Wed, 15 Aug 2018

New package trackr with initial version 0.9.5
Package: trackr
Type: Package
Title: Semantic Annotation and Discoverability System for R-Based Artifacts
Version: 0.9.5
Date: 2018-07-17
Authors@R: c( person("Gabriel", "Becker", role = c("aut", "cre"), email = "becker.gabriel@gene.com"), person("Sara", "Moore", role = c("aut"), email = "moore.sara@gene.com"))
Copyright: Genentech, Inc.
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Description: Automatically annotates R-based artifacts with relevant descriptive and provenance-related and provides a backend-agnostic storage and discoverability system for organizing, retrieving, and interrogating such artifacts.
License: Artistic-2.0
Depends: histry (>= 0.2.1)
Imports: fastdigest, ggplot2, lattice, gridGraphics, methods, CodeDepends (>= 0.6.2), RJSONIO, rsolr, htmltools, miniUI, shiny, rmarkdown, roprov (>= 0.0.3), rlang
Suggests: proto, png, httr, knitr, MASS, MEMSS, mlmRev, dplyr, gridExtra, rstudioapi
VignetteBuilder: knitr
Collate: 'Classes.R' 'DocCollectionRef-methods.R' 'Generics.R' 'PlotWrapper.R' 'ObjFeatureSet.R' 'Trackr-main-API.R' 'abbrev.R' 'accessor-methods.R' 'autotrack.R' 'backend-impls.R' 'coercerender.R' 'convenience_constructors.R' 'ggplotversions.R' 'knitr.R' 'makeRStudioExtras.R' 'parseCode.R' 'recordFile.R' 'shiny.R' 'showMethods.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-15 15:20:42 UTC; beckerg4
Author: Gabriel Becker [aut, cre], Sara Moore [aut]
Repository: CRAN
Date/Publication: 2018-08-15 18:00:03 UTC

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Tue, 14 Aug 2018

New package vapour with initial version 0.1.0
Package: vapour
Title: Lightweight Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Version: 0.1.0
Authors@R: c(person("Michael", "Sumner", email = "mdsumner@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-2471-7511")), person("Simon", "Wotherspoon", role = "ctb", comment = "figured out the mechanism for the resampling algorithm"), person("Mark", "Padgham", role = "ctb", comment = "helped get started :)"), person("Edzer", "Pebesma", role = "ctb", comment = "wrote allocate_attribute, copied here from sf"), person("Roger", "Bivand", role = "ctb", comment = "wrote configure.ac, copied here from rgdal"), person("Jim", "Hester", role = "ctb", comment = "wrote CollectorList.h, copied here from fs package"))
Description: Provides low-level access to 'GDAL' functionality for R packages. The aim is to minimize the level of interpretation put on the 'GDAL' facilities, to enable direct use of it for a variety of purposes. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <http://gdal.org/>. Other available packages 'rgdal' and 'sf' also provide access to the 'GDAL' library, but neither can be used for these lower level tasks, and both do many other tasks.
Depends: R (>= 3.3.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, utils
RoxygenNote: 6.0.1
Suggests: covr, dplyr, geojsonsf, testthat, knitr, rbenchmark, rmarkdown
SystemRequirements: GDAL (>= 2.0.0), PROJ.4 (>= 4.8.0)
VignetteBuilder: knitr
URL: https://github.com/hypertidy/vapour
BugReports: https://github.com/hypertidy/vapour/issues
NeedsCompilation: yes
Packaged: 2018-08-09 01:54:22 UTC; mdsumner
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>), Simon Wotherspoon [ctb] (figured out the mechanism for the resampling algorithm), Mark Padgham [ctb] (helped get started :)), Edzer Pebesma [ctb] (wrote allocate_attribute, copied here from sf), Roger Bivand [ctb] (wrote configure.ac, copied here from rgdal), Jim Hester [ctb] (wrote CollectorList.h, copied here from fs package)
Maintainer: Michael Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-14 15:30:03 UTC

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New package ZipRadius with initial version 1.0.1
Package: ZipRadius
Type: Package
Title: Creates a Data Frame of US Zip Codes in a Given Radius from a Given US Zip Code
Version: 1.0.1
Depends: R (>= 2.10)
Author: Stephen Ewing <stephenewing1337@gmail.com>
Maintainer: Stephen Ewing <stephenewing1337@gmail.com>
Imports: dplyr, geosphere, magrittr, testthat, rlang, ggplot2
Description: Generates a data frame of US zip codes and their distance to the given zip code when given a starting zip code and a radius in miles. Also includes functions for use with 'choroplethrZip' which are detailed in the vignette.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-14 11:28:21 UTC; Steve
Repository: CRAN
Date/Publication: 2018-08-14 12:10:07 UTC

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New package Rnmr1D with initial version 1.2.0
Package: Rnmr1D
Type: Package
Title: Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Version: 1.2.0
Date: 2018-08-13
Authors@R: c( person("Daniel", "Jacob", email="daniel.jacob@inra.fr", role=c("cre", "aut"), comment=c(ORCID="0000-0002-6687-7169")), person("Catherine", "Deborde", email="catherine.deborde@inra.fr", role=c("ctb")), person("Marie", "Lefebvre", email="marie.lefebvre@inra.fr", role=c("ctb")))
Copyright: Institut National de la Recherche Agronomique (INRA)
URL: https://github.com/INRA/Rnmr1D
Maintainer: Daniel Jacob <daniel.jacob@inra.fr>
Description: Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.
Depends: R (>= 2.10)
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.7), base64enc (>= 0.1), MASS(>= 7.3), Matrix, methods, doParallel (>= 1.0.11), foreach (>= 1.4.4), igraph (>= 1.2.1), impute (>= 1.54.0), MassSpecWavelet (>= 1.46.0), ptw (>= 1.9), signal (>= 0.7), speaq (>= 2.3.3), XML (>= 3.98)
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-08-14 06:21:07 UTC; djaco
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>), Catherine Deborde [ctb], Marie Lefebvre [ctb]
Repository: CRAN
Date/Publication: 2018-08-14 12:40:07 UTC

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New package epiflows with initial version 0.2.0
Package: epiflows
Title: Predicting Disease Spread from Flow Data
Version: 0.2.0
Authors@R: c(person("Pawel", "Piatkowski", email = "pawel.piatkowski@posteo.net", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0822-5592")), person("Paula", "Moraga", email = "p.e.moraga-serrano@lancaster.ac.uk", role = "aut", comment = c(ORCID = "0000-0001-5266-0201")), person("Isobel", "Blake", email = "isobel.blake@imperial.ac.uk", role = c("ctb", "dtc")), person("Thibaut", "Jombart", email = "thibautjombart@gmail.com", role = "aut"), person("VP", "Nagraj", email = "vpnagraj@virginia.edu", role = "aut"), person("Zhian N.", "Kamvar", email = "zkamvar@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-1458-7108")), person("Salla E.", "Toikkanen", email = "Salla.e.toikkanen@gmail.com", role = "aut"))
Description: Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Imports: epicontacts, leaflet, ggmap, geosphere, ggplot2, tibble, sp, htmlwidgets, stats, htmltools, visNetwork
Suggests: testthat, roxygen2, knitr, outbreaks, vdiffr, curl, rmarkdown
RoxygenNote: 6.1.0
URL: https://www.repidemicsconsortium.org/epiflows
BugReports: https://github.com/reconhub/epiflows/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-14 07:13:32 UTC; jovyan
Author: Pawel Piatkowski [aut, cre] (<https://orcid.org/0000-0002-0822-5592>), Paula Moraga [aut] (<https://orcid.org/0000-0001-5266-0201>), Isobel Blake [ctb, dtc], Thibaut Jombart [aut], VP Nagraj [aut], Zhian N. Kamvar [aut] (<https://orcid.org/0000-0003-1458-7108>), Salla E. Toikkanen [aut]
Maintainer: Pawel Piatkowski <pawel.piatkowski@posteo.net>
Repository: CRAN
Date/Publication: 2018-08-14 12:40:03 UTC

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New package BayesCTDesign with initial version 0.5.0
Package: BayesCTDesign
Type: Package
Title: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data
Version: 0.5.0
Authors@R: c( person("Barry", "Eggleston", email = "beggleston@rti.org", role = c("cre", "aut")), person("Doug", "Wilson", email = "doug.roy.wilson@gmail.com", role = c("aut")), person("Becky", "McNeil", email = "rmcneil@rti.org", role = c("aut")), person("Joseph", "Ibrahim", email = "jibrahim@email.unc.edu", role = c("aut")), person("Diane", "Catellier", email = "dcatellier@rti.org", role = c("fnd", "rth", "aut")))
Description: A set of functions to help clinical trial researchers calculate power and sample size for two-arm Bayesian randomized clinical trials that do or do not incorporate historical control data. At some point during the design process, a clinical trial researcher who is designing a basic two-arm Bayesian randomized clinical trial needs to make decisions about power and sample size within the context of hypothesized treatment effects. Through simulation, the simple_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about treatment effect,control group characteristics, and outcome. If the clinical trial researcher has access to historical control data, then the researcher can design a two-arm Bayesian randomized clinical trial that incorporates the historical data. In such a case, the researcher needs to work through the potential consequences of historical and randomized control differences on trial characteristics, in addition to working through issues regarding power in the context of sample size, treatment effect size, and outcome. If a researcher designs a clinical trial that will incorporate historical control data, the researcher needs the randomized controls to be from the same population as the historical controls. What if this is not the case when the designed trial is implemented? During the design phase, the researcher needs to investigate the negative effects of possible historic/randomized control differences on power, type one error, and other trial characteristics. Using this information, the researcher should design the trial to mitigate these negative effects. Through simulation, the historic_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about historical and randomized control differences as well as treatment effects and outcomes. The results from historic_sim() and simple_sim() can be printed with print_table() and graphed with plot_table() methods. Outcomes considered are Gaussian, Poisson, Bernoulli, Lognormal, Weibull, and Piecewise Exponential.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: http://github.com/begglest/BayesCTDesign
BugReports: http://github.com/begglest/BayesCTDesign/issues
Imports: eha (>= 2.5.1), ggplot2 (>= 2.2.1), survival (>= 2.41-3), reshape2 (>= 1.4.3), stats (>= 3.5.0)
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-13 15:33:35 UTC; beggleston
Author: Barry Eggleston [cre, aut], Doug Wilson [aut], Becky McNeil [aut], Joseph Ibrahim [aut], Diane Catellier [fnd, rth, aut]
Maintainer: Barry Eggleston <beggleston@rti.org>
Repository: CRAN
Date/Publication: 2018-08-14 12:00:25 UTC

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New package touchard with initial version 1.0
Package: touchard
Type: Package
Title: Touchard Model and Regression
Description: Tools for analyzing count data with the Touchard model. It includes univariate estimation (ML and MM) and regression tools, following Matsushita et al. (2018) The Touchard distribution, Communications in Statistics - Theory and Methods <doi:10.1080/03610926.2018.1444177>.
Version: 1.0
Date: 2018-08-07
Author: Bernardo Andrade and Sandro Oliveira
Maintainer: Bernardo Andrade <bbandrade@unb.br>
License: GPL-2
Depends: R (>= 3.2.0)
Imports: MASS, nleqslv, numDeriv, plotrix
NeedsCompilation: no
Packaged: 2018-08-13 12:02:50 UTC; root
Repository: CRAN
Date/Publication: 2018-08-14 09:40:03 UTC

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New package SDALGCP with initial version 0.1.0
Package: SDALGCP
Title: Spatially Discrete Approximation to Log-Gaussian Cox Processes for Aggregated Disease Count Data
Version: 0.1.0
Authors@R: c( person("Olatunji", "Johnson", email = "olatunjijohnson21111@gmail.com", role = c("aut", "cre")), person("Emanuele", "Giorgi", email = "e.giorgi@lancaster.ac.uk", role = "aut"), person("Peter", "Diggle", email = "p.diggle@lancaster.ac.uk", role = "aut"))
Description: Provides a computationally efficient discrete approximation to log-Gaussian Cox process model for spatially aggregated disease count data. It uses Monte Carlo Maximum Likelihood for model parameter estimation as proposed by Christensen (2004) <doi: 10.1198/106186004X2525> and delivers prediction of spatially discrete and continuous relative risk.
Depends: R (>= 3.4.0)
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Imports: pdist(>= 1.2), Matrix(>= 1.2.14), PrevMap(>= 1.4.1), raster(>= 2.6.7), sp(>= 1.2.7), spatstat(>= 1.55.1), splancs(>= 2.1.40), methods(>= 3.4.4), maptools(>= 0.9.2), plyr(>= 1.8.4), pbapply(>= 1.3.4), progress(>= 1.1.2)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-13 09:35:51 UTC; johnsono
Author: Olatunji Johnson [aut, cre], Emanuele Giorgi [aut], Peter Diggle [aut]
Maintainer: Olatunji Johnson <olatunjijohnson21111@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-14 09:30:05 UTC

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New package rfacebookstat with initial version 1.8.3
Package: rfacebookstat
Type: Package
Title: Load Data from Facebook API Marketing
Version: 1.8.3
Date: 2018-08-08
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Depends: R (>= 3.0.0)
BugReports: https://github.com/selesnow/rfacebookstat/issues
Imports: data.table, httr, RCurl, bitops, jsonlite, dplyr
URL: http://selesnow.github.io/rfacebookstat
License: GPL-2
NeedsCompilation: no
Packaged: 2018-08-13 09:35:40 UTC; Alsey
Repository: CRAN
Date/Publication: 2018-08-14 09:30:02 UTC

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New package MRPC with initial version 1.0.0
Package: MRPC
Type: Package
Title: Mendelian Randomization (MR) Based PC Algorithm
Version: 1.0.0
Author: Md Bahadur Badsha <mdbadsha@uidaho.edu> and Audrey Qiuyan Fu <audreyf@uidaho.edu>
Maintainer: Md Bahadur Badsha <mdbadsha@uidaho.edu>
Description: Estimate the causal graph using generalized Mendelian Randomization (MR) based PC (MRPC) Algorithm. See Badsha and Fu (2018) <doi:10.1101/171348>.
License: GPL (>= 2)
LazyData: TRUE
Imports: GGally,Hmisc,WGCNA,bnlearn,dynamicTreeCut,mice,network,pcalg,methods
Suggests: BiocGenerics,fastcluster,Rgraphviz,stats,scales,sna
NeedsCompilation: no
Packaged: 2018-08-12 21:33:14 UTC; mdbadsha
Repository: CRAN
Date/Publication: 2018-08-14 09:10:03 UTC

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New package GmAMisc with initial version 1.0.0
Package: GmAMisc
Title: Gianmarco Alberti Miscellaneous
Version: 1.0.0
Authors@R: person("Gianmarco", "Alberti", email = "gianmarcoalberti@gmail.com", role = c("aut", "cre"))
Description: Contains many functions useful for univariate outlier detection, permutation-based t-test, permutation-based chi-square test, visualization of residuals, and bootstrap Cramer's V, plotting of the results of the Mann-Whitney and Kruskall-Wallis test, calculation of Brainerd-Robinson similarity coefficient and subsequent clustering, validation of logistic regression models, optimism-corrected AUC, robust Bland-Altman plot, calculation of posterior probability for different chronological relationships between two Bayesian radiocarbon phases, point pattern analysis, landform classification, clustering of spatial features.
Depends: R (>= 3.4.0), maptools (>= 0.9-2)
Imports: caTools (>= 1.17.1), classInt (>= 0.2-3), cluster (>= 2.0.7-1), coin (>= 1.2-2), corrplot (>= 0.84), DescTools (>= 0.99.24), dismo (>= 1.1-4), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), graphics (>= 3.4.3), grDevices (>= 3.4.3), gridExtra (>= 2.3), Hmisc (>= 4.1-1), InPosition (>= 0.12.7), kimisc (>= 0.4), lsr (>= 0.5), methods (>= 3.4.3), plyr (>= 1.8.4), pROC (>= 1.12.1), raster (>= 2.6-7), RcmdrMisc (>= 1.0-10), rgdal (>= 1.3-3), rgeos (>= 0.3-28), sp (>= 1.3-1), spatialEco (>= 1.1-0), spatstat (>= 1.56-0), rworldmap (>= 1.3.6), shape (>= 1.4.4), stats (>= 3.4.3), utils (>= 3.4.3)
Suggests: archdata (>= 1.2), gdistance (>= 1.2-2), resample (>= 0.4)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-12 17:11:57 UTC; gianmarcoalberti
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-14 09:10:07 UTC

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New package fc with initial version 0.1.0
Package: fc
Type: Package
Title: Standard Evaluation-Based Multivariate Function Composition
Version: 0.1.0
Authors@R: c(person("Xiaofei (Susan)", "Wang", email="xiaofei.wang@yale.edu", role = c("aut", "cre")), person("Michael", "Kane", email="michael.kane@yale.edu", role="aut"))
Description: Provides a streamlined, standard evaluation-based approach to multivariate function composition. Allows for chaining commands via a forward-pipe operator, %>%.
Encoding: UTF-8
LazyData: true
URL: https://github.com/swang87/fc
BugReports: https://github.com/swang87/fc/issues
License: GPL-2
Imports: codetools
Suggests: magrittr, purrr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-13 13:49:00 UTC; eastie
Author: Xiaofei (Susan) Wang [aut, cre], Michael Kane [aut]
Maintainer: Xiaofei (Susan) Wang <xiaofei.wang@yale.edu>
Repository: CRAN
Date/Publication: 2018-08-14 09:40:06 UTC

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New package DemoDecomp with initial version 1.0.1
Package: DemoDecomp
Type: Package
Title: Decompose Demographic Functions
Version: 1.0.1
Date: 2018-08-13
Author: Tim Riffe
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Description: Two general demographic decomposition methods are offered: Pseudo-continuous decomposition proposed by Horiuchi, Wilmoth, and Pletcher (2008) <doi:10.1353/dem.0.0033> and stepwise replacement decomposition proposed by Andreev, Shkolnikov and Begun (2002) <doi:10.4054/DemRes.2002.7.14>.
License: GPL-3
LazyLoad: yes
RoxygenNote: 6.1.0
Suggests: covr
RdMacros: Rdpack
Imports: Rdpack
Depends: R (>= 2.10)
BugReports: https://github.com/timriffe/DemoDecomp/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-08-13 09:19:15 UTC; tim
Repository: CRAN
Date/Publication: 2018-08-14 09:30:09 UTC

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Mon, 13 Aug 2018

New package quadmatrix with initial version 0.1.0
Package: quadmatrix
Type: Package
Title: Solving Quadratic Matrix Equations
Version: 0.1.0
Author: Kasa
Maintainer: Siva Rajesh Kasa <sivarajesh.kasa@gmail.com>
Description: Given inputs A,B and C, this package solves the matrix equation A*X^2 - B*X - C = 0.
License: GPL-2
Encoding: UTF-8
LazyData: FALSE
Imports: matrixcalc,geigen
Suggests: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-11 01:58:49 UTC; sivarajesh
Repository: CRAN
Date/Publication: 2018-08-13 14:40:03 UTC

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New package patrick with initial version 0.0.1
Package: patrick
Title: Parameterized Unit Testing
Author: Michael Quinn <msquinn@google.com>
Maintainer: Michael Quinn <msquinn@google.com>
Copyright: Copyright (C) 2018 Google LLC
Description: This is an extension of the 'testthat' package that lets you add parameters to your unit tests. Parameterized unit tests are often easier to read and more reliable, since they follow the DNRY (do not repeat yourself) rule.
Version: 0.0.1
Depends: R (>= 3.1)
Imports: dplyr, purrr, rlang, testthat, tibble
License: Apache License 2.0
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-10 17:11:14 UTC; msquinn
Repository: CRAN
Date/Publication: 2018-08-13 14:10:03 UTC

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New package painter with initial version 0.1.0
Package: painter
Type: Package
Title: Creation and Manipulation of Color Palettes
Version: 0.1.0
Authors@R: person("Brody", "Sandel",role = c("aut","cre"), email = "bsandel@scu.edu")
Description: Functions for creating color palettes, visualizing palettes, modifying colors, and assigning colors for plotting.
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-08-10 21:16:23 UTC; bsandel
Author: Brody Sandel [aut, cre]
Maintainer: Brody Sandel <bsandel@scu.edu>
Repository: CRAN
Date/Publication: 2018-08-13 14:20:03 UTC

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New package mccf1 with initial version 1.0
Package: mccf1
Title: Creates the MCC-F1 Curve and Calculates the MCC-F1 Metric and the Best Threshold
Version: 1.0
Date: 2018-07-31
Authors@R: c(person("Chang", "Cao", role = c("aut", "cre"), email = "kirin.cao@mail.utoronto.ca"), person("Michael", "Hoffman", role = "aut", email = "michael.hoffman@utoronto.ca"), person("Davide", "Chicco", role = "aut", email = "davide.chicco@gmail.com"))
Maintainer: Chang Cao <kirin.cao@mail.utoronto.ca>
Depends: R (>= 3.3.3)
Imports: ROCR, ggplot2
Description: The MCC-F1 analysis is a method to evaluate the performance of binary classifications. The MCC-F1 curve is more reliable than the Receiver Operating Characteristic (ROC) curve and the Precision-Recall (PR)curve under imbalanced ground truth. The MCC-F1 analysis also provides the MCC-F1 metric that integrates classifier performance over varying thresholds, and the best threshold of binary classification.
License: GPL (>= 2)
URL: https://bitbucket.org/hoffmanlab/mccf1/
BugReports: https://stackoverflow.com/questions/tagged/mccf1
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-08 05:01:14 UTC; user
Author: Chang Cao [aut, cre], Michael Hoffman [aut], Davide Chicco [aut]
Repository: CRAN
Date/Publication: 2018-08-13 14:40:06 UTC

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New package garray with initial version 1.0.2
Package: garray
Type: Package
Title: Generalized Array Arithmetic for Ragged Arrays with Named Margins
Version: 1.0.2
Date: 2018-08-10
Author: Qingsheng Huang
Maintainer: Qingsheng Huang <huangqqss@126.com>
Depends: R (>= 3.4.0)
Description: Organize a so-called ragged array as generalized arrays, which is simply an array with sub-dimensions denoting the subdivision of dimensions (grouping of members within dimensions). By the margins (names of dimensions and sub-dimensions) in generalized arrays, operators and utility functions provided in this package automatically match the margins, doing map-reduce style calculation along margins. Generalized arrays are also cooperative to R's native functions that work on simple arrays.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-11 03:41:55 UTC; alex
Repository: CRAN
Date/Publication: 2018-08-13 14:40:08 UTC

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New package DSAIRM with initial version 0.4.0
Package: DSAIRM
Type: Package
Title: Dynamical Systems Approach to Immune Response Modeling
Description: A collection of 'shiny' apps that allow for the simulation and exploration of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models. The development of this package was partially supported by NIH grant U19AI117891.
Version: 0.4.0
Date: 2018-08-10
Authors@R: c( person("Andreas", "Handel", email = "ahandel@uga.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4622-1146") ), person("Spencer", "Hall", role = "ctb"), person("Sina", "Solaimanpour", role = "ctb"), person("Henok", "Woldu", role = "ctb") )
Maintainer: Andreas Handel <ahandel@uga.edu>
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
Imports: adaptivetau (>= 2.2), boot (>= 1.3-20), deSolve (>= 1.20), dplyr (>= 0.7.4), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), knitr (>= 1.15), lhs (>= 0.15), nloptr (>= 1.0.4), rmarkdown (>= 1.10), stats (>= 3.4), tidyr (>= 0.7), utils (>= 3.4), XML
Depends: R (>= 3.4), shiny (>= 1.0)
Suggests: covr, testthat
RoxygenNote: 6.1.0
VignetteBuilder: knitr
URL: https://ahgroup.github.io/DSAIRM, https://github.com/ahgroup/DSAIRM/
BugReports: https://github.com/ahgroup/DSAIRM/issues
NeedsCompilation: no
Packaged: 2018-08-10 17:20:31 UTC; andreas
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>), Spencer Hall [ctb], Sina Solaimanpour [ctb], Henok Woldu [ctb]
Repository: CRAN
Date/Publication: 2018-08-13 14:10:15 UTC

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New package brandwatchR with initial version 0.3.0
Package: brandwatchR
Type: Package
Title: 'Brandwatch' API to R
Version: 0.3.0
Authors@R: c(person("Donal", "Phipps", email = "donal.phipps@gmail.com", role = c("aut", "cre")))
URL: https://github.com/Phippsy/brandwatchR
BugReports: https://github.com/Phippsy/brandwatchR/issues
Description: Interact with the 'Brandwatch' API <https://developers.brandwatch.com/docs>. Allows you to authenticate to the API and obtain data for projects, queries, query groups tags and categories. Also allows you to directly obtain mentions and aggregate data for a specified query or query group.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: R (>= 3.4.0)
Imports: httr (>= 1.3.1), jsonlite (>= 1.5), data.table (>= 1.10)
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-08-11 06:53:55 UTC; donal
Author: Donal Phipps [aut, cre]
Maintainer: Donal Phipps <donal.phipps@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-13 14:40:16 UTC

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New package BLOQ with initial version 0.1-0
Package: BLOQ
Type: Package
Version: 0.1-0
Date: 2018-08-09
Title: Impute and Analyze Data with Observations Below the Limit of Quantification
Authors@R: c( person("Vahid","Nassiri", email = "vahid.nassiri@openanalytics.eu", role = "cre"), person("Helen", "Barnett", email= "h.barnett@lancaster.ac.uk", role = "aut"), person("Helena", "Geys", email= "HGEYS@its.jnj.com", role = "aut"), person("Tom", "Jacobs", email= "TJACOBS1@its.jnj.com", role = "aut"), person("Thomas", "Jaki", email= "t.jaki@lancaster.ac.uk", role = "aut"))
Maintainer: Vahid Nassiri <vahid.nassiri@openanalytics.eu>
Description: Methods for non-compartmental pharmacokinetic analysis with observations below the limit of quantification (BLOQ) are implemented as described in Barnett, Helen Yvette. "Optimizing pharmacokinetic studies utilizing microsampling." PhD diss., Lancaster University, 2017. (available online: <http://eprints.lancs.ac.uk/89163/1/2017barnettphd.pdf>). It includes estimating the area under the concentrations versus time curve (AUC) and its standard error using two approaches: direct estimation using censored maximum likelihood, also by first imputing the BLOQ's using various methods, then compute AUC and its standard error using imputed data.
Imports: maxLik, mvnmle, mvtnorm,
Suggests: testthat,
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-13 14:13:50 UTC; vnassiri
Author: Vahid Nassiri [cre], Helen Barnett [aut], Helena Geys [aut], Tom Jacobs [aut], Thomas Jaki [aut]
Repository: CRAN
Date/Publication: 2018-08-13 14:40:20 UTC

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New package sars with initial version 1.0.0
Package: sars
Type: Package
Title: Fit and Compare Species-Area Relationship Models Using Multimodel Inference
Version: 1.0.0
Authors@R: c(person("Thomas J.", "Matthews", email = "txm676@gmail.com", role = c("aut", "cre")), person("François", "Guilhaumon", email = "francois.guilhaumon@ird.fr", role = c("aut")))
Description: Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.
License: GPL-3
URL: https://github.com/txm676/sars
BugReports: https://github.com/txm676/sars/issues
Imports: dplyr, graphics, nortest, stats, utils, crayon, cli, numDeriv
Depends: R(>= 3.0.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-08-10 09:37:53 UTC; Tom
Author: Thomas J. Matthews [aut, cre], François Guilhaumon [aut]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-13 13:50:03 UTC

