos Tsirogiannis [aut, cre], Adrija Kalvisa [aut]
Maintainer: Constantinos Tsirogiannis <tsirogiannis.c@gmail.com>
Description: Efficient computations for null models that require shuffling columns on big matrix data. This package provides functions for faster computation of diversity measure statistics when independent random shuffling is applied to the columns of a given matrix. Given a diversity measure f and a matrix M, the provided functions can generate random samples (shuffled matrix rows of M), the mean and variance of f, and the p-values of this measure for two different null models that involve independent random shuffling of the columns of M. The package supports computations of alpha and beta diversity measures.
License: GPL-3
Imports: Rcpp (>= 0.12.9), ape, PhyloMeasures, Matrix
LinkingTo: Rcpp
LazyLoad: yes
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2017-03-15 15:07:39 UTC; constant
Repository: CRAN
Date/Publication: 2017-03-16 08:43:52

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New package cir with initial version 2.0.0
Package: cir
Type: Package
Title: Centered Isotonic Regression and Dose-Response Utilities
Version: 2.0.0
Date: 2017-03-15
Description: Isotonic regression (IR), as well as a great small-sample improvement to IR called CIR, interval estimates for both, and additional utilities.
License: GPL-2
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@seattlechildrens.org>
Authors@R: person('Assaf P.','Oron', role=c('cre','aut'), email='assaf.oron@seattlechildrens.org')
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-15 15:50:11 UTC; aoron
Repository: CRAN
Date/Publication: 2017-03-16 08:44:02

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New package BLPestimatoR with initial version 0.1.2
Package: BLPestimatoR
Type: Package
Title: Performs a BLP Demand Estimation
Version: 0.1.2
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
License: GPL-3
LazyData: TRUE
Depends: Rcpp (>= 0.12.7), mvQuad, ucminf, numDeriv, randtoolbox
LinkingTo: Rcpp
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-03-15 15:21:57 UTC; brunned
Repository: CRAN
Date/Publication: 2017-03-16 08:43:44

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New package BioInstaller with initial version 0.0.1
Package: BioInstaller
Title: Lightweight Biology Software Installer
Version: 0.0.1
Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre"))
Description: Install and download massive bioinformatics analysis software and database, such as NGS analysis tools with its required database or/and reference genome, is still a complicated task. BioInstaller can be used to install that tools and database in R conveniently.
Depends: R (>= 3.3.0)
URL: https://github.com/Miachol/BioInstaller
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: stringr (>= 1.2.0), futile.logger (>= 1.4.1), configr (>= 0.2.0), git2r (>= 0.0.3), R.utils (>= 2.5.0), RCurl (>= 1.95-4.8)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2017-03-15 18:14:13 UTC; ljf
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Repository: CRAN
Date/Publication: 2017-03-16 08:43:47

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Wed, 15 Mar 2017

New package hNMF with initial version 0.2
Package: hNMF
Title: Hierarchical Non-Negative Matrix Factorization
Version: 0.2
Author: Nicolas Sauwen
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>
Description: Hierarchical non-negative matrix factorization for tumor segmentation based on multi-parametric MRI data.
Depends: R (>= 3.3.2)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: NMF, oro.nifti, tcltk, nnls, R.matlab, spatialfil, rasterImage, stats, graphics, grDevices
RoxygenNote: 6.0.0
Suggests: testthat
NeedsCompilation: no
Packaged: 2017-03-15 08:50:19 UTC; nsauwen
Repository: CRAN
Date/Publication: 2017-03-15 14:36:51

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New package confinterpret with initial version 0.1.0
Package: confinterpret
Type: Package
Title: Descriptive Interpretations of Confidence Intervals
Version: 0.1.0
Authors@R: person("Jim", "Vine", email = "code@jimvine.co.uk", role = c("aut", "cre"))
Description: Produces descriptive interpretations of confidence intervals. Includes (extensible) support for various test types, specified as sets of interpretations dependent on where the lower and upper confidence limits sit.
License: AGPL-3
URL: https://github.com/jimvine/confinterpret
BugReports: https://github.com/jimvine/confinterpret/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: graphics, grDevices, testthat
NeedsCompilation: no
Packaged: 2017-03-15 11:08:24 UTC; jimvi
Author: Jim Vine [aut, cre]
Maintainer: Jim Vine <code@jimvine.co.uk>
Repository: CRAN
Date/Publication: 2017-03-15 14:36:50

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New package gee4 with initial version 0.1.0.0
Package: gee4
Type: Package
Title: Generalised Estimating Equations (GEE/WGEE) using 'Armadillo' and S4
Version: 0.1.0.0
Authors@R: c(person("Jianxin", "Pan", email = "Jianxin.Pan@manchester.ac.uk", role = c("aut")), person("Yi", "Pan", email = "ypan1988@gmail.com", role = c("aut", "cre")))
Maintainer: Yi Pan <ypan1988@gmail.com>
Description: Fit joint mean-covariance models for longitudinal data within the framework of (weighted) generalised estimating equations (GEE/WGEE). The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Armadillo' C++ library for numerical linear algebra and 'RcppArmadillo' glue.
License: GPL (>= 2)
LazyData: TRUE
SystemRequirements: C++11
Depends: R (>= 3.2.2)
Imports: Formula, methods, Rcpp (>= 0.12.4)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
NeedsCompilation: yes
Author: Jianxin Pan [aut], Yi Pan [aut, cre]
URL: https://github.com/ypan1988/gee4/
BugReports: https://github.com/ypan1988/gee4/issues/
Packaged: 2017-03-14 23:38:21 UTC; yipan
Repository: CRAN
Date/Publication: 2017-03-15 08:49:09

