Wed, 19 Dec 2018

New package OmnibusFisher with initial version 1.0
Package: OmnibusFisher
Type: Package
Title: A Modified Fisher’s Method to Test Overall Gene-Level Effect
Version: 1.0
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>
Description: The separate p-values of SNPs, RNA expressions and DNA methylations are calculated by KM regression. The correlation between different omics data are taken into account. This method can be applied to either samples with all three types of omics data or samples with two types.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: CompQuadForm, stringr
Imports: survey
RoxygenNote: 6.0.0
Collate: 'OmnibusFisher_iteration_GM.R' 'OmnibusFisher_iteration_GMR.R' 'OmnibusFisher_iteration_GR.R' 'OmnibusFisher_iteration_MR.R' 'OmnibusFisher_outer.R' 'example_data.R'
Packaged: 2018-12-10 15:52:18 UTC; qiyan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-12-19 08:30:03 UTC

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Tue, 18 Dec 2018

New package waterquality with initial version 0.2.2
Package: waterquality
Title: Satellite Derived Water Quality Detection Algorithms
Version: 0.2.2
Authors@R: c(person("Richard", "Johansen", email = "richard.johansen@uc.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4287-9677")), person("Jakub", "Nowosad", email="nowosad.jakub@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0002-1057-3721")), person("Molly", "Reif", email="Molly.K.Reif@usace.army.mil", role = c("aut"), comment = c(ORCID = "0000-0003-4207-1459")), person("Erich", "Emery", email="Erich.B.Emery@usace.army.mil", role = c("aut")), person("U.S. Army Corps of Engineers", role = c("fnd")))
Description: The goal of 'waterquality' is to convert satellite-reflectance imagery to a host of pre-defined water quality algorithms designed for the detection of chlorophyll-a, blue-green algae (Phycocyanin), and turbidity. This package is able to process the following sensor configurations: WorldView-2, Sentinel-2, Landsat-8, MODIS, and MERIS.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: methods, raster, rgdal
RoxygenNote: 6.1.1
Suggests: testthat, knitr, tibble, rmarkdown, covr
URL: https://github.com/RAJohansen/waterquality
BugReports: https://github.com/RAJohansen/waterquality/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-10 18:44:39 UTC; johansra
Author: Richard Johansen [aut, cre] (<https://orcid.org/0000-0003-4287-9677>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Molly Reif [aut] (<https://orcid.org/0000-0003-4207-1459>), Erich Emery [aut], U.S. Army Corps of Engineers [fnd]
Maintainer: Richard Johansen <richard.johansen@uc.edu>
Repository: CRAN
Date/Publication: 2018-12-18 23:20:03 UTC

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New package VDJgermlines with initial version 0.1
Package: VDJgermlines
Type: Package
Title: Variable, Diversity and Joining Sequences from Various Species
Version: 0.1
Date: 2018-12-10
Author: Alexander Yermanos
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Depends: R(>= 3.1.0), ape, stringdist
Description: Contains variable, diversity, and joining sequences and accompanying functions that enable both the extraction of and comparison between immune V-D-J genomic segments from a variety of species. Sources include IMGT from MP Lefranc (2009) <doi:10.1093/nar/gkn838> and Vgenerepertoire from publication DN Olivieri (2014) <doi:10.1007/s00251-014-0784-3>.
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-12-10 13:36:52 UTC; ayermano
Repository: CRAN
Date/Publication: 2018-12-18 23:30:32 UTC

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New package SIGN with initial version 0.1.0
Package: SIGN
Type: Package
Title: Similarity Identification in Gene Expression
Version: 0.1.0
Date: 2018-12-02
Authors@R: c( person("Seyed Ali", "Madani Tonekaboni", , email = "ali.madanitonekaboni@mail.utoronto.ca", role = c("aut")), person("Gangesh", "Beri", , email = "gangesh.beri@uhnresearch.ca", role = c("aut")), person("Janosch", "Ortmann", , email = "janosch.ortmann@gmail.com", role = c("aut")), person("Benjamin", "Haibe-Kains", , email = "benjamin.haibe.kains@utoronto.ca", role = c("aut", "cre")) )
Description: Provides a classification framework to use expression patterns of pathways as features to identify similarity between biological samples. It provides a new measure for quantifying similarity between expression patterns of pathways.
Depends: R(>= 3.4)
License: GPL (>= 3)
Imports: stats, utils, survcomp, survival, GSVA
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
biocViews: GeneExpression, Classification, Clustering, Survival
Packaged: 2018-12-10 17:53:22 UTC; alimadani
RoxygenNote: 6.1.1
Author: Seyed Ali Madani Tonekaboni [aut], Gangesh Beri [aut], Janosch Ortmann [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Repository: CRAN
Date/Publication: 2018-12-18 23:11:47 UTC

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New package rdhs with initial version 0.6.0
Package: rdhs
Type: Package
Title: API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
Version: 0.6.0
Authors@R: c(person(given = "OJ", family = "Watson", role = c("aut", "cre"), email = "oj.watson@hotmail.co.uk", comment = c(ORCID = "0000-0003-2374-0741")), person(given = "Jeff", family = "Eaton", role = "aut", comment = c(ORCID = "0000-0001-7728-728X")), person(given = "Lucy", family = "D'Agostino McGowan", role = "rev", comment = c(ORCID = "0000-0001-7297-9359")), person(given = "Duncan", family = "Gillespie", role = "rev"))
Maintainer: OJ Watson <oj.watson@hotmail.co.uk>
URL: https://ropensci.github.io/rdhs/
BugReports: https://github.com/ropensci/rdhs/issues
Description: Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.
LazyData: TRUE
Depends: R (>= 3.3.0)
Imports: R6, httr, jsonlite, foreign, magrittr, rappdirs, digest, storr, xml2, qdapRegex, rgdal, getPass, haven, iotools
Suggests: testthat, knitr, rmarkdown, ggplot2, survey, data.table, microbenchmark
License: MIT + file LICENSE
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-GB
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-10 19:20:04 UTC; oj
Author: OJ Watson [aut, cre] (<https://orcid.org/0000-0003-2374-0741>), Jeff Eaton [aut] (<https://orcid.org/0000-0001-7728-728X>), Lucy D'Agostino McGowan [rev] (<https://orcid.org/0000-0001-7297-9359>), Duncan Gillespie [rev]
Repository: CRAN
Date/Publication: 2018-12-18 23:10:03 UTC

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New package NetworkSim with initial version 0.1.0
Package: NetworkSim
Type: Package
Title: Network Comparison Based on Structural Equivalence and Graphlets
Version: 0.1.0
Date: 2018-12-11
Author: Qili Shi, Libing Shen, Qi Liao, Shun Zhang
Maintainer: Qili Shi <qili.shi@hotmail.com>
Description: Functions to evaluate pair-wise similarity of two networks especially on high-dimensional data.
Depends: R (>= 3.4.0)
Imports: igraph, incgraph
Suggests: limma, DESeq2, edgeR, org.Hs.eg.db
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-11 08:53:16 UTC; lenovo
Repository: CRAN
Date/Publication: 2018-12-18 23:31:03 UTC

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New package MTLR with initial version 0.1.0
Package: MTLR
Type: Package
Title: Survival Prediction with Multi-Task Logistic Regression
Version: 0.1.0
Author: Humza Haider
Maintainer: Humza Haider <hshaider@ualberta.ca>
URL: https://github.com/haiderstats/MTLR
BugReports: https://github.com/haiderstats/MTLR/issues
Description: An implementation of Multi-Task Logistic Regression (MTLR) for R. This package is based on the method proposed by Yu et al. (2011) which utilized MTLR for generating individual survival curves by learning feature weights which vary across time. This model was further extended to account for left and interval censored data.
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.18), survival (>= 2.4.0)
Suggests: ggplot2 (>= 3.0.0), reshape2 (>= 1.4.3), testthat, covr, knitr, rmarkdown
Depends: R (>= 3.4.0)
RoxygenNote: 6.1.1
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-12-10 17:58:19 UTC; humza
Repository: CRAN
Date/Publication: 2018-12-18 23:12:36 UTC

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New package MachineLearning with initial version 0.0.2
Package: MachineLearning
Title: Machine Learning Algorithms for Innovation in Tourism
Version: 0.0.2
Authors@R: c( person("Agustin", "Perez-Martin", email = "agustin.perez@umh.es", role = "aut", comment = c(ORCID = "0000-0003-4994-3176")), person("Agustin", "Perez-Torregrosa", email = "agustin.perez01@goumh.umh.es", role =c("cre","aut"), comment = c(ORCID = "0000-0001-5658-4795")), person("Alejandro", "Rabasa-Dolado", email = "a.rabasa@umh.es", role ="aut" , comment = c(ORCID = "0000-0002-6243-9831")), person("Nuria", "Molla-Campello", email = "nuria.molla@goumh.umh.es", role = "aut", comment = c(ORCID = "0000-0002-6448-7116")), person("Jesus Javier", "Rodriguez-Sala", email = "jesuja.rodriguez@umh.es", role = "aut", comment = c(ORCID = "0000-0002-3796-0692")), person(family = "Agencia Valenciana de Turisme", role = c("ctb", "cph", "fnd")), person(family = "Miguel Hernandez University", role = c("ctb", "cph", "fnd")) )
Description: A collection of routines created in the collaboration framework in tourism innovation between the Valencian Tourism Agency (AVT) <http://www.turisme.gva.es/opencms/opencms/turisme/es/index.jsp> and the Miguel Hernandez University. The package provides a set of machine learning tools for pattern detection, association and classification rules and feature selection even under massive data environments. Almiñana, Escudero, Pérez-Martín, Rabasa, and Santamaría (2014) <doi:10.1007/s11750-012-0264-6>.
Depends: R (>= 3.3.0)
Imports: NbClust, dplyr, formula.tools, magrittr, arules, rpart, FSelectorRcpp, crayon, ggplot2, rpart.plot
License: AGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: spelling, testthat
Language: en-GB
NeedsCompilation: no
Packaged: 2018-12-10 17:18:38 UTC; agustin
Author: Agustin Perez-Martin [aut] (<https://orcid.org/0000-0003-4994-3176>), Agustin Perez-Torregrosa [cre, aut] (<https://orcid.org/0000-0001-5658-4795>), Alejandro Rabasa-Dolado [aut] (<https://orcid.org/0000-0002-6243-9831>), Nuria Molla-Campello [aut] (<https://orcid.org/0000-0002-6448-7116>), Jesus Javier Rodriguez-Sala [aut] (<https://orcid.org/0000-0002-3796-0692>), Agencia Valenciana de Turisme [ctb, cph, fnd], Miguel Hernandez University [ctb, cph, fnd]
Maintainer: Agustin Perez-Torregrosa <agustin.perez01@goumh.umh.es>
Repository: CRAN
Date/Publication: 2018-12-18 23:12:17 UTC

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New package fuzzySim with initial version 2.0
Package: fuzzySim
Type: Package
Title: Fuzzy Similarity in Species Distributions
Version: 2.0
Date: 2018-12-05
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <barbosa@uevora.pt>
Suggests: maptools, parallel, PBSmapping, sp, tools, raster
Description: Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.
License: GPL-3
NeedsCompilation: no
Packaged: 2018-12-10 18:39:50 UTC; marcia
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-12-18 23:10:32 UTC

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New package fluspect with initial version 1.0.0
Package: fluspect
Type: Package
Title: Fluspect-B
Version: 1.0.0
Author: Alberto Hornero, Nastassia Vilfan, Christiaan van der Tol, Onno Muller, Uwe Rascher, Wouter Verhoef
Maintainer: Alberto Hornero <alberto@hornero.es>
Description: A model for leaf fluorescence, reflectance and transmittance spectra. It implements the model introduced by Vilfan et al. (2016) <DOI:10.1016/j.rse.2016.09.017>. Fluspect-B calculates the emission of ChlF on both the illuminated and shaded side of the leaf. Other input parameters are chlorophyll and carotenoid concentrations, leaf water, dry matter and senescent material (brown pigments) content, leaf mesophyll structure parameter and ChlF quantum efficiency for the two photosystems, PS-I and PS-II.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: pracma, utils
LazyData: false
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-10 12:19:06 UTC; ahornero
Repository: CRAN
Date/Publication: 2018-12-18 23:30:05 UTC

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New package congressbr with initial version 0.1.5
Package: congressbr
Type: Package
Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Version: 0.1.5
Authors@R: c( person(given = "Robert", family = "McDonnell", email = "mcdonnell.robert5@gmail.com", role = c("aut", "cre")), person(given = "Guilherme", family = "Jardim Duarte", email = "gjardimduarte@gmail.com", role = "aut"), person(given = "Danilo", family = "Freire", email = "danilofreire@gmail.com", role = "aut"), person(given = "Julio", family = "Trecenti", role = "aut") )
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/> respectively.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: dplyr (>= 0.5.0), purrr (>= 0.2.2), xml2 (>= 1.0.0), httr(>= 1.2.1), lubridate (>= 1.6.0), magrittr (>= 1.5), stringi (>= 1.1.2), tidyr (>= 0.6.0), stringr (>= 1.1.0), tibble (>= 1.2), pscl (>= 1.4.9), glue (>= 0.0.1), progress (>= 0.0.1)
RoxygenNote: 6.1.1
Suggests: devtools, ggplot2, httptest, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-18 20:50:33 UTC; robert
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 22:30:17 UTC

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New package readABF with initial version 1.0.1
Package: readABF
Title: Loads Axon Binary Files
Version: 1.0.1
Authors@R: c(person("Stanislav", "Syekirin", role = c("aut", "cre"), email = "syekirin@gmail.com"), person("Florian", "Pein", role = "ctb", email = "fpein@uni-goettingen.de"))
Description: Loads Axon Binary Files (both 'ABF' and 'ABF2') created by Axon Instruments/Molecular Devices software such as 'pClamp'.
Depends: R (>= 3.2.0)
License: GPL-3
Imports: graphics, methods
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-12-10 08:57:38 UTC; zabolekar
Author: Stanislav Syekirin [aut, cre], Florian Pein [ctb]
Maintainer: Stanislav Syekirin <syekirin@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 16:40:03 UTC

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New package probably with initial version 0.0.1
Package: probably
Version: 0.0.1
Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations.
Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", c("aut", "cre")), person("Davis", "Vaughan", , "davis@rstudio.com", c("aut")), person("RStudio", role = "cph"))
Maintainer: Max Kuhn <max@rstudio.com>
URL: https://github.com/tidymodels/probably/
BugReports: https://github.com/tidymodels/probably/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0.9000
Depends: R (>= 2.10)
Imports: dplyr, generics, rlang, tidyselect, vctrs, yardstick
Suggests: testthat, covr, knitr, rmarkdown, parsnip, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 22:00:37 UTC; davis
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], RStudio [cph]
Repository: CRAN
Date/Publication: 2018-12-18 16:40:05 UTC

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New package easyalluvial with initial version 0.1.7
Package: easyalluvial
Title: Generate Alluvial Plots with a Single Line of Code
Version: 0.1.7
Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "datistics@gmail.com", comment = c(ORCID = " 0000-0003-4585-7799") )
URL: https://github.com/erblast/easyalluvial
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many option to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for data exploration.
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R(>= 2.10)
Suggests: testthat, covr, ISLR, nycflights13
RoxygenNote: 6.1.1
Imports: purrr , tidyr , dplyr , forcats , ggalluvial , ggplot2 , RColorBrewer , recipes , rlang , stringr , magrittr , tibble
Language: en-US
NeedsCompilation: no
Packaged: 2018-12-10 00:19:39 UTC; erbla
Author: Bjoern Koneswarakantha [aut, cre] (<https://orcid.org/ 0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 16:50:03 UTC

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New package cansim with initial version 0.2.2
Package: cansim
Type: Package
Title: Accessing Statistics Canada Data Table and Vectors
Version: 0.2.2
Authors@R: c( person("Jens", "von Bergmann", email = "jens@mountainmath.ca", role = c("cre")), person("Dmitry", "Shkolnik", email = "shkolnikd@gmail.com", role = c("aut")))
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for bilingual English or French language data retrieval, and bundles convenience functions to make it easier to work with retrieved table data. Optional caching features are provided.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: dplyr (>= 0.7), httr (>= 1.0.0), readr, rlang, xml2, rvest, stringr, purrr, tibble, utils, jsonlite
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, scales, tidyr, ggplot2
URL: https://github.com/mountainMath/cansim, https://mountainmath.github.io/cansim/
BugReports: https://github.com/mountainMath/cansim/issues
VignetteBuilder: knitr
Language: en-CA
NeedsCompilation: no
Packaged: 2018-12-10 06:40:09 UTC; jens
Author: Jens von Bergmann [cre], Dmitry Shkolnik [aut]
Repository: CRAN
Date/Publication: 2018-12-18 16:40:14 UTC