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New package ltable with initial version 1.0
Package: ltable
Type: Package
Title: Easy to Make (Lazy) Tables
Version: 1.0
Date: 2018-08-10
Author: Ocheredko Oleksandr
Description: Constructs tables of counts and proportions out of data sets. It has simplified syntax appealing for novice and even for advanced user under time pressure. It is particularly suitable for exploratory data analysis or presentation to single out most appropriate pieces of tabulated information. The other important feature is possibility to insert tables to Excel and Word documents.
Maintainer: Ocheredko Oleksandr <Ocheredko@yahoo.com>
License: GPL (>= 2)
Depends: R (>= 3.4.0)
Suggests: utils, stats
NeedsCompilation: no
Packaged: 2018-08-10 11:39:37 UTC; user
Repository: CRAN
Date/Publication: 2018-08-13 14:00:03 UTC

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New package dint with initial version 1.0.0
Type: Package
Package: dint
Title: A Toolkit for Year-Quarter and Year-Month Dates
Version: 1.0.0
Authors@R: person("Stefan", "Fleck", email = "stefan.b.fleck@gmail.com", role = c("aut", "cre"))
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Description: S3 classes and methods to create and work with year-quarter and year-month vectors. Basic arithmetic operations (such as adding and subtracting) are supported, as well as formatting and converting to and from standard R Date types.
License: MIT + file LICENSE
URL: https://github.com/s-fleck/dint
BugReports: https://github.com/s-fleck/dint/issues
Suggests: ggplot2, knitr, lubridate, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-10 16:47:27 UTC; hoelk
Author: Stefan Fleck [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-13 14:00:06 UTC

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New package dials with initial version 0.0.1
Package: dials
Version: 0.0.1
Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", c("aut", "cre")), person("RStudio", role = "cph"))
License: GPL-2
URL: https://tidymodels.github.io/dials
BugReports: https://github.com/tidymodels/dials/issues
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Depends: scales
Imports: glue, purrr, rlang, tibble, dplyr, utils
Suggests: testthat, knitr, rpart, covr
NeedsCompilation: no
Packaged: 2018-08-10 16:42:53 UTC; max
Author: Max Kuhn [aut, cre], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Repository: CRAN
Date/Publication: 2018-08-13 14:00:10 UTC

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New package frailtyHL with initial version 2.2
Package: frailtyHL
Type: Package
Title: Frailty Models via Hierarchical Likelihood
Version: 2.2
Date: 2018-07-25
Author: Il Do Ha, Maengseok Noh, Jiwoong Kim, Youngjo Lee
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>
Description: Implements the h-likelihood estimation procedures for general frailty models including competing-risk models and joint models.
Depends: R (>= 3.4.0), methods, Matrix, survival, cmprsk
License: Unlimited
NeedsCompilation: no
Packaged: 2018-08-12 06:15:34 UTC; Noh
Repository: CRAN
Date/Publication: 2018-08-13 10:50:02 UTC

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New package ammistability with initial version 0.1.0
Package: ammistability
Type: Package
Title: Additive Main Effects and Multiplicative Interaction Model Stability Parameters
Version: 0.1.0
Authors@R: c( person(given = c("B.", "C."), family = "Ajay", email = "ajaygpb@yahoo.co.in", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7222-8483")), person(given = "J.", family = "Aravind", email = "j.aravind@icar.gov.in", role = c("aut"), comment = c(ORCID = "0000-0002-4791-442X")), person(given = "R.", family = c("Abdul Fiyaz"), email = "fiyaz.ra@icar.gov.in", role = "aut"), person("ICAR", role = c("cph"), comment = c(url = "https://www.icar.org.in")))
Description: Computes various stability parameters from Additive Main Effects and Multiplicative Interaction (AMMI) analysis results such as Modified AMMI Stability Value (MASV), Sums of the Absolute Value of the Interaction Principal Component Scores (SIPC), Sum Across Environments of Genotype-Environment Interaction Modelled by AMMI (AMGE), Sum Across Environments of Absolute Value of Genotype-Environment Interaction Modelled by AMMI (AV_(AMGE)), AMMI Stability Index (ASI), Modified ASI (MASI), AMMI Based Stability Parameter (ASTAB), Annicchiarico's D Parameter (DA), Zhang's D Parameter (DZ), Averages of the Squared Eigenvector Values (EV), Stability Measure Based on Fitted AMMI Model (FA), Absolute Value of the Relative Contribution of IPCs to the Interaction (Za). Further calculates the Simultaneous Selection Index for Yield and Stability from the computed stability parameters. See the vignette for complete list of citations for the methods implemented.
Copyright: 2017-2018, ICAR-DGR
License: GPL-2 | GPL-3
Encoding: UTF-8
Depends: R (>= 3.0.1)
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Imports: agricolae, ggcorrplot, ggplot2, methods, reshape2, stats, Rdpack
Suggests: knitr, rmarkdown, pander
RdMacros: Rdpack
URL: http://github.com/ajaygpb/ammistability https://ajaygpb.github.io/ammistability
BugReports: http://github.com/ajaygpb/ammistability/issues
NeedsCompilation: no
Packaged: 2018-08-09 15:42:17 UTC; J. Aravind
Author: B. C. Ajay [aut, cre] (<https://orcid.org/0000-0001-7222-8483>), J. Aravind [aut] (<https://orcid.org/0000-0002-4791-442X>), R. Abdul Fiyaz [aut], ICAR [cph] (https://www.icar.org.in)
Maintainer: B. C. Ajay <ajaygpb@yahoo.co.in>
Repository: CRAN
Date/Publication: 2018-08-13 09:20:03 UTC

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New package SCPME with initial version 1.0
Package: SCPME
Type: Package
Title: Shrinking Characteristics of Precision Matrix Estimators
Version: 1.0
Date: 2018-08-09
Authors@R: person("Matt", "Galloway", email = "gall0441@umn.edu", role = c("aut", "cre"))
Description: Estimates a penalized precision matrix via an augmented ADMM algorithm. This package is an implementation of the methods described in "Shrinking Characteristics of Precision Matrix Estimators" by Aaron J. Molstad, PhD and Adam J. Rothman, PhD. The manuscript can be found here: <doi:10.1093/biomet/asy023> .
URL: https://github.com/MGallow/SCPME
BugReports: https://github.com/MGallow/SCPME/issues
License: GPL (>= 2)
ByteCompile: TRUE
NeedsCompilation: yes
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: stats, parallel, foreach, ggplot2, dplyr
Depends: Rcpp (>= 0.12.10), RcppProgress (>= 0.1), doParallel
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: testthat, knitr, rmarkdown, microbenchmark, glasso, pkgdown
SystemRequirements: GNU make
VignetteBuilder: knitr
Packaged: 2018-08-09 12:27:47 UTC; Matt
Author: Matt Galloway [aut, cre]
Maintainer: Matt Galloway <gall0441@umn.edu>
Repository: CRAN
Date/Publication: 2018-08-13 09:00:09 UTC

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Sat, 11 Aug 2018

New package CalibratR with initial version 0.1.0
Package: CalibratR
Type: Package
Title: Mapping ML Scores to Calibrated Predictions
Version: 0.1.0
Author: Johanna Schwarz
Maintainer: Johanna Schwarz <Schwar4m@students.uni-marburg.de>
Description: Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0).
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10.0)
Imports: ggplot2, pROC, reshape2, parallel, foreach, utils, stats, fitdistrplus, doParallel
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-08 22:52:08 UTC; Johanna
Repository: CRAN
Date/Publication: 2018-08-11 22:10:03 UTC

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New package psychReport with initial version 0.1
Package: psychReport
Type: Package
Title: Reproducible Reports in Psychology
Version: 0.1
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Sweave'/'Knitr' 'Latex' integration within *.Rnw files.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: cli, crayon, dplyr, ez, reshape2, testthat, xtable
Depends: R(>= 2.10)
NeedsCompilation: no
Packaged: 2018-08-09 06:03:20 UTC; ian
Repository: CRAN
Date/Publication: 2018-08-11 21:20:03 UTC

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New package landscapemetrics with initial version 0.1.0
Type: Package
Package: landscapemetrics
Title: Landscape Metrics for Categorical Map Patterns
Version: 0.1.0
Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "maximilian.hesselbarth@uni-goettingen.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")), person("Marco", "Sciaini", email = "sciaini.marco@gmail.com", role = "aut", comment = c(ORCID = '0000-0002-3042-5435')), person("Jakub", "Nowosad", role = "aut", email = "nowosad.jakub@gmail.com", comment = c(ORCID = "0000-0002-1057-3721")), person("Laura J.", "Graham", role = "ctb", comment = c(ORCID = "0000-0002-1057-3721")), person("Kimberly A.", "With", role = "ctb", comment = c(ORCID = "0000-0001-5570-1515")), person("Jeffrey", "Hollister", role = "ctb", comment = c(ORCID = "0000-0002-3611-7281")), person("Jeremy", "VanDerWal", role = "ctb", comment = "Original author of underlying C code for get_patches() function"), person("Florian", "Privé", role = "ctb", comment = "Original author of underlying C++ code for get_nearestneighbour() function"))
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
License: GPL-3
URL: https://r-spatialecology.github.io/landscapemetrics/
BugReports: https://github.com/r-spatialecology/landscapemetrics/issues
Depends: R (>= 3.1)
Imports: dplyr, ggplot2, magrittr, purrr, raster, Rcpp, tibble
Suggests: covr, testthat, knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
ByteCompile: true
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
SystemRequirements: C++11
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-08-09 07:31:37 UTC; Maximilian
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Laura J. Graham [ctb] (<https://orcid.org/0000-0002-1057-3721>), Kimberly A. With [ctb] (<https://orcid.org/0000-0001-5570-1515>), Jeffrey Hollister [ctb] (<https://orcid.org/0000-0002-3611-7281>), Jeremy VanDerWal [ctb] (Original author of underlying C code for get_patches() function), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function)
Repository: CRAN
Date/Publication: 2018-08-11 22:00:03 UTC

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New package sdStaf with initial version 0.1.14
Package: sdStaf
Type: Package
Title: Species Distribution and Stability Future Models
Version: 0.1.14
Authors@R: c(person("P. Joser", "Atauchi", role = c("aut", "cre"), email = "patauchi@gmail.com"))
Maintainer: P. Joser Atauchi <patauchi@gmail.com>
Description: Functions for post processing the outcomes of ecological niche models. It further include methods to build stability maps based on species distribution models under climate change projections and to reduce environmental data.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: methods, stats, dplyr, ggplot2, R (>= 2.10)
Imports: sp, rgdal, rgeos, rasterVis, tidyr, raster, dismo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-08 17:32:07 UTC; p.joseratauchi
Author: P. Joser Atauchi [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-11 16:30:03 UTC

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New package rcites with initial version 0.1.0
Package: rcites
Type: Package
Title: R Interface to the Species+ Database
Version: 0.1.0
Date: 2018-07-23
Authors@R: c(person("Jonas", "Geschke", role = c("aut"), email = "jonas.e.geschke@gmail.com", comment = c(ORCID = "0000-0002-5654-9313")), person("Kevin", "Cazelles", role = c("aut", "cre"), email = "kevin.cazelles@gmail.com", comment = c(ORCID = "0000-0001-6619-9874")), person("Ignasi", "Bartomeus", role = c("aut"), comment = c(ORCID = "0000-0001-7893-4389")), person("Jonathan", "Goldenberg", role = c("ctb")), person("Marie-Bé", "Leduc", role = c("ctb")), person("Yasmine", "Verzelen", role = c("ctb")))
Description: A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
URL: https://ibartomeus.github.io/rcites/, https://github.com/ibartomeus/rcites
BugReports: https://github.com/ibartomeus/rcites/issues
License: MIT + file LICENSE
Depends: R (>= 3.1.0)
Imports: httr, jsonlite, data.table, methods
Encoding: UTF-8
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat, rworldmap
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 14:37:23 UTC; kevcaz
Author: Jonas Geschke [aut] (<https://orcid.org/0000-0002-5654-9313>), Kevin Cazelles [aut, cre] (<https://orcid.org/0000-0001-6619-9874>), Ignasi Bartomeus [aut] (<https://orcid.org/0000-0001-7893-4389>), Jonathan Goldenberg [ctb], Marie-Bé Leduc [ctb], Yasmine Verzelen [ctb]
Maintainer: Kevin Cazelles <kevin.cazelles@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-11 16:30:06 UTC

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New package modopt.matlab with initial version 1.0-1
Package: modopt.matlab
Type: Package
Title: 'MatLab'-Style Modeling of Optimization Problems
Version: 1.0-1
Date: 2018-08-11
Authors@R: c( person("Ronald", "Hochreiter", email = "ron@hochreiter.net", role = c("aut", "cre")))
Maintainer: Ronald Hochreiter <ron@hochreiter.net>
Description: 'MatLab'-Style Modeling of Optimization Problems with 'R'. This package provides a set of convenience functions to transform a 'MatLab'-style optimization modeling structure to its 'ROI' equivalent.
Depends: R (>= 3.4), ROI, ROI.plugin.glpk, ROI.plugin.quadprog
License: GPL-3
URL: http://www.finance-r.com/
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-11 15:56:09 UTC; ron
Author: Ronald Hochreiter [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-11 17:00:02 UTC

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New package fasterElasticNet with initial version 1.1.2
Package: fasterElasticNet
Type: Package
Title: An Amazing Fast Way to Fit Elastic Net
Version: 1.1.2
Date: 2018-08-01
Authors@R: c(person("Jingyi","Ma",email = "jingyima@163.com", role = c("aut")), person("Qiuhong","Lai",email = "lailaqiuhong@gmail.com", role = "ctb"), person("Linyu","Zuo",email = "zuozhe5959@gmail.com", role = c("ctb","cre")), person("Yi","Yang",email = "lucious.stat.y@gmail.com", role = "ctb"), person("Meng","Su",email = "SUmeng97@126.com", role = "ctb"), person("Zhen","Yu", email = "amy.yuzhen@foxmail.com", role = 'ctb'), person("Gege","Gao", email = "gaogege1995@163.com", role = 'ctb'), person("Xiao","Liu", email = "lucinecoco@163.com", role = 'ctb'), person("Xueni","Ruan", email = "ruanxueni96@163.com", role = 'ctb'), person("Xinyuan","Yang", email = "yangxinyuan100@126.com", role = 'ctb'), person("Yu","Bai", email = "yukisunflower@sina.com", role = 'ctb'), person("Zhijun","Liao", email = "econzhijun@163.com", role = 'ctb') )
Description: Fit Elastic Net, Lasso, and Ridge regression and do cross-validation in a fast way. We build the algorithm based on Least Angle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. (2004)(<doi:10.1214/009053604000000067 >) and some algorithms like Givens rotation and Forward/Back Substitution. In this way, many matrices to be computed are retained as triangular matrices which can eventually speed up the computation. The fitting algorithm for Elastic Net is written in C++ using Armadillo linear algebra library.
Depends: R (>= 3.1.0)
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.16)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
URL: https://github.com/CUFESAM/Elastic-Net
BugReports: https://github.com/CUFESAM/Elastic-Net/issues
NeedsCompilation: yes
Packaged: 2018-08-08 13:22:50 UTC; <e8><8b><8f><e8><90><8c>
Author: Jingyi Ma [aut], Qiuhong Lai [ctb], Linyu Zuo [ctb, cre], Yi Yang [ctb], Meng Su [ctb], Zhen Yu [ctb], Gege Gao [ctb], Xiao Liu [ctb], Xueni Ruan [ctb], Xinyuan Yang [ctb], Yu Bai [ctb], Zhijun Liao [ctb]
Maintainer: Linyu Zuo <zuozhe5959@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-11 16:30:10 UTC

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Fri, 10 Aug 2018

New package telefit with initial version 1.0.0
Package: telefit
Type: Package
Title: Estimation and Prediction for Remote Effects Spatial Process Models
Version: 1.0.0
Date: 2018-07-09
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@colostate.edu>
Description: Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <arXiv:1612.06303>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>.
License: GPL-3
Depends: R (>= 3.0.2)
Imports: abind, coda, cowplot, doRNG, dplyr, fields, itertools, mvtnorm, raster, scoringRules, stringr, foreach, ggplot2, gtable, reshape2, scales, sp, SDMTools
LinkingTo: Rcpp (>= 0.12.4), RcppArmadillo, RcppEigen (>= 0.3.3.3.1)
RoxygenNote: 6.0.1
Suggests: testthat
LazyData: true
SystemRequirements: A system with a recent-enough C++11 compiler (such as g++-4.8 or later).
NeedsCompilation: yes
Packaged: 2018-08-07 14:37:34 UTC; pointdex
Repository: CRAN
Date/Publication: 2018-08-10 16:30:02 UTC

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New package esDesign with initial version 1.0.0
Package: esDesign
Type: Package
Title: Adaptive Enrichment Designs with Sample Size Re-Estimation
Version: 1.0.0
Date: 2018-07-27
Author: Zhao Yang, Ruitao Lin, Guosheng Yin and Ying Yuan
Maintainer: Zhao Yang <yangz98@connect.hku.hk>
Description: Software of 'esDesign' is developed to implement the adaptive enrichment designs with sample size re-estimation. In details, three-proposed trial designs are provided, including the AED1-SSR (or ES1-SSR), AED2-SSR (or ES2-SSR) and AED3-SSR (or ES3-SSR). In addition, this package also contains several widely used adaptive designs, such as the Marker Sequential Test (MaST) design proposed Freidlin et al. (2014) <doi:10.1177/1740774513503739>, the adaptive enrichment designs without early stopping (AED or ES), the sample size re-estimation procedure (SSR) based on the conditional power proposed by Proschan and Hunsberger (1995) <doi:10.2307/2533262>, and some useful functions. In details, we can calculate the futility and/or efficacy stopping boundaries, the sample size required, calibrate the value of the threshold of the difference between subgroup-specific test statistics, conduct the simulation studies in AED, SSR, AED1-SSR, AED2-SSR and AED3-SSR.
Depends: R (>= 3.2.0)
Imports: stats
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-07 17:45:54 UTC; yangzhao
Repository: CRAN
Date/Publication: 2018-08-10 16:30:06 UTC

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Thu, 09 Aug 2018

New package hddtools with initial version 0.8.2
Package: hddtools
Title: Hydrological Data Discovery Tools
Version: 0.8.2
Authors@R: c(person(given = "Claudia", family = "Vitolo", role = c("aut", "cre"), email = "cvitolodev@gmail.com", comment = c(ORCID = "0000-0002-4252-1176")), person(given = "Wouter", family = "Buytaert", role = c("ctb"), comment = "This package was developed during Claudia's PhD at Imperial College London and Wouter was the PhD supervisor."), person(given = "Erin", family = "Le Dell", role = c("ctb"), comment = "Erin reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/73"), person(given = "Michael", family = "Sumner", role = c("ctb"), comment = "Michael reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/73"))
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
URL: http://ropensci.github.io/hddtools, https://github.com/ropensci/hddtools
BugReports: https://github.com/ropensci/hddtools/issues
Description: Facilitates discovery and handling of hydrological data, access to catalogues and databases.
Depends: R (>= 3.2.1), rgdal
Imports: zoo, sp, RCurl, XML, rnrfa, Hmisc, raster, stringr, gdata, tibble
Suggests: testthat, leaflet, rmarkdown, knitr, pkgdown
VignetteBuilder: knitr
License: GPL-3
Repository: CRAN
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-08-09 12:19:57 UTC; claudia
Author: Claudia Vitolo [aut, cre] (<https://orcid.org/0000-0002-4252-1176>), Wouter Buytaert [ctb] (This package was developed during Claudia's PhD at Imperial College London and Wouter was the PhD supervisor.), Erin Le Dell [ctb] (Erin reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/73), Michael Sumner [ctb] (Michael reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/73)
Date/Publication: 2018-08-09 21:40:03 UTC

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New package DesignLibrary with initial version 0.1.0
Package: DesignLibrary
Type: Package
Title: Library of Research Designs
Version: 0.1.0
Authors@R: c(person("Graeme", "Blair", email = "graeme.blair@ucla.edu", role = c("aut")), person("Jasper", "Cooper", email = "jjc2247@columbia.edu", role = c("aut", "cre")), person("Alexander", "Coppock", email = "alex.coppock@yale.edu", role = c("aut")), person("Macartan", "Humphreys", email = "macartan@gmail.com", role = c("aut")), person("Clara", "Bicalho", email = "clarabmcorreia@gmail.com", role = c("aut")), person("Neal", "Fultz", email = "nfultz@gmail.com", role = c("aut")), person("Lily", "Medina", email = "lilymiru@gmail.com", role = c("aut")))
Description: A simple interface to build designs using the using the package 'DeclareDesign'. In one line of code, users can specify the parameters of individual designs and diagnose their properties. The designers can also be used to compare performance of a given design across a range of combinations of parameters, such as effect size, sample size, and assignment probabilities.
URL: https://declaredesign.org/library/, https://github.com/DeclareDesign/DesignLibrary
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: DeclareDesign (>= 0.10.0), R (>= 3.4.0), randomizr (>= 0.16.1), fabricatr (>= 0.4.0), estimatr (>= 0.10.0)
Imports: devtools, rlang, methods
Suggests: knitr, testthat, systemfit, ggplot2, broom, rmarkdown
Enhances: Matching
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-05 21:05:19 UTC; jaspercooper
Author: Graeme Blair [aut], Jasper Cooper [aut, cre], Alexander Coppock [aut], Macartan Humphreys [aut], Clara Bicalho [aut], Neal Fultz [aut], Lily Medina [aut]
Maintainer: Jasper Cooper <jjc2247@columbia.edu>
Repository: CRAN
Date/Publication: 2018-08-09 10:50:04 UTC

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New package bioacoustics with initial version 0.1.4
Package: bioacoustics
Type: Package
Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Version: 0.1.4
Authors@R: c(person("Jean", "Marchal", email = "jean.marchal@wavx.ca", role = c("aut","cre")), person("Francois", "Fabianek", email = "francois.fabianek@wavx.ca", role = "aut"), person("Christopher", "Scott", role = "aut"), person("Chris", "Corben", role = c("ctb", "cph"), email = "chris@hoarybat.com", comment = "Read ZC files, original C code"), person("Peter", "Wilson", role = c("ctb", "cph"), email = "peter@peterwilson.id.au", comment = "Read ZC files, original R code"), person(family = "Wildlife Acoustics, Inc.", role = c("ctb", "cph"), comment = "Read WAC files, original C code"), person(family = "WavX Inc.", role = "cph"))
Maintainer: Jean Marchal <jean.marchal@wavx.ca>
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
License: GPL-3
Encoding: UTF-8
LazyData: true
SystemRequirements: C++11, cmake
Depends: R (>= 3.3.0)
LinkingTo: Rcpp
Imports: htmltools, graphics, grDevices, methods, moments, Rcpp (>= 0.12.13), stringr, tools, tuneR (>= 1.3.0)
Suggests: knitr, rmarkdown
URL: https://github.com/wavx/bioacoustics/
BugReports: https://github.com/wavx/bioacoustics/issues/
NeedsCompilation: yes
RoxygenNote: 6.1.0
VignetteBuilder: knitr
Biarch: TRUE
Packaged: 2018-08-08 08:44:34 UTC; JEMAR270
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, Inc. [ctb, cph] (Read WAC files, original C code), WavX Inc. [cph]
Repository: CRAN
Date/Publication: 2018-08-09 09:50:03 UTC

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Wed, 08 Aug 2018

New package hpiR with initial version 0.2.0
Package: hpiR
Type: Package
Title: House Price Indexes
Version: 0.2.0
Authors@R: c(person("Andy", "Krause", role=c("aut", "cre"), email = "andyxkrause@gmail.com"))
Maintainer: Andy Krause <andyxkrause@gmail.com>
Description: Compute house price indexes and series using a variety of different methods and models common through the real estate literature. Evaluate index 'goodness' based on accuracy, volatility and revision statistics. Background on basic model construction for repeat sales models can be found at: Case and Quigley (1991) <doi:10.2307/2109686> and for hedonic pricing models at: Bourassa et al (2006) <doi:10.1016/j.jhe.2006.03.001>.
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, magrittr, lubridate, robustbase, ggplot2, imputeTS, purrr, forecast, caret, gridExtra, knitr, MASS, rlang, plyr, zoo
URL: https://www.github.com/andykrause/hpiR
RoxygenNote: 6.0.1
Suggests: markdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-05 19:18:32 UTC; andyx
Author: Andy Krause [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-08 16:40:03 UTC

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Tue, 07 Aug 2018

New package scBio with initial version 0.1.0
Package: scBio
Type: Package
Title: Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data
Version: 0.1.0
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
biocViews: limma
Depends: R (>= 2.10)
Imports: sp, foreach, parallel, doSNOW, raster, fields, LiblineaR, limma
NeedsCompilation: no
Packaged: 2018-08-02 18:32:24 UTC; IritGNB5
Repository: CRAN
Date/Publication: 2018-08-07 19:40:06 UTC

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New package Mqrcm with initial version 1.0
Package: Mqrcm
Type: Package
Title: M-Quantile Regression Coefficients Modeling
Version: 1.0
Date: 2018-08-02
Author: Paolo Frumento <paolo.frumento@ki.se>
Maintainer: Paolo Frumento <paolo.frumento@ki.se>
Description: Parametric modeling of M-quantile regression coefficient functions.
Imports: stats, utils, graphics, Hmisc
Depends: pch (>= 1.3)
License: GPL-2
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-02 18:22:32 UTC; paofru
Repository: CRAN
Date/Publication: 2018-08-07 19:30:03 UTC

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New package STMotif with initial version 0.1.0
Package: STMotif
Type: Package
Title: Discovery of Motifs in Spatial-Time Series
Version: 0.1.0
Authors@R: c( person("Amin", "Bazaz", email = "stmotif@eic.cefet-rj.br", role = c("aut", "cre")), person("Heraldo", "Heraldo", role = c("aut")), person("Eduardo", "Ogasawara", role = c("aut")))
Maintainer: Amin Bazaz <stmotif@eic.cefet-rj.br>
Description: Discovery of motifs in a dataset containing numeric values. A motif is a previously unknown subsequence of a time series with relevant number of occurrences. To discover motifs the Combined Series Approach [CSA] is used.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Imports: foreach, stats, ggplot2, reshape2, scales, grDevices, shiny
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-06 21:42:12 UTC; gpca
Author: Amin Bazaz [aut, cre], Heraldo Heraldo [aut], Eduardo Ogasawara [aut]
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-08-07 18:50:03 UTC

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New package Rspotify with initial version 0.1.0
Package: Rspotify
Type: Package
Title: Access to Spotify API
Version: 0.1.0
Author: Tiago Mendes Dantas
Maintainer: Tiago Mendes Dantas <t.mendesdantas@gmail.com>
Description: Provides an interface to the Spotify API <https://developer.spotify.com/documentation/web-api/>.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: dplyr, plyr, httr, jsonlite, magrittr
NeedsCompilation: no
Packaged: 2018-08-06 20:50:11 UTC; tiagomendedantas
Repository: CRAN
Date/Publication: 2018-08-07 18:50:06 UTC