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Tue, 14 Mar 2017

New package EpiCurve with initial version 1.0-0
Package: EpiCurve
Type: Package
Title: Plot an Epidemic Curve
Version: 1.0-0
Date: 2017-03-14
Authors@R: c(person("Jean Pierre", "Decorps", role = c("aut", "cre"), email = "jp.decorps@epiconcept.fr"), person("Morgane","Vallee", role = "ctb", email = "m.vallee@epiconcept.fr") )
Description: Creates simple or stacked epidemic curves for daily, weekly or monthly incomes data.
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: ggplot2, dplyr, ISOweek
Imports: RColorBrewer
NeedsCompilation: no
Packaged: 2017-03-14 17:18:13 UTC; kdo
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Repository: CRAN
Date/Publication: 2017-03-14 20:13:24

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New package pkr with initial version 0.1.0
Package: pkr
Version: 0.1.0
Date: 2017-03-15
Title: Pharmacokinetics in R
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Depends: R (>= 2.0.0), foreign, binr, forestplot
Author: Kyun-Seop Bae [aut], Jee Eun Lee [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Copyright: 2017, Kyun-Seop Bae, Jee Eun Lee
License: GPL-3
NeedsCompilation: no
Repository: CRAN
URL: https://cran.r-project.org/package=pkr
Packaged: 2017-03-14 14:20:29 UTC; K
Date/Publication: 2017-03-14 17:36:11

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New package DataEntry with initial version 0.9-1
Package: DataEntry
Type: Package
Title: Make it Easier to Enter Questionnaire Data
Version: 0.9-1
Date: 2017-03-14
Author: Jakson Aquino
Maintainer: Jakson Aquino <jalvesaq@gmail.com>
Depends: gWidgets, RGtk2, gWidgetsRGtk2, digest
URL: https://github.com/jalvesaq/DataEntry
Description: This is a GUI application for defining attributes and setting valid values of variables, and then, entering questionnaire data in a data.frame.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2017-03-14 09:55:34 UTC; aquino
Repository: CRAN
Date/Publication: 2017-03-14 14:20:55

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New package tsxtreme with initial version 0.3
Package: tsxtreme
Type: Package
Title: Bayesian Modelling of Extremal Dependence in Time Series
Version: 0.3
Date: 2017-03-14
Author: Thomas Lugrin
Maintainer: Thomas Lugrin <thomas.lugrin@epfl.ch>
Depends: R (>= 3.3.3)
Imports: evd, mvtnorm, stats, MASS, graphics
Description: Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2017-03-14 08:09:44 UTC; thomas
Repository: CRAN
Date/Publication: 2017-03-14 10:26:26

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New package nmw with initial version 0.1.1
Package: nmw
Version: 0.1.1
Title: Understanding Nonlinear Mixed Effects Modeling for Population Pharmacokinetics
Description: This shows how NONMEM(R) <http://www.iconplc.com/innovation/nonmem/> software works. NONMEM's classical estimation methods like 'First Order(FO) approximation', 'First Order Conditional Estimation(FOCE)', and 'Laplacian approximation' are explained.
Depends: R (>= 3.0.0)
ByteCompile: yes
License: GPL-3
Copyright: 2017, Kyun-Seop Bae
Author: Kyun-Seop Bae
Maintainer: Kyun-Seop Bae <k@acr.kr>
URL: http://optimizer.r-forge.r-project.org/
NeedsCompilation: no
Packaged: 2017-03-14 07:19:18 UTC; K
Repository: CRAN
Date: 2017-03-14
Date/Publication: 2017-03-14 10:26:25

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New package reticulate with initial version 0.7
Package: reticulate
Type: Package
Title: R Interface to Python
Version: 0.7
Authors@R: c( person("JJ", "Allaire", role = c("aut", "cre"), comment = "R interface", email = "jj@rstudio.com"), person("Kevin", "Ushey", role = c("ctb"), email = "kevin@rstudio.com"), person(family = "RStudio", role = "cph"), person("Yuan", "Tang", role = c("ctb", "cph"), email = "terrytangyuan@gmail.com"), person("Dirk", "Eddelbuettel", role = c("ctb", "cph"), email = "edd@debian.org"), person("Bryan", "Lewis", role = c("ctb", "cph"), email = "blewis@illposed.net"), person("Marcus", "Geelnard", role = c("aut", "cph"), comment = "TinyThread library, http://tinythreadpp.bitsnbites.eu/") )
Description: R interface to Python modules, classes, and functions. When calling into Python R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types. Compatible with all versions of Python >= 2.7.
License: Apache License 2.0
URL: https://github.com/rstudio/reticulate
BugReports: https://github.com/rstudio/reticulate/issues
SystemRequirements: Python (>= 2.7.0)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: utils, graphics, Rcpp (>= 0.12.7)
Suggests: testthat, knitr
LinkingTo: Rcpp
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-03-13 16:43:09 UTC; jjallaire
Author: JJ Allaire [aut, cre] (R interface), Kevin Ushey [ctb], RStudio [cph], Yuan Tang [ctb, cph], Dirk Eddelbuettel [ctb, cph], Bryan Lewis [ctb, cph], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>
Repository: CRAN
Date/Publication: 2017-03-14 08:08:13