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New package sensitivityCalibration with initial version 0.0.1
Package: sensitivityCalibration
Type: Package
Title: A Calibrated Sensitivity Analysis for Matched Observational Studies
Version: 0.0.1
Author: Bo Zhang
Maintainer: Bo Zhang <bozhan@wharton.upenn.edu>
Description: Implements the calibrated sensitivity analysis approach for matched observational studies. Our sensitivity analysis framework views matched sets as drawn from a super-population. The unmeasured confounder is modeled as a random variable. We combine matching and model-based covariate-adjustment methods to estimate the treatment effect. The hypothesized unmeasured confounder enters the picture as a missing covariate. We adopt a state-of-art Expectation Maximization (EM) algorithm to handle this missing covariate problem in generalized linear models (GLMs). As our method also estimates the effect of each observed covariate on the outcome and treatment assignment, we are able to calibrate the unmeasured confounder to observed covariates. Zhang, B., Small, D. S. (2018). <arXiv:1812.00215>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, relaimpo, splitstackshape, ggrepel, stringi, plotly
NeedsCompilation: no
Packaged: 2018-12-09 20:48:12 UTC; ASUS
Repository: CRAN
Date/Publication: 2018-12-18 11:20:06 UTC

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New package preputils with initial version 1.0.2
Package: preputils
Type: Package
Title: Utilities for Preparation of Data Analysis
Version: 1.0.2
Date: 2018-12-03
Author: Josef Frank
Maintainer: Josef Frank <josef.frank@gmx.ch>
Description: Miscellaneous small utilities are provided to mitigate issues with messy, inconsistent or high dimensional data and help for preprocessing and preparing analyses.
Imports: data.table
License: GPL-3
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 23:38:32 UTC; josef
Repository: CRAN
Date/Publication: 2018-12-18 11:30:03 UTC

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New package kuiper.2samp with initial version 1.0
Package: kuiper.2samp
Title: Two-Sample Kuiper Test
Version: 1.0
Author: Ying Ruan [aut, cre]
Maintainer: Ying Ruan <y.ruan.16@ucl.ac.uk>
Description: This function performs the two-sample Kuiper test to assess the anomaly of continuous, one-dimensional probability distributions. References used for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-6361:20034220>.
Depends: R (>= 3.3.1)
License: AGPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2018-12-09 17:36:35 UTC; Ying Taylor Ruan
Repository: CRAN
Date/Publication: 2018-12-18 11:20:09 UTC

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New package pcmabc with initial version 1.0
Package: pcmabc
Type: Package
Title: Approximate Bayesian Computations for Phylogenetic Comparative Methods
Version: 1.0
Date: 2018-12-09
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data.
Depends: R(>= 2.9.1)
Imports: ape (>= 3.0.6), distory, geiger, graphics, methods, mvSLOUCH, phangorn, stats, TreeSim, treespace, utils, yuima
License: GPL (>= 2) | file LICENCE
LazyLoad: yes
Collate: ABCdist.R ABCmessage.R ABC.R ABCupdate.R draw.R getTipSample.R rates.R simsde.R simtree.R
Packaged: 2018-12-09 20:22:33 UTC; kbart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-12-18 10:30:03 UTC

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New package metaRMST with initial version 1.0.0
Package: metaRMST
Title: Meta-Analysis of RMSTD
Version: 1.0.0
Author: Isabelle Weir [aut, cre], Lu Tian [aut], Ludovic Trinquart [aut]
Maintainer: Isabelle Weir <iweir@bu.edu>
URL: https://github.com/iweir/metaRMST
Description: R implementation of a multivariate meta-analysis of randomized controlled trials (RCT) with the difference in restricted mean survival times (RMSTD). Use this package with individual patient level data from an RCT for a time-to-event outcome to determine combined effect estimates according to 4 methods: 1) a univariate meta-analysis using observed treatment effects, 2) a univariate meta-analysis using effects predicted by fitted Royston-Parmar flexible parametric models, 3) multivariate meta-analysis with analytically derived covariance, 4) multivariate meta-analysis with bootstrap derived covariance. This package computes all combined effects and provides an RMSTD curve with combined effect estimates and their confidence intervals.
Depends: R (>= 3.4.0), rstpm2
Imports: mvmeta, meta, survival, survRM2, graphics
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-12-09 20:28:46 UTC; Isabelle
Repository: CRAN
Date/Publication: 2018-12-18 10:30:06 UTC

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New package LabRS with initial version 0.1.0
Package: LabRS
Type: Package
Title: Laboratorio di "Ricerca Sociale con R"
Version: 0.1.0
Author: Agnese Vardanega
Maintainer: Agnese Vardanega <avardanega@unite.it>
URL: https://www.agnesevardanega.eu/
Depends: knitr
Suggests: Rcmdr
Description: Dati, scripts e funzioni per il libro "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale" (Datasets, scripts and functions to support the book "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale").
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-29 15:43:44 UTC; avard
Repository: CRAN
Date/Publication: 2018-12-18 09:10:09 UTC

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Mon, 17 Dec 2018

New package textrecipes with initial version 0.0.1
Package: textrecipes
Title: Extra 'Recipes' for Text Processing
Version: 0.0.1
Authors@R: person(given = "Emil", family = "Hvitfeldt", role = c("aut", "cre"), email = "emilhhvitfeldt@gmail.com")
Description: Converting text to numerical features requires specifically created procedures, which are implemented as steps according to the 'recipes' package. These steps allows for tokenization, filtering, counting (tf and tfidf) and feature hashing.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: GNU make, C++11
LazyData: true
URL: https://github.com/tidymodels/textrecipes
BugReports: https://github.com/tidymodels/textrecipes/issues
Depends: R (>= 2.10), recipes (>= 0.1.4)
Suggests: covr, testthat, knitr, rmarkdown
RoxygenNote: 6.1.0.9000
Imports: generics, rlang, tokenizers, dplyr, tibble, purrr, SnowballC, stopwords, magrittr, stringr, text2vec
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 17:47:21 UTC; rstudio-user
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-17 23:30:03 UTC

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New package qcv with initial version 1.0
Package: qcv
Title: Quantifying Construct Validity
Version: 1.0
Authors@R: c( person("R. Michael", "Furr", role = c("aut", "cre"), email = "FurrRM@wfu.edu"), person("Sarah", "Heuckeroth", role = "aut", email = "heucsa16@wfu.edu"))
Author: R. Michael Furr [aut, cre], Sarah Heuckeroth [aut]
Maintainer: R. Michael Furr <FurrRM@wfu.edu>
Date: 2018-11-26
Description: Primarily, the 'qcv' package computes key indices related to the Quantifying Construct Validity procedure (QCV; Westen & Rosenthal, 2003 <doi:10.1037/0022-3514.84.3.608>; see also Furr & Heuckeroth, in press). The qcv() function is the heart of the 'qcv' package, but additional functions in the package provide useful ancillary information related to the QCV procedure.
Depends: R (>= 3.5.1.0)
Imports: graphics, stats
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 16:43:29 UTC; furrrm
Repository: CRAN
Date/Publication: 2018-12-17 23:30:07 UTC

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New package MVTests with initial version 1.0
Package: MVTests
Type: Package
Title: Multivariate Hypothesis Tests
Version: 1.0
Date: 2018-12-09
Author: Hasan BULUT
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Description: Multivariate hypothesis tests and the confidence intervals. This package can be used for hypothesis tests which are The Hotelling T Square Tests (One-Sample, Two Independent Samples, Paired Samples), The One Way MANOVA, The Multivariate Shapiro-Wilk Test for Multivariate Normality Test, The Bartlett Test for One Sample Covariance Matrix, The Box-M Test and The Bartlett's Sphericity Test.
Depends: R (>= 2.0), stats, matrixcalc
LazyData: true
License: GPL-3
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 18:15:51 UTC; user
Repository: CRAN
Date/Publication: 2018-12-17 23:20:20 UTC

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New package jvcoords with initial version 1.0.2
Package: jvcoords
Type: Package
Title: Principal Component Analysis (PCA) and Whitening
Version: 1.0.2
Date: 2018-12-09
Authors@R: person("Jochen", "Voss", email="voss@seehuhn.de", role=c("aut", "cre"), comment = c(ORCID = "0000-0002-2323-3814"))
License: GPL-3
URL: https://github.com/seehuhn/jvcoords
Description: Provides functions to standardize and whiten data, and to perform Principal Component Analysis (PCA). The main advantage of this package over alternatives like prcomp() is, that jvcoords makes it easy to convert (additional) data between the original and the transformed coordinates. The package also provides a class coords, which can represent affine coordinate transformations. This class forms the basis of the transformations provided by the package, but can also be used independently. The implementation has been optimized to be of comparable speed (and sometimes even faster) than existing alternatives.
NeedsCompilation: no
Packaged: 2018-12-09 18:38:07 UTC; voss
Author: Jochen Voss [aut, cre] (<https://orcid.org/0000-0002-2323-3814>)
Maintainer: Jochen Voss <voss@seehuhn.de>
Repository: CRAN
Date/Publication: 2018-12-17 23:20:04 UTC

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New package FLAME with initial version 1.0.0
Package: FLAME
Type: Package
Title: A Fast Large-Scale Almost Matching Exactly Approach to Causal Inference
Version: 1.0.0
Authors@R: c(person("Chia-Rui (Jerry)", "Chang", role=c("aut", "cre"), email = "chiarui424@gmail.com"), person("Cynthia", "Rudin", role = c("aut"), email = "cynthia@cs.duke.edu"), person("Alexander", "Volfovsky", role = c("aut"), email = "alexander.volfovsky@duke.edu"), person("Sudeepa", "Roy", role = c("aut"), email = "sudeepa@cs.duke.edu"), person("Tianyu", "Wang", role = c("ctb"), email = "tianyu@cs.duke.edu"))
Description: The 'FLAME' (Fast Large-scale Almost Matching Exactly) package implements the matching algorithm in Roy, Rudin, Volfovsky, and Wang (2017) <arXiv:1707.06315>. 'FLAME' performs matching of treatment and control units in the potential outcomes framework for large categorical datasets. 'FLAME' creates matches that include as many covariates as possible, and sequentially drops covariates that are less useful based on a match quality measure. Match quality combines two important elements – it considers predictive power from machine learning on a hold out training set, and a balancing factor to ensure that it does not remove a covariate that would ruin overlap between treatment and control groups. Currently the 'FLAME' package applies to categorical data, and provides two approaches for implementation - bit vectors and database management systems (e.g., 'PostgreSQL', 'SQLite'). For data that has been adequately processed and fits in memory, bit vectors should be applied. For extremely large data that does not fit in memory, database systems should be applied.
Maintainer: Chia-Rui (Jerry) Chang <chiarui424@gmail.com>
URL: https://chiarui424.github.io/FLAME/
BugReports: https://github.com/chiarui424/FLAME/issues
Depends: R (>= 3.3)
Imports: reticulate (>= 1.9), graphics, stats, latticeExtra, dplyr, RPostgreSQL, RSQLite, gmp, lattice, rlang
Suggests: knitr, rmarkdown, ggplot2, ggpubr, e1071
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 19:57:40 UTC; Jerry
Author: Chia-Rui (Jerry) Chang [aut, cre], Cynthia Rudin [aut], Alexander Volfovsky [aut], Sudeepa Roy [aut], Tianyu Wang [ctb]
Repository: CRAN
Date/Publication: 2018-12-17 23:40:08 UTC

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New package dbparser with initial version 1.0.0
Package: dbparser
Title: 'DrugBank' Database XML Parser
Version: 1.0.0
Authors@R: c( person("Mohammed", "Ali", email = "moh_fcis@yahoo.com", role = c("aut", "cre")), person("Ali", "Ezzat", email = "ali_ezzat85@yahoo.com", role = "aut"))
Description: This tool is for parsing the 'DrugBank' XML database <http://drugbank.ca/>. The parsed data are then returned in a proper 'R' dataframe with the ability to save them in a given database.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: DBI, dplyr, ggplot2, odbc, purrr, tibble, XML
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/Dainanahan/dbparser
BugReports: https://github.com/Dainanahan/dbparser/issues
NeedsCompilation: no
Packaged: 2018-12-09 16:45:21 UTC; Mohammed
Author: Mohammed Ali [aut, cre], Ali Ezzat [aut]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Repository: CRAN
Date/Publication: 2018-12-17 23:40:03 UTC

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Sun, 16 Dec 2018

New package geohashTools with initial version 0.2.0
Package: geohashTools
Version: 0.2.0
Title: Tools for Working with Geohashes
Author: Michael Chirico, Hiroaki Kawai
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Depends: R (>= 3.0.0)
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, ported to R from Hiroaki Kawai's 'Python' implementation and embellished to sit naturally in the R ecosystem.
URL: https://github.com/MichaelChirico/geohashTools
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.0)
Suggests: sf, sp, testthat, mockery
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-12-07 12:22:49 UTC; michael.chirico
Repository: CRAN
Date/Publication: 2018-12-16 16:10:03 UTC

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New package CornerstoneR with initial version 1.0.0
Package: CornerstoneR
Version: 1.0.0
Title: Collection for 'CornerstoneR' Interface
Description: Collection of scripts for interface between 'Cornerstone' and 'R'. 'Cornerstone' (<https://www.camline.com/>) as a software for engineering analytics supports an interface to 'R'. The scripts are designed to support an easy usage of this interface.
Authors@R: c( person("Dirk", "Surmann", NULL, "dirk.surmann@versuchsplanung.de" , role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0873-137X")) )
URL: https://gitlab.com/camLine/CornerstoneR
BugReports: https://gitlab.com/camLine/CornerstoneR/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.2.1)
Imports: checkmate (>= 1.5) , data.table (>= 1.10) , ranger , vcd
Suggests: knitr , rmarkdown , testthat
ByteCompile: yes
LazyData: yes
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-08 12:08:10 UTC; Dirk
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>
Repository: CRAN
Date/Publication: 2018-12-16 16:50:02 UTC

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New package tinter with initial version 0.0.1
Package: tinter
Title: Generate a Monochromatic Palette
Version: 0.0.1
Authors@R: c( person("Sebastian", "Dalgarno", role = c("aut", "cre"), email = "seb@poissonconsulting.ca"), person("Joe", "Thorley", role = "ctb", email = "joe@poissonconsulting.ca", comment = c(ORCID = "0000-0002-7683-4592")))
Description: Generate a palette of tints, shades or both from a single colour.
URL: https://github.com/poissonconsulting/tinter
BugReports: https://github.com/poissonconsulting/tinter/issues
Imports: checkr, grDevices
Suggests: graphics, covr, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2018-12-06 00:06:41 UTC; sebastiandalgarno
Author: Sebastian Dalgarno [aut, cre], Joe Thorley [ctb] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Sebastian Dalgarno <seb@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-12-16 15:10:03 UTC

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New package lmreg with initial version 1.0
Package: lmreg
Type: Package
Title: Data and Functions Used in Linear Models and Regression with R: An Integrated Approach
Version: 1.0
Date: 2018-11-13
Author: Debasis Sengupta <shairiksengupta@gmail.com>, S. Rao Jammalamadaka <rao@gmail.com>, Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Maintainer: Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Description: Data files and a few functions used in the book 'Linear Models and Regression with R: An Integrated Approach' by Debasis Sengupta and Sreenivas Rao Jammalamadaka (2019).
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Depends: MASS
Packaged: 2018-12-06 20:28:25 UTC; william
Date/Publication: 2018-12-16 16:00:02 UTC

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New package mined with initial version 1.0-1
Package: mined
Type: Package
Title: Minimum Energy Designs
Version: 1.0-1
Date: 2018-11-24
Author: Dianpeng Wang and V. Roshan Joseph
Maintainer: Dianpeng Wang <wdp@bit.edu.cn>
Description: This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2018). The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate.
License: LGPL-2.1
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2018-12-05 08:22:40 UTC; Administrator
Repository: CRAN
Date/Publication: 2018-12-16 14:40:02 UTC

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New package epiGWAS with initial version 1.0.0
Package: epiGWAS
Title: Robust Methods for Epistasis Detection
Version: 1.0.0
Authors@R: c(person("Lotfi", "Slim", email = "lotfi.slim@mines-paristech.fr", role = c("aut", "cre")), person("Clément", "Chatelain", email = "clement.chatelain@sanofi.com", role = "ctb"), person("Chloé-Agathe", "Azencott", email = "chloe-agathe.azencott@mines-paristech.fr", role ="ctb"), person("Jean-Philippe", "Vert", email = "jpvert@google.com", role ="ctb"))
Description: Functions to perform robust epistasis detection in genome-wide association studies, as described in Slim et al. (2018) <doi:10.1101/442749>. The implemented methods identify pairwise interactions between a particular target variant and the rest of the genotype, using a propensity score approach. The propensity score models the linkage disequilibrium between the target and the rest of the genotype. All methods are penalized regression approaches, which differently incorporate the propensity score to only recover the synergistic effects between the target and the genotype.
Depends: R (>= 3.4.0)
Imports: matrixStats, DescTools, glmnet, SNPknock
Suggests: foreach, iterators, precrec, parallel, doParallel, bigmemory, biglasso, testthat, knitr, rmarkdown, kableExtra
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-04 20:00:21 UTC; lotfislim
Author: Lotfi Slim [aut, cre], Clément Chatelain [ctb], Chloé-Agathe Azencott [ctb], Jean-Philippe Vert [ctb]
Maintainer: Lotfi Slim <lotfi.slim@mines-paristech.fr>
Repository: CRAN
Date/Publication: 2018-12-16 14:10:03 UTC