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Mon, 06 Aug 2018

New package nseval with initial version 0.4
Package: nseval
Type: Package
Title: A Clean API for Lazy and Non-Standard Evaluation
Version: 0.4
Date: 2018-08-01
Author: Peter Meilstrup <peter.meilstrup@gmail.com>
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>
Description: Facilities to capture, inspect, manipulate, and create lazy values (promises), "..." lists, and active calls.
License: GPL (>= 2.0)
Depends:
Suggests: testthat (>= 2.0.0), compiler (>= 3.4), roxygen2 (>= 2.2.2), knitr (>= 1.2), plyr (>= 1.8.1), ggplot2(>= 1.0.1), lazyeval(>= 0.2.0), stringr(>= 1.2.0)
Collate: 'arg.R' 'caller.R' 'quo.R' 'dots.R' 'getpromise.R' 'conversions.R' 'format.R' 'force.R' 'shortcut.R' 'missing.R'
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-08-04 04:44:57 UTC; peter
Repository: CRAN
Date/Publication: 2018-08-06 17:10:02 UTC

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New package nsapi with initial version 0.1.0
Package: nsapi
Version: 0.1.0
Title: Connect to the NS (Dutch Railways) API
Description: Access the NS api and download current departure times, disruptions and engineering work, the station list, and travel recommendations from station to station. All results will be returned as a 'data.frame'. NS (Nederlandse Spoorwegen; Dutch Railways) is the largest train travel provider in the Netherlands. for more information about the API itself see <https://www.ns.nl/en/travel-information/ns-api>. To use the API, and this package, you will need to obtain a username and password. More information about authentication and the use of the functions are described in the vignette.
Authors@R: person("Roel M.", "Hogervorst", email ="hogervorst.rm@gmail.com", role = c("cre", "aut"), comment = c(ORCID = "0000-0001-7509-0328"))
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
URL: https://github.com/RMHogervorst/nsapi , https://rmhogervorst.nl/nsapi/
BugReports: https://github.com/RMHogervorst/nsapi/issues
RoxygenNote: 6.1.0
Suggests: testthat, knitr, rmarkdown
Imports: crul, xml2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-04 08:41:01 UTC; roel
Author: Roel M. Hogervorst [cre, aut] (<https://orcid.org/0000-0001-7509-0328>)
Maintainer: Roel M. Hogervorst <hogervorst.rm@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-06 17:10:06 UTC

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New package LadR with initial version 1.0.4
Package: LadR
Type: Package
Title: Routines for Fit, Inference and Diagnostics in LAD Models
Version: 1.0.4
Author: Kévin Allan Sales Rodrigues <kevin.asr@outlook.com>
Maintainer: Kevin Allan Sales Rodrigues <kevin.asr@outlook.com>
Description: LAD (Least Absolute Deviations) estimation for linear regression, confidence intervals, tests of hypotheses, methods for outliers detection, measures of leverage, methods of diagnostics for LAD regression, special diagnostics graphs and measures of leverage. The algorithms are based in Dielman (2005) <doi:10.1080/0094965042000223680>, Elian et al. (2000) <doi:10.1080/03610920008832518> and Dodge (1997) <doi:10.1006/jmva.1997.1666>. This package also has two datasets "houses" and "pollution", respectively, from Narula and Wellington (1977) <doi:10.2307/1268628> and Santos et al. (2016) <doi:10.1371/journal.pone.0163225>.
License: GPL (>= 3.0)
Depends: R (>= 3.4.0)
Encoding: UTF-8
LazyData: true
Imports: stats, grDevices, graphics, L1pack
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-08-02 23:36:38 UTC; kevinx
Repository: CRAN
Date/Publication: 2018-08-06 17:20:03 UTC

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New package exiftoolr with initial version 0.1.0
Package: exiftoolr
Type: Package
Title: ExifTool Functionality from R
Version: 0.1.0
Date: 2018-08-02
Authors@R: c(person("Joshua", "O'Brien", role = c("aut", "cre"), email = "joshmobrien@gmail.com"), person("Phil", "Harvey", role = "aut"))
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Description: Reads, writes, and edits EXIF and other file metadata using ExifTool <http://www.sno.phy.queensu.ca/~phil/exiftool/>, returning read results as a data frame. ExifTool supports many different metadata formats including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP and ID3, as well as the maker notes of many digital cameras by Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo, Sigma/Foveon and Sony.
License: GPL-2
URL: https://github.com/JoshOBrien/exiftoolr#readme
BugReports: https://github.com/JoshOBrien/exiftoolr/issues
SystemRequirements: Perl
LazyData: TRUE
Imports: curl, jsonlite
Encoding: UTF-8
Language: en-US
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-03 19:03:25 UTC; Josh
Author: Joshua O'Brien [aut, cre], Phil Harvey [aut]
Repository: CRAN
Date/Publication: 2018-08-06 15:40:02 UTC

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New package daarem with initial version 0.2
Package: daarem
Type: Package
Title: Damped Anderson Acceleration with Epsilon Monotonicity for Accelerating EM-Like Monotone Algorithms
Version: 0.2
Date: 2018-7-25
Authors@R: c(person("Nicholas", "Henderson", email = "nhender5@jhmi.edu", role = "cre"), person("Ravi", "Varadhan", email = "ravi.varadhan@jhu.edu", role = "aut"))
Maintainer: Nicholas Henderson <nhender5@jhmi.edu>
Imports: stats, utils
Description: Implements the DAAREM method for accelerating the convergence of slow, monotone sequences from smooth, fixed-point iterations such as the EM algorithm. For further details about the DAAREM method. see Henderson, N.C. and Varadhan, R. (2018) <arXiv:1803.06673>.
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-08-03 18:07:22 UTC; nhenders
Author: Nicholas Henderson [cre], Ravi Varadhan [aut]
Repository: CRAN
Date/Publication: 2018-08-06 15:40:05 UTC

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New package TDA with initial version 1.6.4
Package: TDA
Type: Package
Title: Statistical Tools for Topological Data Analysis
Version: 1.6.4
Date: 2018-08-05
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, David L. Millman, Vincent Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan Reininghaus.
Maintainer: Jisu Kim <jisuk1@andrew.cmu.edu>
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries 'GUDHI' <http://gudhi.gforge.inria.fr/>, 'Dionysus' <http://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.
Depends: R (>= 3.1.0)
Repository: CRAN
License: GPL-3
Imports: FNN, Rcpp (>= 0.11.0), igraph, parallel, scales
Suggests: testthat, lintr
Encoding: UTF-8
LinkingTo: BH (>= 1.60.0-2), Rcpp, RcppEigen
SystemRequirements: C++11, gmp
NeedsCompilation: yes
Packaged: 2018-08-06 00:09:09 UTC; Owner
Date/Publication: 2018-08-06 07:00:01 UTC

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New package PhySortR with initial version 1.0.8
Package: PhySortR
Type: Package
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Version: 1.0.8
Date: 2018-07-20
Authors@R: c(person("Timothy", "Stephens", email = "timothy.stephens1@uqconnect.edu.au", role = c("aut", "cre", "trl"), comment = "R port"), person("Debashish", "Bhattacharya", email = "Bhattacharya@AESOP.Rutgers.edu", role = c("aut")), person("Mark", "Ragan", email = "m.ragan@imb.uq.edu.au", role = c("aut")), person("Cheong Xin", "Chan", email = "c.chan1@uq.edu.au", role = c("aut", "cph"), comment = "Original Perl implementation"))
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non- Exclusive clades that includes a defined portion of non-target taxa.
Depends: R (>= 3.0.0)
Imports: phytools, ape
Repository: CRAN
LazyData: true
License: GPL (>= 3)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-20 00:23:12 UTC; timothy.stephens
Author: Timothy Stephens [aut, cre, trl] (R port), Debashish Bhattacharya [aut], Mark Ragan [aut], Cheong Xin Chan [aut, cph] (Original Perl implementation)
Date/Publication: 2018-08-06 07:00:08 UTC

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Sun, 05 Aug 2018

New package tidytransit with initial version 0.2.3
Package: tidytransit
Type: Package
Title: Read, Validate, Analyze, and Map Files in the General Transit Feed Specification
Version: 0.2.3
Authors@R: c( person("Tom", "Buckley", role = c("aut", "cre"), email = "tom@tbuckl.com"), person("Danton", "Noriega-Goodwin", role = c("cph"), email = "danton.noriega@gmail.com"), person("Elaine", "McVey", role = c("cph"), email = "elaine.mcvey@transloc.com"), person("Charles Hans", "Thompson", role = c("cph"), email = "hans.thompson1@gmail.com"), person("Michael", "Sumner", role = c("cph")) )
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
License: GPL
LazyData: TRUE
Depends: R (>= 3.2.4)
Imports: dplyr, tibble, readr, httr, htmltools, magrittr, stringr, assertthat, scales, here, rlang, sf, lubridate, tidyr
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
URL: https://github.com/r-transit/tidytransit
BugReports: https://github.com/r-transit/tidytransit
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-05 16:18:07 UTC; tbuck
Author: Tom Buckley [aut, cre], Danton Noriega-Goodwin [cph], Elaine McVey [cph], Charles Hans Thompson [cph], Michael Sumner [cph]
Maintainer: Tom Buckley <tom@tbuckl.com>
Repository: CRAN
Date/Publication: 2018-08-05 18:10:03 UTC

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New package survsup with initial version 0.0.1
Package: survsup
Title: Plotting Survival Curves with Numbers at Risk Table
Version: 0.0.1
Authors@R: person("Daniel", "Lindholm", email = "daniel.lindholm@me.com", role = c("aut", "cre"))
Description: Implements functions to plot survival curves. Provides the capability to add numbers at risk tables, and allows for using the pipe operator to create more complex plots.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
URL: http://github.com/dlindholm/survsup
BugReports: http://github.com/dlindholm/survsup/issues
LazyData: true
Imports: stats, utils, survival, dplyr, ggplot2, broom, colorspace, gridExtra
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-04 15:23:02 UTC; dl
Author: Daniel Lindholm [aut, cre]
Maintainer: Daniel Lindholm <daniel.lindholm@me.com>
Repository: CRAN
Date/Publication: 2018-08-05 18:30:03 UTC

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New package PELVIS with initial version 1.0.4
Package: PELVIS
Type: Package
Title: Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae
Version: 1.0.4
Date: 2018-08-03
Author: Frédéric Santos
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Depends: R (>= 3.4.0), shiny
Imports: MASS
Description: An R-Shiny application implementing two methods for sexing the human os coxae based on eleven trichotomic traits, following Bruzek (2002) <doi:10.1002/ajpa.10012>.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-08-03 09:12:59 UTC; f.santos
Repository: CRAN
Date/Publication: 2018-08-05 18:20:13 UTC

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New package localIV with initial version 0.1.0
Package: localIV
Type: Package
Title: Estimation of Marginal Treatment Effects using Local Instrumental Variables
Version: 0.1.0
Authors@R: person("Xiang", "Zhou", email = "xiang_zhou@fas.harvard.edu", role = c("aut", "cre"))
Description: In the generalized Roy model, the marginal treatment effect (MTE) can be used as a building block for constructing conventional causal parameters such as the average treatment effect (ATE) and the average treatment effect on the treated (ATT) (Heckman, Urzua, and Vytlacil 2006 <doi:10.1162/rest.88.3.389>). Given a treatment selection model and an outcome model, the function mte() estimates the MTE via local instrumental variables (or via a normal selection model) and also the projection of MTE onto the 2-dimensional space of the propensity score and a latent variable representing unobserved resistance to treatment (Zhou and Xie 2018 <https://scholar.harvard.edu/files/xzhou/files/zhou-xie_mte2.pdf>). The object returned by mte() can be used to estimate conventional parameters such as ATE and ATT (via average()) or marginal policy-relevant treatment effects (via mprte()).
Depends: R (>= 3.3.0)
Imports: KernSmooth (>= 2.5.0), mgcv (>= 1.8-19), sampleSelection (>= 1.2-0), stats
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
URL: https://github.com/xiangzhou09/localIV
BugReports: https://github.com/xiangzhou09/localIV
NeedsCompilation: no
Packaged: 2018-08-04 21:32:33 UTC; Xiang
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2018-08-05 18:20:03 UTC

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New package BMSC with initial version 0.1
Package: BMSC
Title: Bayesian Model Selection under Constraints
Version: 0.1
Authors@R: c( person("Marcus", "Groß", email = "marcus.gross@inwt-statistics.de", role = c("aut", "cre")), person("Ricardo", "Fernandes", email = "ldv1452@gmail.com", role = c("aut")), person("Mira Celine", "Klein", email = "mira.klein@inwt-statistics.de", role = c("ctb")) )
Description: A Bayesian regression package supporting constrained coefficient estimation and variable selection using Stan. This includes a robust variable selection algorithm by a horseshoe prior (<doi:10.1093/biomet/asq017>) that finds the optimal model considering main effects, interactions as well as powers of given variables under potential parameter constraints.
Depends: R (>= 3.4.0), Rcpp (>= 0.12.0)
Imports: dplyr (>= 0.7.4), ggplot2 (>= 2.2.1), loo (>= 2.0.0), methods (>= 3.4.4), rstan (>= 2.17.3), rstantools (>= 1.5.0), R.utils (>= 2.6.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: StanHeaders (>= 2.17.1), rstan (>= 2.17.2), BH (>= 1.65.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0)
Suggests: lintr, testthat
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-08-03 09:19:19 UTC; mgross
Author: Marcus Groß [aut, cre], Ricardo Fernandes [aut], Mira Celine Klein [ctb]
Maintainer: Marcus Groß <marcus.gross@inwt-statistics.de>
Repository: CRAN
Date/Publication: 2018-08-05 18:20:16 UTC

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New package behaviorchange with initial version 0.0.1
Package: behaviorchange
Type: Package
Title: Tools for Behavior Change Researchers and Professionals
Version: 0.0.1
Date: 2018-08-06
Authors@R: c(person("Gjalt-Jorn", "Peters", email = "gjalt-jorn@a-bc.eu", role = c("aut", "cre", "ctb")))
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@a-bc.eu>
License: GPL (>= 3)
Description: Contains specialised analyses and visualisation tools for behavior change science. These facilitate conducting determinant studies (for example, using confidence interval-based estimation of relevance, CIBER, or CIBERlite plots) and systematically developing, reporting, and analysing interventions (for example, using acyclic behavior change diagrams). This package is especially useful for researchers in the field of behavior change or health psychology and to behavior change professionals such as intervention developers and prevention workers.
URL: https://a-bc.eu
BugReports: https://github.com/academy-of-behavior-change/behaviorchange/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 3.0.0)
Imports: data.tree (>= 0.7.5), DiagrammeR (>= 1.0.0), ggplot2 (>= 2.2.1), googlesheets (>= 0.3.0), gridExtra (>= 2.3), gtable (>= 0.2.0), magrittr (>= 0.1.5), ufs (>= 0.0.1), userfriendlyscience (>= 0.7.1), viridis (>= 0.5.1)
NeedsCompilation: no
Packaged: 2018-08-04 13:40:34 UTC; micro
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Repository: CRAN
Date/Publication: 2018-08-05 18:20:10 UTC

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New package nbc4va with initial version 1.1
Package: nbc4va
Type: Package
Title: Bayes Classifier for Verbal Autopsy Data
Version: 1.1
Date: 2018-08-03
Authors@R: c( person(given = "Richard", family = "Wen", email = "rrwen.dev@gmail.com", role = c("aut", "cre")), person(given = "Pierre", family = "Miasnikof", role = "ctb"), person(given = "Vasily", family = "Giannakeas", role = "ctb"), person(given = "Mireille", family = "Gomes", role = "ctb"))
Maintainer: Richard Wen <rrwen.dev@gmail.com>
Description: An implementation of the Naive Bayes Classifier (NBC) algorithm used for Verbal Autopsy (VA) built on code from Miasnikof et al (2015) <DOI:10.1186/s12916-015-0521-2>.
Depends: R (>= 3.0.0)
Imports: graphics, methods, utils
Suggests: bookdown, knitr, rmarkdown, shiny, testthat
Enhances: openVA
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Collate: 'nbc4va.R' 'nbc4va_data.R' 'nbc4va_validation.R' 'nbc4va_internal.R' 'nbc4va_main.R' 'nbc4va_extra.R' 'nbc4va_utility.R' 'nbc4va_wrapper.R'
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-03 17:10:48 UTC; Rich
Author: Richard Wen [aut, cre], Pierre Miasnikof [ctb], Vasily Giannakeas [ctb], Mireille Gomes [ctb]
Repository: CRAN
Date/Publication: 2018-08-05 16:40:03 UTC

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New package TDAstats with initial version 0.3.0
Package: TDAstats
Type: Package
Title: Pipeline for Topological Data Analysis
Version: 0.3.0
Authors@R: c( person("Raoul", "Wadhwa", email = "raoulwadhwa@gmail.com", role = c("aut", "cre")), person("Andrew", "Dhawan", role = "aut"), person("Drew", "Williamson", role = "aut"), person("Jacob", "Scott", role = "aut"))
Description: A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4)
Imports: ggplot2 (>= 2.2.1), Rcpp (>= 0.12.15)
URL: https://github.com/rrrlw/TDAstats
BugReports: https://github.com/rrrlw/TDAstats/issues
LinkingTo: Rcpp
RoxygenNote: 6.0.1
SystemRequirements: C++11
Suggests: testthat (>= 2.0.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-08-05 03:12:01 UTC; rrrlw
Author: Raoul Wadhwa [aut, cre], Andrew Dhawan [aut], Drew Williamson [aut], Jacob Scott [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-05 05:50:03 UTC

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Fri, 03 Aug 2018

New package RobExtremes with initial version 1.1.0
Package: RobExtremes
Version: 1.1.0
Date: 2018-08-03
Title: Optimally Robust Estimation for Extreme Value Distributions
Description: Optimally robust estimation for extreme value distributions using S4 classes and methods (based on packages 'distr', 'distrEx', 'distrMod', 'RobAStBase', and 'ROptEst').
Depends: R (>= 2.14.0), methods, distrMod(>= 2.7.0), ROptEst(>= 1.1.0), robustbase, evd
Suggests: RUnit (>= 0.4.26), ismev (>= 1.39)
Imports: RobAStRDA, distr, distrEx, RandVar, RobAStBase, startupmsg, actuar
Authors@R: c(person("Nataliya", "Horbenko", role=c("aut","cph")), person("Bernhard", "Spangl", role="ctb", comment="contributed smoothed grid values of the Lagrange multipliers"), person("Sascha", "Desmettre", role="ctb", comment="contributed smoothed grid values of the Lagrange multipliers"), person("Eugen", "Massini", role="ctb", comment="contributed an interactive smoothing routine for smoothing the Lagrange multipliers and smoothed grid values of the Lagrange multipliers"), person("Daria", "Pupashenko", role="ctb", comment="contributed MDE-estimation for GEV distribution in the framework of her PhD thesis 2011--14"), person("Gerald", "Kroisandt", role="ctb", comment="contributed testing routines"), person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "aut", "cph"), email="peter.ruckdeschel@uni-oldenburg.de"))
ByteCompile: yes
LazyLoad: yes
License: LGPL-3
Encoding: latin1
URL: http://robast.r-forge.r-project.org/
LastChangedDate: {$LastChangedDate: 2018-08-03 11:00:05 +0200 (Fr, 03 Aug 2018) $}
LastChangedRevision: {$LastChangedRevision: 1092 $}
VCS/SVNRevision: 1091
NeedsCompilation: yes
Packaged: 2018-08-03 14:41:31 UTC; ruckdesc
Author: Nataliya Horbenko [aut, cph], Bernhard Spangl [ctb] (contributed smoothed grid values of the Lagrange multipliers), Sascha Desmettre [ctb] (contributed smoothed grid values of the Lagrange multipliers), Eugen Massini [ctb] (contributed an interactive smoothing routine for smoothing the Lagrange multipliers and smoothed grid values of the Lagrange multipliers), Daria Pupashenko [ctb] (contributed MDE-estimation for GEV distribution in the framework of her PhD thesis 2011--14), Gerald Kroisandt [ctb] (contributed testing routines), Matthias Kohl [aut, cph], Peter Ruckdeschel [cre, aut, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Repository: CRAN
Date/Publication: 2018-08-03 16:50:21 UTC

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New package rare with initial version 0.1.1
Package: rare
Type: Package
Title: Linear Model with Tree-Based Lasso Regularization for Rare Features
Version: 0.1.1
Author: Xiaohan Yan [aut, cre], Jacob Bien [aut, cre]
Maintainer: Xiaohan Yan <xy257@cornell.edu>
Description: Implementation of an alternating direction method of multipliers algorithm for fitting a linear model with tree-based lasso regularization, which is proposed in Algorithm 1 of Yan and Bien (2018) <arXiv:1803.06675>. The package allows efficient model fitting on the entire 2-dimensional regularization path for large datasets. The complete set of functions also makes the entire process of tuning regularization parameters and visualizing results hassle-free.
Depends: R (>= 3.2.1)
Imports: Matrix, glmnet, Rcpp
Suggests: knitr, dendextend, rmarkdown
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.0
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/yanxht/rare
BugReports: https://github.com/yanxht/rare/issues
NeedsCompilation: yes
Packaged: 2018-08-03 14:45:47 UTC; xy257
Repository: CRAN
Date/Publication: 2018-08-03 16:50:09 UTC

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Thu, 02 Aug 2018

New package pcgen with initial version 0.1.0.0
Package: pcgen
Type: Package
Title: Reconstruction of Causal Networks for Data with Random Genetic Effects
Version: 0.1.0.0
Author: Willem Kruijer, Pariya Behrouzi, Maria Xose Rodriguez-Alvarez
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Depends: R (>= 3.1.0)
Imports: pcalg, graph, Matrix, stats, MASS, utils, Hmisc, methods, lme4, sommer, ggm
Description: Implements the pcgen algorithm, which is a modified version of the standard pc-algorithm, with specific conditional independence tests and modified orientation rules.
License: GPL-3
Date: 2018-08-01
NeedsCompilation: no
Packaged: 2018-08-01 14:39:27 UTC; behro001
Repository: CRAN
Date/Publication: 2018-08-02 21:20:03 UTC

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New package ufs with initial version 0.0.1
Package: ufs
Type: Package
Title: Quantitative Analysis Made Accessible
Version: 0.0.1
Date: 2018-08-01
Authors@R: c(person("Gjalt-Jorn", "Peters", email = "gjalt-jorn@userfriendlyscience.com", role = c("aut", "cre", "ctb")))
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
License: GPL (>= 3)
Description: This is a new version of the 'userfriendlyscience' package, which has grown a bit unwieldy. This first submission contains a number of basic functions to easily format values, work with scales, and format vectors in a single character value. Over time, more functions presently in 'userfriendlyscience' will be migrated over to this package.
URL: https://userfriendlyscience.com
BugReports: https://github.com/matherion/userfriendlyscience/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-02 14:45:04 UTC; micro
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Repository: CRAN
Date/Publication: 2018-08-02 15:30:03 UTC

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New package rolocISCCNBS with initial version 0.1
Package: rolocISCCNBS
Type: Package
Title: A Colour List and Colour Metric Based on the ISCC-NBS System of Color Designation
Version: 0.1
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Description: A colour list and colour metric based on the ISCC-NBS System of Color Designation for use with the 'roloc' package for converting colour specifications to colour names.
License: GPL-2 | GPL-3
Depends: roloc
Imports: methods, colorspace
NeedsCompilation: no
Packaged: 2018-07-30 21:15:35 UTC; pmur002
Repository: CRAN
Date/Publication: 2018-08-02 15:30:06 UTC

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New package polyRAD with initial version 0.5-0
Package: polyRAD
Version: 0.5-0
Date: 2018-07-31
Title: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Authors@R: c(person("Lindsay V.", "Clark", email = "lvclark@illinois.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3881-9252")), person("U.S. National Science Foundation", role = "fnd"))
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>), U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Imports: fastmatch, pcaMethods, methods, Rcpp
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures
LinkingTo: Rcpp
VignetteBuilder: knitr, rmarkdown
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2018) <doi:10.1101/380899>.
License: GPL (>= 2)
URL: https://github.com/lvclark/polyRAD
NeedsCompilation: yes
Packaged: 2018-08-02 14:21:52 UTC; lvclark
Repository: CRAN
Date/Publication: 2018-08-02 15:30:10 UTC

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New package tidybayes with initial version 1.0.1
Package: tidybayes
Title: Tidy Data and 'Geoms' for Bayesian Models
Version: 1.0.1
Date: 2018-07-30
Authors@R: c(person("Matthew", "Kay", role = c("aut", "cre"), email = "mjskay@umich.edu"))
Maintainer: Matthew Kay <mjskay@umich.edu>
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Depends: R (>= 2.10)
Imports: plyr, dplyr, tidyr, ggplot2 (>= 3.0.0), stringi, stringr, LaplacesDemon, coda, purrr (>= 0.2.3), tibble, MASS, rlang, ggstance, ggridges, grid, forcats, HDInterval, arrayhelpers, tidyselect, magrittr
Suggests: knitr, import, testthat, vdiffr, rstan (>= 2.17.0), runjags, rjags, jagsUI, rstanarm (>= 2.17.2), rstantools, emmeans, broom (>= 0.4.3), dotwhisker, MCMCglmm, bayesplot, modelr, brms (>= 2.4.0), cowplot, covr, gdtools, rmarkdown, bindrcpp
License: GPL (>= 3)
Language: en-US
BugReports: https://github.com/mjskay/tidybayes/issues/new
URL: http://mjskay.github.io/tidybayes, https://github.com/mjskay/tidybayes
VignetteBuilder: knitr
RoxygenNote: 6.1.0
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-08-02 12:27:13 UTC; matth
Author: Matthew Kay [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-02 13:10:03 UTC

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New package SparseMDC with initial version 0.99.5
Package: SparseMDC
Type: Package
Title: Implementation of SparseMDC Algorithm
Version: 0.99.5
Authors@R: c( person("Martin", "Barron", email = "mbarron2@nd.edu",role = c("aut")), person("Jun", "Li", email = "jun.li@nd.edu",role = c("aut","cre")) )
Description: Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
License: GPL-3
Imports: stats, foreach, parallel, doParallel
Depends: R (>= 3.1.0), doRNG
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-01 16:44:39 UTC; Martin
Author: Martin Barron [aut], Jun Li [aut, cre]
Maintainer: Jun Li <jun.li@nd.edu>
Repository: CRAN
Date/Publication: 2018-08-02 12:40:16 UTC

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New package omu with initial version 1.0.2
Package: omu
Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Version: 1.0.2
Authors@R: person("Connor", "Tiffany", email = "crtiffany@ucdavis.edu", role = c("aut", "cre"))
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data using the package 'KEGGREST' to access the 'KEGG' API.
Depends: R (>= 3.3.0)
biocViews:
Imports: plyr, dplyr, stringr, KEGGREST, reshape2, ggfortify, ggplot2, magrittr, tidyr
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/connor-reid-tiffany/Omu, https://www.kegg.jp/kegg/rest/keggapi.html
BugReports: https://github.com/connor-reid-tiffany/Omu/issues
NeedsCompilation: no
Packaged: 2018-08-02 02:18:17 UTC; connor
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>
Repository: CRAN
Date/Publication: 2018-08-02 12:40:03 UTC