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New package scalpel with initial version 1.0.0
Package: scalpel
Type: Package
Title: Processes Calcium Imaging Data
Version: 1.0.0
Author: Ashley Petersen
Maintainer: Ashley Petersen <ashleyjpete@gmail.com>
Description: Identifies the locations of neurons, and estimates their calcium concentrations over time using the SCALPEL method proposed in Petersen, A., Simon, N., and Witten, D. SCALPEL: Extracting Neurons from Calcium Imaging Data <https://ajpetecom.files.wordpress.com/2017/01/petersenscalpel.pdf>.
License: GPL (>= 2)
URL: www.ajpete.com/software
Imports: Matrix, R.matlab, protoclust, igraph, SDMTools, gam
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2017-03-13 22:02:43 UTC; ashleypetersen
Repository: CRAN
Date/Publication: 2017-03-14 06:58:35

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New package outreg with initial version 0.2.2
Package: outreg
Type: Package
Title: Regression Table for Publication
Version: 0.2.2
Authors@R: c( person("Kota", "Mori", email = "kmori05@gmail.com", role = c("aut", "cre")) )
Description: Create regression tables for publication. Currently supports 'lm', 'glm', 'survreg', and 'ivreg' outputs.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: magrittr, reshape2, sandwich, stats, stringr, tidyr, utils
Suggests: AER, survival, testthat
RoxygenNote: 5.0.1
URL: https://github.com/kota7/outreg
BugReports: https://github.com/kota7/outreg/issues
NeedsCompilation: no
Packaged: 2017-03-14 03:08:42 UTC; Kota.Mori
Author: Kota Mori [aut, cre]
Maintainer: Kota Mori <kmori05@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-14 06:58:31

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Mon, 13 Mar 2017

New package radmixture with initial version 0.0.1
Package: radmixture
Title: Calculate Population Stratification
Version: 0.0.1
Date: 2017-02-20
Authors@R: c( person("Beilei", "Bian", role = c("aut", "cre"), email = "bianbeilei@wegene.com"), person("Dajun", "Luo", role = "ctb", comment = "R's C API"), person("Gang", "Chen", role = "ctb"), person("Senwei", "Tang", role = "ctb"), person(family = "WeGene", role = "cph") )
Maintainer: Beilei Bian <bianbeilei@wegene.com>
Description: Implementation of ADMIXTURE for individual ancestry inference in R. Specifically, ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets, see <https://www.genetics.ucla.edu/software/admixture/>. Users can use 'radmixture' to calculate ancestry components with different public datasets. It is very convenient and fast for personal genotype data. For more details, see <https://github.com/wegene-llc/radmixture/blob/master/README.md>.
Depends: R (>= 3.1.0)
Imports: quadprog, plyr, magrittr, MCMCpack
Suggests: rmarkdown, knitr, testthat
License: MIT + file LICENSE
URL: https://github.com/wegene-llc/radmixture
BugReports: https://github.com/wegene-llc/radmixture/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
VignetteBuilder: knitr
ByteCompile: true
Packaged: 2017-03-13 16:25:07 UTC; bianbeilei
Author: Beilei Bian [aut, cre], Dajun Luo [ctb] (R's C API), Gang Chen [ctb], Senwei Tang [ctb], WeGene [cph]
Repository: CRAN
Date/Publication: 2017-03-13 19:25:45

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New package EcoIndR with initial version 1.0
Package: EcoIndR
Version: 1.0
Title: Ecological Indicators
Author: Cástor Guisande González
Maintainer: Cástor Guisande González <castor@uvigo.es>
Description: Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.
License: GPL (>= 2)
Encoding: latin1
Depends: R (>= 3.1.1)
Suggests: vegan, shape, Rarity, splancs, plotrix, FD, picante
Repository: CRAN
NeedsCompilation: no
Packaged: 2017-03-13 15:59:42 UTC; castor
Date/Publication: 2017-03-13 17:18:49

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New package collpcm with initial version 1.0
Package: collpcm
Version: 1.0
Type: Package
Title: Collapsed Latent Position Cluster Model for Social Networks
Date: 2017-03-10
Authors@R: c( person( "Jason", "Wyse", email = "wyseja@tcd.ie", role = c( "aut", "cre" ) ), person( "Caitriona", "Ryan", email = "Caitriona.Ryan@ul.ie", role = c( "aut" ) ), person( "Nial", "Friel", email="nial.friel@ucd.ie", role=c("ths") ) )
Description: Markov chain Monte Carlo based inference routines for collapsed latent position cluster models or social networks, which includes searches over the model space (number of clusters in the latent position cluster model). The label switching algorithm used is that of Nobile and Fearnside (2007) <doi:10.1007/s11222-006-9014-7> which relies on the algorithm of Carpaneto and Toth (1980) <doi:10.1145/355873.355883>.
Depends: R (>= 2.10), vegan, network, latentnet
License: GPL-3
NeedsCompilation: yes
Maintainer: Jason Wyse <wyseja@tcd.ie>
Packaged: 2017-03-10 19:40:12 UTC; jason
Author: Jason Wyse [aut, cre], Caitriona Ryan [aut], Nial Friel [ths]
Repository: CRAN
Date/Publication: 2017-03-13 17:11:04