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New package cliapp with initial version 0.1.0
Package: cliapp
Title: Create Rich Command Line Applications
Version: 0.1.0
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Description: Create rich command line applications, with colors, headings, lists, alerts, progress bars, etc. It uses CSS for custom themes.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/r-lib/cliapp#readme
BugReports: https://github.com/r-lib/cliapp/issues
RoxygenNote: 6.1.1
Imports: cli, crayon, fansi, glue (>= 1.3.0), prettycode, progress (>= 1.2.0), R6, selectr, utils, withr, xml2
Suggests: callr, covr, rstudioapi, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-05 09:41:39 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2018-12-16 14:40:05 UTC

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New package bfsl with initial version 0.1.0
Package: bfsl
Title: Best-Fit Straight Line
Version: 0.1.0
Authors@R: person("Patrick", "Sturm", email = "sturm@tofwerk.com", role = c("aut", "cre"))
Description: Provides the solution from York (1968) <doi:10.1016/S0012-821X(68)80059-7> for fitting a straight line to bivariate data with errors in both coordinates. It gives unbiased estimates of the intercept, slope and standard errors of the best-fit straight line to independent points with (possibly correlated) normally distributed errors in both x and y. Other commonly used errors-in-variables methods, such as orthogonal distance regression, geometric mean regression or Deming regression are special cases of York’s solution.
Depends: R (>= 3.5.0)
License: GPL-3
URL: https://github.com/pasturm/bfsl
BugReports: https://github.com/pasturm/bfsl/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-12-05 12:58:44 UTC; pst
Author: Patrick Sturm [aut, cre]
Maintainer: Patrick Sturm <sturm@tofwerk.com>
Repository: CRAN
Date/Publication: 2018-12-16 14:50:03 UTC

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Fri, 14 Dec 2018

New package bioRad with initial version 0.4.0
Package: bioRad
Title: Biological Analysis and Visualization of Weather Radar Data
Version: 0.4.0
Description: Extract, visualize and summarize aerial movements of birds and insects from weather radar data.
Authors@R: c( person("Adriaan M.", "Dokter", role = c("aut", "cre"), email = "amd427@cornell.edu", comment = c(ORCID = "0000-0001-6573-066X")), person("Peter", "Desmet", role = "aut", email = "peter.desmet@inbo.be", comment = c(ORCID = "0000-0002-8442-8025")), person("Stijn", "Van Hoey", role = "aut", email = "stijn.vanhoey@inbo.be", comment = c(ORCID = "0000-0001-6413-3185")), person("Jurriaan", "Spaaks", role = "ctb", email = "j.spaaks@esciencecenter.nl"), person("Lourens", "Veen", role = "ctb", email = "l.veen@esciencecenter.nl"), person("Liesbeth", "Verlinden", role = "ctb", email = "l.verlinden@uva.nl", comment = c(ORCID = "0000-0003-1744-9325")), person("Hidde", "Leijnse", role = "ctb", email = "hidde.leijnse@knmi.nl", comment = c(ORCID = "0000-0001-7835-4480")) )
License: MIT + file LICENSE
URL: https://github.com/adokter/bioRad, https://adokter.github.io/bioRad
BugReports: https://github.com/adokter/bioRad/issues
biocViews:
Depends: R (>= 2.10)
Imports: curl, fields, ggmap, ggplot2, graphics, methods, raster, rgdal, rhdf5, sp, stats, utils, maptools
Suggests: knitr, testthat
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-14 20:54:42 UTC; amd427
Author: Adriaan M. Dokter [aut, cre] (<https://orcid.org/0000-0001-6573-066X>), Peter Desmet [aut] (<https://orcid.org/0000-0002-8442-8025>), Stijn Van Hoey [aut] (<https://orcid.org/0000-0001-6413-3185>), Jurriaan Spaaks [ctb], Lourens Veen [ctb], Liesbeth Verlinden [ctb] (<https://orcid.org/0000-0003-1744-9325>), Hidde Leijnse [ctb] (<https://orcid.org/0000-0001-7835-4480>)
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Repository: CRAN
Date/Publication: 2018-12-14 21:30:04 UTC

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Thu, 13 Dec 2018

New package norm2 with initial version 2.0.2
Package: norm2
Type: Package
Title: Analysis of Incomplete Multivariate Data under a Normal Model
Version: 2.0.2
Date: 2018-12-12
Author: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Maintainer: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Description: Functions for parameter estimation, Bayesian posterior simulation and multiple imputation from incomplete multivariate data under a normal model.
Depends: R (>= 3.1.0)
Imports: stats
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2018-12-13 11:25:36 UTC; schaf310
Repository: CRAN
Date/Publication: 2018-12-14 00:00:03 UTC

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Tue, 11 Dec 2018

New package RTest with initial version 1.2.1
Package: RTest
Version: 1.2.1
Date: 2018-12-09
Title: A XML-Based Testing Framework for Automated Component Tests of R Packages
Authors@R: c( person("Sebastian", "Wolf", , "sebastian@mail-wolf.de", role = c("aut","cre")), person("Matthias", "Pfeifer", , "matthiaspfeifer@gmx.net", role = c("aut", "ctb")), person("Sergej", "Potapov", , "sergej.potapov@roche.com", role = c("ctb")), person("Roche", role = c("cph", "fnd")) )
Depends: R (>= 3.1.3), testthat (>= 1.0.0), magick(>= 1.3), methods, XML, stringr
Imports: base64, jsonlite
Suggests: knitr, rmarkdown
Description: This provides a framework for R packages developed for a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter functionalities for XML-based test case definition as well as for standardized reporting of the test results.
Collate: RTest-package.R utils.R utils.test.R utils.xmlRead.R utils.xmlWrite.R RTestCollection.R RTestCase.R RTestCase.test-adapter.R
SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb)
VignetteBuilder: knitr
License: GPL (>= 2)
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-10 09:54:38 UTC; news
Author: Sebastian Wolf [aut, cre], Matthias Pfeifer [aut, ctb], Sergej Potapov [ctb], Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian@mail-wolf.de>
Repository: CRAN
Date/Publication: 2018-12-11 09:30:08 UTC

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Mon, 10 Dec 2018

New package mistr with initial version 0.0.1
Package: mistr
Type: Package
Title: Mixture and Composite Distributions
Version: 0.0.1
Depends: R (>= 3.0.1)
Authors@R: c( person("Lukas", "Sablica", email = "lsablica@wu.ac.at", role = c("aut", "cre")), person("Kurt", "Hornik", email = "Kurt.Hornik@wu.ac.at", role = "aut", comment = c(ORCID = "0000-0003-4198-9911")) )
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Description: A flexible computational framework for mixture distributions with the focus on the composite models.
License: GPL-3
Imports: bbmle, stats, graphics, grDevices
Suggests: ggplot2, grid, knitr, rmarkdown, pinp
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-07 10:54:45 UTC; sablica
Author: Lukas Sablica [aut, cre], Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>)
Repository: CRAN
Date/Publication: 2018-12-10 15:00:02 UTC

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Sun, 09 Dec 2018

New package transformr with initial version 0.1.1
Package: transformr
Type: Package
Title: Polygon and Path Transformations
Version: 0.1.1
Date: 2018-12-04
Authors@R: person(given = "Thomas Lin", family = "Pedersen", role = c("cre", "aut"), email = "thomasp85@gmail.com")
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Description: In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The 'transformr' package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the 'tweenr' package.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: C++11
LazyData: true
Imports: Rcpp (>= 0.12.15), tweenr, rlang, sf, lpSolve
Suggests: magrittr
LinkingTo: Rcpp
RoxygenNote: 6.1.1
URL: https://github.com/thomasp85/transformr
BugReports: https://github.com/thomasp85/transformr/issues
NeedsCompilation: yes
Packaged: 2018-12-04 10:53:59 UTC; thomas
Author: Thomas Lin Pedersen [cre, aut]
Repository: CRAN
Date/Publication: 2018-12-09 16:30:02 UTC

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New package ProjectManagement with initial version 1.0
Package: ProjectManagement
Type: Package
Title: Management of Deterministic and Stochastic Projects
Date: 2018-12-04
Version: 1.0
Authors@R: c( person("Juan Carlos","Gonçalves Dosantos",role=c("aut","cre"), email="juan.carlos.goncalves@udc.es"), person("Ignacio","García Jurado",role=c("aut")), person("Julián","Costa Bouzas",role=c("aut")) )
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot a histogram of this duration. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Depends: R (>= 3.5.0), triangle, plotly, cooptrees
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Author: Juan Carlos Gonçalves Dosantos [aut, cre], Ignacio García Jurado [aut], Julián Costa Bouzas [aut]
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-12-04 12:07:13 UTC; User
Repository: CRAN
Date/Publication: 2018-12-09 16:40:02 UTC

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New package NTS with initial version 1.0.0
Package: NTS
Title: Nonlinear Time Series Analysis
Version: 1.0.0
Authors@R: c( person("Ruey", "Tsay", email = "ruey.tsay@chicagobooth.edu", role = "aut"), person("Rong", "Chen", email = "rongchen@stat.rutgers.edu", role = "aut"), person("Xialu", "Liu", email = "xialu.liu@sdsu.edu", role = c("aut", "cre")))
Author: Ruey Tsay [aut], Rong Chen [aut], Xialu Liu [aut, cre]
Maintainer: Xialu Liu <xialu.liu@sdsu.edu>
Description: Simulation, estimation, prediction procedure, and model identification methods for nonlinear time series analysis, including threshold autoregressive models, Markov-switching models, convolutional functional autoregressive models, nonlinearity tests, Kalman filters and various sequential Monte Carlo methods. More examples and details about this package can be found in the book "Nonlinear Time Series Analysis" by Ruey S. Tsay and Rong Chen, Wiley, 2018 (ISBN: 978-1-119-26407-1).
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: base,dlm,graphics,MASS,MSwM,Rdpack,parallel,splines,stats,tensor
RdMacros: Rdpack
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-04 01:44:20 UTC; xliu
Repository: CRAN
Date/Publication: 2018-12-09 16:20:03 UTC

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New package LinkedGASP with initial version 1.0
Package: LinkedGASP
Type: Package
Title: Linked Emulator of a Coupled System of Simulators
Version: 1.0
Date: 2018-11-24
Author: Ksenia N. Kyzyurova, kseniak.ucoz.net
Maintainer: Ksenia N. Kyzyurova <ksenia.kyzyurova@gmail.com>
Depends: nloptr, spBayes
Suggests: MASS
Description: Prototypes for construction of a Gaussian Stochastic Process emulator (GASP) of a computer model. This is done within the objective Bayesian implementation of the GASP. The package allows for construction of a linked GASP of the composite computer model. Computational implementation follows the mathematical exposition given in publication: Ksenia N. Kyzyurova, James O. Berger, Robert L. Wolpert. Coupling computer models through linking their statistical emulators. SIAM/ASA Journal on Uncertainty Quantification, 6(3): 1151-1171, (2018).<DOI:10.1137/17M1157702>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2018-12-04 15:02:55 UTC; kseniak
Repository: CRAN
Date/Publication: 2018-12-09 16:50:03 UTC

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New package smurf with initial version 1.0.0
Type: Package
Package: smurf
Title: Sparse Multi-Type Regularized Feature Modeling
Version: 1.0.0
Date: 2018-12-03
Authors@R: c( person("Tom", "Reynkens", email = "tomreynkens@hotmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5516-5107")), person("Sander", "Devriendt", email = "sander.devriendt@kuleuven.be", role = "aut"), person("Katrien", "Antonio", role = "aut") )
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
URL: https://gitlab.com/TReynkens/smurf
License: GPL (>= 2)
BugReports: https://gitlab.com/TReynkens/smurf/issues
Depends: R (>= 3.1)
Imports: catdata, glmnet, graphics, MASS, Matrix, methods, mgcv, parallel, RColorBrewer, Rcpp (>= 0.12.12), speedglm, stats
Suggests: bookdown, knitr, roxygen2 (>= 6.0.0), testthat
LinkingTo: Rcpp, RcppArmadillo (>= 0.8.300.1.0)
VignetteBuilder: knitr
ByteCompile: yes
Encoding: UTF-8
LazyData: yes
NeedsCompilation: yes
RoxygenNote: 6.1.1
Packaged: 2018-12-03 19:39:26 UTC; tom
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>), Sander Devriendt [aut], Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Repository: CRAN
Date/Publication: 2018-12-09 16:00:03 UTC

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New package rSPARCS with initial version 0.0.1
Package: rSPARCS
Type: Package
Title: Data Management for the SPARCS
Version: 0.0.1
Author: Wangjian Zhang, Zhicheng Du, Ziqiang Lin, David Q. Rich, Sally W. Thurston, Jijin Yao, Xiaobo Xue, Shao Lin, Yuantao Hao
Maintainer: Wangjian Zhang <wzhang27@albany.edu>
Description: To clean and analyze the data from the Statewide Planning and Research Cooperative System (SPARCS), and generate sets for statistical modeling. Additionally, other data with similar format or study objectives can also be handled.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: foreign,data.table,spatialEco,geosphere,tigris,raster,sp
NeedsCompilation: no
Packaged: 2018-12-02 17:48:38 UTC; zwjed
Repository: CRAN
Date/Publication: 2018-12-09 15:10:09 UTC

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New package RCarb with initial version 0.1.2
Package: RCarb
Type: Package
Title: Dose Rate Modelling of Carbonate-Rich Samples
Version: 0.1.2
Date: 2018-12-02
Author: Sebastian Kreutzer [aut, trl, cre, dtc] (<https://orcid.org/0000-0002-0734-2199>), Roger P. Nathan [aut, cph], Barbara Mauz [aut, cph] (<https://orcid.org/0000-0003-1504-333X>)
Authors@R: c( person("Sebastian", "Kreutzer", role = c("aut", "trl", "cre", "dtc"), email = "sebastian.kreutzer@u-bordeaux-montaigne.fr", comment = c(ORCID = "0000-0002-0734-2199")), person("Roger P.", "Nathan", role = c("aut", "cph")), person("Barbara", "Mauz", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1504-333X")))
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Description: Translation of the 'MATLAB' program 'Carb' (Nathan and Mauz 2008 <DOI:10.1016/j.radmeas.2007.12.012>; Mauz and Hoffmann 2014) for dose rate modelling for carbonate-rich samples in the context of trapped charged dating (e.g., luminescence dating) applications.
Depends: R (>= 3.3.0), utils
Imports: interp (>= 1.0), matrixStats (>= 0.50.0)
Suggests: testthat (>= 2.0), R.rsp (>= 0.42.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: R.rsp
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-02 20:56:32 UTC; kreutzer
Repository: CRAN
Date/Publication: 2018-12-09 15:10:12 UTC

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New package optionstrat with initial version 1.0.0
Package: optionstrat
Type: Package
Title: Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies
Version: 1.0.0
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>
Description: Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: graphics, stats
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-03 01:39:56 UTC; John Buynak
Repository: CRAN
Date/Publication: 2018-12-09 15:30:02 UTC

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New package viewshed3d with initial version 1.0.0
Package: viewshed3d
Title: Compute Viewshed in 3D Terrestrial Laser Scanner Scenes of Ecosystems
Version: 1.0.0
Authors@R: c(person("Bastien", "Lecigne", email = "lecignebastien@gmail.com", role = c("aut", "cre")), person("Jan", "Eitel", role=c("aut")))
Description: A set of tools to compute viewshed in 3D from Terrestrial Laser Scanner data and prepare the data prior to visibility calculation.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: VoxR (>= 0.5.1), rgl (>= 0.99.16), doParallel (>= 1.0.14), foreach (>= 1.4.4), tcltk2 (>= 1.2.9), iterators (>= 1.0.9), tcltk (>= 3.4.4), utils (>= 3.4.4)
NeedsCompilation: no
Packaged: 2018-12-01 07:14:51 UTC; bastien
Author: Bastien Lecigne [aut, cre], Jan Eitel [aut]
Maintainer: Bastien Lecigne <lecignebastien@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-09 14:20:03 UTC

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New package parglm with initial version 0.1.0
Package: parglm
Type: Package
Title: Parallel GLM
Version: 0.1.0
Authors@R: c( person("Benjamin", "Christoffersen", email = "boennecd@gmail.com", role = c("cre", "aut")), person("Anthony", "Williams", role = c("cph")), person("Boost developers", role = c("cph")))
Description: Provides a parallel estimation method for generalized linear models without compiling with a multithreaded LAPACK or BLAS.
License: GPL-2
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, Matrix
SystemRequirements: C++11
Suggests: testthat, SuppDists, knitr, rmarkdown, speedglm, microbenchmark, R.rsp
RoxygenNote: 6.0.1
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2018-11-30 23:35:28 UTC; User
Author: Benjamin Christoffersen [cre, aut], Anthony Williams [cph], Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-09 14:10:02 UTC