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New package jsonstat with initial version 0.0.1
Package: jsonstat
Type: Package
Title: Interface to 'JSON-stat'
Version: 0.0.1
Author: Kim Seonghyun [aut, cre]
Maintainer: Kim Seonghyun <zedoul@gmail.com>
Authors@R: c( person("Kim", "Seonghyun", "", "zedoul@gmail.com", c("aut", "cre")) )
Description: Interface to 'JSON-stat' <https://json-stat.org/>, a simple lightweight 'JSON' format for data dissemination.
URL: https://github.com/zedoul/jsonstat
BugReports: https://github.com/zedoul/jsonstat/issues
Depends: R (>= 3.3.0)
Imports: cli, dplyr, jsonlite, rlang
Suggests: knitr, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-02 07:27:47 UTC; zedoul
Repository: CRAN
Date/Publication: 2018-08-02 12:40:06 UTC

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New package HCT with initial version 0.1.0
Package: HCT
Type: Package
Title: Calculates Significance Criteria and Power for a Single Arm Trial
Version: 0.1.0
Author: David A. Schoenfeld
Maintainer: David A. Schoenfeld <dschoenfeld@mgh.harvard.edu>
Description: Given a database of previous treatment/placebo estimates, their standard errors and sample sizes, the program calculates a significance criteria and power estimate that takes into account the among trial variation.
Depends: R (>= 2.10), rstan
Suggests: testthat
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-01 14:37:03 UTC; das15
Repository: CRAN
Date/Publication: 2018-08-02 12:30:12 UTC

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New package GFE with initial version 0.1.0
Package: GFE
Type: Package
Title: Gross Flows Estimation under Complex Surveys
Version: 0.1.0
Author: Acero William <wfaceror@unal.edu.co>, Gutirrez Andrs <andres.gutierrez@un.org>, Trujillo Leonardo <ltrujillo@unal.edu.co>
Maintainer: Acero William <wfaceror@unal.edu.co>
Description: The philosophy in the package is described in Stasny (1988) <doi:10.2307/1391558> and Gutirrez, A., Trujillo, L. & Silva, N. (2014), <ISSN:1492-0921> to estimate the gross flows under complex surveys using a Markov chain approach with non response.
Depends: R (>= 3.3.1)
License: GPL (>= 2)
Encoding: latin1
LazyData: true
RoxygenNote: 6.0.1
Repository: CRAN
Imports: dplyr, data.table, TeachingSampling
NeedsCompilation: no
Packaged: 2018-08-01 14:29:18 UTC; wacero
Date/Publication: 2018-08-02 12:10:10 UTC

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New package fieldRS with initial version 0.1.0
Package: fieldRS
Type: Package
Title: Remote Sensing Field Work Tools
Version: 0.1.0
Date: 2018-08-01
Authors@R: person("Ruben", "Remelgado", role = c("aut", "cre"), email="ruben.remelgado@uni-wuerzburg.de")
URL: https://github.com/RRemelgado/fieldRS/
BugReports: https://github.com/RRemelgado/fieldRS/issues/
Maintainer: Ruben Remelgado <ruben.remelgado@uni-wuerzburg.de>
Description: In remote sensing, designing a field campaign to collect ground-truth data can be a challenging task. We need to collect representative samples while accounting for issues such as budget constraints and limited accessibility created by e.g. poor infrastructure. As suggested by Olofsson et al. (2014) <doi:10.1016/j.rse.2014.02.015>, this demands the establishment of best-practices to collect ground-truth data that avoid the waste of time and funds. 'fieldRS' addresses this issue by helping scientists and practitioners design field campaigns through the identification of priority sampling sites, the extraction of potential sampling plots and the conversion of plots into consistent training and validation samples that can be used in e.g. land cover classification.
LazyData: TRUE
Imports: raster, sp, caret, rgdal, ggplot2, grDevices, rsMove, spatialEco, rgeos, RStoolbox
RoxygenNote: 6.0.1
License: GPL (>= 3)
Suggests: knitr, rmarkdown, kableExtra, imager
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-01 15:22:53 UTC; rus14jh
Author: Ruben Remelgado [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-02 12:10:06 UTC

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New package cromwellDashboard with initial version 0.5.1
Package: cromwellDashboard
Type: Package
Title: A Dashboard to Visualize Scientific Workflows in 'Cromwell'
Version: 0.5.1
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Description: A dashboard supports the usage of 'cromwell'. 'Cromwell' is a scientific workflow engine for command line users. This package utilizes 'cromwell' REST APIs and provides these convenient functions: timing diagrams for running workflows, 'cromwell' engine status, a tabular workflow list. For more information about 'cromwell', visit <http://cromwell.readthedocs.io>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinydashboard, stringr, httr, dplyr, DT
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-02 05:42:05 UTC; xzhan9
Repository: CRAN
Date/Publication: 2018-08-02 12:40:13 UTC

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New package BivGeo with initial version 1.0.1
Package: BivGeo
Type: Package
Title: Basu-Dhar Bivariate Geometric Distribution
Version: 1.0.1
Author: Ricardo Puziol de Oliveira and Jorge Alberto Achcar
Maintainer: Ricardo Puziol de Oliveira <rpuziol.oliveira@gmail.com>
Description: Computes the joint probability mass function, the joint cumulative distribution, the correlation coefficient and generate random deviates from the Basu-Dhar bivariate geometric distribution. The package also computes the joint survival function in presence of cure fraction using the mixture model approach (For more details, see Achcar et. al (2016) <doi:10.1080/02664763.2015.1117589> and de Oliveira et. al (2018) <doi:10.1080/02664763.2018.1495701>).
Depends: R (>= 3.0.2)
Imports: stats
RoxygenNote: 6.0.1
Encoding: UTF-8
NeedsCompilation: no
LazyData: TRUE
License: GPL (>= 2)
Packaged: 2018-08-01 17:36:53 UTC; ricky
Repository: CRAN
Date/Publication: 2018-08-02 12:30:15 UTC

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New package sparkbq with initial version 0.1.0
Package: sparkbq
Type: Package
Title: Google 'BigQuery' Support for 'sparklyr'
Version: 0.1.0
Date: 2018-07-31
Authors@R: c(person(family = "Mirai Solutions GmbH", role = "aut", email = "info@mirai-solutions.com"), person("Martin", "Studer", role = "cre", email = "martin.studer@mirai-solutions.com"), person("Nicola", "Lambiase", role = "ctb", email = "nicola.lambiase@mirai-solutions.com"), person("Omer", "Demirel", role = "ctb"))
URL: http://www.mirai-solutions.com, https://github.com/miraisolutions/sparkbq
BugReports: https://github.com/miraisolutions/sparkbq/issues
Description: A 'sparklyr' extension package providing an integration with Google 'BigQuery'. It supports direct import/export where records are directly streamed from/to 'BigQuery'. In addition, data may be imported/exported via intermediate data extracts on Google 'Cloud Storage'.
Depends: R (>= 3.3.2)
Imports: sparklyr (>= 0.7.0)
Suggests: dplyr
License: GPL-3 | file LICENSE
SystemRequirements: Spark (>= 2.2.x)
Encoding: UTF-8
LazyData: yes
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-31 16:17:56 UTC; mstuder
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], Nicola Lambiase [ctb], Omer Demirel [ctb]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Repository: CRAN
Date/Publication: 2018-08-02 11:40:02 UTC

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New package simode with initial version 1.0.1
Package: simode
Type: Package
Title: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching
Version: 1.0.1
Authors@R: c( person("Itai", "Dattner", email = "idattner@stat.haifa.ac.il", role = c("aut", "cre")), person("Rami", "Yaari", email = "ramiyaari@gmail.com", role = "aut"))
Description: Implements statistical inference for systems of ordinary differential equations, that uses the integral-matching criterion and takes advantage of the separability of parameters, in order to obtain initial parameter estimates for nonlinear least squares optimization. Dattner & Yaari (2018) <arXiv:1807.04202>. Dattner et al. (2017) <doi:10.1098/rsif.2016.0525>. Dattner & Klaassen (2015) <doi:10.1214/15-EJS1053>.
Depends: R (>= 3.4.0)
Imports: deSolve, pracma, quadprog
Suggests: parallel, Rcgmin, Rvmmin, R.rsp
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2018-07-31 12:10:40 UTC; ramiy
Author: Itai Dattner [aut, cre], Rami Yaari [aut]
Maintainer: Itai Dattner <idattner@stat.haifa.ac.il>
Repository: CRAN
Date/Publication: 2018-08-02 12:00:03 UTC

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New package rmi with initial version 0.1.1
Package: rmi
Title: Mutual Information Estimators
Version: 0.1.1
Author: Isaac Michaud [cre, aut]
Maintainer: Isaac Michaud <ijmichau@ncsu.edu>
Description: Provides mutual information estimators based on k-nearest neighbor estimators by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138>, S. Gao, et al. (2015) <http://proceedings.mlr.press/v38/gao15.pdf> and local density estimators by W. Gao, et al. (2017) <doi:10.1109/ISIT.2017.8006749>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
LinkingTo: Rcpp, RcppArmadillo, BH
Imports: Rcpp, stats, graphics
Suggests: testthat, parallel, tgp
NeedsCompilation: yes
Packaged: 2018-07-31 17:15:50 UTC; isaacmichaud
Repository: CRAN
Date/Publication: 2018-08-02 11:40:06 UTC

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New package readmnist with initial version 1.0.6
Package: readmnist
Type: Package
Title: Read MNIST Dataset
Version: 1.0.6
Author: Jiang Junfeng
Maintainer: Jiang Junfeng <a412133593@gmail.com>
Description: You can use the function Read.mnist() to read data and arrange them properly from MNIST dataset (the open handwriting digit database <http://yann.lecun.com/exdb/mnist/>). With this package, you can conveniently get all of necessary informations and then immediately start to check whether your machine learning algorithm works well. It can automatically recognize the type of dataset and returns the informations in corresponding structure.
License: GPL
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-07-31 16:32:37 UTC; coldog
Repository: CRAN
Date/Publication: 2018-08-02 11:40:09 UTC

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Wed, 01 Aug 2018

New package aws.kms with initial version 0.1.2
Package: aws.kms
Type: Package
Title: 'AWS Key Management Service' Client Package
Version: 0.1.2
Date: 2018-07-31
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com", comment = c(ORCID = "0000-0003-4097-6326")))
Description: Client package for the 'AWS Key Management Service' <https://aws.amazon.com/kms/>, a cloud service for managing encryption keys.
License: GPL (>= 2)
URL: https://github.com/cloudyr/aws.kms
BugReports: https://github.com/cloudyr/aws.kms/issues
Imports: httr, jsonlite, base64enc, aws.signature (>= 0.4.0)
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-31 15:51:24 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>)
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-01 13:10:03 UTC

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New package nodbi with initial version 0.1.0
Package: nodbi
Title: 'NoSQL' Database Connector
Description: Simplified document database manipulation and analysis, including support for many 'NoSQL' databases, including document databases ('Elasticsearch', 'CouchDB', 'MongoDB'), 'key-value' databases ('Redis'), and other 'NoSQL' types ('etcd').
Version: 0.1.0
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "sckott@protonmail.com", comment = c(ORCID = "0000-0003-1444-9135")), person("Rich", "FitzJohn", role = "aut"), person("Jeroen", "Ooms", role = "aut") )
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/ropensci/nodbi
BugReports: https://github.com/ropensci/nodbi/issues
Depends: R (>= 2.10)
Imports: data.table, jsonlite
Suggests: sofa (>= 0.3.0), etseed (>= 0.1.0), elastic (>= 0.8.4), mongolite (>= 1.6), redux, testthat
RoxygenNote: 6.0.1
X-schema.org-applicationCategory: Databases
X-schema.org-keywords: database, MongoDB, Redis, Elasticsearch, CouchDB, NoSQL, JSON, documents
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2018-07-24 21:17:04 UTC; sckott
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Rich FitzJohn [aut], Jeroen Ooms [aut]
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Repository: CRAN
Date/Publication: 2018-08-01 13:00:03 UTC

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New package lfl with initial version 1.4.2
Package: lfl
Type: Package
Title: Linguistic Fuzzy Logic
Version: 1.4.2
Date: 2018-08-02
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE) - see Burda (2015) <doi:10.1109/FUZZ-IEEE.2015.7337826>.
License: GPL (>= 3.0)
Suggests: testthat
Depends: R (>= 3.4.0)
Imports: Rcpp (>= 0.11.0), foreach, forecast (>= 5.5), plyr, tseries, e1071, zoo, utils
LinkingTo: Rcpp
NeedsCompilation: yes
SystemRequirements: C++11
Encoding: UTF-8
Packaged: 2018-08-01 10:07:43 UTC; michal
Repository: CRAN
Date/Publication: 2018-08-01 11:20:03 UTC

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Tue, 31 Jul 2018

New package anyflights with initial version 0.1.0
Package: anyflights
Title: Download Air Travel Data for Specified Years and Airports
Version: 0.1.0
Authors@R: c( person("Simon P.", "Couch", , "simonpatrickcouch@gmail.com", c("aut", "cre")), person("Jay", "Lee", , "jaylee@reed.edu", "aut"), person("Hadley", "Wickham", , "hadley@rstudio.com", "aut"), person("RStudio", role = "cph") )
Description: Supplies a set of functions to query air travel data for user- specified years and airports. Datasets include on-time flights, airlines, airports, and weather.
License: CC0
LazyData: true
Depends: R (>= 2.10)
Imports: httr, dplyr, readr, RCurl, utils, tibble, lubridate
URL: http://github.com/simonpcouch/anyflights
BugReports: https://github.com/simonpcouch/anyflights/issues
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-07-31 15:23:40 UTC; simonpcouch
Author: Simon P. Couch [aut, cre], Jay Lee [aut], Hadley Wickham [aut], RStudio [cph]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 16:10:03 UTC

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New package phylotaR with initial version 1.0.0
Package: phylotaR
Type: Package
Title: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
Version: 1.0.0
Authors@R: c(person("Hannes", "Hettling", role = "aut"), person("Rutger", "Vos", role = "aut"), person("Alexander", "Zizka", role = "aut"), person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com"), person("Alexandre", "Antonelli", role = c("aut")))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
License: MIT + file LICENSE
URL: https://github.com/ropensci/phylotaR#readme
BugReports: https://github.com/ropensci/phylotaR/issues
SystemRequirements: BLAST+ (>=2.0)
Depends: R (>= 3.3.0), methods,
Imports: igraph, rentrez, XML, ggplot2, sys, treeman, treemapify, R.utils
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2018-07-31 14:02:27 UTC; dom
Author: Hannes Hettling [aut], Rutger Vos [aut], Alexander Zizka [aut], Dom Bennett [aut, cre], Alexandre Antonelli [aut]
Repository: CRAN
Date/Publication: 2018-07-31 15:50:03 UTC

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New package jmdl with initial version 0.1.0
Package: jmdl
Type: Package
Title: Joint Mean-Correlation Regression Approach for Discrete Longitudinal Data
Version: 0.1.0
Author: Jane Lee
Maintainer: Jane Lee <mote@mail.ustc.edu.cn>
Description: Fit joint mean-correlation models for discrete longitudinal data (Tang CY,Zhang W, Leng C, 2017 <doi:10.5705/ss.202016.0435>).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
Imports: Formula, methods, minqa, boot, mnormt, MASS, mvtnorm, abind
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-07-31 13:37:36 UTC; ThinkPad
Repository: CRAN
Date/Publication: 2018-07-31 15:50:17 UTC

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New package alpaca with initial version 0.2
Package: alpaca
Type: Package
Title: Fit GLM's with High-Dimensional k-Way Fixed Effects
Version: 0.2
Authors@R: c(person("Amrei", "Stammann", email = "amrei.stammann@hhu.de", role = c("aut", "cre")), person("Daniel", "Czarnowske", email = "daniel.czarnowske@hhu.de", role = c("aut")))
Description: Provides a routine to concentrate out factors with many levels during the optimization of the log-likelihood function of the corresponding generalized linear model (glm). The package is based on the algorithm proposed by Stammann (2018) <arXiv:1707.01815> and is restricted to glm's that are based on maximum likelihood estimation and non-linear. It also offers an efficient algorithm to recover estimates of the fixed effects in a post-estimation routine. The package also includes robust and multi-way clustered standard errors.
License: GPL-3
Depends: R (>= 3.1.0)
Imports: data.table, Formula, MASS, Rcpp, stats, utils
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/amrei-stammann/alpaca
BugReports: https://github.com/amrei-stammann/alpaca/issues
RoxygenNote: 6.1.0
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-31 15:12:05 UTC; daniel
Author: Amrei Stammann [aut, cre], Daniel Czarnowske [aut]
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Repository: CRAN
Date/Publication: 2018-07-31 16:00:02 UTC

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New package ARIbrain with initial version 0.1
Package: ARIbrain
Version: 0.1
Date: 2018-07-27
Title: All-Resolution Inference
Author: Livio Finos, Jelle Goeman, Wouter Weeda, Jonathan Rosenblatt, Aldo Solari
Maintainer: Livio Finos <livio.finos@unipd.it>
Description: It performs All-Resolutions Inference (ARI) on functional Magnetic Resonance Image (fMRI) data. As a main feature, it estimates lower bounds for the proportion of active voxels in a set of clusters as, for example, given by a cluster-wise analysis. The method is described in Rosenblatt, Finos, Weeda, Solari, Goeman (2018) <doi:10.1016/j.neuroimage.2018.07.060>.
License: GPL (>= 2)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
Imports: hommel, RNifti, plyr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 13:22:45 UTC; livio
Repository: CRAN
Date/Publication: 2018-07-31 14:50:03 UTC

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New package uniformly with initial version 0.1.0
Package: uniformly
Type: Package
Title: Uniform Sampling
Version: 0.1.0
Date: 2018-07-31
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Description: Uniform sampling on various geometric shapes, such as spheres, ellipsoids, simplices.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/stla/uniformly
BugReports: https://github.com/stla/uniformly/issues
RoxygenNote: 6.0.1
Imports: stats, pgnorm
Suggests: knitr, rmarkdown, geometry, rgl, misc3d, scatterplot3d
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 06:53:14 UTC; SDL96354
Repository: CRAN
Date/Publication: 2018-07-31 12:10:03 UTC

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New package tm1r with initial version 1.0.0
Package: tm1r
Type: Package
Title: The Integration Between 'IBM COGNOS TM1' and R
Version: 1.0.0
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: jsonlite, httr
NeedsCompilation: no
Packaged: 2018-07-31 10:19:17 UTC; MAnd58
Repository: CRAN
Date/Publication: 2018-07-31 12:30:03 UTC

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New package EMSHS with initial version 1.0.0
Package: EMSHS
Type: Package
Title: EM Algorithm for Bayesian Shrinkage Approach with Structural Information Incorporated
Version: 1.0.0
Author: Changgee Chang and Praveen Suthaharan
Maintainer: Praveen Suthaharan <psuthah@emory.edu>
Description: Fits a Bayesian shrinkage regression model that can incorporate structural information. Changgee Chang, Suprateek Kundu, Qi Long (2018) <doi:10.1111/biom.12882>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: Rdpack
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2018-07-31 10:44:34 UTC; prave
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2018-07-31 12:40:02 UTC

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New package cxhull with initial version 0.1.0
Package: cxhull
Type: Package
Title: Convex Hull
Version: 0.1.0
Date: 2018-07-31
Authors@R: c( person("C. B.", "Barber", role="cph", comment="author of the Qhull library"), person("The Geometry Center", role="cph"), person("Stéphane", "Laurent", role=c("cph","aut","cre"), email="laurent_step@yahoo.fr"))
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Description: Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/stla/cxhull
BugReports: https://github.com/stla/cxhull/issues
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, rgl
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-31 07:02:21 UTC; SDL96354
Author: C. B. Barber [cph] (author of the Qhull library), The Geometry Center [cph], Stéphane Laurent [cph, aut, cre]
Repository: CRAN
Date/Publication: 2018-07-31 12:20:02 UTC

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New package BDP2 with initial version 0.1.3
Package: BDP2
Type: Package
Title: Bayesian Adaptive Designs for Phase II Trials with Binary Endpoint
Version: 0.1.3
Date: 2018-07-31
Author: Annette Kopp-Schneider, Manuel Wiesenfarth, Ulrich Abel
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>
Description: Tools and workflow to choose design parameters in Bayesian adaptive single-arm phase II trial designs with binary endpoint (response, success) with possible stopping for efficacy and futility at interim analyses. Also contains routines to determine and visualize operating characteristics. See Kopp-Schneider et al. (2018) <doi:10.1002/bimj.201700209>.
License: GPL-2
Depends: rmarkdown, shiny, shinyBS
LazyData: TRUE
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 09:11:34 UTC; wiesenfa
Repository: CRAN
Date/Publication: 2018-07-31 12:30:06 UTC

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New package adaptMT with initial version 1.0.0
Package: adaptMT
Type: Package
Title: Adaptive P-Value Thresholding for Multiple Hypothesis Testing with Side Information
Version: 1.0.0
Authors@R: person("Lihua", "Lei", email = "lihua.lei@berkeley.edu", role = c("aut", "cre"))
Maintainer: Lihua Lei <lihua.lei@berkeley.edu>
Description: Implementation of adaptive p-value thresholding (AdaPT), including both a framework that allows the user to specify any algorithm to learn local false discovery rate and a pool of convenient functions that implement specific algorithms. See Lei, Lihua and Fithian, William (2016) <arXiv:1609.06035>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://arxiv.org/abs/1609.06035, https://github.com/lihualei71/adaptMT
BugReports: https://github.com/lihualei71/adaptMT/issues
Suggests: glmnet, HDtweedie, mgcv, splines, testthat, knitr, rmarkdown, dplyr
RoxygenNote: 6.0.1
Imports: methods
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-31 06:40:07 UTC; Leo
Author: Lihua Lei [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-31 12:00:03 UTC

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New package SingleCaseES with initial version 0.4.0
Package: SingleCaseES
Type: Package
Title: A Calculator for Single-Case Effect Sizes
Version: 0.4.0
Date: 2018-07-28
Authors@R: c( person(c("James","E."), "Pustejovsky", email = "jepusto@gmail.com", role = c("aut", "cre")), person(c("Daniel","M."), "Swan", email = "dswan@utexas.edu", role = "aut") )
Description: Provides R functions for calculating basic effect size indices for single-case designs, including several non-overlap measures and parametric effect size measures, and for estimating the gradual effects model developed by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>. Standard errors and confidence intervals (based on the assumption that the outcome measurements are mutually independent) are provided for the subset of effect sizes indices with known sampling distributions.
URL: https://github.com/jepusto/SingleCaseES
BugReports: https://github.com/jepusto/SingleCaseES/issues
License: GPL-3
Imports: stats, purrr, magrittr, dplyr, tidyr, rlang, tidyselect
Suggests: spelling, shiny, ggplot2, testthat, markdown, knitr, rmarkdown, prettydoc, kableExtra
LazyData: TRUE
RoxygenNote: 6.0.1
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 21:08:57 UTC; jep2963
Author: James E. Pustejovsky [aut, cre], Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 10:20:06 UTC

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New package robmixglm with initial version 1.0-2
Package: robmixglm
Type: Package
Title: Robust Generalized Linear Models (GLM) using Mixtures
Version: 1.0-2
Date: 2018-07-31
Authors@R: c(person("Ken","Beath",email="ken.beath@mq.edu.au", role=c("aut","cre")))
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Contact: Ken Beath <ken.beath@mq.edu.au>
Author: Ken Beath [aut, cre]
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Depends: R(>= 3.2.0)
Suggests: R.rsp, robustbase, lattice, forward
VignetteBuilder: R.rsp
Imports: fastGHQuad, stats, bbmle, MASS, VGAM, actuar, Rcpp (>= 0.12.15), methods, boot, numDeriv
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
License: GPL (>= 2)
LinkingTo: Rcpp
Packaged: 2018-07-31 02:18:23 UTC; kjbeath1
Repository: CRAN
Date/Publication: 2018-07-31 10:40:03 UTC

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New package makeParallel with initial version 0.1.1
Package: makeParallel
Version: 0.1.1
Date: 2018-07-18
Title: Transform Serial R Code into Parallel R Code
Authors@R: person("Clark", "Fitzgerald", role = c("aut", "cre"), email = "clarkfitzg@gmail.com", comment = c(ORCID = "0000-0003-3446-6389"))
Maintainer: Clark Fitzgerald <clarkfitzg@gmail.com>
Depends: R (>= 3.1.0)
Imports: methods, utils, graphics, parallel, codetools, CodeDepends, whisker
Suggests: igraph, roxygen2, knitr, rmarkdown, testthat
Description: Writing parallel R code can be difficult, particularly for code that is not "embarrassingly parallel". This experimental package automates the transformation of serial R code into more efficient parallel versions. It identifies task parallelism by statically analyzing entire scripts to detect dependencies between statements. It implements an extensible system for scheduling and generating new code. It includes a reference implementation of the 'List Scheduling' approach to the general task scheduling problem of scheduling statements on multiple processors.
License: MIT + file LICENSE
URL: https://github.com/clarkfitzg/makeParallel
BugReports: https://github.com/clarkfitzg/makeParallel
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 19:23:01 UTC; clark
Author: Clark Fitzgerald [aut, cre] (<https://orcid.org/0000-0003-3446-6389>)
Repository: CRAN
Date/Publication: 2018-07-31 10:30:03 UTC

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New package LVGP with initial version 2.1.3
Package: LVGP
Type: Package
Title: Latent Variable Gaussian Process Modeling with Qualitative and Quantitative Input Variables
Version: 2.1.3
Author: Siyu Tao, Yichi Zhang
Maintainer: Siyu Tao <siyutao2020@u.northwestern.edu>
Description: Fit response surfaces for datasets with latent-variable Gaussian process modeling, predict responses for new inputs, and plot latent variables locations in the latent space (1D or 2D). The input variables of the datasets can be quantitative, qualitative/categorical or mixed. The output variable of the datasets is a scalar (quantitative). The method is published in "A Latent Variable Approach to Gaussian Process Modeling with Qualitative and Quantitative Factors" by Yichi Zhang, Siyu Tao, Wei Chen, and Daniel W. Apley (2018) <arXiv:1806.07504>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: lhs(>= 0.14), randtoolbox(>= 1.17), lattice(>= 0.20-34)
Depends: R (>= 3.5.0), stats (>= 3.2.5), parallel (>= 3.2.5)
Repository: CRAN
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-07-30 22:42:42 UTC; SiyuTao
Date/Publication: 2018-07-31 10:20:10 UTC

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New package geodetector with initial version 1.0-1
Package: geodetector
Title: Stratified Heterogeneity Measure, Dominant Driving Force Detection, Interaction Relationship Investigation
Version: 1.0-1
Authors@R: c(person("Chengdong", "Xu", email = "xucd@Lreis.ac.cn", role = c("aut", "cre")),person("Jinfeng", "Wang", email = "wangjf@Lreis.ac.cn", role = c("aut")),person("Yue", "Hou" , role = "ctb"),person("Qian", "Yin", role = "ctb"))
Description: Spatial stratified heterogeneity (SSH), referring to the within strata are more similar than the between strata, a model with global parameters would be confounded if input data is SSH. Note that the "spatial" here can be either geospatial or the space in mathematical meaning. Geographical detector is a novel tool to investigate SSH: (1) measure and find SSH of a variable Y; (2) test the power of determinant X of a dependent variable Y according to the consistency between their spatial distributions; and (3) investigate the interaction between two explanatory variables X1 and X2 to a dependent variable Y (Wang et al 2014 <doi:10.1080/13658810802443457>, Wang, Zhang, and Fu 2016 <doi:10.1016/j.ecolind.2016.02.052>).
Depends: R (>= 2.10)
Imports: sp (>= 1.2-7),rgeos (>= 0.3-26),rgdal (>= 1.2-16),maptools
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Author: Chengdong Xu [aut, cre], Jinfeng Wang [aut], Yue Hou [ctb], Qian Yin [ctb]
Maintainer: Chengdong Xu <xucd@Lreis.ac.cn>
Repository: CRAN
Packaged: 2018-07-31 01:56:47 UTC; lenovo
Date/Publication: 2018-07-31 10:40:06 UTC