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New package bioOED with initial version 0.1.1
Package: bioOED
Type: Package
Title: Sensitivity Analysis and Optimum Experiment Design for Microbial Inactivation
Version: 0.1.1
Date: 2017-03-12
Authors@R: c(person("Alberto", "Garre", email = "garre.alberto@gmail.com", role = c("aut", "cre")), person("Jose Lucas", "Penalver", email = "", role = "aut"), person("Pablo S.", "Fernandez", email = "pablo.fernandez@upct.es", role = "aut"), person("Jose A.", "Egea", email = "josea.egea@upct.es", role = "aut") )
Description: Extends the bioinactivation package with functions for Sensitivity Analysis and Optimum Experiment Design.
License: GPL-3
LazyData: TRUE
Imports: FME (>= 1.3.2), bioinactivation (>= 1.1.2), corrplot(>= 0.73), dplyr (>= 0.5.0), ggplot2 (>= 2.1.0), MEIGOR (>= 1.0.0), stats (>= 3.3.2), graphics(>= 3.3.2)
Suggests: knitr (>= 1.9), testthat (>= 0.9.1), rmarkdown
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-12 21:46:29 UTC; Alberto
Author: Alberto Garre [aut, cre], Jose Lucas Penalver [aut], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-13 08:45:26

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Sun, 12 Mar 2017

New package taxonomizr with initial version 0.2.2
Package: taxonomizr
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
License: GPL-2
Title: Functions to Work with NCBI Accessions and Taxonomy
Type: Package
LazyLoad: yes
Author: Scott Sherrill-Mix [aut, cre]
Authors@R: c(person("Scott", "Sherrill-Mix", role = c("aut", "cre"), email = "shescott@upenn.edu"))
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
Version: 0.2.2
Date: 2017-03-08
Suggests: testthat, knitr, rmarkdown
Depends: R (>= 3.0.0)
Imports: parallel, RSQLite, data.table, R.utils
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-03-08 16:28:47 UTC; scott
Repository: CRAN
Date/Publication: 2017-03-09 08:18:40

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New package SymTS with initial version 1.0
Package: SymTS
Type: Package
Title: Symmetric Tempered Stable Distributions
Version: 1.0
Date: 2017-03-06
Author: Michael Grabchak <mgrabcha@uncc.edu> and Lijuan Cao <lcao2@uncc.edu>
Maintainer: Michael Grabchak <mgrabcha@uncc.edu>
Description: Contains methods for simulation and for evaluating the pdf, cdf, and quantile functions for symmetric stable, symmetric classical tempered stable, and symmetric power tempered stable distributions.
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2017-03-09 05:07:06 UTC; lcao2
Repository: CRAN
Date/Publication: 2017-03-09 08:18:28

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New package Stickbreaker with initial version 1.0.0
Package: Stickbreaker
Type: Package
Title: Fits Stickbreaking, Multiplicative and Additive Models to Data
Version: 1.0.0
Authors@R: c( person("Craig", "Miller", email = "crmiller@uidaho.edu", role = "aut"), person("James", "Van Leuven", email = "jtvanleuven@gmail.com", role = "cre"))
Description: Genetically modified organisms are used to test the phenotypic effects of mutation. Often, multiple substitutions impact organismal fitness differently than single substitutions (epistatic interactions). This package fits three basic models (additive, multiplicative, and stickbreaking) to fitness data and suggests the best fitting model by multinomial regression. Stickbreaker can also be used to simulate fitness data.
Depends: R (>= 3.3.1)
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: nnet, lattice, xtable
Suggests: knitr, rmarkdown
Packaged: 2017-03-07 22:59:32 UTC; james
Author: Craig Miller [aut], James Van Leuven [cre]
Maintainer: James Van Leuven <jtvanleuven@gmail.com>
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2017-03-10 08:50:10

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New package spmoran with initial version 0.1.0
Package: spmoran
Type: Package
Title: Moran's Eigenvector-Based Spatial Regression Models
Version: 0.1.0
Author: Daisuke Murakami
Maintainer: Daisuke Murakami <murakami_daisuke_t@yahoo.co.jp>
Description: Functions for estimating fixed and random effects eigenvector spatial filtering models.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: fields, vegan, Matrix,
Suggests: spdep, R.rsp,
VignetteBuilder: R.rsp,
NeedsCompilation: no
Packaged: 2017-03-12 09:16:22 UTC; murakami
Repository: CRAN
Date/Publication: 2017-03-12 18:43:11

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New package spec with initial version 0.1.1
Package: spec
Type: Package
Title: A Data Specification Format and Interface
Version: 0.1.1
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Description: Creates a data specification that describes the columns of a table (data.frame). Provides methods to read, write, and update the specification. Checks whether a table matches its specification. See specification.data.frame(),read.spec(), write.spec(), as.csv.spec(), respecify.character(), and %matches%.data.frame().
Imports: encode, csv, magrittr, utils
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-10 03:22:28 UTC; tbergsma
Repository: CRAN
Date/Publication: 2017-03-10 08:50:28

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New package SigOptR with initial version 0.0.1
Package: SigOptR
Title: R API Wrapper for SigOpt
Version: 0.0.1
Author: Alexandra Johnson [aut, cre]
Maintainer: Alexandra Johnson <alexandra@sigopt.com>
Description: Interfaces with the 'SigOpt' API. More info at <https://sigopt.com>.
Imports: httr, jsonlite
Depends: R (>= 3.2.0)
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2017-03-09 22:41:37 UTC; root
Repository: CRAN
Date/Publication: 2017-03-10 08:50:09