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New package ChemoSpec2D with initial version 0.2.0
Package: ChemoSpec2D
Type: Package
Title: Exploratory Chemometrics for 2D Spectroscopy
Version: 0.2.0
Date: 2018-11-30
Authors@R: c( person("Bryan A.", "Hanson", role = c("aut", "cre"), email = "hanson@depauw.edu", comment = "ORCID 0000-0003-3536-8246"))
Description: A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.
License: GPL-3
Depends: R (>= 3.5.0), ChemoSpecUtils (>= 0.2)
Imports: R.utils, tools, utils, plyr, ThreeWay, multiway, matrixStats
Suggests: knitr, testthat
URL: https://github.com/bryanhanson/ChemoSpec2D
BugReports: https://github.com/bryanhanson/ChemoSpec2D/issues
ByteCompile: TRUE
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-30 15:25:18 UTC; bryanhanson
Author: Bryan A. Hanson [aut, cre] (ORCID 0000-0003-3536-8246)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Repository: CRAN
Date/Publication: 2018-12-09 14:10:06 UTC

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New package pedigreeTools with initial version 0.1
Package: pedigreeTools
Version: 0.1
Date: 2018-11-14
Title: Versatile Functions for Working with Pedigrees
Author: Ana Ines Vazquez, Douglas Bates, Siddharth Avadhanam, Paulino Perez
Maintainer: Ana Ines Vazquez <avazquez@msu.edu>
Description: Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients and the relationship matrix (includes code for pedigrees from self-pollinated species). The use of pedigree data is central to genetics research within the animal and plant breeding communities to predict breeding values. The relationship matrix between the individuals can be derived from pedigree structure following the algorithms described for example in Vazquez et al., 2010 <doi:10.2527/jas.2009-1952>.
Depends: R(>= 3.0.0), methods
Imports: Matrix (>= 1.0)
LazyLoad: yes
LazyData: yes
License: GPL-3
URL: https://github.com/Rpedigree/pedigreeTools/
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-11-30 18:18:27 UTC; pperez
Repository: CRAN
Date/Publication: 2018-12-09 13:50:06 UTC

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New package multiRDPG with initial version 1.0.1
Package: multiRDPG
Version: 1.0.1
Type: Package
Title: Multiple Random Dot Product Graphs
Authors@R: c(person("Agnes Martine", "Nielsen", email = "agni@dtu.dk", role = c("aut", "cre")),person("Daniela", "Witten", role = "aut"))
Description: Fits the Multiple Random Dot Product Graph Model and performs a test for whether two networks come from the same distribution. Both methods are proposed in Nielsen, A.M., Witten, D., (2018) "The Multiple Random Dot Product Graph Model", arXiv preprint <arXiv:1811.12172> (Submitted to Journal of Computational and Graphical Statistics).
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-30 16:37:58 UTC; agni
Author: Agnes Martine Nielsen [aut, cre], Daniela Witten [aut]
Maintainer: Agnes Martine Nielsen <agni@dtu.dk>
Repository: CRAN
Date/Publication: 2018-12-09 13:40:03 UTC

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Sat, 08 Dec 2018

New package R2STATS with initial version 0.68-39
Package: R2STATS
Title: A GTK GUI for Fitting and Comparing GLM and GLMM
Version: 0.68-39
Encoding: UTF-8
Date: 2018-11-30
Author: Yvonnick Noel [aut, cre]
Maintainer: Yvonnick Noel <yvonnick.noel@univ-rennes2.fr>
Description: A 'gWidgetsRGtk2' GUI for fitting and comparing GLM or GLMM (based on Douglas Bates' 'lme4' package). It is designed to make comparisons between numerous models easy, both numerically and graphically, which may be useful for teaching. Relevant plots are automatically produced for each model family. 'R2STATS' is *not* a generic graphical interface for R, but a GUI for statistical modelling in a model comparison approach.
URL: http://yvonnick.noel.free.fr/r2stats
License: GPL (>= 2)
Depends: R (>= 3.1.0), proto, Matrix
Imports: grDevices, lattice, lme4, cairoDevice, gWidgets, gWidgetsRGtk2, RGtk2Extras, MASS, utils, latticeExtra, statmod
SystemRequirements: Cairo (>= 1.0.0), ATK (>= 1.10.0), Pango (>=1.10.0), GTK+ (>= 2.8.0), GLib (>= 2.8.0)
NeedsCompilation: no
Packaged: 2018-12-08 08:34:12 UTC; noel
Repository: CRAN
Date/Publication: 2018-12-08 23:22:34 UTC

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Tue, 04 Dec 2018

New package biospear with initial version 1.0.2
Package: biospear
Type: Package
Title: Biomarker Selection in Penalized Regression Models
Version: 1.0.2
Author: Nils Ternes [aut], Federico Rotolo [aut], Stefan Michiels [aut, cre]
Maintainer: Stefan Michiels <stefan.michiels@gustaveroussy.fr>
Depends: R (>= 2.10), pkgconfig
Description: Provides some tools for developing and validating prediction models, estimate expected survival of patients and visualize them graphically. Most of the implemented methods are based on penalized regressions such as: the lasso (Tibshirani R (1996)), the elastic net (Zou H et al. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>), the adaptive lasso (Zou H (2006) <doi:10.1198/016214506000000735>), the stability selection (Meinshausen N et al. (2010) <doi:10.1111/j.1467-9868.2010.00740.x>), some extensions of the lasso (Ternes et al. (2016) <doi:10.1002/sim.6927>), some methods for the interaction setting (Ternes N et al. (2016) <doi:10.1002/bimj.201500234>), or others. A function generating simulated survival data set is also provided.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: cobs, corpcor, devtools, glmnet, graphics, grplasso, MASS, Matrix, mboost, parallel, plsRcox, pROC, PRROC, RCurl, stats, survAUC, survival
NeedsCompilation: no
Packaged: 2018-12-04 09:16:42 UTC; s_michiels
Repository: CRAN
Date/Publication: 2018-12-04 10:20:19 UTC

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Mon, 03 Dec 2018

New package ParBayesianOptimization with initial version 0.0.1
Package: ParBayesianOptimization
Title: Parallel Bayesian Optimization of Hyperparameters
Version: 0.0.1
Authors@R: person("Samuel", "Wilson", email = "samwilson303@gmail.com", role = c("aut", "cre"))
Description: Fast, flexible framework for implementing Bayesian optimization of model hyperparameters according to the methods described in Snoek et al. <arXiv:1206.2944>. The package allows the user to run scoring function in parallel, save intermediary results, and tweak other aspects of the process to fully utilize the computing resources available to the user.
URL: https://github.com/AnotherSamWilson/ParBayesianOptimization
BugReports: https://github.com/AnotherSamWilson/ParBayesianOptimization/issues
Depends: R (>= 3.5.0), data.table (>= 1.11.8), GauPro, stats, foreach, dbscan
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0.9000
Suggests: knitr,rmarkdown,xgboost,doParallel,ggplot2
VignetteBuilder: knitr
Maintainer: Samuel Wilson <samwilson303@gmail.com>
NeedsCompilation: no
Packaged: 2018-11-23 23:55:38 UTC; swilson
Author: Samuel Wilson [aut, cre]
Repository: CRAN
Date/Publication: 2018-12-03 22:40:06 UTC

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New package qccrs with initial version 0.1.0
Package: qccrs
Type: Package
Title: Quality Control Charts under Repetitive Sampling
Version: 0.1.0
Authors@R: c( person(c("Muhammad", "Yaseen"), email = "myaseen208@gmail.com", role = c("aut", "cre")) , person(c("Muhammad", "Aslam"), email = "aslam_ravian@hotmail.com", role = c("aut", "ctb")) , person(c("Sami", "Ullah"), email = "samiullahuos@gmail.com", role = c("aut", "ctb")) , person(c("Muhammad", "Azam"), email = "mazam@uvas.edu.pk", role = c("aut", "ctb")) , person(c("Chi-Hyuck", "Jun"), email = "chjun@postech.ac.kr", role = c("aut", "ctb")) , person(c("Muhammad", "Kashif"), email = "mkashif@uaf.edu.pk", role = c("aut", "ctb")) )
Author: Muhammad Yaseen [aut, cre], Muhammad Aslam [aut, ctb], Sami Ullah [aut, ctb], Muhammad Azam [aut, ctb], Chi-Hyuck Jun [aut, ctb], Muhammad Kashif [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Functions to calculate Average Sample Numbers (ASN), Average Run Length (ARL1) and value of k, k1 and k2 for quality control charts under repetitive sampling as given in Aslam et al. (2014) (<DOI:10.7232/iems.2014.13.1.101>).
Depends: R (>= 3.1)
Imports: dplyr, magrittr, purrr, stats, tibble
License: GPL-2
URL: https://github.com/myaseen208/qccrs, https://myaseen208.github.io/qccrs/
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Note: Department of Mathematics and Statistics, University of Agriculture Faisalabad, Faisalabad-Pakistan.
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-11-29 13:14:17 UTC; myaseen
Repository: CRAN
Date/Publication: 2018-12-03 19:50:03 UTC

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New package FAMoS with initial version 0.1.0
Package: FAMoS
Type: Package
Title: A Flexible Algorithm for Model Selection (FAMoS)
Version: 0.1.0
Author: Michael Gabel, Tobias Hohl
Maintainer: Michael Gabel <m_gabel@gmx.de>
Description: Given a set of parameters describing model dynamics and a corresponding cost function, FAMoS attempts to find the most suitable parameter subset in terms of a specified information criterion. Works on any cost function that returns a negative log-likelihood.
License: GPL-3
Depends: R (>= 3.4)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: future, R.utils
Suggests: future.batchtools, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-30 11:53:23 UTC; work
Repository: CRAN
Date/Publication: 2018-12-03 19:50:16 UTC

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New package ev.trawl with initial version 0.1.0
Package: ev.trawl
Type: Package
Title: Extreme Value Trawls
Version: 0.1.0
Author: Valentin Courgeau
Maintainer: Valentin Courgeau <valentin.courgeau15@imperial.ac.uk>
Description: Implementation of trawl processes and an extension of such processes into a univariate latent model for extreme values. Inference, simulation and initialization tools are available. See Noven et al. (2018) <DOI:10.21314/JEM.2018.179> which can be found on arXiv (<arXiv:1511.08190>) .
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: R (>= 2.10)
Imports: testthat, fExtremes, hypergeo, stats, ghyp, evir, eva
NeedsCompilation: no
Packaged: 2018-11-29 15:44:01 UTC; Valentin
Repository: CRAN
Date/Publication: 2018-12-03 19:40:08 UTC

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New package emstreeR with initial version 2.0.0
Package: emstreeR
Type: Package
Title: Fast Computing Euclidean Minimum Spanning Trees
Version: 2.0.0
Date: 2018-11-15
Authors@R: c( person(given="Allan", family="Quadros", email = "allanvcq@gmail.com", role = c("aut", "cre")), person(given="Andre", family="Cancado", email = "cancado@unb.br", role = c("ctb")), person(given="Pedro", family="Brom", email = "pcbrom@gmail.com", role = c("ctb")), person(given="Eduardo", family="Hellas", email = "ehellas@gmail.com", role = c("ctb")) )
Description: Computes an Euclidean Minimum Spanning Tree using the Dual-Tree Boruvka algorithm (March, Ram, Gray, 2010, doi:<10.1145/1835804.1835882>) implemented in 'mlpack' - the C++ Machine Learning library (Curtin, 2005, <doi:10.21105/joss.00726>). 'emstreeR' works as a wrapper so that R users can benefit from the fast C++ function for computing an Euclidean Minimum Spanning Tree without touching the C++ code. The package also provides functions and an S3 method for readily plotting the Minimum Spanning Trees (MST) using either 'base' R, 'scatterplot3d' or 'ggplot2' style.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Imports: Rcpp (>= 0.12.18), scatterplot3d, ggplot2, BBmisc
Depends: R (>= 3.5.0)
LinkingTo: Rcpp, RcppMLPACK, RcppArmadillo, BH
BugReports: https://github.com/allanvc/emstreeR/issues
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-28 19:52:28 UTC; allan
Author: Allan Quadros [aut, cre], Andre Cancado [ctb], Pedro Brom [ctb], Eduardo Hellas [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-03 19:40:12 UTC

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New package cvmgof with initial version 1.0.0
Title: Cramer-von Mises Goodness-of-Fit Tests
Package: cvmgof
Type: Package
Version: 1.0.0
Author: Romain Azais, Sandie Ferrigno and Marie-Jose Martinez
Maintainer: Romain Azais <romain.azais@inria.fr>
Description: It is devoted to Cramer-von Mises goodness-of-fit tests. It implements three statistical methods based on Cramer-von Mises statistics to estimate and test a regression model.
License: CeCILL
Encoding: UTF-8
LazyData: FALSE
Imports: lattice
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-29 12:48:23 UTC; romain
Repository: CRAN
Date/Publication: 2018-12-03 19:50:09 UTC

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New package BeyondBenford with initial version 1.0
Package: BeyondBenford
Type: Package
Title: Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset
Version: 1.0
Date: 2018-11-17
Author: Blondeau Da Silva Stephane
Maintainer: Blondeau Da Silva Stephane <Stephane.Blondeau-Da-Silva@ac-limoges.fr>
Description: Allows to compare the goodness of fit of Benford's and Blondeau Da Silva's digit distributions in a dataset. It is used to check whether the data distribution is consistent with theoretical distributions highlighted by Blondeau Da Silva or not (through the dat.distr() function): this ideal theoretical distribution must be at least approximately followed by the data for the use of Blondeau Da Silva's model to be well-founded. It also enables to plot histograms of digit distributions, both observed in the dataset and given by the two theoretical approaches (with the digit.ditr() function). Finally, it proposes to quantify the goodness of fit via Pearson's chi-squared test (with the chi2() function).
License: GPL-2
NeedsCompilation: no
Packaged: 2018-11-29 09:02:33 UTC; anne
Repository: CRAN
Date/Publication: 2018-12-03 19:40:17 UTC

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New package aGE with initial version 0.0.9
Package: aGE
Type: Package
Title: Adaptive Set-Based Gene-Environment Interaction Test for Rare Variants
Version: 0.0.9
Description: Tests gene-environment interaction for rare genetic variants within the framework of adaptive sum of powered score test. The package includes two tests: adaptive gene-by-environment interaction test, and joint test for genetic main effects and gene-environment interaction. See Yang et al (2018) <doi:10.1002/sim.8037>.
Depends: R (>= 3.4)
License: GPL-3
Encoding: UTF-8
Imports: nlme, MASS, survey, stats
NeedsCompilation: no
Date: 2018-11-11
Packaged: 2018-11-20 04:55:49 UTC; yang
Authors@R: c(person("Tianzhong", "Yang", role = c("aut", "cre"), email = "tianzhong.yang@uth.tmc.edu"), person("Han", "Chen", role = "aut"), person("Peng", "Wei", role = "aut") )
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
Author: Tianzhong Yang [aut, cre], Han Chen [aut], Peng Wei [aut]
Maintainer: Tianzhong Yang <tianzhong.yang@uth.tmc.edu>
Repository: CRAN
Date/Publication: 2018-12-03 19:50:13 UTC

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New package PeakSegDisk with initial version 2018.11.28
Package: PeakSegDisk
Type: Package
Title: Disk-Based Implementation of PeakSegFPOP
Version: 2018.11.28
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Description: Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints <arXiv:1810.00117> for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).
License: GPL-3
Depends: R (>= 2.10)
Imports: data.table (>= 1.9.8), parallel
Suggests: testthat, ggplot2, penaltyLearning
NeedsCompilation: yes
Packaged: 2018-11-28 19:07:33 UTC; tdhock
Repository: CRAN
Date/Publication: 2018-12-03 12:42:36 UTC

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New package mlergm with initial version 0.1
Package: mlergm
Title: Multilevel Exponential-Family Random Graph Models
Version: 0.1
Authors@R: c( person("Jonathan", "Stewart", email = "jonathan.stewart@rice.edu", role = c("cre", "aut")), person("Michael", "Schweinberger", email = "michael.schweinberger@rice.edu", role = c("ctb")))
Description: Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.
Depends: R (>= 3.5.0), ergm, network
Imports: parallel, Matrix, stringr, stats, GGally, ggplot2, cowplot, reshape2, plyr, methods, graphics, sna
Suggests: RColorBrewer, knitr, rmarkdown
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-28 22:39:17 UTC; jstew
Author: Jonathan Stewart [cre, aut], Michael Schweinberger [ctb]
Maintainer: Jonathan Stewart <jonathan.stewart@rice.edu>
Repository: CRAN
Date/Publication: 2018-12-03 12:10:03 UTC

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New package clr with initial version 0.1.0
Package: clr
Type: Package
Title: Curve Linear Regression via Dimension Reduction
Version: 0.1.0
Author: Amandine Pierrot with contributions and/or help from Qiwei Yao, Haeran Cho, Yannig Goude and Tony Aldon.
Maintainer: Amandine Pierrot <amandine.m.pierrot@gmail.com>
Copyright: EDF R&D 2017
Description: A new methodology for linear regression with both curve response and curve regressors, which is described in Cho, Goude, Brossat and Yao (2013) <doi:10.1080/01621459.2012.722900> and (2015) <doi:10.1007/978-3-319-18732-7_3>. The key idea behind this methodology is dimension reduction based on a singular value decomposition in a Hilbert space, which reduces the curve regression problem to several scalar linear regression problems.
License: LGPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 2.10)
Imports: magrittr, lubridate, dplyr, stats
NeedsCompilation: no
Packaged: 2018-11-28 23:16:59 UTC; amandinepierrot
Repository: CRAN
Date/Publication: 2018-12-03 12:12:44 UTC