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New package circumplex with initial version 0.1.1
Type: Package
Package: circumplex
Title: Analysis and Visualization of Circular Data
Version: 0.1.1
Authors@R: c( person("Jeffrey", "Girard", email = "me@jmgirard.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7359-3746")), person("Johannes", "Zimmermann", role = "aut", comment = c(ORCID = "0000-0001-6975-2356")), person("Aidan", "Wright", role = "aut", comment = c(ORCID = "0000-0002-2369-0601")) )
Description: Tools for analyzing and visualizing circular data, including a generalization of the bootstrapped structural summary method from Zimmermann & Wright (2017) <doi:10.1177/1073191115621795> and functions for creating publication-ready tables and figures from the results. Future versions will include tools for circular fit and reliability analyses, as well as greatly enhanced visualization methods.
License: GPL-3
URL: https://github.com/jmgirard/circumplex
BugReports: https://github.com/jmgirard/circumplex/issues
Depends: R (>= 3.5.0)
Imports: assertthat (>= 0.2.0), boot (>= 1.3.20), dplyr (>= 0.7.6), ggforce (>= 0.1.3), ggplot2 (>= 3.0.0), htmlTable (>= 1.12), magrittr (>= 1.5), purrr (>= 0.2.5), Rcpp (>= 0.12.18), rlang (>= 0.2.1), stats, tibble (>= 1.4.2), tidyr (>= 0.8.1)
LinkingTo: Rcpp (>= 0.12.18), RcppArmadillo (>= 0.8.600.0.0)
RoxygenNote: 6.1.0
Suggests: covr (>= 3.1.0), forcats (>= 0.3.0), kableExtra (>= 0.9.0), knitr (>= 1.20), psych (>= 1.8.4), rmarkdown (>= 1.10), testthat (>= 2.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-30 19:06:29 UTC; Eleventh
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>), Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>), Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>
Repository: CRAN
Date/Publication: 2018-07-31 10:10:02 UTC

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New package biglmm with initial version 0.9-1
Package: biglmm
Type: Package
Title: Bounded Memory Linear and Generalized Linear Models
Version: 0.9-1
Authors@R: c(person(given="Thomas", family="Lumley", email="tlumley@u.washington.edu", role="aut"), person(given="Christophe", family="Dutang", email="christophe.dutang@ensimag.fr", role="ctb"), person(given="Alan", family="Miller", role="ctb", comment="Algorithm AS 274"), person(given="Morven", family="Gentleman", role="ctb", comment="Algorithm AS 75"), person(given="Mark", family="Purver", email="mark_purver@hotmail.com", role="cre"))
Author: Thomas Lumley [aut], Christophe Dutang [ctb], Alan Miller [ctb] (Algorithm AS 274), Morven Gentleman [ctb] (Algorithm AS 75), Mark Purver [cre]
Maintainer: Mark Purver <mark_purver@hotmail.com>
Description: Regression for data too large to fit in memory. This package functions exactly like the 'biglm' package, but works with later versions of R.
License: GPL
Suggests: RSQLite, RODBC
Depends: DBI, methods
Enhances: leaps
Packaged: 2018-07-30 20:45:22 UTC
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2018-07-31 10:20:03 UTC
RoxygenNote: 6.0.1

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New package whitechapelR with initial version 0.2.1
Package: whitechapelR
Title: Advanced Policing Techniques for the Board Game "Letters from Whitechapel"
Version: 0.2.1
Authors@R: person("Mark", "Ewing", email = "b.mark@ewingsonline.com", role = c("aut", "cre"))
Description: Provides a set of functions to make tracking the hidden movements of the 'Jack' player easier. By tracking every possible path Jack might have traveled from the point of the initial murder including special movement such as through alleyways and via carriages, the police can more accurately narrow the field of their search. Additionally, by tracking all possible hideouts from round to round, rounds 3 and 4 should have a vastly reduced field of search.
Depends: R (>= 3.3)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: plyr, igraph
Suggests: covr, testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-30 14:31:10 UTC; u772700
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Repository: CRAN
Date/Publication: 2018-07-31 09:40:03 UTC

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New package VFP with initial version 1.0
Package: VFP
Version: 1.0
Date: 2018-07-30
Title: Variance Function Program
Author: Andre Schuetzenmeister [cre, aut], Florian Dufey [aut], Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Authors@R: c( person(given="Andre", family="Schuetzenmeister", email="andre.schuetzenmeister@roche.com", role = c("cre", "aut")), person(given="Florian", family="Dufey", email="florian.dufey@roche.com", role = c("aut")), person(given="Andrea", family="Geistanger", email="andrea.geistanger@roche.com", role = c("ctb")) )
Depends: R (>= 3.1.0), gnm
Imports: MASS, utils, stats, graphics, grDevices
Suggests: VCA, RUnit
Description: Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is to fit multiple variance functions to a data set and consequently assess which function reflects the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship is of great importance when individual test-results are used for defining follow-up treatment of patients.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-07-30 15:06:36 UTC; schueta6
Repository: CRAN
Date/Publication: 2018-07-31 09:40:09 UTC

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New package MultiFit with initial version 0.1.0
Package: MultiFit
Type: Package
Title: Multivariate Multiscale Framework for Independence Tests
Version: 0.1.0
Author: S. Gorsky, L. Ma
Maintainer: S. Gorsky <s.gorsky@duke.edu>
Description: Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky and Ma (2018) <arXiv:1806.06777>.
License: CC0
Imports: Rcpp (>= 0.12.17), data.table
LinkingTo: Rcpp, RcppArmadillo
Suggests: png, qgraph, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-30 16:15:22 UTC; hhh
Repository: CRAN
Date/Publication: 2018-07-31 09:50:09 UTC

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New package jarbes with initial version 1.7.0
Package: jarbes
Type: Package
Title: Just a Rather Bayesian Evidence Synthesis
Version: 1.7.0
Date: 2018-07-30
Authors@R: c(person("Pablo Emilio", "Verde", role=c("aut","cre"), email="pabloemilio.verde@hhu.de"))
Depends: R (>= 3.4.0)
Imports: rjags (>= 3.4.0), R2jags (>= 0.04-03), stats, graphics, ggplot2, ggExtra, MASS, grid, gridExtra, mcmcplots
SystemRequirements: JAGS (>= 3.4.0) (see http://mcmc-jags.sourceforge.net)
Description: Provides a new class of Bayesian meta-analysis models that we called "The Hierarchical Meta-Regression" (HMR). The aim of HMR is to incorporate into the meta-analysis, the data collection process, which results in a model for the internal and external validity bias. In this way, it is possible to combine studies of different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS). The statistical methods and their applications are described in Verde, Ohmann, Morbach and Icks (2016) <doi:10.1002/sim.6809> and in Verde (2017) <doi:10.5772/intechopen.70231>.
License: GPL (>= 2)
Packaged: 2018-07-30 16:20:35 UTC; verde
Repository: CRAN
RoxygenNote: 6.0.1
NeedsCompilation: no
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Date/Publication: 2018-07-31 09:50:03 UTC

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New package dhh with initial version 0.0.1
Package: dhh
Title: A Heavy-Headed Distribution
Version: 0.0.1
Authors@R: person("Runlong", "Tang", email = "tangrunlong@gmail.com", role = c("aut", "cre"))
Description: The density, cumulative distribution, quantiles, and i.i.d random variables of a heavy-headed distribution. For more information, please see the vignette.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 16:36:16 UTC; rltang_dell7510
Author: Runlong Tang [aut, cre]
Maintainer: Runlong Tang <tangrunlong@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-31 09:50:06 UTC

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New package bnviewer with initial version 0.1.0
Package: bnviewer
Type: Package
Title: Interactive Visualization of Bayesian Networks
Version: 0.1.0
Depends: R (>= 3.0)
Author: Robson Fernandes
Maintainer: Robson Fernandes <robs.fernandes@outlook.com>
Description: Interactive visualization of Bayesian Networks. The 'bnviewer' package reads various structure learning algorithms provided by the 'bnlearn' package and allows you to view them interactively.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Repository: CRAN
Imports: visNetwork (>= 2.0.4), bnlearn (>= 4.3), methods, igraph (>= 1.2.1)
NeedsCompilation: no
Packaged: 2018-07-30 14:14:23 UTC; robsonfernandes
Date/Publication: 2018-07-31 09:40:07 UTC

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New package beezdemand with initial version 0.1.0
Package: beezdemand
Version: 0.1.0
Date: 2018-07-14
Title: Behavioral Economic Easy Demand
Authors@R: c(person("Brent", "Kaplan", email = "bkaplan.ku@gmail.com", role = c("aut", "cre")), person("Shawn", "Gilroy", email = "shawn.gilroy@temple.edu", role = "ctb"))
Author: Brent Kaplan [aut, cre], Shawn Gilroy [ctb]
Maintainer: Brent Kaplan <bkaplan.ku@gmail.com>
Description: Facilitates many of the analyses performed in studies of behavioral economic demand. The package supports commonly-used options for modeling operant demand including (1) data screening proposed by Stein, Koffarnus, Snider, Quisenberry, & Bickel (2015; <doi:10.1037/pha0000020>), (2) fitting models of demand such as linear (Hursh, Raslear, Bauman, & Black, 1989, <doi:10.1007/978-94-009-2470-3_22>), exponential (Hursh & Silberberg, 2008, <doi:10.1037/0033-295X.115.1.186>) and modified exponential (Koffarnus, Franck, Stein, & Bickel, 2015, <doi:10.1037/pha0000045>), and (3) calculating numerous measures relevant to applied behavioral economists (Intensity, Pmax, Omax). Also supports plotting and comparing data.
Depends: R (>= 2.5)
Imports: nlmrt, nlstools, nls2, ggplot2, reshape2, stats
Suggests: openxlsx, knitr, dplyr, tidyr, rmarkdown
License: GPL-2 | file LICENSE
URL: https://github.com/brentkaplan/beezdemand
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 17:17:24 UTC; brent
Repository: CRAN
Date/Publication: 2018-07-31 10:00:02 UTC

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Mon, 30 Jul 2018

New package glycanr with initial version 0.3.1
Package: glycanr
Title: Tools for Analysing N-Glycan Data
Version: 0.3.1
Authors@R: c( person("Ivo", "Ugrina", role=c("aut", "cre", "cph"), email="ivougrina@gmail.com"), person("Lucija", "Klaric", role="aut"), person("Alyce", "Russell", role="aut"), person("Frano", "Vuckovic", role="aut"))
Maintainer: Ivo Ugrina <ivougrina@gmail.com>
Description: Useful utilities in N-glycan data analysis. This package tries to fill the gap in N-glycan data analysis by providing easy to use functions for basic operations on data (see <https://en.wikipedia.org/wiki/Glycomics> for more details on Glycomics). At the moment 'glycanr' is mostly oriented to data obtained by UPLC (Ultra Performance Liquid Chromatography) and LCMS (Liquid chromatography–mass spectrometry) analysis of Plasma and IgG glycome.
Depends: R (>= 3.1.2)
Imports: ggplot2, tidyr (>= 0.3.1), dplyr (>= 0.4.3), coin
License: MIT + file LICENSE
LazyData: true
Suggests: knitr, preprocessCore, testthat
VignetteBuilder: knitr
URL: https://github.com/iugrina/glycanr
BugReports: https://github.com/iugrina/glycanr/issues
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-30 17:37:10 UTC; iugrina
Author: Ivo Ugrina [aut, cre, cph], Lucija Klaric [aut], Alyce Russell [aut], Frano Vuckovic [aut]
Repository: CRAN
Date/Publication: 2018-07-30 21:00:03 UTC

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New package poolVIM with initial version 1.0.0
Package: poolVIM
Type: Package
Title: Gene-Based Association Tests using the Actual Impurity Reduction (AIR) Variable Importance
Version: 1.0.0
Date: 2018-07-25
Author: Stefano Nembrini <stefanonembrini@gmail.com>
Maintainer: Stefano Nembrini <stefanonembrini@gmail.com>
Description: Gene-based association tests using the actual impurity reduction (AIR) variable importance. The function aggregates AIR importance measures from a group of SNPs or probes and outputs a p-value for each gene. The procedures builds upon the method described in <doi:10.1093/Bioinformatics/Bty373> and will be published soon.
License: GPL (>= 2)
LazyData: TRUE
Imports: stats, ranger
Depends: R(>= 3.3.1), EmpiricalBrownsMethod(>= 1.6.0), Hmisc(>= 4.1)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-30 07:18:24 UTC; S
Repository: CRAN
Date/Publication: 2018-07-30 17:30:08 UTC

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New package syt with initial version 0.1.0
Package: syt
Type: Package
Title: Standard Young Tableaux
Version: 0.1.0
Date: 2018-07-30
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Description: Deals with standard Young tableaux (field of combinatorics). Performs enumeration, counting, random generation, the Robinson-Schensted correspondence, and conversion to and from paths on the Young lattice.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: Matrix, partitions, utils
Suggests: testthat
URL: https://github.com/stla/syt
BugReports: https://github.com/stla/syt/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-30 14:57:13 UTC; SDL96354
Repository: CRAN
Date/Publication: 2018-07-30 16:10:03 UTC

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New package Rspc with initial version 1.2.2
Package: Rspc
Type: Package
Title: Nelson Rules for Control Charts
Version: 1.2.2
Maintainer: Stanislav Matousek (MSD) <rspc@merck.com>
Description: Implementation of Nelson rules for control charts in 'R'. The 'Rspc' implements some Statistical Process Control methods, namely Levey-Jennings type of I (individuals) chart, Shewhart C (count) chart and Nelson rules (as described in Montgomery, D. C. (2013) Introduction to statistical quality control. Hoboken, NJ: Wiley.). Typical workflow is taking the time series, specify the control limits, and list of Nelson rules you want to evaluate. There are several options how to modify the rules (one sided limits, numerical parameters of rules, etc.). Package is also capable of calculating the control limits from the data (so far only for i-chart and c-chart are implemented).
Authors@R: c( person("Martin", "Vagenknecht (MSD)", role = "aut"), person("Jindrich", "Soukup (MSD)", role = "aut"), person("Stanislav", "Matousek (MSD)", email = "rspc@merck.com", role = c("aut", "cre")), person("Janet", "Alvarado (MSD)", role = c("ctb", "rev")), person("Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA", role = "cph"))
BugReports: https://github.com/Merck/SPC_Package/issues
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Suggests: knitr
NeedsCompilation: no
Packaged: 2018-07-30 11:52:34 UTC; soukupj
Author: Martin Vagenknecht (MSD) [aut], Jindrich Soukup (MSD) [aut], Stanislav Matousek (MSD) [aut, cre], Janet Alvarado (MSD) [ctb, rev], Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA [cph]
Repository: CRAN
Date/Publication: 2018-07-30 16:20:06 UTC

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New package collections with initial version 0.1.0
Package: collections
Type: Package
Title: High Performance Container Data Types
Version: 0.1.0
Date: 2018-07-29
Authors@R: c( person("Randy", "Lai", , "randy.cs.lai@gmail.com", role = c("aut", "cre")) )
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
URL: https://randy3k.github.io/collections
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
NeedsCompilation: yes
ByteCompile: yes
Imports: R6
Suggests: testthat
LazyData: true
RoxygenNote: 6.1.0
Packaged: 2018-07-30 14:33:57 UTC; Randy
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 16:20:02 UTC

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New package roloc with initial version 0.1-1
Package: roloc
Type: Package
Title: Convert Colour Specification to Colour Name
Version: 0.1-1
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Description: Functions to convert an R colour specification to a colour name. The user can select and create different lists of colour names and different colour metrics for the conversion.
License: GPL-2 | GPL-3
Imports: grDevices, methods, parallel, colorspace
Suggests: grid, ggplot2, testthat
NeedsCompilation: no
Packaged: 2018-07-26 22:15:04 UTC; pmur002
Repository: CRAN
Date/Publication: 2018-07-30 14:20:03 UTC

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New package SIRE with initial version 1.0.2
Package: SIRE
Type: Package
Title: Finding Feedback Effects in SEM and Testing for Their Significance
Version: 1.0.2
Authors@R: person("Gianmarco", "Vacca", email = "gianmarco.vacca@unicatt.it", role = c("aut","cre"))
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>
Description: Provides two main functionalities. 1 - Given a system of simultaneous equation, it decomposes the matrix of coefficients weighting the endogenous variables into three submatrices: one includes the subset of coefficients that have a causal nature in the model, two include the subset of coefficients that have a interdependent nature in the model, either at systematic level or induced by the correlation between error terms. 2 - Given a decomposed model, it tests for the significance of the interdependent relationships acting in the system, via Maximum likelihood and Wald test, which can be built starting from the function output. For theoretical reference see Faliva (1992) <doi:10.1007/BF02589085> and Faliva and Zoia (1994) <doi:10.1007/BF02589041>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0)
Imports: systemfit, psych, igraph, matrixcalc, MASS, numDeriv, Matrix, stringr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-28 17:41:17 UTC; JimmyMac
Author: Gianmarco Vacca [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-30 13:20:03 UTC

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New package NitrogenUptake2016 with initial version 0.2.0
Package: NitrogenUptake2016
Type: Package
Title: Data and Source Code From: Nitrogen Uptake and Allocation Estimates for Spartina Alterniflora and Distichlis Spicata
Version: 0.2.0
Author: Troy D. Hill, Nathalie R. Sommer, Caroline R. Kanaskie, Emily A. Santos, and Autumn J. Oczkowski
Maintainer: Troy D. Hill <Hill.Troy@gmail.com>
Description: Contains data, code, and figures from Hill et al. (in press; Journal of Experimental Marine Biology and Ecology) and Hill et al. (submitted; Data In Brief). Datasets document plant allometry, stem heights, nutrient and stable isotope content, and sediment denitrification enzyme assays. The data and analysis offer an examination of nitrogen uptake and allocation in two salt marsh plants.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/troyhill/NitrogenUptake2016
LazyData: true
Depends: R (>= 3.0), zoo, car, MASS
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, plyr, reshape2, ggplot2, scales, MuMIn, rsq
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-28 23:22:32 UTC; tdh
Repository: CRAN
Date/Publication: 2018-07-30 13:30:03 UTC

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New package gren with initial version 0.0.1
Package: gren
Type: Package
Title: Adaptive Group-Regularized Logistic Elastic Net Regression
Version: 0.0.1
Date: 2018-07-19
Author: Magnus M. Münch
Maintainer: Magnus M. Münch <m.munch@vumc.nl>
Description: Allows the user to incorporate multiple sources of co-data (e.g., previously obtained p-values, published gene lists, and annotation) in the estimation of a logistic regression model to enhance predictive performance and feature selection, as described in Münch, Peeters, van der Vaart, and van de Wiel (2018) <arXiv:1805.00389>.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.14), glmnet, Iso, pROC
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
VignetteBuilder: knitr
URL: https://github.com/magnusmunch/gren/
Suggests: knitr, rmarkdown
Encoding: UTF-8
RoxygenNote: 6.0.1
LazyData: true
Packaged: 2018-07-28 16:45:07 UTC; magnusmunch
Repository: CRAN
Date/Publication: 2018-07-30 13:10:03 UTC

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New package DecisionAnalysis with initial version 0.1.0
Package: DecisionAnalysis
Type: Package
Title: Implementation of Multi Objective Decision Analysis
Version: 0.1.0
Authors@R: c( person("Josh", "Deehr", email = "josh.deehr@gmail.com", role = c("aut","cre")), person("Christopher", "Smith", email = "Cms3am@virginia.edu", role = c("aut")), person("Jason", "Freels", email = "auburngrads@live.com", role = c("aut")), person("Emily", "Meyer", email = "emily.meyer@theperducogroup.com", role = c("aut")) )
Maintainer: Josh Deehr <josh.deehr@gmail.com>
BugReports: https://github.com/AFIT-R/DecisionAnalysis
Date: 2018-07-19
Description: Aides in the multi objective decision analysis process by simplifying the creation of value hierarchy tree plots, calculating and plotting single and multi attribute value function scores, and conducting sensitivity analysis. Linear, exponential, and categorical single attribute value functions are supported. For details see Parnell (2013, ISBN:978-1-118-17313-8) Kirkwood (1997, ISBN:0-534-51692-0).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: stats, ggplot2, tidyr, dplyr, graphics, data.tree, gridExtra, viridisLite, Cairo
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-28 23:17:44 UTC; ktdeehr
Author: Josh Deehr [aut, cre], Christopher Smith [aut], Jason Freels [aut], Emily Meyer [aut]
Repository: CRAN
Date/Publication: 2018-07-30 13:20:05 UTC

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New package swdft with initial version 0.0.1
Package: swdft
Title: Sliding Window Discrete Fourier Transform (SWDFT)
Version: 0.0.1
Authors@R: person("Lee F. Richardson", email = "leerichardson2013@gmail.com", role = c("aut", "cre"))
Description: Implements the Sliding Window Discrete Fourier Transform (SWDFT). Also provides statistical and graphical tools for analyzing the output. For details see Richardson, L.F., Eddy W.F. (2018) <arXiv:1807.07797>.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, fftwtools, fields
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 11:56:35 UTC; lee
Author: Lee F. Richardson [aut, cre]
Maintainer: Lee F. Richardson <leerichardson2013@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 12:20:03 UTC

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New package ruin with initial version 0.1.1
Package: ruin
Type: Package
Title: Simulation of Various Risk Processes
Version: 0.1.1
Date: 2018-07-20
Authors@R: person("Iegor", "Rudnytskyi", email = "iegor.rudnytskyi@gmail.com", role = c("aut", "cre"))
Description: A (not yet exhaustive) collection of common models of risk processes in actuarial science, represented as formal S4 classes. Each class (risk model) has a simulator of its path, and a plotting function. Further, a Monte-Carlo estimator of a ruin probability for a finite time is implemented, using a parallel computation. Currently, the package extends two classical risk models Cramer-Lundberg and Sparre Andersen models by including capital injections, that are positive jumps (see Breuer L. and Badescu A.L. (2014) <doi:10.1080/03461238.2011.636969>). The intent of the package is to provide a user-friendly interface for ruin processes' simulators, as well as a solid and extensible structure for future extensions.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: http://github.com/irudnyts/ruin
BugReports: http://github.com/irudnyts/ruin/issues
Depends: R (>= 3.5.0)
Imports: methods, parallel, ggplot2 (>= 2.2.1)
Collate: 'AllClass.R' 'AllGeneric.R' 'methods-CramerLundberg.R' 'methods-CramerLundbergCapitalInjections.R' 'methods-SparreAndersen.R' 'methods-SparreAndersenCapitalInjections.R' 'plot_path.R' 'ruin_probability.R' 'zzz.R'
RoxygenNote: 6.0.1
Suggests: testthat, actuar (>= 2.3.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 12:22:58 UTC; irudnyts
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 12:56:18 UTC

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New package helminthR with initial version 1.0.5
Package: helminthR
Type: Package
Title: Access London Natural History Museum Host-Helminth Record Database
Version: 1.0.5
Author: Tad Dallas
Imports: xml2, rvest, httr, magrittr, plyr, ggmap, utils, knitr, rmarkdown
Suggests: testthat, ggplot2,
VignetteBuilder: knitr
Maintainer: Tad Dallas <tad.a.dallas@gmail.com>
URL: https://github.com/rOpenSci/helminthR
BugReports: https://github.com/rOpenSci/helminthR/issues
Description: Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently <http://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.
License: GPL-3
LazyData: yes
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-26 06:50:11 UTC; tad
Repository: CRAN
Date/Publication: 2018-07-30 12:10:09 UTC

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New package glassoFast with initial version 1.0
Package: glassoFast
Type: Package
Title: Fast Graphical LASSO
Version: 1.0
Date: 2018-07-17
Suggests: glasso, rbenchmark
Author: Matyas A Sustik [aut, cph], Ben Calderhead [aut, cph], Julien Clavel [com, ctb]
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Description: A fast and improved implementation of the graphical LASSO.
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2018-07-26 11:48:33 UTC; julienclavel
Repository: CRAN
Date/Publication: 2018-07-30 12:10:12 UTC

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New package cregg with initial version 0.3.0
Package: cregg
Type: Package
Title: Simple Conjoint Tidying, Analysis, and Visualization
Version: 0.3.0
Date: 2018-07-27
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com", comment = c(ORCID = "0000-0003-4097-6326")))
Description: Simple tidying, analysis, and visualization of conjoint (factorial) experiments, including estimation and visualization of average marginal component effects ('AMCEs') and marginal means ('MMs') for weighted and un-weighted survey data, along with useful reference category diagnostics and statistical tests. Estimation of 'AMCEs' is based upon methods described by Hainmueller, Hopkins, and Yamamoto (2014) <doi:10.1093/pan/mpt024>.
License: MIT + file LICENSE
URL: https://github.com/leeper/cregg
BugReports: https://github.com/leeper/cregg/issues
Depends: R (>= 3.5.0)
Imports: stats, sandwich (>= 2.4-0), survey (>= 3.33), lmtest, ggplot2 (>= 2.0), ggstance, scales
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-27 10:54:46 UTC; THOMAS
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>)
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 12:30:03 UTC

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New package bigreadr with initial version 0.1.0
Package: bigreadr
Version: 0.1.0
Date: 2018-07-27
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Authors@R: person("Florian", "Privé", , "florian.prive.21@gmail.com", c("aut", "cre"))
License: GPL-3
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0
Imports: data.table, Rcpp, parallel, fpeek
Suggests: spelling, testthat, covr
LinkingTo: Rcpp
Language: en-US
URL: https://github.com/privefl/bigreadr
BugReports: https://github.com/privefl/bigreadr/issues
NeedsCompilation: yes
Packaged: 2018-07-27 11:08:45 UTC; privef
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 12:30:07 UTC

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New package lilikoi with initial version 0.1.0
Package: lilikoi
Title: Metabolomics Personalized Pathway Analysis Tool
Version: 0.1.0
Authors@R: c( person("Fadhl", "Alakwaa", email = "falakwaa@hawaii.edu", role = c("aut", "cre")), person("Sijia", "Huang", email = "scarlettcanny@gmail.com", role = c( "aut")))
Description: Computes the pathway deregulation score for a given set of metabolites, selects the pathways with the highest mutual information and then uses them to build a classifier. F. Alakwaa, S. Huang, and L. Garmire (2018) <doi:10.1101/283408>.
Imports: caret, corrplot, devtools, dplyr, e1071, gbm, ggplot2, glmnet, hash, Hmisc, infotheo, Matrix, pamr, R.oo, princurve, pROC, randomForest, reshape2, RWeka, stringr
Depends: R (>= 3.4.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
URL: https://github.com/lanagarmire/lilikoi
BugReports: https://github.com/lanagarmire/lilikoi/issues
RoxygenNote: 6.0.1.9000
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-07-24 22:16:04 UTC; byunits
Author: Fadhl Alakwaa [aut, cre], Sijia Huang [aut]
Maintainer: Fadhl Alakwaa <falakwaa@hawaii.edu>
Repository: CRAN
Date/Publication: 2018-07-30 11:10:03 UTC