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New package rmcfs with initial version 1.2.4
Package: rmcfs
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency Discovery
Version: 1.2.4
Date: 2017-03-09
Authors@R: c(person('Michal', 'Draminski', role = c('aut', 'cre'), email = 'michal.draminski@ipipan.waw.pl'), person('Jacek', 'Koronacki', role = c('aut'), email = 'jacek.koronacki@ipipan.waw.pl'), person('Julian', 'Zubek', role = c('ctb'), email = 'j.zubek@phd.ipipan.waw.pl'))
Depends: rJava (>= 0.5-0), R (>= 2.70)
Imports: yaml, ggplot2, reshape2, dplyr, igraph (>= 1.0.1)
SystemRequirements: Java (>= 6.0)
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
License: GPL-3
URL: http://www.ipipan.eu/staff/m.draminski/mcfs.htm
LazyData: yes
NeedsCompilation: no
Packaged: 2017-03-09 17:09:11 UTC; mdraminski
Author: Michal Draminski [aut, cre], Jacek Koronacki [aut], Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Repository: CRAN
Date/Publication: 2017-03-10 11:49:57

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New package rdataretriever with initial version 1.0.0
Package: rdataretriever
Title: R Interface to the Data Retriever
Description: Provides an R interface to the Data Retriever <http://data-retriever.org/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.
Version: 1.0.0
Date: 2017-02-21
Authors@R: c(person("Daniel", "McGlinn", role = c("aut", "cre"), email = "danmcglinn@gmail.com"), person("Henry", "Senyondo", role = "aut", email = "henrykironde@gmail.com"), person("Shawn", "Taylor", role = "aut", email = "shawntaylor@weecology.org"), person("Ethan", "White", role = "aut", email = "ethan@weecology.org"))
BugReports: https://github.com/ropensci/rdataretriever/issues
URL: https://github.com/ropensci/rdataretriever/
Depends: R (>= 3.0.0)
Imports: utils
SystemRequirements: Data Retriever (>= 1.8)
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-10 22:50:50 UTC; mcglinnd
Author: Daniel McGlinn [aut, cre], Henry Senyondo [aut], Shawn Taylor [aut], Ethan White [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-11 09:18:44

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New package quantoptr with initial version 0.1.2
Package: quantoptr
Type: Package
Title: Algorithms for Quantile- And Mean-Optimal Treatment Regimes
Authors@R: c( person("Yu", "Zhou", , "zhou0269@umn.edu", role = c("cre", "aut")), person("Lan", "Wang", , "wangx346@umn.edu ", role = "ctb"), person("Ben", "Sherwood", , "ben.sherwood@ku.edu", role = "ctb"), person("Rui", "Song", , "rsong@ncsu.edu ", role = "ctb") )
Author: Yu Zhou [cre, aut], Lan Wang [ctb], Ben Sherwood [ctb], Rui Song [ctb]
Maintainer: Yu Zhou <zhou0269@umn.edu>
Description: Estimation methods for optimal treatment regimes under three different criteria, namely marginal quantile, marginal mean, and mean absolute difference. For the first two criteria, both one-stage and two-stage estimation method are implemented. A doubly robust estimator for estimating the quantile-optimal treatment regime is also included.
Version: 0.1.2
License: GPL (>= 2)
LazyData: TRUE
Imports: stringr, rgenoud (>= 5.7), quantreg (>= 5.18), parallel, stats, methods, Rdpack
Depends: R (>= 3.2)
RoxygenNote: 5.0.1.9000
Suggests: faraway
NeedsCompilation: no
Packaged: 2017-03-11 09:41:36 UTC; yuzhou
RdMacros: Rdpack
Repository: CRAN
Date/Publication: 2017-03-11 18:17:45

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New package PWFSLSmoke with initial version 0.99.9
Type: Package
Package: PWFSLSmoke
Version: 0.99.9
Title: Utilities for Working with Air Quality Monitoring Data
Authors@R: c( person("Jonathan", "Callahan", email="jonathan.s.callahan@gmail.com", role=c("aut","cre")), person("Rohan", "Aras", email="rohana@uw.edu", role=c("aut")), person("Zach", "Dingels", email="dingelsz@uw.edu", role=c("aut")), person("Jon", "Hagg", email="jhagg314@gmail.com", role=c("aut")), person("Jimin", "Kim", email="jk55@uw.edu", role=c("aut")), person("Rex", "Thompson", email="rexs.thompson@gmail.com", role=c("aut")), person("Alice", "Yang", email="wenhuy@uw.edu", role=c("aut")) )
Author: Jonathan Callahan [aut, cre], Rohan Aras [aut], Zach Dingels [aut], Jon Hagg [aut], Jimin Kim [aut], Rex Thompson [aut], Alice Yang [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Depends: R (>= 3.1.0), dplyr, maps, MazamaSpatialUtils (>= 0.4.4)
Imports: cluster, dygraphs (>= 1.1.1.4), futile.logger, ggmap, httr, leaflet (>= 1.0.0), lubridate, maptools, mapproj, openair, png, RColorBrewer, RCurl, RgoogleMaps, readr, reshape2, sp, stringr, xts, zoo
Suggests: knitr, rmarkdown
Description: Utilities for working with air quality monitoring data with a focus on small particulates (PM2.5) generated by wildfire smoke. Functions are provided for downloading available data from the United States Environmental Protection Agency (US EPA) and it's AirNow air quality site. Additional sources of PM2.5 data made accessible by the package include: AIRSIS (password protected), the Western Regional Climate Center (WRCC) and the open source site OpenAQ.
License: GPL-3
VignetteBuilder: knitr
Repository: CRAN
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-10 17:00:45 UTC; jonathan
Date/Publication: 2017-03-11 09:18:25