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New package ical with initial version 0.1.5
Package: ical
Type: Package
Title: 'iCalendar' Parsing
Version: 0.1.5
Date: 2018-11-27
Author: c( person( "Peter", "Meissner", role = c("aut", "cre"), email = "retep.meissner@gmail.com" ), person( "Philipp", "Kewisch", role = "cph", comment = "Ical.js file is is licences under MPL. Source: https://github.com/mozilla-comm/ical.js" ) )
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Description: A simple wrapper around the 'ical.js' library executing 'Javascript' code via 'V8' (the 'Javascript' engine driving the 'Chrome' browser and 'Node.js' and accessible via the 'V8' R package). This package enables users to parse 'iCalendar' files ('.ics', '.ifb', '.iCal', '.iFBf') into lists and 'data.frames' to ultimately do statistics on events, meetings, schedules, birthdays, and the like.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: V8 (>= 1.5)
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2018-11-27 20:48:38 UTC; peter
Repository: CRAN
Date/Publication: 2018-12-03 11:22:41 UTC

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New package DIMORA with initial version 0.1.0
Package: DIMORA
Date: 2018-11-25
Type: Package
Title: Diffusion Models R Analysis
Version: 0.1.0
Author: Zanghi Federico
Depends: R (>= 3.1.0), minpack.lm, numDeriv, stats
Maintainer: Zanghi Federico <federico.zanghi@studenti.unipd.it>
Description: The implemented methods are: Bass Standard model, Bass Generalized model (with rectangular shock, exponential shock, mixed shock and armonic shock. You can choose to add from 1 to 3 shocks), Guseo-Guidolin model and Variable Potential Market model. The Bass model consists of a simple differential equation that describes the process of how new products get adopted in a population, the Generalized Bass model is a generalization of the Bass model in which there is a "carrier" function x(t) that allows to change the speed of time sliding. In some real processes the reachable potential of the resource available in a temporal instant may appear to be not constant over time, because of this we use Variable Potential Market model, in which the Guseo-Guidolin has a particular specification for the market function.
Encoding: UTF-8
License: GPL | file LICENSE
RoxygenNote: 6.1.0.9000
NeedsCompilation: no
Packaged: 2018-11-26 15:24:14 UTC; federicozanghi
Repository: CRAN
Date/Publication: 2018-12-03 11:03:09 UTC

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New package twosamples with initial version 1.0.0
Package: twosamples
Type: Package
Title: Fast Permutation Based Two Sample Tests
Version: 1.0.0
Author: Connor Dowd
Maintainer: Connor Dowd <cdowd@chicagobooth.edu>
Description: Fast randomization based two sample tests. Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, and Anderson-Darling. There is also a very efficient test based on the Wasserstein Distance. The default test 'two_sample' builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. We also include the permutation scheme to make test building simple for others.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
URL: https://github.com/cdowd/twosamples
BugReports: https://github.com/cdowd/twosamples/issues
NeedsCompilation: yes
Packaged: 2018-11-21 15:44:35 UTC; connorjdowd
Repository: CRAN
Date/Publication: 2018-12-03 09:30:03 UTC

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New package tabula with initial version 1.0.0
Package: tabula
Title: Analysis, Seriation and Visualization of Archaeological Count Data
Version: 1.0.0
Date: 2018-11-22
Authors@R: c(person("Nicolas", "Frerebeau", email = "data@archaeo.science", role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0001-5759-4944")), person("Brice", "Lebrun", email = "brice.lebrun@u-bordeaux-montaigne.fr", role = c("ctb"), comment = c(ORCID = "https://orcid.org/0000-0001-7503-8685")), person("Matthew", "Peeples", email = "matthew.peeples@asu.edu", role = c("ctb"), comment = c(ORCID = "https://orcid.org/0000-0003-4496-623X")) )
Maintainer: Nicolas Frerebeau <data@archaeo.science>
Description: An easy way to examine archaeological count data (artifacts, faunal remains, etc.). This package includes several measures of diversity, e.g. richness, rarefaction, diversity, turnover, similarity, etc. It also provides matrix seriation methods for chronological modeling and dating. The package make it easy to visualize count data and statistical thresholds: rank/abundance plots, Ford and Bertin diagrams, etc.
URL: http://github.com/nfrerebeau/tabula
BugReports: http://github.com/nfrerebeau/tabula/issues
Depends: R (>= 3.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
Collate: 'utilities.R' 'tabula.R' 'AllClasses.R' 'AllGenerics.R' 'LogicalMatrix.R' 'NumericMatrix.R' 'index-richness.R' 'index-diversity.R' 'alpha-diversity.R' 'index-turnover.R' 'index-similarity.R' 'beta-diversity.R' 'data.R' 'method-seriation.R' 'statistics.R' 'plot.R' 'seriation.R'
RoxygenNote: 6.1.1
Suggests: testthat, knitr, rmarkdown
Imports: dplyr (>= 0.7), FactoMineR, ggplot2 (>= 3.0.0), grDevices, magrittr, methods, rlang, stats, tidyr, utils
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-22 17:10:58 UTC; nicolas
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>), Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>), Matthew Peeples [ctb] (<https://orcid.org/0000-0003-4496-623X>)
Repository: CRAN
Date/Publication: 2018-12-03 09:40:03 UTC

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New package solartime with initial version 0.0.1
Package: solartime
Title: Utilities Dealing with Solar Time Such as Sun Position and Time of Sunrise
Version: 0.0.1
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Description: Provide utilities to work with solar time, i.e. where noon is exactly when sun culminates. Provides functions for computing sun position and times of sunrise and sunset.
Depends: R (>= 3.2.0)
URL: https://github.com/bgctw/solartime
Imports: lubridate
Suggests: testthat, knitr
License: GPL-3
LazyLoad: yes
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-22 09:12:42 UTC; twutz
Repository: CRAN
Date/Publication: 2018-12-03 09:30:06 UTC

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New package RProbSup with initial version 1.0
Package: RProbSup
Type: Package
Title: Calculates Probability of Superiority
Version: 1.0
Author: John Ruscio
Maintainer: John Ruscio <ruscio@tcnj.edu>
Description: The A() function calculates the A statistic, a nonparametric measure of effect size for two independent groups that’s also known as the probability of superiority (Ruscio, 2008), along with its standard error and a confidence interval constructed using bootstrap methods (Ruscio & Mullen, 2012). Additional functions are provided to calculate variants of the A statistic developed for other research designs (e.g., related samples, more than two independent groups or related samples; Ruscio & Gera, 2013). <DOI: 10.1037/1082-989X.13.1.19>. <DOI: 10.1080/00273171.2012.658329>. <DOI: 10.1080/00273171.2012.738184>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-22 16:56:17 UTC; oliviaortelli
Repository: CRAN
Date/Publication: 2018-12-03 09:32:48 UTC

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New package remedy with initial version 0.1.0
Package: remedy
Title: 'RStudio' Addins to Simplify 'Markdown' Writing
Version: 0.1.0
Authors@R: c(person("Colin", "Fay", email = "contact@colinfay.me", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7343-1846")), person("Jonathan", "Sidi", email = "yonicd@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0002-4222-1819")), person("Luke", "Smith", email = "luke@protocolvital.info", role = c("aut"), comment = "author of seasmith/AlignAssign"), person("Jonathan", "Carroll", email = "rpkg@jcarroll.com.au", role = c("ctb"), comment = c(ORCID = "0000-0002-1404-5264")), person("Andrzej", "Oleś", email = "andrzej.oles@gmail.com", role = c("ctb"), comment = c(ORCID = "0000-0003-0285-2787")), person("Daniel", "Possenriede", email = "possenriede@gmail.com", role = c("ctb"), comment = c(ORCID = "0000-0002-6738-9845")))
Description: An 'RStudio' addin providing shortcuts for writing in 'Markdown'. This package provides a series of functions that allow the user to be more efficient when using 'Markdown'. For example, you can select a word, and put it in bold or in italics, or change the alignment of elements inside you Rmd. The idea is to map all the functionalities from 'remedy' on keyboard shortcuts, so that it provides an interface close to what you can find in any other text editor.
License: MIT + file LICENSE
URL: https://github.com/ThinkR-open/remedy
BugReports: https://github.com/ThinkR-open/remedy/issues
Imports: knitr, rstudioapi, rematch2, utils, stats
Suggests: testthat, rmarkdown
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-22 16:23:08 UTC; colin
Author: Colin Fay [aut, cre] (<https://orcid.org/0000-0001-7343-1846>), Jonathan Sidi [aut] (<https://orcid.org/0000-0002-4222-1819>), Luke Smith [aut] (author of seasmith/AlignAssign), Jonathan Carroll [ctb] (<https://orcid.org/0000-0002-1404-5264>), Andrzej Oleś [ctb] (<https://orcid.org/0000-0003-0285-2787>), Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Colin Fay <contact@colinfay.me>
Repository: CRAN
Date/Publication: 2018-12-03 09:20:03 UTC

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New package pkgcond with initial version 0.1.0
Package: pkgcond
Type: Package
Title: Classed Error and Warning Conditions
Version: 0.1.0
Authors@R: c( person("Andrew", "Redd", email="Andrew.Redd@hsc.utah.edu", role=c("aut", "cre")), person("R Documentation Task Force", role=c("aut")) )
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Description: This provides utilities for creating classed error and warning conditions based on where the error originated.
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R(>= 3.5.0)
Imports: methods
Suggests: covr, testthat
Enhances: assertthat
RoxygenNote: 6.1.1
Language: en-US
Collate: 'assert_that.R' 'conditions.R' 'comma_list.R' 'find_scope.R' 'infix.R' 'skip_scope.R' 'suppress.R' 'translate.R'
URL: https://github.com/RDocTaskForce/pkgcond
BugReports: https://github.com/RDocTaskForce/pkgcond/issues
NeedsCompilation: no
Packaged: 2018-11-26 22:39:01 UTC; u0092104
Author: Andrew Redd [aut, cre], R Documentation Task Force [aut]
Repository: CRAN
Date/Publication: 2018-12-03 10:40:03 UTC

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New package PKconverter with initial version 1.3
Package: PKconverter
Type: Package
Title: The Parameter Converter of the Pharmacokinetic Models
Version: 1.3
Author: Eun-Kyung Lee, Hye-sun Cho
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Description: Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion. The pharmacokinetics model explains that how the drug concentration change as the drug moves through the different compartments of the body. For pharmacokinetic modeling and analysis, it is essential to understand the basic pharmacokinetic parameters. All parameters are considered, but only some of parameters are used in the model. Therefore, we need to convert the estimated parameters to the other parameters after fitting the specific pharmacokinetic model. This package is developed to help this converting work. For more detailed explanation of pharmacokinetic parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001"; "Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>; "Mould and Upton" (2012) <doi:10.1038/psp.2012.4>; "Mould and Upton" (2013) <doi:10.1038/psp.2013.14>.
License: GPL (>= 2)
Imports: shiny, shinythemes, shinydashboard
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-23 07:59:40 UTC; leeeu
Repository: CRAN
Date/Publication: 2018-12-03 09:52:49 UTC

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New package npExact with initial version 0.2
Package: npExact
Type: Package
Title: Exact Nonparametric Hypothesis Tests for the Mean, Variance and Stochastic Inequality
Version: 0.2
Date: 2018-11-12
Authors@R: c( person(given = "Oliver", family = "Reiter", role = c("cre", "aut"), comment = c(ORCID = "0000-0001-6338-5428"), email = "oliver.reiter@snapdragon.cc"), person(given = "Karl", family = "Schlag", role = c("aut"), email = "karl.schlag@univie.ac.at"), person(given = "Peter", family = "Saffert", role = "ctb"), person(given = "Christian", family = "Pechhacker", role = "ctb"), person(given = "Simona", family = "Jokubauskaite", role = "ctb"), person(given = "Tautvilas", family = "Janusauskas", role = "ctb"))
Description: Provides several novel exact hypothesis tests with minimal assumptions on the errors. The tests are exact, meaning that their p-values are correct for the given sample sizes (the p-values are not derived from asymptotic analysis). The test for stochastic inequality is for ordinal comparisons based on two independent samples and requires no assumptions on the errors. The other tests include tests for the mean and variance of a single sample and comparing means in independent samples. All these tests only require that the data has known bounds (such as percentages that lie in [0,100]. These bounds are part of the input.
Depends: R (>= 3.2)
Imports: stats
Suggests: testthat
URL: https://github.com/zauster/npExact
BugReports: https://github.com/zauster/npExact/issues
License: GPL-2
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-09 18:23:11 UTC; reitero
Author: Oliver Reiter [cre, aut] (<https://orcid.org/0000-0001-6338-5428>), Karl Schlag [aut], Peter Saffert [ctb], Christian Pechhacker [ctb], Simona Jokubauskaite [ctb], Tautvilas Janusauskas [ctb]
Maintainer: Oliver Reiter <oliver.reiter@snapdragon.cc>
Repository: CRAN
Date/Publication: 2018-12-03 09:10:03 UTC

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New package mixRaschTools with initial version 1.1
Package: mixRaschTools
Title: Plotting and Average Theta Functions for Multiple Class Mixed Rasch Models
Version: 1.1
Authors@R: c(person("Pamela", "Trantham", role = c("aut", "cre"), email = "pamelapsc@yahoo.com"))
Author: Pamela Trantham [aut, cre]
Description: Provides supplemental functions for the 'mixRasch' package (Willse, 2014), <https://cran.r-project.org/package=mixRasch/mixRasch.pdf> including a plotting function to compare item parameters for multiple class models and a function that provides average theta values for each class in a mixture model.
Depends: R (>= 3.3.0)
License: GPL
Encoding: UTF-8
LazyData: true
Imports: graphics
Suggests: knitr, rmarkdown, mixRasch, testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-25 18:52:55 UTC; pamela
Maintainer: Pamela Trantham <pamelapsc@yahoo.com>
Repository: CRAN
Date/Publication: 2018-12-03 10:10:03 UTC

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New package misaem with initial version 0.9.0
Package: misaem
Title: Stochastic Approximation EM for Logistic Regression with Missing Values
Version: 0.9.0
Date: 2018-11-26
Authors@R: person("Wei", "Jiang", email = "wei.jiang@polytechnique.edu", role = c("aut", "cre"))
Description: Estimate parameters of logistic regression with missing data and perform model selection, using algorithm Stochastic Approximation EM.
Depends: R (>= 3.4.0)
Encoding: UTF-8
License: GPL-3
URL: https://github.com/wjiang94/misaem.git
Imports: magrittr, mvtnorm, stats, MASS
Suggests: knitr, rmarkdown
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-27 11:02:25 UTC; wjiang
Author: Wei Jiang [aut, cre]
Maintainer: Wei Jiang <wei.jiang@polytechnique.edu>
Repository: CRAN
Date/Publication: 2018-12-03 10:50:03 UTC

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New package icsurvROC with initial version 0.1.0
Package: icsurvROC
Type: Package
Title: Interval Censored Survival ROC
Version: 0.1.0
Author: Yunro Chung [cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Description: Nonparametric and semiparametric estimations of the time-dependent ROC curve for the interval-censored failure time data.
Depends: R (>= 3.5.0), survival, Iso, icenReg
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-25 22:10:20 UTC; roy
Repository: CRAN
Date/Publication: 2018-12-03 10:22:41 UTC

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New package GENMETA with initial version 0.1
Package: GENMETA
Title: Implements Generalized Meta-Analysis Using Iterated Reweighted Least Squares Algorithm
Version: 0.1
Authors@R: c(person("Prosenjit", "Kundu", role = c("aut", "cre"), email = "pkundu@jhu.edu"), person("Runlong", "Tang", role = "aut"), person("Nilanjan", "Chatterjee", role = "aut"))
Description: Generalized meta-analysis is a technique for estimating parameters associated with a multiple regression model through meta-analysis of studies which may have information only on partial sets of the regressors. It estimates the effects of each variable while fully adjusting for all other variables that are measured in at least one of the studies. Using algebraic relationships between regression parameters in different dimensions, a set of moment equations is specified for estimating the parameters of a maximal model through information available on sets of parameter estimates from a series of reduced models available from the different studies. The specification of the equations requires a reference dataset to estimate the joint distribution of the covariates. These equations are solved using the generalized method of moments approach, with the optimal weighting of the equations taking into account uncertainty associated with estimates of the parameters of the reduced models. The proposed framework is implemented using iterated reweighted least squares algorithm for fitting generalized linear regression models. For more details about the method, please see pre-print version of the manuscript on generalized meta-analysis by Prosenjit Kundu, Runlong Tang and Nilanjan Chatterjee (2018) <arXiv:1708.03818>.
Depends: R (>= 2.15.3), MASS, graphics
Imports: Matrix, magic
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Collate: 'myoptim.R' 'sign.star.R' 'GENMETA.R' 'GENMETA.control.R' 'GENMETA.summary.R' 'GENMETA.plot.R'
NeedsCompilation: no
Packaged: 2018-11-21 20:37:35 UTC; prosenjitkundu
Author: Prosenjit Kundu [aut, cre], Runlong Tang [aut], Nilanjan Chatterjee [aut]
Maintainer: Prosenjit Kundu <pkundu@jhu.edu>
Repository: CRAN
Date/Publication: 2018-12-03 09:10:07 UTC