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New package draw with initial version 1.0.0
Package: draw
Type: Package
Title: Wrapper Functions for Producing Graphics
Version: 1.0.0
Author: Richard Wen <rrwen.dev@gmail.com>
Maintainer: Richard Wen <rrwen.dev@gmail.com>
Description: A set of user-friendly wrapper functions for creating consistent graphics and diagrams with lines, common shapes, text, and page settings. Compatible with and based on the R 'grid' package.
Imports: grDevices, grid, tools
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
URL: https://github.com/rrwen/draw
BugReports: https://github.com/rrwen/draw/issues
NeedsCompilation: no
Packaged: 2018-07-24 22:07:42 UTC; Rich
Repository: CRAN
Date/Publication: 2018-07-30 11:10:06 UTC

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New package debugr with initial version 0.0.1
Package: debugr
Title: Debug Tool to Watch Objects/Expressions While Running an R Script
Version: 0.0.1
Authors@R: person("Joachim", "Zuckarelli", email = "joachim@zuckarelli.de", role = c("aut", "cre"))
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Description: Tool to print out the value of R objects/expressions while running an R script. Outputs can be made dependent on user-defined conditions/criteria. Debug messages only appear when a global option for debugging is set. This way, 'debugr' code can even remain in the debugged code for later use without any negative effects during normal runtime.
BugReports: https://github.com/jsugarelli/debugr/issues
URL: https://github.com/jsugarelli/debugr/
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: utils, rprojroot, rstudioapi
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-25 19:46:41 UTC; Joachim
Author: Joachim Zuckarelli [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-30 11:50:03 UTC

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New package cytofan with initial version 0.1.0
Package: cytofan
Type: Package
Title: Plot Fan Plots for Cytometry Data using 'ggplot2'
Version: 0.1.0
Authors@R: person("Yann", "Abraham", email = "yann.abraham@gmail.com", role = c("aut", "cre"))
Description: An implementation of Fan plots for cytometry data in 'ggplot2'. For reference see Britton, E.; Fisher, P. & J. Whitley (1998) The Inflation Report Projections: Understanding the Fan Chart <https://www.bankofengland.co.uk/quarterly-bulletin/1998/q1/the-inflation-report-projections-understanding-the-fan-chart>).
License: GPL-3
LazyData: true
Depends: R (>= 3.0.0), ggplot2 (>= 2.2.0)
Imports: RColorBrewer
Suggests: dplyr, reshape2, bodenmiller, knitr, rmarkdown
URL: https://github.com/yannabraham/cytofan
BugReports: https://github.com/yannabraham/cytofan/issues
Encoding: UTF-8
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-25 19:48:34 UTC; ayann
Author: Yann Abraham [aut, cre]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 11:40:03 UTC

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New package trafo with initial version 1.0.0
Package: trafo
Title: Estimation, Comparison and Selection of Transformations
Version: 1.0.0
Date: 2018-07-16
Authors@R: c(person("Lily", "Medina", email = "lilymiru@gmail.com", role = "aut"), person("Piedad", "Castro", role="aut", email = "p25castro@gmail.com"), person("Ann-Kristin", "Kreutzmann", role=c("aut", "cre"), email="ann-kristin.kreutzmann@fu-berlin.de"), person("Natalia", "Rojas-Perilla", role="aut", email = "natalia.rojas@fu-berlin.de"))
Description: Estimation, selection and comparison of several families of transformations. The families of transformations included in the package are the following: Bickel-Doksum (Bickel and Doksum 1981 <doi:10.2307/2287831>), Box-Cox, Dual (Yang 2006 <doi:10.1016/j.econlet.2006.01.011>), Glog (Durbin et al. 2002 <doi:10.1093/bioinformatics/18.suppl_1.S105>), Gpower1, Log, Log-shift opt (Feng et al. 2016 <doi:10.1002/sta4.104>), Manly, Modulus (John and Draper 1980 <doi:10.2307/2986305>), Neglog (Whittaker et al. 2005 <doi:10.1111/j.1467-9876.2005.00520.x>), Reciprocal and Yeo-Johnson. The package simplifies to compare linear models with untransformed and transformed dependent variable as well as linear models where the dependent variable is transformed with different transformations. Furthermore, the package employs maximum likelihood approaches, moments optimization and divergence minimization to estimate the optimal transformation parameter.
Depends: R (>= 3.2.4)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: FNN, moments, pryr, graphics, grDevices, lmtest
Suggests: testthat, R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2018-07-24 08:47:31 UTC; Ann-Kristin
Author: Lily Medina [aut], Piedad Castro [aut], Ann-Kristin Kreutzmann [aut, cre], Natalia Rojas-Perilla [aut]
Maintainer: Ann-Kristin Kreutzmann <ann-kristin.kreutzmann@fu-berlin.de>
Repository: CRAN
Date/Publication: 2018-07-30 10:50:02 UTC

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New package rLandsat with initial version 0.1.0
Package: rLandsat
Type: Package
Title: Landsat Data Complete Download Process
Version: 0.1.0
Author: Himanshu Sikaria - SocialCops [aut, cre], Shilpa Arora [rev], Akash Tandon [rev], Kriti Kathuria [rev]
Maintainer: Himanshu Sikaria<himanshu.sikaria@socialcops.com>
Description: Easily acquire Landsat <https://landsat.usgs.gov>, a remote sensing satellite, data from R. Search for Landsat scenes and download the Landsat data using this library which uses API built by Development Seed <https://api.developmentseed.org/satellites> and U.S. Geological Survey <https://espa.cr.usgs.gov/api>.
License: GPL-3 | file LICENSE
URL: https://github.com/socialcopsdev/rLandsat
BugReports: https://github.com/socialcopsdev/rLandsat/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: R (>= 3.1.2)
Suggests: testthat
Imports: RCurl, svMisc, httr, jsonlite, dplyr, readr, stringr
NeedsCompilation: no
Packaged: 2018-07-24 10:52:26 UTC; Himanshu
Repository: CRAN
Date/Publication: 2018-07-30 11:00:02 UTC

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New package qsub with initial version 1.0.3
Package: qsub
Title: Running Commands Remotely on 'Gridengine' Clusters
Version: 1.0.3
Authors@R: c( person( "Robrecht", "Cannoodt", email = "rcannood@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood") ), person( "Wouter", "Saelens", email = "wouter.saelens@ugent.be", role = c("aut"), comment = c(ORCID = "0000-0002-7114-6248", github = "zouter") ) )
Description: Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.
Depends: R (>= 3.0)
License: GPL-3
LazyData: true
Imports: dplyr, glue, methods, processx, purrr, random, readr, ssh, stringr, tidyr, utils
URL: http://github.com/rcannood/qsub
BugReports: https://github.com/rcannood/qsub/issues
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-07-24 13:39:39 UTC; rcannood
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-30 11:00:05 UTC

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New package PHEindicatormethods with initial version 1.0.8
Package: PHEindicatormethods
Type: Package
Version: 1.0.8
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and their confidence intervals using methods approved for use in the production of Public Health England indicators such as those presented via Fingertips (<http://fingertips.phe.org.uk/>). It provides functions for the generation of proportions, crude rates, means, directly standardised rates, indirectly standardised rates and standardised mortality ratios. Statistical methods are referenced in the following publications. Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>. Dobson et al (1991) <doi:10.1002/sim.4780100317>. Armitage P, Berry G (2002) <doi:10.1002/9780470773666>. Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>. Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Authors@R: c(person("Anderson", "Georgina", , "georgina.anderson@phe.gov.uk", c("aut", "cre")), person("Fox", "Sebastian", , "sebastian.fox@phe.gov.uk", c("ctb")), person("Francis", "Matthew", , "matthew.francis@phe.gov.uk", c("ctb")), person("Fryers", "Paul", , "paul.fryers@phe.gov.uk", c("ctb")))
BugReports: https://github.com/PublicHealthEngland/PHEindicatormethods/issues
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, rlang
Suggests: knitr, readxl, rmarkdown, RODBC, testthat,
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-24 10:51:22 UTC; Georgina.Anderson
Author: Anderson Georgina [aut, cre], Fox Sebastian [ctb], Francis Matthew [ctb], Fryers Paul [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>
Repository: CRAN
Date/Publication: 2018-07-30 10:50:13 UTC

More information about PHEindicatormethods at CRAN
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New package hipread with initial version 0.1.0
Package: hipread
Type: Package
Title: Read Hierarchical Fixed Width Files
Version: 0.1.0
Authors@R: c( person("Greg", "Freedman Ellis", , "gfellis@umn.edu", c("aut", "cre")), person("Derek Burk", role = "ctb"), person("Joe Grover", role = "ctb"), person("Mark Padgham", role = "ctb"), person("Hadley", "Wickham", , "hadley@rstudio.com", "ctb", comment = "Code adapted from readr"), person("Jim", "Hester", , "james.hester@rstudio.com", c("ctb"), comment = "Code adapted from readr"), person("Romain", "Francois", role = "ctb", comment = "Code adapted from readr"), person("R Core Team", role = "ctb", comment = "Code adapted from readr"), person("RStudio", role = c("cph", "fnd"), comment = "Code adapted from readr"), person("Jukka", "Jylänki", role = c("ctb", "cph"), comment = "Code adapted from readr"), person("Mikkel", "Jørgensen", role = c("ctb", "cph"), comment = "Code adapted from readr"), person("University of Minnesota", role = "cph"))
Maintainer: Greg Freedman Ellis <gfellis@umn.edu>
Description: Read hierarchical fixed width files like those commonly used by many census data providers. Also allows for reading of data in chunks, and reading 'gzipped' files without storing the full file in memory.
License: GPL (>= 2) | file LICENSE
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, BH
Imports: Rcpp, dplyr, R6, rlang
Suggests: readr, testthat
SystemRequirements: C++11
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-07-24 14:43:43 UTC; greg
Author: Greg Freedman Ellis [aut, cre], Derek Burk [ctb], Joe Grover [ctb], Mark Padgham [ctb], Hadley Wickham [ctb] (Code adapted from readr), Jim Hester [ctb] (Code adapted from readr), Romain Francois [ctb] (Code adapted from readr), R Core Team [ctb] (Code adapted from readr), RStudio [cph, fnd] (Code adapted from readr), Jukka Jylänki [ctb, cph] (Code adapted from readr), Mikkel Jørgensen [ctb, cph] (Code adapted from readr), University of Minnesota [cph]
Repository: CRAN
Date/Publication: 2018-07-30 11:00:09 UTC

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New package QuClu with initial version 0.1.0
Package: QuClu
Type: Package
Title: Quantile-Based Clustering Algorithms
Version: 0.1.0
Date: 2018-07-20
Author: Christian Hennig, Cinzia Viroli and Laura Anderlucci
Maintainer: Laura Anderlucci <laura.anderlucci@unibo.it>
Description: Various quantile-based clustering algorithms: algorithm CU (Common theta and Unscaled variables), algorithm CS (Common theta and Scaled variables through lambda_j), algorithm VU (Variable-wise theta_j and Unscaled variables) and algorithm VW (Variable-wise theta_j and Scaled variables through lambda_j). Hennig, Viroli, Anderlucci (2018) <arXiv:1806.10403v1>.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 6.0.1
Imports: stats
NeedsCompilation: no
Packaged: 2018-07-30 08:19:51 UTC; laura
Repository: CRAN
Date/Publication: 2018-07-30 09:00:03 UTC

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Sun, 29 Jul 2018

New package pssmooth with initial version 1.0.0
Package: pssmooth
Type: Package
Title: Flexible and Efficient Evaluation of Principal Surrogates/Treatment Effect Modifiers
Version: 1.0.0
Author: Michal Juraska
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
BugReports: https://github.com/mjuraska/pssmooth/issues
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB, Inference on treatment effect modification by biomarker response in a three-phase sampling design (under review). The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response (see the flexible three-phase sampling design in the paper for details). Bootstrap-based procedures are available for pointwise and simultaneous confidence intervals and testing of four relevant hypotheses. Summary and plotting functions are provided for estimation results.
License: GPL-2
URL: https://github.com/mjuraska/pssmooth
Encoding: UTF-8
LazyData: true
Imports: graphics, stats, osDesign, np, chngpt, MASS
Suggests: knitr, rmarkdown
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 18:12:40 UTC; mjuraska
Repository: CRAN
Date/Publication: 2018-07-29 22:00:03 UTC

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New package HDclust with initial version 1.0
Package: HDclust
Type: Package
Title: Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks
Version: 1.0
Date: 2018-07-19
Authors@R: c( person("Yevhen", "Tupikov", email = "yzt116@psu.edu", role = c("aut", "cre")), person("Lin", "Lin", email = "llin@psu.edu", role = "aut"), person("Jia", "Li", email = "jiali@psu.edu", role = "aut"))
Description: Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <http://jmlr.org/papers/v18/16-342.html>.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.16), RcppProgress (>= 0.1)
Depends: methods
LinkingTo: Rcpp, RcppProgress
Collate: 'AllClass.R' 'AllGeneric.R' 'AllMethod.R' 'clustControl.R' 'trainControl.R' 'hmmvbClust.R' 'hmmvbTrain.R' 'vbSearchControl.R' 'package-HDclust.R' 'RcppExports.R' 'sim3.R' 'sim2.R' 'hmmvbBIC.R'
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-23 20:35:01 UTC; eugene
Author: Yevhen Tupikov [aut, cre], Lin Lin [aut], Jia Li [aut]
Maintainer: Yevhen Tupikov <yzt116@psu.edu>
Repository: CRAN
Date/Publication: 2018-07-29 22:00:07 UTC

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New package DeclareDesign with initial version 0.10.0
Package: DeclareDesign
Title: Declare and Diagnose Research Designs
Version: 0.10.0
Authors@R: c(person("Graeme", "Blair", email = "graeme.blair@ucla.edu", role = c("aut", "cre")), person("Jasper", "Cooper", email = "jaspercooper@gmail.com", role = c("aut")), person("Alexander", "Coppock", email = "acoppock@gmail.com", role = c("aut")), person("Macartan", "Humphreys", email = "macartan@gmail.com", role = c("aut")), person("Neal", "Fultz", email = "nfultz@gmail.com", role = c("aut")))
Description: Researchers can characterize and learn about the properties of research designs before implementation using `DeclareDesign`. Ex ante declaration and diagnosis of designs can help researchers clarify the strengths and limitations of their designs and to improve their properties, and can help readers evaluate a research strategy prior to implementation and without access to results. It can also make it easier for designs to be shared, replicated, and critiqued.
Depends: R (>= 3.4.0), randomizr (>= 0.16.1), fabricatr (>= 0.4.0), estimatr (>= 0.10.0)
Imports: rlang, methods
License: MIT + file LICENSE
URL: https://declaredesign.org, https://github.com/DeclareDesign/DeclareDesign
BugReports: https://github.com/DeclareDesign/DeclareDesign/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat, knitr, rmarkdown, AER, dplyr, data.table, ggplot2, future.apply, broom, MASS, Matching, betareg, biglm, gam, lfe, sf, reshape2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-23 18:12:40 UTC; gdblair
Author: Graeme Blair [aut, cre], Jasper Cooper [aut], Alexander Coppock [aut], Macartan Humphreys [aut], Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Repository: CRAN
Date/Publication: 2018-07-29 21:50:03 UTC

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New package metaDigitise with initial version 1.0.0
Package: metaDigitise
Title: Extract and Summarise Data from Published Figures
Version: 1.0.0
Authors@R: c(person("Joel", "Pick", email = "joel.l.pick@gmail.com", role = c("aut")), person("Shinichi", "Nakagawa", email = "s.nakagawa@unsw.edu.au", role = c("aut")), person("Daniel", "Noble", email = "daniel.wa.noble@gmail.com", role = c("aut", "cre")))
Description: High-throughput, flexible and reproducible extraction of data from figures in primary research papers. metaDigitise() can extract data and / or automatically calculate summary statistics for users from box plots, bar plots (e.g., mean and errors), scatter plots and histograms.
Depends: R (>= 3.4)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: magick, stats, graphics, utils, purrr
Suggests: mockery, testthat, knitr, rmarkdown
BugReports: https://github.com/daniel1noble/metaDigitise/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-23 01:11:06 UTC; danielnoble
Author: Joel Pick [aut], Shinichi Nakagawa [aut], Daniel Noble [aut, cre]
Maintainer: Daniel Noble <daniel.wa.noble@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-29 08:40:03 UTC

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New package bcf with initial version 1.2
Package: bcf
Type: Package
Title: Causal Inference for a Binary Treatment and Continuous Outcome using Bayesian Causal Forests
Version: 1.2
Date: 2018-07-24
Author: P. Richard Hahn, Jared S. Murray, and Carlos Carvalho
Maintainer: Jared S. Murray <jared.murray@mccombs.utexas.edu>
Description: Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2017) <arXiv:1706.09523> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
License: GPL-3
Depends: Rcpp (>= 0.10.4)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-07-24 21:41:44 UTC; jared
Repository: CRAN
Date/Publication: 2018-07-29 08:40:07 UTC

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New package rerf with initial version 1.1.3
Package: rerf
Type: Package
Title: Randomer Forest
Version: 1.1.3
Date: 2018-07-05
Authors@R: c(person("James", "Browne", role = c("aut", "cre"), email = "jbrowne6@jhu.edu"), person("Tyler", "Tomita", role = "aut", email = "ttomita2@jhmi.edu"), person("Joshua", "Vogelstein", role = "ths", email = "jovo@jhu.edu"))
Description: Random Forester (RerF) is an algorithm developed by Tomita (2016) <arXiv:1506.03410v2> which is similar to Random Forest - Random Combination (Forest-RC) developed by Breiman (2001) <doi:10.1023/A:1010933404324>. Random Forests create axis-parallel, or orthogonal trees. That is, the feature space is recursively split along directions parallel to the axes of the feature space. Thus, in cases in which the classes seem inseparable along any single dimension, Random Forests may be suboptimal. To address this, Breiman also proposed and characterized Forest-RC, which uses linear combinations of coordinates rather than individual coordinates, to split along. This package, 'rerf', implements RerF which is similar to Forest-RC. The difference between the two algorithms is where the random linear combinations occur: Forest-RC combines features at the per tree level whereas RerF takes linear combinations of coordinates at every node in the tree.
License: GPL-2
URL: https://github.com/neurodata/R-RerF
Imports: parallel, RcppZiggurat, utils, stats, dummies
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: GNU make
ByteCompile: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-07-28 17:48:47 UTC; james
Author: James Browne [aut, cre], Tyler Tomita [aut], Joshua Vogelstein [ths]
Maintainer: James Browne <jbrowne6@jhu.edu>
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-07-29 06:10:03 UTC

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New package rise with initial version 1.0.3
Package: rise
Version: 1.0.3
Title: Conduct RISE Analysis
Description: Implements techniques for educational resource inspection, selection, and evaluation (RISE) described in Bodily, Nyland, and Wiley (2017) <doi:10.19173/irrodl.v18i2.2952>. Automates the process of identifying learning materials that are not effectively supporting student learning in technology-mediated courses by synthesizing information about access to course content and performance on assessments.
Authors@R: c(person("David", "Wiley", email= "david.wiley@gmail.com", role = c("aut", "cre")), person("Lumen Learning", role= "cph"))
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.0.1
Depends: R(>= 2.10.0), ggplot2, stats
Suggests: testthat
BugReports: https://github.com/lumenlearning/rise/issues
NeedsCompilation: no
Packaged: 2018-07-23 15:08:02 UTC; david
Author: David Wiley [aut, cre], Lumen Learning [cph]
Maintainer: David Wiley <david.wiley@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-29 06:00:03 UTC

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Sat, 28 Jul 2018

New package SurvTrunc with initial version 0.1.0
Package: SurvTrunc
Type: Package
Title: Analysis of Doubly Truncated Data
Version: 0.1.0
Date: 2018-07-13
Author: Lior Rennert
Maintainer: Lior Rennert <liorr@clemson.edu>
Description: Package performs Cox regression and survival distribution function estimation when the survival times are subject to double truncation. The estimation procedure for each method involves inverse probability weighting, where the weights correspond to the inverse of the selection probabilities and are estimated using the survival times and truncation times only. Both methods require that the survival and truncation times are quasi-independent. A test for checking this independence assumption is also included in this package. The functions available in this package for Cox regression, survival distribution function estimation, and testing independence under double truncation are based on the following methods, respectively: Rennert and Xie (2017) <doi:10.1111/biom.12809>, Shen (2010) <doi:10.1007/s10463-008-0192-2>, Martin and Betensky (2005) <doi:10.1198/016214504000001538>.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Depends: survival
Imports: stats, grDevices, graphics
NeedsCompilation: no
Packaged: 2018-07-23 13:45:01 UTC; Lior
Repository: CRAN
Date/Publication: 2018-07-28 16:40:08 UTC

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New package gmvarkit with initial version 1.0.0
Package: gmvarkit
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Version: 1.0.0
Authors@R: person("Savi", "Virolainen", email = "savi.virolainen@helsinki.fi", role = c("aut", "cre"))
Description: Maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics, forecasting and simulations. Applying general linear constraints to the autoregressive parameters is supported. Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: Brobdingnag (>= 1.2-5), mvnfast (>= 0.2.5), parallel (>= 3.4.0), stats (>= 3.4.0), pbapply (>= 1.3-4), graphics (>= 3.4.0), grDevices (>= 3.4.0)
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-23 13:39:53 UTC; savi
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Repository: CRAN
Date/Publication: 2018-07-28 16:30:03 UTC

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New package ggsom with initial version 0.2.0
Package: ggsom
Type: Package
Title: New Data Visualisations for SOMs Cluster
Version: 0.2.0
Authors@R: c(person("Felipe","Carvalho", role=c("aut","cre"), email="lipecaso@gmail.com"), person("Rafael", "Santos", role = "ctb", email="rafael.santos@inpe.br"))
Description: Contains parallel coordinate and attribute mapping visualisations for cluster data.
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
Depends: R (>= 3.4.0)
Imports: tidyverse, kohonen, ggthemes, ggplot2, dplyr, tidyr
Suggests: RCurl, knitr, rmarkdown, testthat
URL: https://github.com/oldlipe/ggsom
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Collate: 'utils.R' 'aes_som.R' 'ggsom.R' 'ggsom_line.R' 'ggsom_rect.R' 'ggsom_ribbon.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2018-07-23 17:10:56 UTC; asainpe
Author: Felipe Carvalho [aut, cre], Rafael Santos [ctb]
Maintainer: Felipe Carvalho <lipecaso@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-28 16:50:03 UTC

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New package fedregs with initial version 0.1.0
Package: fedregs
Type: Package
Title: Text Analysis of the US Code of Federal Regulations
Version: 0.1.0
Authors@R: person("Scott", "Large", email = "scott.large@noaa.gov", role = c("cre", "aut"))
Description: The Code of Federal Regulations (CFR) annual edition is the codification of the general and permanent rules published in the Federal Register by the departments and agencies of the Federal Government of the United States of America. Simply, the 'fedregs' package facilitates word processing and sentiment analysis of the CFR using tidy principles. Note: According to the Code of Federal Regulations XML Rendition User Guide Document: "In general, there are no restrictions on re-use of information in Code of Federal Regulations material because U.S. Government works are not subject to copyright. OFR and GPO do not restrict downstream uses of Code of Federal Regulations data, except that independent providers should be aware that only the OFR and GPO are entitled to represent that they are the providers of the official versions of the Code of Federal Regulations and related Federal Register publications."
License: GPL-3
BugReports: https://github.com/slarge/fedregs/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0),
Imports: dplyr (>= 0.7.4), magrittr (>= 1.5), xml2 (>= 1.2.0), purrr(>= 0.2.5), rvest(>= 0.3.2), stringi(>= 1.1.7), httr (>= 1.3.1), tidytext (>= 0.1.9)
Suggests: ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), testthat (>= 2.0.0)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 13:55:40 UTC; scott.large
Author: Scott Large [cre, aut]
Maintainer: Scott Large <scott.large@noaa.gov>
Repository: CRAN
Date/Publication: 2018-07-28 16:40:06 UTC

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New package ems with initial version 1.2.0
Package: ems
Title: Epimed Solutions Collection for Data Editing, Analysis, and Benchmark of Health Units
Version: 1.2.0
Date: 2018-07-23
Authors@R: c(person("Lunna", "Borges", role = c("aut","cre"), email = "lunna.borges@epimedsolutions.com"), person("Pedro", "Brasil", role = c("aut"), email = "pedro.brasil@epimedsolutions.com"), person("Camila", "Cardoso", role = c("aut"), email = "camila.cardoso@epimedsolutions.com"), person("Caio", "Ferreira", role = c("aut"), email = "caio.ferreira@epimedsolutions.com"))
Description: Collection of functions for data analysis and editing of clinical and epidemiological data. Most of them are related to benchmark with prediction models.
Depends: R (>= 3.2.2)
License: GPL (>= 2)
LazyData: true
RoxygenNote: 6.0.1
Author: Lunna Borges [aut, cre], Pedro Brasil [aut], Camila Cardoso [aut], Caio Ferreira [aut]
Maintainer: Lunna Borges <lunna.borges@epimedsolutions.com>
Repository: CRAN
Repository/R-Forge/Project: ems
Repository/R-Forge/Revision: 85
Repository/R-Forge/DateTimeStamp: 2018-07-23 13:56:30
Date/Publication: 2018-07-28 16:50:06 UTC
NeedsCompilation: no
Packaged: 2018-07-23 14:10:10 UTC; rforge

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New package Hapi with initial version 0.0.3
Package: Hapi
Type: Package
Title: Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
Version: 0.0.3
Author: Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia
Maintainer: Ruidong Li <rli012@ucr.edu>
Description: Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: false
Imports: HMM, ggplot2
Suggests: knitr, testthat
VignetteBuilder: knitr
biocViews: SNP, GenomicVariation, Genetics, HiddenMarkovModel, SingleCell, Sequencing, Microarray
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 04:15:32 UTC; ruidong
Repository: CRAN
Date/Publication: 2018-07-28 15:10:07 UTC

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New package fredr with initial version 1.0.0
Package: fredr
Title: An R Client for the 'FRED' API
Version: 1.0.0
Authors@R: c( person("Sam", "Boysel", email = "sboysel@gmail.com", role = c("aut", "cre")), person("Davis", "Vaughan", email = "dvaughan@business-science.io", role = c("aut")) )
Maintainer: Sam Boysel <sboysel@gmail.com>
Description: An R client for the 'Federal Reserve Economic Data' ('FRED') API <https://api.stlouisfed.org>. Functions to retrieve economic time series and other data from 'FRED'.
URL: https://github.com/sboysel/fredr
BugReports: https://github.com/sboysel/fredr/issues
Depends: R (>= 3.2.2)
Imports: httr, jsonlite, tibble, rlang
Suggests: covr, dplyr, ggplot2, knitr, purrr, rmarkdown, testthat, zoo, xts
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-23 01:57:40 UTC; sboysel
Author: Sam Boysel [aut, cre], Davis Vaughan [aut]
Repository: CRAN
Date/Publication: 2018-07-28 15:20:03 UTC