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New package POUMM with initial version 1.2.1
Package: POUMM
Type: Package
Title: The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Version: 1.2.1
Date: 2017-03-10
Authors@R: person("Venelin", "Mitov", email = "vmitov@gmail.com", role = c("aut", "cre", "cph"))
Description: Combined maximum likelihood and Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed Model; Fast POUMM likelihood calculation. Maximum likelihood inference of the genotypic values at the tips of a phylogeny assuming that the trait has evolved on it according to a POUMM with specified genotypic value at the root. Functions for summarizing and plotting the inference results; Functions for simulation of univariate continuous trait evolution along a phylogenetic tree.
License: GPL (>= 3.0)
LazyData: true
Depends: R (>= 3.1.0), stats, Rcpp, methods
LinkingTo: Rcpp, RcppArmadillo
Imports: ape, data.table, coda, foreach, ggplot2, gsl, Matrix
Suggests: testthat, TreeSim (>= 2.2), Rmpfr, mvtnorm, lmtest, knitr, rmarkdown, parallel, doParallel
RoxygenNote: 5.0.1
VignetteBuilder: knitr
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2017-03-10 14:49:07 UTC; vmitov
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Repository: CRAN
Date/Publication: 2017-03-11 09:18:21

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New package mrgsolve with initial version 0.8.2
Package: mrgsolve
Type: Package
Version: 0.8.2
Title: Simulate from ODE-Based Population PK/PD and Systems Pharmacology Models
Authors@R: c( person("Kyle T", "Baron", "", "kyleb@metrumrg.com", c("aut", "cre")), person("Alan C", "Hindmarsh", "", "", c("ctb")), person("Linda R", "Petzold", "", "", c("ctb")), person("Bill", "Gillespie", "", "", c("ctb")), person("Charles", "Margossian", "", "", c("ctb")), person("Devin", "Pastoor", "", "", c("ctb")), person("Metrum Research Group LLC", role = c("cph")) )
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
URL: https://github.com/metrumresearchgroup/mrgsolve
BugReports: https://github.com/metrumresearchgroup/mrgsolve/issues
Copyright: Metrum Research Group, LLC 2017
Description: Facilitates simulation from hierarchical, ordinary differential equation (ODE) based models typically employed in drug development. A model specification file is created consisting of R and C++ code that is parsed, compiled, and dynamically loaded into the R session. Input data are passed in and simulated data are returned as R objects. A dosing event engine allows interventions (bolus and infusion) to be managed separately from the model code. Differential equations are solved with the 'DLSODA' routine in 'ODEPACK' (<https://computation.llnl.gov/casc/odepack/>).
License: GPL (>= 2)
Depends: R (>= 3.1.2), methods
Imports: Rcpp (>= 0.12.3), dplyr (>= 0.5.0), magrittr (>= 1.5), lazyeval (>= 0.1.10), RcppArmadillo (>= 0.5.600.2.0), tibble (>= 1.2)
LinkingTo: Rcpp (>= 0.12.1), RcppArmadillo (>= 0.5.600.2.0), BH
Suggests: lattice, testthat, XML, rmarkdown
LazyLoad: yes
NeedsCompilation: yes
Collate: 'RcppExports.R' 'utils.R' 'package.R' 'generics.R' 'class_modlist.R' 'class_tgrid.R' 'class_numericlist.R' 'class_matlist.R' 'class_ev.R' 'class_derived.R' 'class_mrgmod.R' 'class_mrgsims.R' 'Aaaa.R' 'altname.R' 'annot.R' 'chain.R' 'class_build.R' 'compile.R' 'complog.R' 'covset.R' 'data_set.R' 'datasets.R' 'env.R' 'events.R' 'example.R' 'funset.R' 'idata_set.R' 'init.R' 'knobs.R' 'library.R' 'matlist.R' 'matrix.R' 'mcache.R' 'model_include.R' 'modlib.R' 'modspec.R' 'mread.R' 'mrgindata.R' 'mrgsims.R' 'mrgsolve.R' 'nmxml.R' 'param.R' 'print.R' 'qsim.R' 'render.R' 'simtime.R' 'update.R'
RoxygenNote: 6.0.1
Packaged: 2017-03-11 02:22:23 UTC; kyleb
Author: Kyle T Baron [aut, cre], Alan C Hindmarsh [ctb], Linda R Petzold [ctb], Bill Gillespie [ctb], Charles Margossian [ctb], Devin Pastoor [ctb], Metrum Research Group LLC [cph]
Repository: CRAN
Date/Publication: 2017-03-11 09:18:40