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New package customsteps with initial version 0.7.1.0
Package: customsteps
Title: Customizable Higher-Order Recipe Step Functions
Version: 0.7.1.0
Authors@R: person("Lars", "Kjeldgaard", email = "lars_kjeldgaard@hotmail.com", role = c("aut", "cre"))
Description: Customizable higher-order recipe step functions for the 'recipes' package. These step functions take 'prep' and 'bake' helper functions as inputs and create specifications of customized recipe steps as output.
URL: https://github.com/smaakage85/customsteps
Depends: R (>= 3.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: recipes, dplyr, tibble, magrittr, purrr, tidyselect, methods, generics, rlang
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-25 19:03:11 UTC; lars_
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Repository: CRAN
Date/Publication: 2018-12-03 10:12:42 UTC

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New package CpDyna with initial version 1.0
Package: CpDyna
Type: Package
Title: Change Point Detection in Dynamic Graphs
Version: 1.0
Date: 2018-11-08
Author: Marco Corneli, Pierre Latouche, Fabrice Rossi, Margot Selosse
Maintainer: Margot Selosse <margot.selosse@gmail.com>
Description: Implementation of a model-based approach for clustering and multiple change points in dynamic graphs (Marco Corneli, Pierre Latouche and Fabrice Rossi (2018) <doi.org/10.1007/s11222-017-9775-1>).
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.17), mclust, RColorBrewer, igraph
LinkingTo: Rcpp, RcppProgress, RcppArmadillo
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, mapview, sp
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2018-11-22 10:03:36 UTC; margot
Depends: R (>= 2.10)
RoxygenNote: 6.1.0
Repository: CRAN
Date/Publication: 2018-12-03 09:10:11 UTC

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New package CopCTS with initial version 1.0.0
Package: CopCTS
Type: Package
Title: Copula-Based Semiparametric Analysis for Time Series Data with Detection Limits
Version: 1.0.0
Author: Fuyuan David Li
Maintainer: Fuyuan David Li <LFY@gwmail.gwu.edu>
Description: Semiparametric estimation for censored time series with lower detection limit. The latent response is a sequence of stationary process with Markov property of order one. Estimation of copula parameter(COPC) and Conditional quantile estimation are included for five available copula functions. Copula selection methods based on L2 distance from empirical copula function are also included.
Depends: copula
Imports: msm,copBasic,methods
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-27 15:02:18 UTC; lfy
Repository: CRAN
Date/Publication: 2018-12-03 10:52:46 UTC

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New package cglm with initial version 1.0
Package: cglm
Type: Package
Title: Fits Conditional Generalized Linear Models
Version: 1.0
Date: 2018-11-26
Author: Arvid Sjolander
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>
Description: Estimates the ratio of the regression coefficients and the dispersion parameter in conditional generalized linear models for clustered data.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.18), stats, nleqslv, data.table
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2018-11-26 07:17:23 UTC; arvsjo
Repository: CRAN
Date/Publication: 2018-12-03 10:32:41 UTC

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New package argonDash with initial version 0.1.0
Package: argonDash
Type: Package
Title: Argon Shiny Dashboard Template
Version: 0.1.0
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com", role = c("aut", "cre")), person(family = "RinteRface", role = "cph"), person(family = "Creative Tim", role = c("ctb", "cph"), comment = "Argon theme for Bootstrap 4"))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: Create awesome 'Bootstrap 4' dashboards powered by 'Argon'. See more here <https://rinterface.github.io/argonDash/>.
License: GPL-2
Imports: shiny, htmltools, argonR
Suggests: magrittr
URL: https://github.com/RinteRface/argonDash
BugReports: https://github.com/RinteRface/argonDash/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-21 10:49:12 UTC; davidgranjon
Author: David Granjon [aut, cre], RinteRface [cph], Creative Tim [ctb, cph] (Argon theme for Bootstrap 4)
Repository: CRAN
Date/Publication: 2018-12-03 09:20:07 UTC

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Sun, 02 Dec 2018

New package pmd with initial version 0.1.1
Package: pmd
Type: Package
Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis
Version: 0.1.1
Date: 2018-10-29
Authors@R: person(given = "Miao", family = "YU", role = c("aut", "cre"), email = "yufreecas@gmail.com", comment = c(ORCID = "0000-0002-2804-6014"))
Maintainer: Miao YU <yufreecas@gmail.com>
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. A GUI for PMD analysis is also included as a 'shiny' application.
URL: https://yufree.github.io/pmd
BugReports: https://github.com/yufree/pmd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, enviGCMS
VignetteBuilder: knitr
biocViews:
Depends: R (>= 2.10)
Imports: RColorBrewer, shiny, rmarkdown
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-08 04:11:35 UTC; yufree
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Repository: CRAN
Date/Publication: 2018-12-02 17:20:03 UTC

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New package compas with initial version 0.1
Package: compas
Type: Package
Title: Conformational Manipulations of Protein Atomic Structures
Version: 0.1
Date: 2018-11-20
Author: Samuel W.K. Wong, Dylan Shi, Megan Hazlett, Jasmine Cheng
Maintainer: Samuel W.K. Wong <samuel.wong@uwaterloo.ca>
Description: Manipulate and analyze 3-D structural geometry of Protein Data Bank (PDB) files.
License: GPL-3
Imports: Rcpp (>= 0.12.18), bio3d
LinkingTo: Rcpp, RcppEigen
Depends: R (>= 3.2.0)
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-11-20 19:13:20 UTC; Samuel
Repository: CRAN
Date/Publication: 2018-12-02 17:30:03 UTC

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New package AzureRMR with initial version 1.0.0
Package: AzureRMR
Title: Interface to 'Azure Resource Manager'
Version: 1.0.0
Authors@R: c( person("Hong", "Ooi", , "hongooi@microsoft.com", role = c("aut", "cre")), person("Microsoft", role="cph") )
Description: A lightweight but powerful R interface to the 'Azure Resource Manager' REST API. The package exposes classes and methods for 'OAuth' authentication and working with subscriptions and resource groups. It also provides functionality for creating and deleting 'Azure' resources and deploying templates. While 'AzureRMR' can be used to manage any 'Azure' service, it can also be extended by other packages to provide extra functionality for specific services.
URL: https://github.com/cloudyr/AzureRMR
BugReports: https://github.com/cloudyr/AzureRMR/issues
License: MIT + file LICENSE
VignetteBuilder: knitr
Depends: R (>= 3.3)
Imports: utils, httr (>= 1.3), jsonlite, R6
Suggests: knitr, testthat
RoxygenNote: 6.1.0.9000
NeedsCompilation: no
Packaged: 2018-11-20 19:46:15 UTC; hongooi
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Repository: CRAN
Date/Publication: 2018-12-02 17:20:07 UTC

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New package ar.matrix with initial version 0.1.0
Package: ar.matrix
Type: Package
Title: Simulate Auto Regressive Data from Precision Matricies
Version: 0.1.0
Authors@R: c(person("Neal","Marquez",role=c("aut","cre","cph"),email="nmarquez@uw.edu"))
Author: Neal Marquez [aut, cre, cph]
Maintainer: Neal Marquez <nmarquez@uw.edu>
Description: Using sparse precision matricies and Choleski factorization simulates data that is auto-regressive.
Depends: R (>= 3.3.0)
Imports: MASS, Matrix, sparseMVN, sp
Suggests: ggplot2, leaflet
License: GPL (>= 2)
BugReports: https://github.com/nmmarquez/ar.matrix/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-20 20:44:39 UTC; nmarquez
Repository: CRAN
Date/Publication: 2018-12-02 17:30:06 UTC

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Fri, 30 Nov 2018

New package snfa with initial version 0.0.1
Package: snfa
Title: Smooth Non-Parametric Frontier Analysis
Version: 0.0.1
Authors@R: person("Taylor", "McKenzie", email = "tkmckenzie@gmail.com", role = c("aut", "cre"))
Description: Fitting of non-parametric production frontiers for use in efficiency analysis. Methods are provided for both a smooth analogue of Data Envelopment Analysis (DEA) and a non-parametric analogue of Stochastic Frontier Analysis (SFA). Frontiers are constructed for multiple inputs and a single output using constrained kernel smoothing as in Racine et al. (2009), which allow for the imposition of monotonicity and concavity constraints on the estimated frontier.
Maintainer: Taylor McKenzie <tkmckenzie@gmail.com>
Depends: R (>= 3.5.0)
Imports: abind (>= 1.4.5), ggplot2 (>= 3.1.0), prodlim (>= 2018.4.18), quadprog (>= 1.5.5), Rdpack (>= 0.10.1), rootSolve (>= 1.7)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2018-11-20 16:08:34 UTC; tmcken
Author: Taylor McKenzie [aut, cre]
Repository: CRAN
Date/Publication: 2018-12-01 00:00:03 UTC

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New package smartR with initial version 0.62.0
Package: smartR
Type: Package
Title: Spatial Management and Assessment of Demersal Resources for Trawl Fisheries
Version: 0.62.0
Date: 2018-11-20
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea <dandrea.lorenz@gmail.com>
Description: A tool for assessing bio-economic feedback in different management scenarios. 'smartR' (Spatial Management and Assessment of demersal Resources for Trawl fisheries) combines information from different tasks gathered within the European Data Collection Framework for the fishery sector. The 'smartR' package implements the SMART model (Russo et al., 2014 <doi:10.1371/journal.pone.0086222>), through the object-oriented programming paradigm, and within this package it is possible to achieve the complete set of analyses required by the SMART approach: from the editing and formatting of the raw data; the construction and maintenance of coherent datasets; the numerical and visual inspection of the generated metadata; to the final simulation of management scenarios and the forecast of their effects. The interaction between the user and the application could take place through invocation of methods via the command line or could be entirely committed to the graphical user interfaces (GUI).
License: GPL (>= 2)
Depends: R6, rjags, maptools, mapdata
Imports: PBSmapping, gWidgets2, gWidgets2RGtk2, gstat, lattice, plyr, sp, maps, clues, cluster, spdep, marmap, shape, jpeg, grid, ggplot2, sqldf, gsubfn, chron, reshape2, foreign, ROCR, caret, nnls, mtsdi, gridExtra, rgeos, scales, grDevices, ggthemes, vegan, rpart, ggrepel, rgdal, RColorBrewer, jsonlite, igraph, mapproj
LazyData: true
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-11-20 13:51:26 UTC; Lomo
Repository: CRAN
Date/Publication: 2018-11-30 23:40:03 UTC

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New package SeedCalc with initial version 1.0.0
Package: SeedCalc
Type: Package
Title: Seed Germination and Seedling Growth Indexes
Version: 1.0.0
Author: Laercio Junio da Silva, Andre Danta de Medeiros e Ariadne Morbeck Santos Oliveira
Maintainer: Laercio Junio da Silva <laerciojdsilva@gmail.com>
Description: Functions to calculate seed germination and seedling emergence and growth indexes. The main indexes for germination and seedling emergence, considering the time for seed germinate are: T10, T50 and T90, in Farooq et al. (2005) <10.1111/j.1744-7909.2005.00031.x>; and MGT, in Labouriau (1983). Considering the germination speed are: Germination Speed Index, in Maguire (1962), Mean Germination Rate, in Labouriau (1983); considering the homogeneity of germination are: Coefficient of Variation of the Germination Time, in Carvalho et al. (2005) <10.1590/S0100-84042005000300018>, and Variance of Germination, in Labouriau (1983); Uncertainty, in Labouriau and Valadares (1976) <ISSN:0001-3765>; and Synchrony, in Primack (1980). The main seedling indexes are Growth, in Sako (2001), Uniformity, in Sako (2001) and Castan et al. (2018) <doi:10.1590/1678-992x-2016-0401>; and Vigour, in Medeiros and Pereira (2018) <doi:10.1590/1983-40632018v4852340>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-20 13:19:23 UTC; laerc
Repository: CRAN
Date/Publication: 2018-12-01 00:00:16 UTC

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New package PCMBase with initial version 1.2.7
Package: PCMBase
Type: Package
Title: Simulation and Likelihood Calculation of Phylogenetic Comparative Models
Version: 1.2.7
Authors@R: c(person("Venelin", "Mitov", email = "vmitov@gmail.com", role = c("aut", "cre", "cph")), person("Krzysztof", "Bartoszek", role = c("ctb")), person("Georgios", "Asimomitis", role = c("ctb")), person("Tanja", "Stadler", role = c("ctb")))
Maintainer: Venelin Mitov <vmitov@gmail.com>
Description: Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for ML and Bayesian fit of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.
Encoding: UTF-8
License: GPL (>= 3.0)
LazyData: true
Depends: R (>= 3.1.0)
Imports: ape, expm, mvtnorm, data.table, ggplot2
Suggests: testthat, knitr, rmarkdown, abind, ggtree, covr
RoxygenNote: 6.1.1
ByteCompile: yes
VignetteBuilder: knitr, rmarkdown
URL: https://venelin.github.io/PCMBase/, https://github.com/venelin/PCMBase
BugReports: https://github.com/venelin/PCMBase/issues
NeedsCompilation: no
Packaged: 2018-11-20 15:10:33 UTC; vmitov
Author: Venelin Mitov [aut, cre, cph], Krzysztof Bartoszek [ctb], Georgios Asimomitis [ctb], Tanja Stadler [ctb]
Repository: CRAN
Date/Publication: 2018-11-30 23:50:04 UTC

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New package ggnormalviolin with initial version 0.1.1
Package: ggnormalviolin
Title: A 'ggplot2' Extension to Make Normal Violin Plots
Version: 0.1.1
Authors@R: person(given = "W. Joel", family = "Schneider", role = c("aut", "cre"), email = "w.joel.schneider@gmail.com", comment = c(ORCID = "0000-0002-8393-5316"))
Description: Uses 'ggplot2' to create normally distributed violin plots with specified means and standard deviations. This function can be useful in showing hypothetically normal distributions and confidence intervals.
License: CC0
URL: https://github.com/wjschne/ggnormalviolin
BugReports: https://github.com/wjschne/ggnormalviolin/issues
Imports: dplyr, ggplot2, grid, magrittr, scales
Suggests: spelling
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-20 12:49:56 UTC; renee
Author: W. Joel Schneider [aut, cre] (<https://orcid.org/0000-0002-8393-5316>)
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-30 23:40:06 UTC

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New package bamp with initial version 2.0.4
Package: bamp
Type: Package
Title: Bayesian Age-Period-Cohort Modeling and Prediction
Version: 2.0.4
Date: 2018-11-20
Author: Volker Schmid [aut, cre], Florian Geressen [ctb], Leonhard Held [ctb], Evi Rainer [ctb]
Authors@R: c(person("Volker","Schmid",email="volker.schmid@lmu.de", role=c("aut","cre")),person("Florian","Geressen",role="ctb"), person("Leonhard","Held",role="ctb"),person("Evi","Rainer",role="ctb"))
Maintainer: Volker Schmid <volker.schmid@lmu.de>
Description: Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov Chain Monte Carlo Methods. This is the R version of the previous BAMP software as described in Volker Schmid and Leonhard Held (2007) <DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and Prediction - BAMP, Journal of Statistical Software 21:8. This package includes checks of convergence using Gelman's R.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: coda, graphics, parallel, stats, abind
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr, R.rsp
Suggests: knitr, rmarkdown, R.rsp
URL: https://volkerschmid.github.io/bamp/
BugReports: https://github.com/volkerschmid/bamp/issues
NeedsCompilation: yes
Packaged: 2018-11-20 15:50:56 UTC; schmid
Repository: CRAN
Date/Publication: 2018-11-30 23:40:11 UTC

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New package vistributions with initial version 0.1.0
Package: vistributions
Type: Package
Title: Visualize Probability Distributions
Version: 0.1.0
Authors@R: person("Aravind", "Hebbali", email = "hebbali.aravind@gmail.com", role = c("aut", "cre"))
Description: Visualize and compute percentiles/probabilities of normal, t, f, chi square and binomial distributions.
Depends: R(>= 3.1)
Imports: ggplot2, magrittr, shiny, stats, tibble
Suggests: testthat, knitr, rmarkdown, shinyBS, shinycssloaders, shinythemes
License: MIT + file LICENSE
URL: https://github.com/rsquaredacademy/vistributions, https://vistributions.rsquaredacademy.com
BugReports: https://github.com/rsquaredacademy/vistributions/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-20 10:38:13 UTC; HP
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-30 16:50:03 UTC