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New package FossilSim with initial version 2.0.0
Package: FossilSim
Type: Package
Title: Simulation of Fossil and Taxonomy Data
Version: 2.0.0
Authors@R: c(person("Rachel", "Warnock", email="rachel.warnock@bsse.ethz.ch", role=c("aut","cph")), person("Joelle", "Barido-Sottani", email="joelle.barido-sottani@m4x.org",role=c("aut","cre","cph")), person("Walker", "Pett",role=c("aut","cph")))
Description: Simulating taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.0.1
Imports: ape, TreeSim,
Suggests: paleotree, knitr, rmarkdown, devtools
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2018-07-23 09:27:05 UTC; Joelle
Author: Rachel Warnock [aut, cph], Joelle Barido-Sottani [aut, cre, cph], Walker Pett [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Repository: CRAN
Date/Publication: 2018-07-28 15:50:16 UTC

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New package fingertipscharts with initial version 0.0.1
Package: fingertipscharts
Type: Package
Version: 0.0.1
Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Authors@R: c(person("Sebastian", "Fox", , "sebastian.fox@phe.gov.uk", c("aut", "cre")))
BugReports: https://github.com/PublicHealthEngland/fingertipscharts/issues
Imports: broom, dplyr, fingertipsR, geojsonio, ggplot2 (>= 3.0), leaflet, lemon, mapproj, purrr, rlang, scales, stats, stringr, tibble, tidyr, utils
Suggests: knitr, rmarkdown, testthat, vdiffr
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 08:54:08 UTC; sebastian.fox
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Repository: CRAN
Date/Publication: 2018-07-28 15:30:02 UTC

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New package dexterMST with initial version 0.1.0
Package: dexterMST
Type: Package
Title: CML Calibration of Multi Stage Tests
Version: 0.1.0
Date: 2018-07-12
Authors@R: c(person("Timo", "Bechger", role = c("aut", "cre"), email = "tmbechger@gmail.com"), person("Jesse","Koops", role = "aut"), person("Ivailo","Partchev", role = "aut"), person("Gunter", "Maris", role = "aut"), person("Robert", "Zwitser", role = "ctb"))
Maintainer: Timo Bechger <tmbechger@gmail.com>
Description: Conditional Maximum Likelihood Calibration and data management of multistage tests. Functions for calibration of the Extended Nominal Response and the Interaction models, DIF and profile analysis. See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
License: GPL (>= 2)
URL: http://dexterities.netlify.com
BugReports: https://github.com/jessekps/dexter/issues
Imports: Rcpp (>= 0.12.14), dexter (>= 0.8.0), dplyr (>= 0.7.4), RSQLite (>= 2.0), rlang (>= 0.2.0), dbplyr (>= 1.2.0), fastmatch, igraph (>= 1.2.1), tidyr (>= 0.8.0), tibble, DBI, crayon, graphics, methods, stats, utils
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: knitr, testthat, mirt, ggplot2, Cairo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-19 20:11:19 UTC; timo
Author: Timo Bechger [aut, cre], Jesse Koops [aut], Ivailo Partchev [aut], Gunter Maris [aut], Robert Zwitser [ctb]
Repository: CRAN
Date/Publication: 2018-07-28 15:10:03 UTC

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New package demu with initial version 0.2.0
Package: demu
Type: Package
Title: Optimal Design Emulators via Point Processes
Version: 0.2.0
Date: 2018-07-06
Author: Matthew T. Pratola <mpratola@stat.osu.edu> [aut, cre, cph]
Maintainer: Matthew T. Pratola <mpratola@stat.osu.edu>
Description: Implements the Determinantal point process (DPP) based optimal design emulator described in Pratola, Lin and Craigmile (2018) <arXiv:1804.02089> for Gaussian process regression models. See <http://www.matthewpratola.com/software> for more information and examples.
Depends: R (>= 3.2.3)
Imports: Rcpp (>= 0.12.12), stats, fields, spam, Matrix, ClusterR
LinkingTo: Rcpp, RcppArmadillo
License: AGPL-3
LazyData: true
NeedsCompilation: yes
Packaged: 2018-07-23 09:49:45 UTC; mpratola
Repository: CRAN
Date/Publication: 2018-07-28 15:40:02 UTC

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New package cgraph with initial version 1.0.1
Package: cgraph
Type: Package
Title: Computational Graphs
Version: 1.0.1
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
URL: https://cgraph.org/
BugReports: https://github.com/triepels/cgraph/issues
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various functions including basic arithmetic, trigonometry functions, and linear algebra functions. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: R6
Suggests: Rgraphviz, testthat
RoxygenNote: 6.0.1
Collate: 'session.R' 'array.R' 'cgraph.R' 'fun.R' 'math.R' 'misc.R' 'print.R' 'transform.R' 'trig.R'
NeedsCompilation: yes
Packaged: 2018-07-23 11:07:06 UTC; ron
Repository: CRAN
Date/Publication: 2018-07-28 15:50:08 UTC

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New package ActisoftR with initial version 0.0.1
Package: ActisoftR
Type: Package
Title: A Toolbox for Parsing Scored Actigraphy Data
Version: 0.0.1
Date: 2018-07-01
Depends: R (>= 3.1.0)
Authors@R: c(person("Edgar", "Santos-Fernandez", , "edgar.santosfdez@gmail.com", c("aut", "cre")), person("Lora", "Wu", , "L.Wu@massey.ac.nz", c("aut")), person("Margo", "van den Berg", , "M.J.vandenBerg@massey.ac.nz", c("aut" )) )
Description: 'Actigraphy' is a cost-effective and convenient tool for activity-based monitoring. 'ActisoftR' was designed for parsing 'actigraphy' outputs and to summarise scored data across user-defined intervals. It consists of several functions for importing, generating reports and statistics, and for data visualization.
URL: https://github.com/SWRC/ActisoftR
Imports: ggplot2, dplyr, scales, tibble, lubridate, data.table, magrittr, methods, RColorBrewer, tidyr
Suggests: DT, Rcpp, rmarkdown, roxygen2, knitr, testthat, readr, plotly, devtools
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-23 04:48:01 UTC; santosfe
Author: Edgar Santos-Fernandez [aut, cre], Lora Wu [aut], Margo van den Berg [aut]
Maintainer: Edgar Santos-Fernandez <edgar.santosfdez@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-28 15:20:08 UTC

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Fri, 27 Jul 2018

New package rrtable with initial version 0.1.0
Package: rrtable
Type: Package
Title: Reproducible Research with a Table of R Codes
Version: 0.1.0
Imports: stringr, ggplot2 (>= 2.2.0), officer (>= 0.3.0), purrr (>= 0.2.4), flextable (>= 0.4.4), rvg, magrittr, devEMF, moonBook (>= 0.1.8), rmarkdown, shiny, editData, readr (>= 1.1.1), ztable (>= 0.1.8)
Authors@R: person("Keon-Woong", "Moon", email = "cardiomoon@gmail.com", role = c("aut", "cre"))
Description: Makes documents containing plots and tables from a table of R codes. Can make "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS powerpoint')" documents with or without R code. In the package, modularized 'shiny' app codes are provided. These modules are intended for reuse across applications.
Depends: R(>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Suggests: knitr
NeedsCompilation: no
Packaged: 2018-07-22 23:19:44 UTC; cardiomoon
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-27 22:20:03 UTC

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New package mable with initial version 1.0
Package: mable
Title: Maximum Approximate Bernstein Likelihood Estimation
Version: 1.0
Date: 2018-07-11
Author: Zhong Guan [aut, cre]
Maintainer: Zhong Guan <zguan@iu.edu>
Depends: R (>= 3.0.0)
Suggests: graphics, mixtools, stats
Description: Fit raw or grouped continuous data from a population with a smooth density on unit interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>.
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2018-07-22 23:20:25 UTC; zguan
Repository: CRAN
Date/Publication: 2018-07-27 22:20:16 UTC

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New package UnitCircle with initial version 0.1.3
Package: UnitCircle
Type: Package
Title: Check if Roots of a Polynomial Lie Outside the Unit Circle
Version: 0.1.3
Author: Jonathan Berrisch
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Description: The uc.check() function checks whether the roots of a given polynomial lie outside the Unit circle. You can also easily draw an unit circle.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.0.1
URL: https://github.com/BerriJ/UnitCircle
BugReports: https://github.com/BerriJ/UnitCircle/issues
NeedsCompilation: no
Packaged: 2018-07-22 21:45:15 UTC; Jonathan
Repository: CRAN
Date/Publication: 2018-07-27 21:30:02 UTC

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New package postal with initial version 0.1.0
Package: postal
Type: Package
Title: United States Postal Service API Interface
Version: 0.1.0
Author: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>
Maintainer: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>
Description: An interface to the United States Postal Service Post Calc and Zone Calc APIs, postal allows users to find the postage price, delivery day, and other information for packages and envelopes, as well as to find the postal zone for an origin and a destination zip code pair.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
URL: https://github.com/aedobbyn/postal/
BugReports: https://github.com/aedobbyn/postal/issues/
Imports: curl, dplyr, glue, janitor, jsonlite, lubridate, magrittr, purrr, readr, stringr, tibble (>= 1.2), tidyr
Suggests: covr, cowsay, ggplot2, here, knitr, maps, rmarkdown, stats, testthat, zipcode
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-22 20:58:37 UTC; amanda
Repository: CRAN
Date/Publication: 2018-07-27 21:20:02 UTC

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New package MMDvariance with initial version 0.0.9
Package: MMDvariance
Type: Package
Title: Detecting Differentially Variable Genes Using the Mixture of Marginal Distributions
Version: 0.0.9
Date: 2018-07-22
Authors@R: c( person("Xuan", "Li", role=c("aut", "ctb"), email = "lixuan0759@gmail.com"), person("Yuejiao", "Fu", role=c("aut", "ctb"), email = "yuejiao@mathstat.yorku.ca"), person("Xiaogang", "Wang", role = c("aut", "ctb"), email = "stevenw@mathstat.yorku.ca"), person("Dawn L.", "DeMeo", role = c("aut", "ctb"), email = "redld@channing.harvard.edu"), person("Kelan", "Tantisira", role = c("aut", "ctb"), email = "rekgt@channing.harvard.edu"), person("Scott T.", "Weiss", role = c("aut", "ctb"), email = "restw@channing.harvard.edu"), person("Weiliang", "Qiu", role=c("aut", "cre"), email = "weiliang.qiu@gmail.com") )
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
Depends: R (>= 3.4.0), Biobase, lawstat
Imports: MASS, graphics, stats
Suggests: ALL
biocViews: Bioinformatics, DifferentialExpression
Description: Gene selection based on variance using the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions. Please see the reference: Li X, Fu Y, Wang X, DeMeo DL, Tantisira K, Weiss ST, Qiu W. (2018) <doi:10.1155/2018/6591634>.
License: GPL (>= 2)
Packaged: 2018-07-22 18:10:43 UTC; weiliangqiu
NeedsCompilation: no
Author: Xuan Li [aut, ctb], Yuejiao Fu [aut, ctb], Xiaogang Wang [aut, ctb], Dawn L. DeMeo [aut, ctb], Kelan Tantisira [aut, ctb], Scott T. Weiss [aut, ctb], Weiliang Qiu [aut, cre]
Repository: CRAN
Date/Publication: 2018-07-27 21:10:14 UTC

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New package ggpage with initial version 0.2.2
Package: ggpage
Type: Package
Title: Creates Page Layout Visualizations
Version: 0.2.2
Authors@R: person("Emil", "Hvitfeldt", email = "emilhhvitfeldt@gmail.com", role = c("aut", "cre"))
Description: Facilitates the creation of page layout visualizations in which words are represented as rectangles with sizes relating to the length of the words. Which then is divided in lines and pages for easy overview of up to quite large texts.
Depends: R (>= 3.0.0),
Imports: dplyr, ggplot2 (>= 2.0.0), stringr, tidytext (>= 0.1.0), magrittr, purrr, rlang
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: testthat, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-22 18:04:17 UTC; Emilhvitfeldthansen
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-27 21:10:07 UTC

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New package funLBM with initial version 1.0
Package: funLBM
Type: Package
Title: Model-Based Co-Clustering of Functional Data
Version: 1.0
Date: 2018-07-18
Author: Charles Bouveyron and Julien Jacques
Maintainer: Charles Bouveyron <charles.bouveyron@math.cnrs.fr>
Depends: fda, parallel, funFEM, R (>= 3.1.0)
Description: The funLBM algorithm allows to simultaneously cluster the rows and the columns of a data matrix where each entry of the matrix is a function or a time series.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-07-22 15:38:53 UTC; bouveyro
Repository: CRAN
Date/Publication: 2018-07-27 21:10:11 UTC

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New package trread with initial version 0.2.4
Package: trread
Type: Package
Title: Transit File Reader
Version: 0.2.4
Authors@R: c( person("Tom", "Buckley", role = c("aut", "cre"), email = "tom@tbuckl.com"), person("Danton", "Noriega-Goodwin", role = c("aut"), email = "danton.noriega@gmail.com"), person("Elaine", "McVey", role = c("aut"), email = "elaine.mcvey@transloc.com"), person("Charles Hans", "Thompson", role = c("ctb"), email = "hans.thompson1@gmail.com"), person("Michael", "Sumner", role = c("ctb")) )
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
License: GPL
LazyData: TRUE
Depends: R (>= 3.2.4)
Imports: dplyr, tibble, readr, httr, htmltools, magrittr, stringr, assertthat, scales, here
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.0.1
URL: https://github.com/r-gtfs/trread
BugReports: https://github.com/r-gtfs/trread/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-22 18:28:12 UTC; tbuck
Author: Tom Buckley [aut, cre], Danton Noriega-Goodwin [aut], Elaine McVey [aut], Charles Hans Thompson [ctb], Michael Sumner [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Repository: CRAN
Date/Publication: 2018-07-27 21:00:03 UTC

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New package tidymodels with initial version 0.0.1
Package: tidymodels
Title: Easily Install and Load the 'Tidymodels' Packages
Version: 0.0.1
Authors@R: c( person("Kuhn", "Max", , "max@rstudio.com", role = c("aut", "cre")), person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut")), person("RStudio", role = c("cph", "fnd")) )
Description: The tidy modeling "verse" is a collection of package for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.
License: GPL-3 | file LICENSE
URL: https://github.com/tidymodels/tidymodels
BugReports: https://github.com/tidymodels/tidymodels/issues
Depends: R (>= 3.1)
Imports: broom (>= 0.5.0), cli (>= 1.0.0), crayon (>= 1.3.4), dplyr (>= 0.7.6), ggplot2 (>= 3.0.0), infer (>= 0.3.0), magrittr (>= 1.5), pillar (>= 1.3.0), purrr (>= 0.2.5), recipes (>= 0.1.3), rlang (>= 0.2.1), rsample (>= 0.0.2), rstudioapi (>= 0.7), tibble (>= 1.4.2), tidytext (>= 0.1.9), tidypredict (>= 0.2.0), tidyposterior (>= 0.0.1), yardstick (>= 0.0.1)
Suggests: covr, knitr, rmarkdown, testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-22 16:04:08 UTC; max
Author: Kuhn Max [aut, cre], Hadley Wickham [aut], RStudio [cph, fnd]
Maintainer: Kuhn Max <max@rstudio.com>
Repository: CRAN
Date/Publication: 2018-07-27 21:00:06 UTC

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New package rviewgraph with initial version 1.2
Package: rviewgraph
Type: Package
Title: Animated Graph Layout Viewer
Version: 1.2
Date: 2018-07-06
Author: Alun Thomas
Maintainer: Alun Thomas <Alun.Thomas@utah.edu>
Description: This is an 'R' interface to Alun Thomas's 'ViewGraph' 'Java' graph viewing program. It takes a graph specified as an incidence matrix, list of edges, or in 'igraph' format and runs a graphical user interface that shows an animation of a force directed algorithm positioning the vertices in two dimensions. It works well for graphs of various structure of up to a few thousand vertices. It's not fazed by graphs that comprise several components. The coordinates can be read as an 'igraph' style layout matrix at any time. The user can mess with the layout using a mouse, preferably one with 3 buttons, and some keyed commands. The 'Java' program 'ViewGraph' is contained in Alun Thomas's 'JPSGCS' collection of 'Java' programs for statistical genetics and computational statistics. The homepage for 'JPSGCS' is <http://www-genepi.med.utah.edu/~alun/software/index.html>. The documentation page for 'ViewGraph' is at <http://www-genepi.med.utah.edu/~alun/software/docs/ViewGraph.html>.
Suggests:
Enhances: igraph, Matrix
Depends: rJava
License: GPL-2
LazyLoad: yes
Packaged: 2018-07-22 15:54:06 UTC; alun
Collate: 'onLoad.R' 'rViewGraph.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-07-27 21:00:09 UTC

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New package RaceID with initial version 0.0.9
Package: RaceID
Title: Identification of Cell Types and Inference of Lineage Trees from Single-Cell RNA-Seq Data
Version: 0.0.9
Date: 2018-07-14
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Depends: R (>= 3.3)
biocViews:
Imports: coop, cluster, FateID, fpc, grDevices, ica, igraph, irlba, locfit, methods, MASS, Matrix, pheatmap, quadprog, randomForest, RColorBrewer, Rtsne, vegan
Suggests: DESeq2, destiny, knitr, rmarkdown, scran
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-22 13:41:10 UTC; d.grun
Repository: CRAN
Date/Publication: 2018-07-27 13:40:02 UTC

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New package mdir.logrank with initial version 0.0.2
Package: mdir.logrank
Type: Package
Title: Multiple-Direction Logrank Test
Version: 0.0.2
Date: 2018-07-22
Author: Marc Ditzhaus and Sarah Friedrich
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>
Depends: R (>= 3.5.0)
Description: Implemented is the multiple-direction logrank test for two-sample right censored data. In addition to the statistic two p-values are calculated: the first one is based on a chi-squared approximation and the second one is based on a permutation approach. Ditzhaus, M. and Friedrich, S. (2018) <arXiv:1807.05504>.
License: GPL-2 | GPL-3
Imports: plyr (>= 1.8.3), stats, MASS (>= 7.3-47)
LazyData: TRUE
BugReports: http://github.com/marcdii/mdir.logrank/issues
Suggests: RGtk2 (>= 2.20.34), coin
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-22 15:53:17 UTC; sarah
Repository: CRAN
Date/Publication: 2018-07-27 13:50:02 UTC

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Thu, 26 Jul 2018

New package CEC with initial version 0.10.2
Package: CEC
Title: Cross-Entropy Clustering
Version: 0.10.2
Date: 2018-07-26
Author: Konrad Kamieniecki [aut, cre], Przemyslaw Spurek [ctb]
Maintainer: Konrad Kamieniecki <konrad.kamieniecki@alumni.uj.edu.pl>
Description: CEC divides data into Gaussian type clusters. The implementation allows the simultaneous use of various type Gaussian mixture models, performs the reduction of unnecessary clusters and it's able to discover new groups. Based on Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>.
ByteCompile: true
URL: https://github.com/azureblue/cec
Encoding: UTF-8
NeedsCompilation: yes
SystemRequirements: C++11
License: GPL-3
Imports: graphics, methods, stats, utils
Packaged: 2018-07-26 20:10:44 UTC; konrad
Repository: CRAN
Date/Publication: 2018-07-26 22:00:06 UTC

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Wed, 25 Jul 2018

New package RTransferEntropy with initial version 0.2.5
Package: RTransferEntropy
Type: Package
Title: Measuring Information Flow Between Time Series with Shannon and Renyi Transfer Entropy
Version: 0.2.5
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Authors@R: c( person("Simon", "Behrendt", , "simon.behrendt@zu.de", role = c("aut", "cre")), person("David", "Zimmermann", role = c("aut")), person("Thomas", "Dimpfl", role = c("aut")), person("Franziska", "Peter", role = c("aut")) )
License: GPL-3
URL: https://github.com/BZPaper/RTransferEntropy
BugReports: https://github.com/BZPaper/RTransferEntropy/issues
Encoding: UTF-8
Depends: R (>= 3.1.2)
Imports: future, future.apply, Rcpp
LazyData: true
RoxygenNote: 6.0.1
LinkingTo: Rcpp
Suggests: data.table, ggplot2, gridExtra, knitr, quantmod, rmarkdown, testthat, vars
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-22 13:51:32 UTC; david
Author: Simon Behrendt [aut, cre], David Zimmermann [aut], Thomas Dimpfl [aut], Franziska Peter [aut]
Maintainer: Simon Behrendt <simon.behrendt@zu.de>
Repository: CRAN
Date/Publication: 2018-07-25 22:40:09 UTC

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New package Nmisc with initial version 0.3.2
Package: Nmisc
Type: Package
Title: Miscellaneous Functions Used at 'Numeract LLC'
Version: 0.3.2
Authors@R: c( person("Mike", "Badescu", email = "mike.badescu@numeract.com", role = c("aut", "cre")), person("Ana-Maria", "Niculescu", role = "aut"), person("Teodor", "Ciuraru", role = "ctb"), person("Numeract LLC", role = "cph") )
Description: Contains functions useful for debugging, set operations on vectors, and 'UTC' date and time functionality. It adds a few vector manipulation verbs to 'purrr' and 'dplyr' packages. It can also generate an R file to install and update packages to simplify deployment into production. The functions were developed at the data science firm 'Numeract LLC' and are used in several packages and projects.
URL: https://github.com/numeract/Nmisc
BugReports: https://github.com/numeract/Nmisc/issues
License: MIT + file LICENCE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Depends: R (>= 3.4)
Imports: dplyr, magrittr, purrr, rappdirs, rlang, tibble, stringr
Suggests: lubridate, testthat, covr
NeedsCompilation: no
Packaged: 2018-07-22 15:45:48 UTC; Mike
Author: Mike Badescu [aut, cre], Ana-Maria Niculescu [aut], Teodor Ciuraru [ctb], Numeract LLC [cph]
Maintainer: Mike Badescu <mike.badescu@numeract.com>
Repository: CRAN
Date/Publication: 2018-07-25 22:20:09 UTC

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New package weibulltools with initial version 0.5.4
Package: weibulltools
Type: Package
Title: Statistical Methods for Life Data Analysis
Version: 0.5.4
Authors@R: person("Hensel", "Tim-Gunnar", email = "tim-gunnar.hensel@tu-berlin.de", role = c("aut", "cre"))
Description: Contains methods for examining bench test or field data using the well-known Weibull Analysis. It includes Monte Carlo simulation for estimating the life span of products that have not failed, taking account of registering and reporting delays as stated in (Verband der Automobilindustrie e.V. (VDA), 2016, <ISSN:0943-9412>). If the products looked upon are vehicles, the covered mileage can be estimated as well. It also provides non-parametric estimators like Median Ranks, Kaplan-Meier (Abernethy, 2006, <ISBN:978-0-9653062-3-2>), Johnson (Johnson, 1964, <ISBN:978-0444403223>), and Nelson-Aalen for failure probability estimation within samples that contain failures as well as censored data. Methods for estimating the parameters of lifetime distributions, like Maximum Likelihood and Median-Rank Regression, (Genschel and Meeker, 2010, <DOI:10.1080/08982112.2010.503447>) as well as the computation of confidence intervals of quantiles and probabilities using the delta method related to Fisher's confidence intervals (Meeker and Escobar, 1998, <ISBN:9780471673279>) and the beta-binomial confidence bounds are also included. If desired, the data can automatically be divided into subgroups using segmented regression. Besides the calculation, methods for interactive visualization of the edited data using *Plotly* are provided as well. These visualizations include the layout of a probability plot for a specified distribution, the graphical technique of probability plotting and the possibility of adding regression lines and confidence bounds to existing plots.
License: GPL-2
Imports: dplyr, magrittr, plotly, Rcpp, sandwich, segmented, SPREDA, survival
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: yes
Packaged: 2018-07-25 12:05:59 UTC; Tim.Hensel
Author: Hensel Tim-Gunnar [aut, cre]
Maintainer: Hensel Tim-Gunnar <tim-gunnar.hensel@tu-berlin.de>
Repository: CRAN
Date/Publication: 2018-07-25 21:50:03 UTC

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New package jetpack with initial version 0.3.1
Package: jetpack
Type: Package
Title: A Friendly Package Manager
Version: 0.3.1
Date: 2018-07-10
Authors@R: person("Andrew", "Kane", email = "andrew@chartkick.com", role = c("aut", "cre"))
Description: Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
URL: https://github.com/ankane/jetpack
BugReports: https://github.com/ankane/jetpack/issues
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 6.0.1
Imports: packrat (>= 0.4.9), devtools (>= 1.4), httr (>= 1.1.0), crayon (>= 1.0.0), desc (>= 1.2.0), docopt (>= 0.4)
Suggests: testthat, withr
NeedsCompilation: no
Packaged: 2018-07-19 18:29:50 UTC; andrew
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Repository: CRAN
Date/Publication: 2018-07-25 16:10:03 UTC

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New package stars with initial version 0.1-1
Package: stars
Version: 0.1-1
Title: Scalable, Spatiotemporal Tidy Arrays for R
Description: Support for Scalable, Spatiotemporal Tidy Arrays in R, using GDAL bindings.
Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"), email = "edzer.pebesma@uni-muenster.de", comment = c(ORCID = "0000-0001-8049-7069")), person("Michael", "Sumner", role = "ctb"), person("Etienne", "Racine", role = "ctb"), person("Adriano", "Fantini", role = "ctb") )
Depends: R (>= 3.3.0), abind, sf (>= 0.6-3)
Imports: methods, Rcpp, rlang, units, classInt (>= 0.2-2)
Suggests: lwgeom, covr, ggplot2, ggthemes, gstat, dplyr (>= 0.7-0), knitr, maps, plm, rmarkdown, sp, zoo, xts, spacetime, raster, testthat, viridis
VignetteBuilder: knitr
License: Apache License
URL: https://github.com/r-spatial/stars/
BugReports: https://github.com/r-spatial/stars/issues/
Collate: init.R stars.R meta.R sf.R dimensions.R plot.R tidyverse.R transform.R ops.R write.R raster.R spacetime.R
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-19 07:39:50 UTC; edzer
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Michael Sumner [ctb], Etienne Racine [ctb], Adriano Fantini [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Repository: CRAN
Date/Publication: 2018-07-25 16:00:02 UTC

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New package bnclassify with initial version 0.4.1
Package: bnclassify
Title: Learning Discrete Bayesian Network Classifiers from Data
Description: State-of-the art algorithms for learning discrete Bayesian network classifiers from data, including a number of those described in Bielza & Larranaga (2014) <doi:10.1145/2576868>, with functions for prediction, model evaluation and inspection.
Version: 0.4.1
Authors@R: c(person("Mihaljevic","Bojan",email="bmihaljevic@fi.upm.es",role=c("aut","cre")), person("Bielza","Concha",email="mcbielza@fi.upm.es",role="aut"), person("Larranaga","Pedro",email="pedro.larranaga@fi.upm.es",role="aut"), person("Wickham", "Hadley", role="ctb", comment="some code extracted from memoise package"))
URL: http://github.com/bmihaljevic/bnclassify
BugReports: http://github.com/bmihaljevic/bnclassify/issues
Depends: R (>= 3.2.0)
Imports: assertthat (>= 0.1), entropy(>= 1.2.0), matrixStats(>= 0.14.0), rpart(>= 4.1-8), Rcpp,
Suggests: graph(>= 1.42.0), gRain(>= 1.2-3), gRbase(>= 1.7-0.1), mlr(>= 2.2), testthat(>= 0.8.1), knitr(>= 1.10.5), ParamHelpers(>= 1.5), Rgraphviz(>= 2.8.1), rmarkdown(>= 0.7), mlbench, covr
License: GPL (>= 2)
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
VignetteBuilder: knitr
RoxygenNote: 6.0.1
LinkingTo: Rcpp, BH
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2018-07-17 18:19:09 UTC; bmihaljevic
Author: Mihaljevic Bojan [aut, cre], Bielza Concha [aut], Larranaga Pedro [aut], Wickham Hadley [ctb] (some code extracted from memoise package)
Repository: CRAN
Date/Publication: 2018-07-25 09:50:03 UTC