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New package mlrMBO with initial version 1.0.0
Package: mlrMBO
Title: A Toolbox for Model-Based Optimization of Expensive Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization ('MBO'), also known as Bayesian optimization. It is designed for both single- and multi-objective optimization with mixed continuous, categorical and conditional parameters. The machine learning toolbox 'mlr' provide dozens of regression learners to model the performance of the target algorithm with respect to the parameter settings. It provides many different infill criteria to guide the search process. Additional features include multipoint batch proposal, parallel execution as well as visualization and sophisticated logging mechanisms, which is especially useful for teaching and understanding of algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that single components can be easily replaced or adapted by the user for specific use cases.
Authors@R: c( person("Bernd", "Bischl", email = "bernd_bischl@gmx.net", role = c("aut")), person("Jakob", "Bossek", email = "jakob.bossek@tu-dortmund.de", role = "aut"), person("Jakob", "Richter", email = "code@jakob-r.de", role = c("aut", "cre")), person("Daniel", "Horn", email = "daniel.horn@tu-dortmund.de", role = "aut"), person("Michel", "Lang", email = "michellang@gmail.com", role = "aut"), person("Janek", "Thomas", email = "janek.thomas@stat.uni-muenchen.de", role = "aut"))
License: BSD_2_clause + file LICENSE
URL: https://github.com/mlr-org/mlrMBO
BugReports: https://github.com/mlr-org/mlrMBO/issues
Depends: mlr (>= 2.10), ParamHelpers (>= 1.10), smoof (>= 1.4)
Imports: backports, BBmisc (>= 1.11), checkmate (>= 1.8.2), data.table, lhs, parallelMap (>= 1.3)
Suggests: akima, cmaesr (>= 1.0.3), ggplot2, RColorBrewer, DiceKriging, DiceOptim, earth, emoa, GGally, gridExtra, kernlab, kknn, knitr, mco, nnet, party, randomForest, rmarkdown, rpart, testthat, eaf, covr
LazyData: yes
Encoding: UTF-8
ByteCompile: yes
Version: 1.0.0
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2017-03-10 19:49:34 UTC; jakob
Author: Bernd Bischl [aut], Jakob Bossek [aut], Jakob Richter [aut, cre], Daniel Horn [aut], Michel Lang [aut], Janek Thomas [aut]
Maintainer: Jakob Richter <code@jakob-r.de>
Repository: CRAN
Date/Publication: 2017-03-12 18:43:06

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New package iSDM with initial version 1.0
Package: iSDM
Type: Package
Title: Invasive Species Distribution Modelling
Version: 1.0
Date: 2016-04-05
Author: Tarek Hattab & Jonathan Lenoir
Maintainer: Tarek Hattab <hattab.tarek@gmail.com>
Description: Functions for predicting and mapping potential and realized distributions of invasive species within the invaded range.
Depends: R (>= 3.2.0)
Imports: stats, utils, graphics, ade4, geometry, geosphere, maptools, MASS, pdist, raster, rgdal, sp, colorRamps, virtualspecies, rgl
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-09 09:02:51 UTC; natha
Repository: CRAN
Date/Publication: 2017-03-09 18:08:43

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New package iNextPD with initial version 0.3.2
Package: iNextPD
Type: Package
Title: Interpolation and Extrapolation for Phylogenetic Diversity
Version: 0.3.2
Date: 2017-03-11
Authors@R: c(person("T. C.", "Hsieh", role = c("aut", "cre", "cph"), email = "euler96@gmail.com"), person("Chun-Huo", "Chiu", role = "ths", email = "otterfinder@yahoo.com.tw"), person("Anne", "Chao", role = "ths", email = "chao@stat.nthu.edu.tws"))
Maintainer: T. C. Hsieh <euler96@gmail.com>
Description: Interpolation and extrapolation for phylogenetic diversity.
URL: http://chao.stat.nthu.edu.tw/blog/software-download/
License: GPL (>= 3)
Depends: R (>= 3.1.2)
Imports: stats, graphics, ade4, ggplot2, Rcpp, iNEXT
BugReports: https://github.com/JohnsonHsieh/iNextPD/issues
LazyLoad: yes
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown, gridExtra, ggthemes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-11 03:58:23 UTC; johnson
Author: T. C. Hsieh [aut, cre, cph], Chun-Huo Chiu [ths], Anne Chao [ths]
Repository: CRAN
Date/Publication: 2017-03-11 09:18:39

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New package imputeR with initial version 2.0
Package: imputeR
Title: A General Imputation Framework in R
Version: 2.0
Date: 2017-02-07
Author: Lingbing Feng, Steffen Moritz, Gen Nowak, Alan. H. Welsh, Terry. J. O'Neill
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Description: General imputation framework based on variable selection methods including regularisation methods, tree-based models and dimension reduction methods.
LazyData: yes
Type: Package
ByteCompile: TRUE
BugReports: https://github.com/SteffenMoritz/imputeR/issues
URL: http://github.com/SteffenMoritz/imputeR
Repository: CRAN
Depends: R (>= 3.1.0),
Imports: caret, reshape2, glmnet, pls, rda, Cubist, ridge, gbm, mboost, rpart
Suggests: testthat
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-03-09 01:30:20 UTC; Steve
Date/Publication: 2017-03-09 08:22:01

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New package iMessager with initial version 1.0
Package: iMessager
Title: Send 'iMessages' from R
Version: 1.0
Authors@R: person("Scott", "Lougheed", email = "info@scottlougheed.com", role = c("aut", "cre"))
Description: Send 'iMessages' from R running 'macOS' 10.8.x or later. You must have 'Messages.app' configured for the user account you are running R on.
Depends: R (>= 3.3.2)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2017-03-08 20:00:55 UTC; scottlougheed
Author: Scott Lougheed [aut, cre]
Maintainer: Scott Lougheed <info@scottlougheed.com>
Repository: CRAN
Date/Publication: 2017-03-09 08:18:31

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New package huxtable with initial version 0.1.0
Package: huxtable
Type: Package
Title: Simply Create LaTeX and HTML Tables
Version: 0.1.0
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Description: Creates HTML and LaTeX tables. Provides similar functionality to 'xtable', but does more, with a simpler interface.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, dplyr
RoxygenNote: 6.0.1
URL: https://hughjonesd.github.io/huxtable
BugReports: https://github.com/hughjonesd/huxtable/issues
Imports: knitr, rmarkdown, xtable, devtools, htmltools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-03-09 12:38:34 UTC; david
Repository: CRAN
Date/Publication: 2017-03-09 15:23:59