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New package rSEA with initial version 1.0
Package: rSEA
Type: Package
Title: Simultaneous Enrichment Analysis
Version: 1.0
Author: Mitra Ebrahimpoor
Maintainer: Mitra Ebrahimpoor<m.ebrahimpoor@lumc.nl>
Description: SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to make use of three databases for genomics, GO, Reactome and Wikipathways.
Depends: R (>= 2.10), hommel (>= 1.2)
License: GPL (>= 2)
Date: 2018-11-16
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-20 09:11:50 UTC; mebrahimpoor
Repository: CRAN
Date/Publication: 2018-11-30 16:50:10 UTC

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New package rdbnomics with initial version 0.4.3
Package: rdbnomics
Type: Package
Title: Download DBnomics Data
Version: 0.4.3
Authors@R: c(person("Thomas", "Brand", role = c("aut"), email = "thomas.brand@cepremap.org"), person("Sebastien", "Galais", role = c("cre", "ctb"), email = "Sebastien.GALAIS@banque-france.fr"))
Description: R access to hundreds of millions data series from DBnomics API (<https://db.nomics.world/>).
Depends: R (>= 3.1.0)
License: AGPL-3
URL: https://github.com/dbnomics/rdbnomics
BugReports: https://github.com/dbnomics/rdbnomics/issues
Encoding: UTF-8
LazyData: true
Imports: jsonlite, data.table
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, dplyr, magrittr, ggplot2, DT, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-19 22:48:28 UTC; sebas
Author: Thomas Brand [aut], Sebastien Galais [cre, ctb]
Maintainer: Sebastien Galais <Sebastien.GALAIS@banque-france.fr>
Repository: CRAN
Date/Publication: 2018-11-30 16:50:06 UTC

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New package rCRM with initial version 0.1
Package: rCRM
Type: Package
Title: Regularized Continual Reassessment Method
Version: 0.1
Author: Xiang Li, Hong Tian, Kevin Liu, Pilar Lim
Maintainer: Xiang Li <xli256@its.jnj.com>
Description: Fit a 2-parameter continual reassessment method (CRM) model (O'Quigley and Shen (1996), <doi: 10.2307/2532905>) regularized with L2 norm (Friedman et al. (2010), <doi: 10.18637/jss.v033.i01>) adjusted by the distance with the target dose limiting toxicity (DLT) rate.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.19)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2018-11-19 19:48:02 UTC; xli256
Repository: CRAN
Date/Publication: 2018-11-30 16:40:03 UTC

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New package MetaboLouise with initial version 1.0.0
Package: MetaboLouise
Version: 1.0.0
Date: 2018-11-20
Title: METABOlomics LOngitudinal SimUlation Engine
Author: Charlie Beirnaert
Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>
Description: Simulating dynamic (longitudinal, time-resolved) metabolomics data based on an underlying biological network. The network is initiating with certain concentrations and evolves over a simulated time period. Optionally external influxes (concentration drivers) can be added.
Depends: R (>= 3.1.0),
Imports: igraph, graphics, stats
Suggests: knitr, rmarkdown
LazyData: true
VignetteBuilder: knitr
License: GPL-3
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-20 10:54:21 UTC; Charlie
Repository: CRAN
Date/Publication: 2018-11-30 16:50:13 UTC

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New package rdtLite with initial version 1.0.2
Package: rdtLite
Title: Provenance Collector
Version: 1.0.2
Date: 2018-11-08
Authors@R: c( person("Barbara", "Lerner", role = c("aut", "cre"), email = "blerner@mtholyoke.edu"), person("Emery", "Boose", role = "aut", email = "boose@fas.harvard.edu"), person("Elizabeth", "Fong", role = "aut", email = "fong22e@mtholyoke.edu"), person("Luis", "Perez", role = "aut", email = "luis.perez.live@gmail.com"), person("Thomas", "Pasquier", role = "ctb", email = "thomas.francis.pasquier@gmail.com"), person("Matthew", "Lau", role = "ctb", email = "matthewklau@fas.harvard.edu"), person("Yada", "Pruksachatkun", role = "ctb", email = "pruks22y@mtholyoke.edu"), person("Alex", "Liu", role = "ctb", email = "uilxela7@gmail.com"), person("Moe Pwint Phyu", role = "ctb", email = "phyu22m@mtholyoke.edu"), person("Connor", "Gregorich-Trevor", role = "ctb", email = "gregoric@grinnell.edu"), person("Aaron", "Ellison", role = "res", email = "aellison@fas.harvard.edu"), person("Margo", "Seltzer", role = "res", email = "margo@eecs.harvard.edu"), person("Joe", "Wonsil", role = "res", email = "jwonsil@carthage.edu"), person("Orenna", "Brand", role = "res", email = "o.brand@columbia.edu") )
Copyright: President and Fellows of Harvard College, Trustees of Mount Holyoke College
Depends: R (>= 3.5.0)
Description: Defines functions that can be used to collect provenance as an R script executes or during a console session. The output is a text file in PROV-JSON format.
License: GPL-3 | file LICENSE
URL: https://github.com/End-to-end-provenance/rdtLite
BugReports: https://github.com/End-to-end-provenance/rdtLite/issues
Imports: curl, digest, ggplot2, grDevices, gtools, jsonlite, knitr, methods, sessioninfo, tools, utils, XML
Suggests: roxygen2, testthat
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-19 18:43:49 UTC; blerner
Author: Barbara Lerner [aut, cre], Emery Boose [aut], Elizabeth Fong [aut], Luis Perez [aut], Thomas Pasquier [ctb], Matthew Lau [ctb], Yada Pruksachatkun [ctb], Alex Liu [ctb], Moe Pwint Phyu [ctb], Connor Gregorich-Trevor [ctb], Aaron Ellison [res], Margo Seltzer [res], Joe Wonsil [res], Orenna Brand [res]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Repository: CRAN
Date/Publication: 2018-11-30 12:50:02 UTC

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New package nCopula with initial version 0.1.1
Package: nCopula
Type: Package
Title: Hierarchical Archimedean Copulas Constructed with Multivariate Compound Distributions
Version: 0.1.1
Authors@R: c(person("Simon-Pierre", "Gadoury", role=c("cre", "aut"), email="spgadou@me.com"), person("David", "Beauchemin", role="ctb", email="david.beauchemin.5@ulaval.ca"))
Maintainer: Simon-Pierre Gadoury <spgadou@me.com>
Description: Construct and manipulate hierarchical Archimedean copulas with multivariate compound distributions. The model used is the one of Cossette et al. (2017) <doi:10.1016/j.insmatheco.2017.06.001>.
Depends: R (>= 3.4.0), copula
Imports: Deriv, stringr, stringi, compiler, methods,
License: GPL (>= 2)
LazyData: FALSE
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-11-19 20:48:52 UTC; Simon-Pierre
Author: Simon-Pierre Gadoury [cre, aut], David Beauchemin [ctb]
Repository: CRAN
Date/Publication: 2018-11-30 12:40:07 UTC

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New package HMB with initial version 1.0
Package: HMB
Type: Package
Title: Hierarchical Model-Based Estimation Approach
Version: 1.0
Date: 2018-11-20
Authors@R: c( person("Svetlana", "Saarela", role = c("cre", "aut"), email = "admin@svetlanasaarela.com"), person("Sören", "Holm", role = "aut"), person("Zhiqiang", "Yang", role = "aut", email='zhiqiangyang@fs.fed.us'), person("Wilmer", "Prentius", role = "ctb") )
Description: For estimation of a variable of interest using two sources of auxiliary information available in a nested structure. For reference see Saarela et al. (2016)<doi:10.1007/s13595-016-0590-1> and Saarela et al. (2018) <doi:10.3390/rs10111832>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: TRUE
Imports: Rcpp (>= 0.12.16)
Depends: methods, stats, R (>= 3.5)
LinkingTo: Rcpp, RcppArmadillo
Collate: RcppExports.R helper_functions.R HMB-class.R SummaryHMB-class.R ghmb.R gtsmb.R hmb.R tsmb.R
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-19 19:12:33 UTC; svla0001
Author: Svetlana Saarela [cre, aut], Sören Holm [aut], Zhiqiang Yang [aut], Wilmer Prentius [ctb]
Maintainer: Svetlana Saarela <admin@svetlanasaarela.com>
Repository: CRAN
Date/Publication: 2018-11-30 12:50:06 UTC

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New package fishtree with initial version 0.1.0
Package: fishtree
Type: Package
Title: Interface to the Fish Tree of Life API
Version: 0.1.0
Authors@R: c( person("Jonathan", "Chang", role = c("aut", "cre"), email = "jonathan.chang@ucla.edu", comment = c("ORCID" = "0000-0002-3811-1254")), person("Michael E", "Alfaro", role = "ctb"), person("Daniel L", "Rabosky", role = "ctb"), person("Stephen A", "Smith", role = "ctb") )
Description: An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information.
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
URL: https://fishtreeoflife.org/
BugReports: https://github.com/jonchang/fishtree/issues
Depends: R (>= 3.4)
Imports: ape (>= 5.1), rlang (>= 0.2.2), jsonlite (>= 1.5), utils
Suggests: rfishbase, hisse, geiger, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-19 15:52:32 UTC; jonchang
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>), Michael E Alfaro [ctb], Daniel L Rabosky [ctb], Stephen A Smith [ctb]
Maintainer: Jonathan Chang <jonathan.chang@ucla.edu>
Repository: CRAN
Date/Publication: 2018-11-30 12:40:10 UTC

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Thu, 29 Nov 2018

New package vctrs with initial version 0.1.0
Package: vctrs
Title: Vector Helpers
Version: 0.1.0
Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph") )
Description: Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analyzing function interfaces.
License: GPL-3
URL: https://github.com/r-lib/vctrs
BugReports: https://github.com/r-lib/vctrs/issues
Depends: R (>= 3.1)
Imports: backports, digest, glue, rlang, zeallot
Suggests: covr, generics, knitr, pillar, pkgdown, rmarkdown, testthat, tibble
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2018-11-19 14:40:32 UTC; hadley
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Repository: CRAN
Date/Publication: 2018-11-29 17:10:03 UTC

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New package wiseR with initial version 1.0.1
Package: wiseR
Type: Package
Title: A Shiny Application for End-to-End Bayesian Decision Network Analysis and Web-Deployment
Version: 1.0.1
Author: Tavpritesh Sethi [aut, cre], Shubham Maheshwari [aut]
Authors@R: c( person("Tavpritesh", "Sethi", role = c("aut", "cre"), email = "tavpriteshsethi@iiitd.ac.in"), person("Shubham", "Maheshwari", role = c("aut"), email = "shubham14101@iiitd.ac.in") )
Maintainer: Tavpritesh Sethi <tavpriteshsethi@iiitd.ac.in>
Contact: Tavpritesh Sethi<tavpriteshsethi@iiitd.ac.in>,Shubham Maheshwari<shubham14101@iiitd.ac.in>
Description: A Shiny application for learning Bayesian Decision Networks from data. This package can be used for probabilistic reasoning (in the observational setting), causal inference (in the presence of interventions) and learning policy decisions (in Decision Network setting). Functionalities include end-to-end implementations for data-preprocessing, structure-learning, exact inference, approximate inference, extending the learned structure to Decision Networks and policy optimization using statistically rigorous methods such as bootstraps, resampling, ensemble-averaging and cross-validation. In addition to Bayesian Decision Networks, it also features correlation networks, community-detection, graph visualizations, graph exports and web-deployment of the learned models as Shiny dashboards.
biocViews:
Depends: R (>= 3.5.0)
Imports: Rgraphviz, RBGL, graph, bnlearn, HydeNet, rhandsontable, shiny, shinydashboard, dplyr, visNetwork, shinyWidgets, missRanger, tools, shinyalert, shinycssloaders, rintrojs, arules, psych, DescTools, DT, linkcomm, igraph, parallel, shinyBS
URL: https://github.com/SAFE-ICU/wiseR
BugReports: https://github.com/SAFE-ICU/wiseR/issues
Suggests: knitr,rmarkdown, rcompanion
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-19 04:50:39 UTC; JOHAN LIBERT
Repository: CRAN
Date/Publication: 2018-11-29 16:10:03 UTC

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New package textfeatures with initial version 0.3.0
Package: textfeatures
Type: Package
Title: Extracts Features from Text
Version: 0.3.0
Authors@R: person("Michael Wayne", "Kearney", , "kearneymw@missouri.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0730-4694"))
Description: A tool for extracting some generic features (e.g., number of words, line breaks, characters per word, URLs, lower case, upper case, commas, periods, exclamation points, etc.) from strings of text.
License: MIT + file LICENSE
URL: https://github.com/mkearney/textfeatures
BugReports: https://github.com/mkearney/textfeatures/issues
Depends: R (>= 3.1.0)
Imports: dplyr, purrr, rlang, syuzhet, text2vec, tfse, tibble, tokenizers, utils, stats
Suggests: knitr, roxygen2, testthat, covr
Encoding: UTF-8
LazyData: yes
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-29 15:15:55 UTC; kearneymw
Author: Michael Wayne Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael Wayne Kearney <kearneymw@missouri.edu>
Repository: CRAN
Date/Publication: 2018-11-29 15:50:03 UTC

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New package MCI2 with initial version 1.0.0
Package: MCI2
Type: Package
Title: Market Area Models for Retail and Service Locations
Version: 1.0.0
Date: 2018-11-19
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Description: Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package is a more user-friendly wrapper of the functions in the package 'MCI' (Wieland 2017) providing market area analysis using the Huff Model or the Multiplicative Competitive Interaction (MCI) Model. In 'MCI2', also a function for creating transport costs matrices is provided.
Imports: MCI, REAT, tmaptools, osrm, reshape
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-19 12:48:37 UTC; User
Repository: CRAN
Date/Publication: 2018-11-29 16:00:13 UTC

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New package leaflet.opacity with initial version 0.1.0
Package: leaflet.opacity
Type: Package
Title: Opacity Controls for Leaflet Maps
Version: 0.1.0
Date: 2018-11-07
Authors@R: c( person("Marc", "Becker", ,"marc.becker@uni-jena.de", role = c("aut", "cre"), comment = "R interface"), person(family = "LizardTech", role = c("aut", "cph"), comment = "Leaflet.OpacityControls JavaScript library") )
Description: Extends the 'leaflet' R package with the 'Leaflet.OpacityControls' JavaScript plugin. Adds controls to the leaflet map for adjusting the opacity of a layer.
BugReports: https://github.com/be-marc/leaflet.opacity
License: GPL-3
Imports: htmltools, htmlwidgets
Suggests: leaflet, raster, rgdal, magrittr, testthat, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-19 14:02:57 UTC; marc
Author: Marc Becker [aut, cre] (R interface), LizardTech [aut, cph] (Leaflet.OpacityControls JavaScript library)
Maintainer: Marc Becker <marc.becker@uni-jena.de>
Repository: CRAN
Date/Publication: 2018-11-29 16:00:10 UTC

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Wed, 28 Nov 2018

New package riskPredictClustData with initial version 0.2.6
Package: riskPredictClustData
Type: Package
Title: Assessing Risk Predictions for Clustered Data
Version: 0.2.6
Date: 2018-11-18
Authors@R: c( person("Bernard", "Rosner", role=c("aut", "ctb"), email = "stbar@channing.harvard.edu"), person("Weiliang", "Qiu", role=c("aut", "cre"), email = "Weiliang.Qiu@gmail.com"), person("Meiling T.", "Lee", role = c("aut", "ctb"), email = "MLTLEE@umd.edu") )
Maintainer: Weiliang Qiu <Weiliang.Qiu@gmail.com>
Depends: R (>= 3.4.0)
Imports: MASS, stats, gee, Hmisc, mvtnorm, utils
Description: Assessing and comparing risk prediction rules for clustered data. The method is based on the paper: Rosner B, Qiu W, and Lee MLT.(2013) <doi: 10.1007/s10985-012-9240-6>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-18 15:10:36 UTC; ICSA
Author: Bernard Rosner [aut, ctb], Weiliang Qiu [aut, cre], Meiling T. Lee [aut, ctb]
Repository: CRAN
Date/Publication: 2018-11-28 08:50:03 UTC

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New package rchie with initial version 1.0.0
Package: rchie
Type: Package
Title: A Parser for 'ArchieML'
Version: 1.0.0
Authors@R: c( person(given = "Noam", family = "Ross", role = c("aut", "cre"), email = "noam.ross@gmail.com", comment = c(ORCID = "0000-0002-2136-0000")), person(given = "Michael", family = "Strickland", role = "aut", comment = "Author of archieml-js library") )
Description: Parses the 'ArchieML' format from the New York Times <http://archieml.org>. Also provides utilities for retrieving Google Drive documents for parsing.
License: Apache License (>= 2.0)
URL: https://github.com/noamross/rchie, https://github.com/newsdev/archieml-js
BugReports: https://github.com/noamross/rchie/issues
Encoding: UTF-8
Imports: V8, jsonlite
Suggests: testthat, covr, googledrive, curl
SystemRequirements: V8 <= 3.15: libv8-3.14-dev (deb), v8-314-devel (rpm), v8-3.14 (arch), v8@3.15 (homebrew)
LazyData: TRUE
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-18 01:56:47 UTC; noamross
Author: Noam Ross [aut, cre] (<https://orcid.org/0000-0002-2136-0000>), Michael Strickland [aut] (Author of archieml-js library)
Maintainer: Noam Ross <noam.ross@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-28 08:40:02 UTC