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New package forward with initial version 1.0.4
Package: forward
Version: 1.0.4
Date: 2018-07-24
Title: Robust Analysis using Forward Search
Author: Originally written for S-Plus by: Kjell Konis <kkonis@insightful.com> and Marco Riani <mriani@unipr.it> Ported to R by Luca Scrucca <luca@stat.unipg.it> Ken Beath <ken.beath@mq.edu.au>
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Depends: R (>= 3.5), MASS
Description: Robust analysis using forward search in linear and generalized linear regression models, as described in Atkinson, A.C. and Riani, M. (2000), Robust Diagnostic Regression Analysis, First Edition. New York: Springer.
License: GPL-2
NeedsCompilation: no
Packaged: 2018-07-25 04:51:47 UTC; kjbeath1
Repository: CRAN
Date/Publication: 2018-07-25 07:20:08 UTC

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Tue, 24 Jul 2018

New package bacistool with initial version 0.9.5
Package: bacistool
Type: Package
Title: Bayesian Classification and Information Sharing (BaCIS) Tool for the Design of Multi-Group Phase II Clinical Trials
Version: 0.9.5
Author: Nan Chen and J. Jack Lee
Maintainer: Nan Chen <nchen2@mdanderson.org>
Description: Provides the design of multi-group phase II clinical trials with binary outcomes using the hierarchical Bayesian classification and information sharing (BaCIS) model. Subgroups are classified into two clusters on the basis of their outcomes mimicking the hypothesis testing framework. Subsequently, information sharing takes place within subgroups in the same cluster, rather than across all subgroups. This method can be applied to the design and analysis of multi-group clinical trials with binary outcomes.
Depends: R (>= 3.3.0)
SystemRequirements: JAGS (>= 4.3.0)
Imports: rjags
License: GNU General Public License (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-07-24 19:25:10 UTC; NChen2
Repository: CRAN
Date/Publication: 2018-07-24 21:40:10 UTC

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Mon, 23 Jul 2018

New package samplesize4surveys with initial version 3.6.1.0
Package: samplesize4surveys
Type: Package
Title: Sample Size Calculations for Complex Surveys
Version: 3.6.1.0
Date: 2018-07-20
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas <hagutierrezro@gmail.com>
Description: Computes the required sample size for estimation of totals, means and proportions under complex sampling designs.
License: GPL (>= 2)
Depends: R (>= 3.1), TeachingSampling, timeDate
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-20 17:32:38 UTC; psirusteam
Repository: CRAN
Date/Publication: 2018-07-23 15:10:03 UTC

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New package TeachingSampling with initial version 3.4.2
Package: TeachingSampling
Type: Package
Title: Selection of Samples and Parameter Estimation in Finite Population
License: GPL (>= 2)
Version: 3.4.2
Date: 2018-07-22
Author: Hugo Andres Gutierrez Rojas <hagutierrezro@gmail.com>
Maintainer: Hugo Andres Gutierrez Rojas <hagutierrezro@gmail.com>
Depends: R (>= 3.1)
Description: Allows the user to draw probabilistic samples and make inferences from a finite population based on several sampling designs.
Encoding: latin1
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-23 01:21:12 UTC; psirusteam
Repository: CRAN
Date/Publication: 2018-07-23 07:30:15 UTC

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Sun, 22 Jul 2018

New package sundialr with initial version 0.1.1
Package: sundialr
Type: Package
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
Version: 0.1.1
Authors@R: c( person("Satyaprakash", "Nayak", "", "sn248@cornell.edu", c("aut", "cre")), person("Scott D", "Cohen", "", "", c("ctb")), person("Alan C", "Hindmarsh", "", "", c("ctb")), person("Radu", "Serban", "", "", c("ctb")), person("Dan", "Shumaker", "", "", c("ctb")), person("Daniel R", "Reynolds", "", "", c("ctb")), person("Aaron", "Collier", "", "", c("ctb")), person("David", "Gardner", "", "", c("ctb")), person("Carol", "Woodward", "", "", c("ctb")), person("Slaven", "Peles", "", "", c("ctb")), person("Peter", "Brown", "", "", c("ctb")), person("Hilari C", "Tiedeman", "", "", c("ctb")), person("Ting", "Yan", "", "", c("ctb")), person("Lawrence Livermore National Security", role = c("cph")), person("Southern Methodist University", role = c("cph")) )
Maintainer: Satyaprakash Nayak <sn248@cornell.edu>
URL: https://github.com/sn248/sundialr
BugReports: https://github.com/sn248/sundialr/issues
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computation.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE' from the library can be accessed. The package requires ODE to be written using 'Rcpp' and does not require the libraries to be installed on the system.
License: GPL (>= 2)
LazyData: TRUE
Imports: Rcpp (>= 0.12.5)
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-07-22 15:42:39 UTC; nayaks16
Author: Satyaprakash Nayak [aut, cre], Scott D Cohen [ctb], Alan C Hindmarsh [ctb], Radu Serban [ctb], Dan Shumaker [ctb], Daniel R Reynolds [ctb], Aaron Collier [ctb], David Gardner [ctb], Carol Woodward [ctb], Slaven Peles [ctb], Peter Brown [ctb], Hilari C Tiedeman [ctb], Ting Yan [ctb], Lawrence Livermore National Security [cph], Southern Methodist University [cph]
Repository: CRAN
Date/Publication: 2018-07-22 21:10:03 UTC

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New package ps with initial version 1.0.0
Package: ps
Version: 1.0.0
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.
Authors@R: c( person("Jay", "Loden", role = "aut"), person("Dave", "Daeschler", role = "aut"), person("Giampaolo", "Rodola'", role = "aut"), person("Gábor", "Csárdi", , "csardi.gabor@gmail.com", c("aut", "cre")), person("RStudio", role = "cph"))
License: BSD_3_clause + file LICENSE
URL: https://github.com/r-lib/ps#readme
BugReports: https://github.com/r-lib/ps/issues
Encoding: UTF-8
Depends: R (>= 3.1)
Imports: utils
Suggests: callr, covr, processx, testthat, tibble
RoxygenNote: 6.0.1
Biarch: true
NeedsCompilation: yes
Packaged: 2018-07-22 11:04:14 UTC; gaborcsardi
Author: Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gábor Csárdi [aut, cre], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-22 21:10:07 UTC

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New package fpeek with initial version 0.1.0
Package: fpeek
Type: Package
Title: Check Text Files Content at a Glance
Version: 0.1.0
Authors@R: c( person("David", "Gohel", role = c("aut", "cre"), email = "david.gohel@ardata.fr"))
Description: Tools to help text files importation. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files. This package provides an alternative to a simple use of the 'head', 'tail', 'wc' and 'iconv' programs that are not always available on machine where R is installed.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.12)
LinkingTo: Rcpp
RoxygenNote: 6.0.1.9000
Suggests: testthat, covr
NeedsCompilation: yes
Packaged: 2018-07-18 21:25:20 UTC; davidgohel
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Repository: CRAN
Date/Publication: 2018-07-22 21:10:09 UTC

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New package NormalBetaPrime with initial version 1.0
Package: NormalBetaPrime
Type: Package
Title: Normal Beta Prime Prior
Version: 1.0
Date: 2018-07-12
Author: Ray Bai, Malay Ghosh
Maintainer: Ray Bai <raybai07@ufl.edu>
Description: Implements Bayesian linear regression, variable selection, normal means estimation, and multiple hypothesis testing using the normal-beta prime prior, as introduced by Bai and Ghosh (2018) <arXiv:1807.02421> and Bai and Ghosh (2018) <arXiv:1807.06539>. Normal means estimation and multiple testing for the Dirichlet-Laplace <doi:10.1080/01621459.2014.960967> and horseshoe+ priors <doi:10.1214/16-BA1028> are also available in this package.
License: GPL-3
LazyData: true
Depends: R (>= 3.1.0)
Imports: stats, utils, Matrix, MASS, glmnet, pscl, GIGrvg, pracma
NeedsCompilation: yes
Repository: CRAN
Packaged: 2018-07-22 13:58:15 UTC; rayba
Date/Publication: 2018-07-22 15:10:03 UTC

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New package eplusr with initial version 0.8.2
Package: eplusr
Title: A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
Version: 0.8.2
Authors@R: person(given = "Hongyuan", family = "Jia", role = c("aut", "cre"), email = "hongyuanjia@cqu.edu.cn", comment = c(ORCID = "0000-0002-0075-8183"))
Description: A rich toolkit of using the whole building simulation program 'EnergyPlus', which enables programmatic navigation, modification of 'EnergyPlus' models and makes it less painful to do parametric simulations and analysis.
License: GPL-3
URL: https://hongyuanjia.github.io/eplusr
BugReports: https://github.com/hongyuanjia/eplusr/issues
Depends: R (>= 3.2.0)
Imports: R6, RSQLite, assertthat, cli, clisymbols, data.table (>= 1.9.8), fasttime, furrr, future, gh, lubridate, processx, progress, purrr, readr, stringr, units, uuid
Suggests: testthat, covr
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Collate: 'constants.R' 'utils.R' 'units.R' 'assertions.R' 'impl.R' 'parse.R' 'epw.R' 'idd.R' 'idd_object.R' 'idf.R' 'idf_object.R' 'validate.R' 'format.R' 'run.R' 'job.R' 'param.R' 'install.R' 'eplusr.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2018-07-22 02:43:40 UTC; hongy
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuanjia@cqu.edu.cn>
Repository: CRAN
Date/Publication: 2018-07-22 15:20:03 UTC

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New package envnames with initial version 0.3.0
Package: envnames
Type: Package
Title: Track User-Defined Environment Names
Version: 0.3.0
Date: 2018-07-15
Author: Daniel Mastropietro
Maintainer: Daniel Mastropietro <mastropi@uwalumni.com>
Description: Set of functions to keep track of user-defined environment names which cannot be retrieved with the built-in function environmentName. The main function in this package for this purpose has a similar name: environment_name(), which returns the name of the environment given as parameter, be it a system, package, user-defined, or function execution environment. The package also provides additional functionality, the most important ones being: - A function (obj_find()) to search for objects. This function extends the functionality of exists() as follows: objects are searched recursively within all user-defined environments. - A way to get the stack of calling function names (get_fun_calling_chain()), in an easier way than the built-in function sys.call(), which requires further non-intuitive parsing of the output. - A function (get_obj_address()) to retrieve the memory address of an object. This package was inspired by an "R for developers" course given by Andrea Spano from Quantide (<http://www.quantide.com/courses-overview/r-for-developers>) and by a post by Gabor Grothendieck at the R-Help forum (<https://stat.ethz.ch/pipermail/r-help/2010-July/245646.html>).
URL: https://github.com/mastropi/envnames
BugReports: https://github.com/mastropi/envnames/issues
License: GPL
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2018-07-20 14:53:50 UTC; lundinmatlab
Repository: CRAN
Date/Publication: 2018-07-22 15:30:03 UTC

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New package CAinterprTools with initial version 1.0.0
Package: CAinterprTools
Title: Graphical Aid in Correspondence Analysis Interpretation and Significance Testings
Version: 1.0.0
Authors@R: person("Gianmarco", "Alberti", email = "gianmarcoalberti@gmail.com", role = c("aut", "cre"))
Description: Allows to plot a number of information related to the interpretation of Correspondence Analysis' results. It provides the facility to plot the contribution of rows and columns categories to the principal dimensions, the quality of points display on selected dimensions, the correlation of row and column categories to selected dimensions, etc. It also allows to assess which dimension(s) is important for the data structure interpretation by means of different statistics and tests. The package also offers the facility to plot the permuted distribution of the table total inertia as well as of the inertia accounted for by pairs of selected dimensions. Different facilities are also provided that aim to produce interpretation-oriented scatterplots. Reference: <doi:10.1016/j.softx.2015.07.001>.
Depends: R (>= 3.1.0)
Imports: ca (>= 0.70), classInt (>= 0.2-3), cluster (>= 2.0.7), FactoMineR (>= 1.40), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), graphics (>= 3.4.3), Hmisc (>= 4.1-1), RcmdrMisc (>= 1.0), reshape2 (>= 1.4.3), stats (>= 3.4.3), utils (>= 3.4.3)
License: GPL
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-22 06:36:49 UTC; gianmarcoalberti
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-22 15:10:06 UTC

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New package MSMwRA with initial version 1.2
Package: MSMwRA
Type: Package
Title: Multivariate Statistical Methods with R Applications
Version: 1.2
Date: 2018-07-17
Author: Hasan BULUT
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Description: Data sets in the book entitled "Multivariate Statistical Methods with R Applications", H.Bulut (2018). The book will be published in Turkish and the original name of this book be "R Uygulamalari ile Cok Degiskenli Istatistiksel Yontemler".
LazyData: true
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-21 18:54:24 UTC; TOSHIBA
Repository: CRAN
Date/Publication: 2018-07-22 14:50:02 UTC

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New package movecost with initial version 0.1
Package: movecost
Title: Calculation of Accumulated Cost Surface and Least-Cost Paths Related to Human Movement Across the Landscape
Version: 0.1
Authors@R: person("Gianmarco", "Alberti", email = "gianmarcoalberti@gmail.com", role = c("aut", "cre"))
Description: Provides the facility to calculate accumulated cost surface and least-cost paths using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain model, a start location and (optionally) destination locations.
Depends: R (>= 3.4.0)
Imports: gdistance (>= 1.2-2), raster (>= 2.6-7), rgdal (>= 1.3-3), rgeos (>= 0.3-28), sp (>= 1.3-1)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-20 22:29:15 UTC; gianmarcoalberti
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-22 14:30:03 UTC

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New package dsr with initial version 0.1.0
Package: dsr
Type: Package
Title: Compute Directly Standardized Rates, Ratios and Differences
Version: 0.1.0
Author: Matthew Kumar <mattkumar@gmail.com>
Maintainer: Matthew Kumar <mattkumar@gmail.com>
Description: A set of functions to compute and compare directly standardized rates, rate differences and ratios. A variety of user defined options for analysis (e.g confidence intervals) and formatting are included.
Imports: stats, dplyr (>= 0.7.4) , rlang, utils
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-20 20:04:40 UTC; Kumar
Repository: CRAN
Date/Publication: 2018-07-22 14:20:07 UTC

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New package rbit with initial version 1.0.0
Package: rbit
Title: Binary Indexed Tree
Version: 1.0.0
Author: Jialun Zhang, Zhilan Fan, Hang Zhang
Maintainer: Jialun Zhang <reatank@foxmail.com>
Description: A simple implementation of Binary Indexed Tree by R. The BinaryIndexedTree class supports construction of Binary Indexed Tree from a vector, update of a value in the vector and query for the sum of a interval of the vector.
License: MIT + file LICENSE
LazyData: true
Imports: R6
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-07-20 08:38:26 UTC; Konata
Repository: CRAN
Date/Publication: 2018-07-22 13:50:03 UTC

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New package BRISC with initial version 0.1.0
Package: BRISC
Type: Package
Title: Fast Inference for Large Spatial Datasets using BRISC
Version: 0.1.0
Authors@R: c(person("Arkajyoti", "Saha", role=c("aut", "cre"), email="arkajyotisaha93@gmail.com"), person("Abhirup", "Datta", role="aut", email="abhidatta@jhu.edu"), person("Jorge", "Nocedal", role="ctb", email="j-nocedal@northwestern.edu"), person("Naoaki", "Okazaki", role="ctb", email="okazaki@c.titech.ac.jp"))
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Author: Arkajyoti Saha [aut, cre], Abhirup Datta [aut], Jorge Nocedal [ctb], Naoaki Okazaki [ctb]
Depends: R (>= 3.3.0), RANN, parallel, stats, rdist, matrixStats, pbapply
Description: Fits Bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using Nearest Neighbor Gaussian Processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
License: GPL (>= 2)
URL: https://github.com/ArkajyotiSaha/BRISC
BugReports: https://github.com/ArkajyotiSaha/BRISC/issues
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-07-20 17:16:35 UTC; arkajyotisaha
Repository: CRAN
Date/Publication: 2018-07-22 14:00:02 UTC

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New package linkspotter with initial version 1.2.0
Package: linkspotter
Type: Package
Title: Bivariate Correlations Calculation and Visualization
Version: 1.2.0
Date: 2018-07-18
Authors@R: c( person("Alassane", "Samba", role = c("aut", "cre"),email = "alassane.samba@orange.com"), person(family="Orange", role = c("cph")) )
Description: Compute and visualize using the 'visNetwork' package all the bivariate correlations of a dataframe. Several and different types of correlation coefficients (Pearson's r, Spearman's rho, Kendall's tau, distance correlation, maximal information coefficient and equal-freq discretization-based maximal normalized mutual information) are used according to the variable couple type (quantitative vs categorical, quantitative vs quantitative, categorical vs categorical).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2.0)
Imports: shiny, visNetwork, infotheo, minerva, energy, mclust, rAmCharts, Hmisc, pbapply, ggplot2, dplyr, tidyr
Collate: 'linkspotterComplete.R' 'boostedBoxplot.R' 'clusterVariables.R' 'emptyVar.R' 'linkspotterDurationEstimator.R' 'linkspotterGraph.R' 'linkspotterGraphOnMatrix.R' 'linkspotterOnFile.R' 'linkspotterUI.R' 'corCouplesToMatrix.R' 'matrixToCorCouples.R' 'maxNMI.R' 'BeEFdiscretization_numfact.R' 'BeEFdiscretization_numnum.R' 'multiBivariateCorrelation.R' 'NormalizedMI.R' 'uselessVar.R' 'createShinyAppFolder.R'
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-19 08:15:19 UTC; XXGB1668
Author: Alassane Samba [aut, cre], Orange [cph]
Maintainer: Alassane Samba <alassane.samba@orange.com>
Repository: CRAN
Date/Publication: 2018-07-22 12:20:03 UTC

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New package jmvconnect with initial version 1.0.1
Package: jmvconnect
Type: Package
Title: Connect to the 'jamovi' Statistical Spreadsheet
Version: 1.0.1
Date: 2018-07-12
Authors@R: person('Jonathon', 'Love', role = c("aut", "cre", "cph"), email = "jon@thon.cc")
Maintainer: Jonathon Love <jon@thon.cc>
Description: Methods to access data sets from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information) from R.
License: GPL (>= 2)
Imports: jmvcore (>= 0.9.1), evaluate, rappdirs, httr, Rcpp (>= 0.12.16)
LinkingTo: Rcpp, BH
RoxygenNote: 6.0.1
SystemRequirements: jamovi, C++11
NeedsCompilation: yes
Packaged: 2018-07-19 00:17:19 UTC; jonathon
Author: Jonathon Love [aut, cre, cph]
Repository: CRAN
Date/Publication: 2018-07-22 11:50:03 UTC

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New package double.truncation with initial version 1.0
Package: double.truncation
Type: Package
Title: Analysis of Doubly-Truncated Data
Version: 1.0
Date: 2018-07-18
Author: Takeshi Emura, Hu Ya-Hsuan
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models. Parametric models from the special exponential family (SEF) are based on Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
License: GPL-2
NeedsCompilation: no
Packaged: 2018-07-18 08:09:01 UTC; user
Repository: CRAN
Date/Publication: 2018-07-22 11:20:02 UTC

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Sat, 21 Jul 2018

New package wdman with initial version 0.2.4
Package: wdman
Type: Package
Title: 'Webdriver'/'Selenium' Binary Manager
Version: 0.2.4
Authors@R: c( person("John", "Harrison", , "johndharrison0@gmail.com", role = "aut", comment = "original author"), person("Ju Yeong", "Kim", , "jkim2345@fredhutch.org", role = "cre", comment = "rOpenSci maintainer"))
Description: There are a number of binary files associated with the 'Webdriver'/'Selenium' project (see <http://www.seleniumhq.org/download/>, <https://sites.google.com/a/chromium.org/chromedriver/>, <https://github.com/mozilla/geckodriver>, <http://phantomjs.org/download.html> and <https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver> for more information). This package provides functions to download these binaries and to manage processes involving them.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.2)
Suggests: testthat, covr, knitr, rmarkdown
Imports: binman, assertthat, subprocess (>= 0.8.0), yaml, semver(>= 0.2.0), utils
URL: https://github.com/ropensci/wdman
URLNote: https://github.com/ropensci/wdman
BugReports: https://github.com/ropensci/wdman/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-21 17:32:38 UTC; jkim
Author: John Harrison [aut] (original author), Ju Yeong Kim [cre] (rOpenSci maintainer)
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>
Repository: CRAN
Date/Publication: 2018-07-21 21:50:03 UTC

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New package rda with initial version 1.0.2-2.1
Package: rda
Version: 1.0.2-2.1
Date: 2012-06-30
Title: Shrunken Centroids Regularized Discriminant Analysis
Author: Yaqian Guo <yaqiang@stat.stanford.edu> Trevor Hastie <hastie@stat.stanford.edu> Robert Tibshirani <tibs@stanford.edu>
Maintainer: ORPHANED
Depends: R (>= 2.10)
Description: Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.
License: GPL (>= 2)
Packaged: 2018-07-21 16:59:24 UTC; hornik
Repository: CRAN
Date/Publication: 2018-07-21 17:12:01 UTC
NeedsCompilation: no
X-CRAN-Original-Maintainer: Rob Tibshirani <tibs@stanford.edu>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package plsdof with initial version 0.2-7.1
Package: plsdof
Type: Package
Title: Degrees of Freedom and Statistical Inference for Partial Least Squares Regression
Depends: MASS
Version: 0.2-7.1
Date: 2014-09-04
Author: Nicole Kraemer, Mikio L. Braun
Maintainer: ORPHANED
Description: The plsdof package provides Degrees of Freedom estimates for Partial Least Squares (PLS) Regression. Model selection for PLS is based on various information criteria (aic, bic, gmdl) or on cross-validation. Estimates for the mean and covariance of the PLS regression coefficients are available. They allow the construction of approximate confidence intervals and the application of test procedures. Further, cross-validation procedures for Ridge Regression and Principal Components Regression are available.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2018-07-21 16:59:31 UTC; hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-07-21 17:11:59 UTC
X-CRAN-Original-Maintainer: Nicole Kraemer <kraemer_r_packages@yahoo.de>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package penalizedSVM with initial version 1.1.1
Package: penalizedSVM
Type: Package
Title: Feature Selection SVM using Penalty Functions
Version: 1.1.1
Date: 2010-08-02
Depends: e1071, MASS, corpcor, statmod, tgp, mlegp, lhs
Author: Natalia Becker, Wiebke Werft, Axel Benner
Maintainer: ORPHANED
Description: Provides feature selection SVM using penalty functions. The smoothly clipped absolute deviation (SCAD), 'L1-norm', 'Elastic Net' ('L1-norm' and 'L2-norm') and 'Elastic SCAD' (SCAD and 'L2-norm') penalties are available. The tuning parameters can be found using either a fixed grid or a interval search.
License: GPL (>= 2)
LazyLoad: yes
Encoding: latin1
Packaged: 2018-07-21 17:04:21 UTC; hornik
Repository: CRAN
Date/Publication: 2018-07-21 17:11:57 UTC
NeedsCompilation: no
X-CRAN-Original-Maintainer: Natalia Becker <natalia.becker@dkfz.de>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package diffusionMap with initial version 1.1-0.1
Package: diffusionMap
Version: 1.1-0.1
Date: 2014-02-19
Title: Diffusion Map
Author: Joseph Richards <joeyrichar@gmail.com>
Maintainer: ORPHANED
Description: Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model.
Depends: R (>= 2.4.0)
Imports: scatterplot3d, igraph, Matrix
License: GPL-2
URL: http://www.stat.berkeley.edu/~jwrichar/software.html
Packaged: 2018-07-21 17:16:50 UTC; hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-07-21 17:26:23 UTC
X-CRAN-Original-Maintainer: Joseph Richards <joeyrichar@gmail.com>
X-CRAN-Comment: Orphaned and corrected on 2018-07-21 as check problems were not corrected despite reminders.

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New package cleandata with initial version 0.1.0
Package: cleandata
Type: Package
Title: Functions to Inspect, Impute, and Encode Data, and to Keep Track of This Process
Version: 0.1.0
Author: Sherry Zhao
Maintainer: Sherry Zhao <sxzhao@gwu.edu>
Description: Functions to work with data frames to prepare data further analysis. The functions for imputation and encoding can produce log files to keep track of data manipulation process.
BugReports: https://github.com/sherrisherry/cleandata/issues
Depends: R (>= 3.0.0)
Imports: stats
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-07-17 22:58:52 UTC; Admin
Repository: CRAN
Date/Publication: 2018-07-21 18:00:03 UTC

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New package c060 with initial version 0.2-4
Package: c060
Version: 0.2-4
Date: 2014-12-09
Author: Martin Sill, Thomas Hielscher, Manuela Zucknick, Natalia Becker.
Maintainer: Martin Sill <m.sill@dkfz.de>
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and Generalized Linear Models
Depends:
Imports: glmnet, survival, parallel, mlegp, tgp, peperr, penalizedSVM, lattice
Suggests:
Description: c060 provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: c060
Repository/R-Forge/Revision: 185
Repository/R-Forge/DateTimeStamp: 2014-12-11 13:09:54
Date/Publication: 2014-12-11 17:04:38
Packaged: 2014-12-11 13:30:10 UTC; rforge
NeedsCompilation: no

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Fri, 20 Jul 2018

New package TDAstats with initial version 0.1.0
Package: TDAstats
Type: Package
Title: Pipeline for Topological Data Analysis
Version: 0.1.0
Authors@R: c( person("Raoul", "Wadhwa", email = "raoulwadhwa@gmail.com", role = c("aut", "cre")), person("Andrew", "Dhawan", role = "aut"), person("Drew", "Williamson", role = "aut"), person("Jacob", "Scott", role = "aut"))
Description: A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2 (>= 2.2.1), Rcpp (>= 0.12.15)
URL: https://github.com/rrrlw/TDAstats
BugReports: https://github.com/rrrlw/TDAstats/issues
LinkingTo: Rcpp
RoxygenNote: 6.0.1
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2018-07-20 16:46:18 UTC; rrrlw
Author: Raoul Wadhwa [aut, cre], Andrew Dhawan [aut], Drew Williamson [aut], Jacob Scott [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2018-07-20 17:50:02 UTC

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New package SpNetPrep with initial version 1.0
Package: SpNetPrep
Title: Linear Network Preprocessing for Spatial Statistics
Version: 1.0
Author: Alvaro Briz-Redon
Maintainer: Alvaro Briz-Redon <alvaro.briz@uv.es>
Description: Launches a Shiny application that allows users to carry out some of the steps that are required to curate both a linear network object based on a road structure and a point pattern that lies on such a network, becoming two previous steps to the performance of a spatial statistics analysis.
Depends: R (>= 3.5.0)
License: GPL-2
Imports: spatstat, leaflet, shiny, sp, raster, maptools
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2018-07-20 15:47:37 UTC; Alvaro
Repository: CRAN
Date/Publication: 2018-07-20 18:00:07 UTC

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