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New package gsynth with initial version 1.0.2
Package: gsynth
Type: Package
Title: Generalized Synthetic Control Method
Version: 1.0.2
Date: 2017-3-8
Author: Yiqing Xu, University of California, San Diego
Maintainer: Yiqing Xu <yiqingxu@ucsd.edu>
Description: Generalized synthetic control method: causal inference with interactive fixed-effect models. It imputes counterfactuals for each treated unit using control group information based on a linear interactive fixed effects model that incorporates unit-specific intercepts interacted with time-varying coefficients. This method generalizes the synthetic control method to the case of multiple treated units and variable treatment periods, and improves efficiency and interpretability. Data must be in form of a balanced panel with a dichotomous treatment.
URL: http://yiqingxu.org/software/gsynth/gsynth_examples.html
NeedsCompilation: yes
License: GPL-2
Imports: Rcpp (>= 0.12.3), ggplot2 (>= 2.1.0), GGally (>= 1.0.1), doParallel (>= 1.0.10), foreach (>= 1.4.3), abind (>= 1.4.5)
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2017-03-12 03:35:42 UTC; lenovo
Repository: CRAN
Date/Publication: 2017-03-12 09:02:35

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New package GADMTools with initial version 2.0-1
Package: GADMTools
Type: Package
Title: Easy Use of 'GADM' Shapefiles
Version: 2.0-1
Date: 2017-03-10
Authors@R: c(person("Jean Pierre", "Decorps", role = c("aut", "cre"), email = "jp.decorps@epiconcept.fr"), person("Morgane","Vallee", role = "ctb", email = "m.vallee@epiconcept.fr") )
Description: Manipulate, assemble,export <www.gadm.org> shapefiles. Create choroplethe, heatmaps, dots plot, proportional dots and more.
License: GPL-3
Depends: sp,ggplot2, dplyr, classInt, rgdal
Imports: RColorBrewer, maptools, scales, stringr, lattice, jsonlite, gridExtra, rgeos, ggmap
NeedsCompilation: no
Packaged: 2017-03-11 11:45:22 UTC; kdo
Author: Jean Pierre Decorps [aut, cre], Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Repository: CRAN
Date/Publication: 2017-03-11 18:17:38

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New package envDocument with initial version 2.3.0
Package: envDocument
Type: Package
Title: Document the R Working Environment
Version: 2.3.0
Date: 2017-03-08
Author: c( person("Donald", "Jackson", , "donald.jackson@bms.com", role = c("aut", "cre")), person("Bristol-Myers Squibb, role = "cph") )
Maintainer: Donald Jackson <donald.jackson@bms.com>
Description: Prints out information about the R working environment (system, R version,loaded and attached packages and versions) from a single function "env_doc()". Optionally adds information on git repository, tags, commits and remotes (if available).
License: GPL (>= 3.0)
Repository: CRAN
Suggests: git2r(>= 0.15.0), knitr(>= 1.13)
RoxygenNote: 5.0.1
VignetteBuilder: knitr
Imports: utils, methods
NeedsCompilation: no
Packaged: 2017-03-10 16:47:05 UTC; jacksod
Date/Publication: 2017-03-11 09:18:37

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New package DMMF with initial version 0.2.8.0
Package: DMMF
Type: Package
Title: Daily Based Morgan--Morgan--Finney (DMMF) Soil Erosion Model
Version: 0.2.8.0
Date: 2017-02-28
Authors@R: c(person("Kwanghun", "Choi", role = c("aut", "cre"), email="kwanghun.choi@yahoo.com"), person("Sebastian", "Arnhold", role = c("dtc", "ctb")), person("Bjoern", "Reineking", role = c("ths", "ctb")))
Author: Kwanghun Choi [aut, cre], Sebastian Arnhold [dtc, ctb], Bjoern Reineking [ths, ctb]
Maintainer: Kwanghun Choi <kwanghun.choi@yahoo.com>
Description: Implements the daily based Morgan--Morgan--Finney (DMMF) soil erosion model for estimating surface runoff and sediments budgets from a field or a catchment on a daily basis.
License: GPL (>= 2)
Depends: R (>= 3.2.3), raster, sp, rgdal, methods
NeedsCompilation: yes
Packaged: 2017-03-09 13:18:50 UTC; kwanghun
Repository: CRAN
Date/Publication: 2017-03-10 11:49:40

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New package CrossScreening with initial version 0.0.1
Package: CrossScreening
Type: Package
Title: Cross-Screening in Observational Studies that Test Many Hypotheses
Version: 0.0.1
Date: 2017-03-02
Authors@R: c(person("Paul", "Rosenbaum", email = "rosenbap@wharton.upenn.edu", role = c("aut")), person("Qingyuan", "Zhao", email = "qyzhao@wharton.upenn.edu", role = c("aut", "cre")))
Description: Cross-screening is a new method that uses both random halves of the sample to screen and test many hypotheses. It generally improves statistical power in observational studies when many hypotheses are tested simultaneously.
Imports: stats, sensitivitymw, parallel, plyr, tables
Suggests:
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-03-08 19:43:08 UTC; qyzhao
Author: Paul Rosenbaum [aut], Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@wharton.upenn.edu>
Repository: CRAN
Date/Publication: 2017-03-09 08:18:15

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