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New package ezpickr with initial version 0.1.1
Package: ezpickr
Title: Import Various Data File Types as a Rectangular Form Using a File Picker Dialogue Box
Version: 0.1.1
Author: JooYoung Seo [aut, cre], Soyoung Choi [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Authors@R: c(person("JooYoung", "Seo", role=c("aut", "cre"), email="jooyoung@psu.edu"), person("Soyoung Choi", email = "sxc940@psu.edu", role = "ctb"))
Description: Easy data importing for the most frequently used file formats in a 'tibble' form.
License: GPL-3
VignetteBuilder: knitr
URL: https://github.com/jooyoungseo/ezpickr
BugReports: https://github.com/jooyoungseo/ezpickr/issues
Encoding: UTF-8
LazyData: true
Imports: readr, haven, rvest, jsonlite, readxl, magrittr, xml2, textreadr, tesseract, docxtractr, dplyr, tibble, striprtf, antiword
RoxygenNote: 6.1.0.9000
Suggests: testthat, knitr, rmarkdown, webshot, covr
NeedsCompilation: no
Packaged: 2018-11-18 21:29:36 UTC; JooYoung
Repository: CRAN
Date/Publication: 2018-11-28 08:50:10 UTC

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New package ed50 with initial version 0.1.0
Package: ed50
Type: Package
Title: Estimate ED50 and Its Confidence Interval
Version: 0.1.0
Author: Yongbo Gan, Zhijian Yang, Wei Mei
Maintainer: Yongbo Gan <yongbogan@whu.edu.cn>
Description: Functions of five estimation method for ED50 (50 percent effective dose) are provided, and they are respectively Dixon-Mood method (1948) <doi:10.2307/2280071>, Choi's original turning point method (1990) <doi:10.2307/2531453> and it's modified version given by us, as well as logistic regression and isotonic regression. Besides, the package also supports comparison between two estimation results.
Imports: stats, boot
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-19 07:27:59 UTC; Lenovo
Repository: CRAN
Date/Publication: 2018-11-28 09:00:03 UTC

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Tue, 27 Nov 2018

New package TAShiny with initial version 0.1.0
Package: TAShiny
Type: Package
Title: 'Text Analyzer Shiny'
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive shiny application for working with textmining and text analytics. Various visualizations are provided.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.0.3)
Imports: shiny,igraph,tm,SnowballC,dplyr,wordcloud2
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-17 10:28:27 UTC; KARTIKEYA
Repository: CRAN
Date/Publication: 2018-11-27 17:30:03 UTC

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New package RDFTensor with initial version 1.0
Package: RDFTensor
Type: Package
Title: Different Tensor Factorization (Decomposition) Techniques for RDF Tensors (Three-Mode-Tensors)
Version: 1.0
Date: 2018-11-16
Author: Abdelmoneim Amer Desouki
Maintainer: Abdelmoneim Amer Desouki <desouki@mail.upb.de>
Depends: R (>= 3.2.0), Matrix, methods, pracma
Description: Different Tensor Factorization techniques suitable for RDF Tensors. RDF Tensors are three-mode-tensors, binary tensors and usually very sparse. Currently implemented methods are 'RESCAL' Maximilian Nickel, Volker Tresp, and Hans-Peter Kriegel (2012) <doi:10.1145/2187836.2187874>, 'NMU' Daniel D. Lee and H. Sebastian Seung (1999) <doi:10.1038/44565>, 'ALS', Alternating Least Squares 'parCube' Papalexakis, Evangelos, C. Faloutsos, and N. Sidiropoulos (2012) <doi:10.1007/978-3-642-33460-3_39>, 'CP_APR' C. Chi and T. G. Kolda (2012) <doi:10.1137/110859063>. The code is mostly converted from MATLAB and Python implementations of these methods. The package also contains functions to get Boolean (Binary) transformation of the real-number-decompositions. These methods also are for general tensors, so with few modifications they can be applied for other types of tensor.
License: GPL-3
NeedsCompilation: no
Packaged: 2018-11-17 04:55:34 UTC; Abdelmonem
Repository: CRAN
Date/Publication: 2018-11-27 17:20:03 UTC

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New package plot.matrix with initial version 1.0
Package: plot.matrix
Type: Package
Title: Visualizes a Matrix as Heatmap
Version: 1.0
Date: 2018-11-15
Author: Sigbert Klinke
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Description: Visualizes a matrix object plainly as heatmap. It provides a single S3 function plot for matrices.
License: GPL-3
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-15 12:00:52 UTC; sigbert
Repository: CRAN
Date/Publication: 2018-11-27 09:20:03 UTC

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Mon, 26 Nov 2018

New package Z10 with initial version 0.1.0
Package: Z10
Type: Package
Title: Simple Ecological Statistics from the NEON Network
Version: 0.1.0
Author: Robert Lee <rhlee@colorado.edu>
Maintainer: Robert Lee <rhlee@colorado.edu>
Description: Provides simple statistics from instruments and observations at sites in the NEON network, and acts as a simple interface for v0 of the National Ecological Observatory Network (NEON) API. Statistics are generated for meteorologic and soil-based observations, and are presented for daily, annual, and one-time observations at all available NEON sites. Users can also retrieve any dataset publicly hosted by NEON. Metadata for NEON sites and data products can be returned, as well as information on data product availability by site and date. For more information on NEON, please visit <https://www.neonscience.org>. For detailed data product information, please see the NEON data product catalog at <https://data.neonscience.org/data-product-catalog>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: rjson, stringr, magrittr, lubridate, dplyr
Suggests: RNRCS, metScanR, rnoaa, neonUtilities
NeedsCompilation: no
Packaged: 2018-11-16 20:22:36 UTC; rlee
Repository: CRAN
Date/Publication: 2018-11-26 20:40:07 UTC

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New package TRES with initial version 0.1.0
Package: TRES
Type: Package
Title: Tensor Regression with Envelope Structure and Three Generic Envelope Estimation Approaches
Version: 0.1.0
Author: Wenjing Wang [aut, cre] <wenjing.wang@stat.fsu.edu>, Xin Zhang [aut, cre] <henry@stat.fsu.edu>
Maintainer: Wenjing Wang <wenjing.wang@stat.fsu.edu>
Description: Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0), ManifoldOptim, rTensor, MASS
Imports: pracma, mvtnorm, methods
RcppModules: ManifoldOptim_module
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 18:32:05 UTC; wenja
Repository: CRAN
Date/Publication: 2018-11-26 20:20:06 UTC

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New package SMFilter with initial version 1.0.0
Package: SMFilter
Title: Filtering Algorithms for the State Space Model on the Stiefel Manifold
Version: 1.0.0
Authors@R: person("Yukai", "Yang", email = "yukai.yang@statistik.uu.se",role = c("aut", "cre"))
Description: Provides the filtering algorithms for the state space model on the Stiefel manifold.
Depends: R (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
URL: https://github.com/yukai-yang/SMFilter
BugReports: https://github.com/yukai-yang/SMFilter/issues
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-16 19:59:04 UTC; yyang
Author: Yukai Yang [aut, cre]
Maintainer: Yukai Yang <yukai.yang@statistik.uu.se>
Repository: CRAN
Date/Publication: 2018-11-26 20:40:11 UTC

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New package FSMUMI with initial version 1.0
Package: FSMUMI
Type: Package
Title: Imputation of Time Series Based on Fuzzy Logic
Version: 1.0
Date: 2018-11-16
Author: Thi-Thu-Hong Phan, Andre Bigand, Emilie Poisson-Caillault
Maintainer: Thi Thu Hong Phan <ptthong@vnua.edu.vn>
Description: Filling large gaps in low or uncorrelated multivariate time series uses a new fuzzy weighted similarity measure. It contains all required functions to create large missing consecutive values within time series and then fill these gaps, according to the paper Phan et al. (2018), <DOI:10.1155/2018/9095683>. Performance indicators are also provided to compare similarity between two univariate signals (incomplete signal and imputed signal).
Depends: R (>= 3.0.0)
Imports: FuzzyR, stats, lsa
License: GPL (>= 2)
RoxygenNote: 6.0.1
URL: http://mawenzi.univ-littoral.fr/FSMUMI/
NeedsCompilation: no
Packaged: 2018-11-16 09:45:10 UTC; camille
Repository: CRAN
Date/Publication: 2018-11-26 20:10:06 UTC

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New package bipartiteD3 with initial version 0.1.0
Package: bipartiteD3
Type: Package
Title: Interactive Bipartite Graphs
Version: 0.1.0
Authors@R: person("Chris", "Terry", email = "christerry3@btinternet.com", role = c("aut", "cre"))
Description: Generates interactive bipartite graphs using the D3 library. Designed for use with the 'bipartite' analysis package. Sources open source 'vis-js' library (<http://visjs.org/>). Adapted from examples at <https://bl.ocks.org/NPashaP> (released under GPL-3).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: RColorBrewer (>= 1.1), r2d3 (>= 0.2.2), purrr (>= 0.2.5), dplyr (>= 0.7.5), tidyr (>= 0.8), stringr(>= 1.3), tibble (>= 1.4), bipartite (>= 2.08),
Depends:
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-16 13:31:28 UTC; pemb4504
Author: Chris Terry [aut, cre]
Maintainer: Chris Terry <christerry3@btinternet.com>
Repository: CRAN
Date/Publication: 2018-11-26 20:10:03 UTC

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New package ypr with initial version 0.3.0
Package: ypr
Version: 0.3.0
Title: Yield Per Recruit
Description: An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
Authors@R: person("Joe", "Thorley", email = "joe@poissonconsulting.ca", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7683-4592"))
License: MIT + file LICENSE
URL: https://github.com/poissonconsulting/ypr
BugReports: https://github.com/poissonconsulting/ypr/issues
Depends: R (>= 3.4.0)
Imports: checkr, ggplot2, graphics, scales, stats, tools,
Suggests: covr, testthat, tibble, knitr, rmarkdown, tidyr
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2018-11-16 03:31:41 UTC; joe
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-11-26 20:00:03 UTC

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New package suropt with initial version 0.1.0
Package: suropt
Type: Package
Title: Surrogate-Based Optimization
Version: 0.1.0
Authors@R: c( person("Adriano", "Passos", email="adriano.utfpr@gmail.com", role=c("aut","cre")), person("Marco", "Luersen", email="luersen@utfpr.edu.br", role="ctb"))
Description: Multi-Objective optimization based on surrogate models. Important functions: build_surmodel, train_hego, train_mego, train_sme.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.4.0)
Imports: methods, lhs, ggplot2, dplyr, tidyr, purrr, tibble, DiceKriging, DiceOptim, GPareto, emoa, mco, rgenoud, pso, GenSA
NeedsCompilation: no
Packaged: 2018-11-15 21:28:39 UTC; Adriano
Author: Adriano Passos [aut, cre], Marco Luersen [ctb]
Maintainer: Adriano Passos <adriano.utfpr@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-26 20:00:08 UTC

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New package restez with initial version 1.0.0
Package: restez
Type: Package
Title: Create and Query a Local Copy of 'GenBank' in R
Version: 1.0.0
Authors@R: person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com", comment = c(ORCID = "0000-0003-2722-1359"))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
URL: https://github.com/ropensci/restez#readme
BugReports: https://github.com/ropensci/restez/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: utils, rentrez, MonetDBLite (>= 0.6.0), DBI (>= 1.0.0), downloader, RCurl, cli, crayon, callr (>= 3.0.0), devtools
Suggests: testthat, knitr, R.utils, rmarkdown
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-16 09:19:36 UTC; djb208
Author: Dom Bennett [aut, cre] (<https://orcid.org/0000-0003-2722-1359>)
Repository: CRAN
Date/Publication: 2018-11-26 20:00:12 UTC

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New package read.gb with initial version 1.6
Package: read.gb
Type: Package
Title: Open GenBank Files
Version: 1.6
Author: Robin Mercier
Maintainer: Robin Mercier <robin.largon.mercier@hotmail.fr>
Description: Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at <https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Collate: 'CDS.F.R' 'C_region.F.R' 'DNA.treatment.R' 'D_loop.F.R' 'D_segment.F.R' 'F_UTR.F.R' 'variation.F.R' 'V_segment.F.R' 'V_region.F.R' 'unsure.F.R' 'tRNA.F.R' 'transit_peptide.F.R' 'tmRNA.F.R' 'telomere.F.R' 'T_UTR.F.R' 'STS.F.R' 'stem_loop.F.R' 'source.F.R' 'sig_peptide.F.R' 'S_region.F.R' 'rRNA.F.R' 'repeat_region.F.R' 'rep_origin.F.R' 'regulatory.F.R' 'protein_bind.F.R' 'propeptide.F.R' 'primer_bind.F.R' 'prim_transcript.F.R' 'precursor_RNA.F.R' 'polyA_site.F.R' 'oriT.F.R' 'operon.F.R' 'old_sequence.F.R' 'ncRNA.F.R' 'N_region.F.R' 'mRNA.F.R' 'modified_base.F.R' 'mobile_element.F.R' 'misc_structure.F.R' 'misc_RNA.F.R' 'misc_recomb.F.R' 'misc_feature.F.R' 'misc_difference.F.R' 'misc_binding.F.R' 'mat_peptide.F.R' 'J_segment.F.R' 'intron.F.R' 'iDNA.F.R' 'gene.F.R' 'gap.F.R' 'exon.F.R' 'centromere.F.R' 'assembly_gap.F.R' 'Feature.sep.R' 'Reference.sep.R' 'Reorganize.report.R' 'read.gb-internal.R' 'read.gb.R'
NeedsCompilation: no
Packaged: 2018-11-15 13:59:16 UTC; Largon
Repository: CRAN
Date/Publication: 2018-11-26 19:50:03 UTC

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New package postlogic with initial version 0.1.0
Package: postlogic
Type: Package
Title: Infix and Postfix Logic Operators
Version: 0.1.0
Authors@R: person("Andrew", "Redd", role = c("aut", "cre") , email = "Andrew.Redd@hsc.utah.edu" , comment = c(ORCID = "https://orcid.org/000-0002-6149-2438") )
Maintainer: Andrew Redd <Andrew.Redd@hsc.utah.edu>
Description: Provides adds postfix and infix logic operators for if, then, unless, and otherwise.
Language: en-US
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr
URL: https://github.com/RDocTaskForce/postlogic
BugReports: https://github.com/RDocTaskForce/postlogic/issues
NeedsCompilation: no
Packaged: 2018-11-16 00:30:54 UTC; u0092104
Author: Andrew Redd [aut, cre] (<https://orcid.org/000-0002-6149-2438>)
Repository: CRAN
Date/Publication: 2018-11-26 20:00:23 UTC

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New package PDShiny with initial version 0.1.0
Package: PDShiny
Type: Package
Title: 'Probability Distribution Shiny'
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: Interactive shiny application for working with Probability Distributions. Calculations and Graphs are provided.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.0.3)
Imports: shiny
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 07:14:19 UTC; KARTIKEYA
Repository: CRAN
Date/Publication: 2018-11-26 19:50:06 UTC

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New package coveffectsplot with initial version 0.0.1
Package: coveffectsplot
Title: Produce Forest Plots to Visualize Covariate Effects
Version: 0.0.1
Authors@R: c( person("Samer", "Mouksassi", email = "samermouksassi@gmail.com", role = c("aut", "cre")), person("Dean", "Attali", email = "daattali@gmail.com", role = c("ctb")) )
Description: Produce forest plots to visualize covariate effects using either the command line or an interactive 'Shiny' application.
URL: https://github.com/smouksassi/interactiveforestplot
BugReports: https://github.com/smouksassi/interactiveforestplot/issues
Depends: R (>= 3.1.0)
Imports: colourpicker, dplyr, egg, ggplot2, ggstance, markdown, shiny, shinyjs, stats, tidyr, utils
Suggests: MASS, knitr, rmarkdown, ggridges
License: MIT + file LICENSE
SystemRequirements: pandoc with https support
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-15 13:30:01 UTC; smouksas
Author: Samer Mouksassi [aut, cre], Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-26 19:40:03 UTC

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New package changepoint.mv with initial version 1.0.0
Package: changepoint.mv
Type: Package
Title: Changepoint Analysis for Multivariate Time Series
Version: 1.0.0
Date: 2018-11-15
Author: Lawrence Bardwell <l.bardwell@lancaster.ac.uk> [aut], Idris Eckley <i.eckley@lancaster.ac.uk> [ths,ctb], Paul Fearnhead <p.fearnhead@lancaster.ac.uk> [ths,ctb], Daniel Grose <dan.grose@lancaster.ac.uk> [aut,cre]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Description: Detects the Most Recent Changepoints (mrc) for panel data consisting of many related univariate timeseries.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.12),methods,zoo,tbart,Rdpack,ggplot2,reshape2,assertive
LinkingTo: Rcpp
Suggests: gridExtra
RdMacros: Rdpack
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-15 10:58:50 UTC; grosedj1
Repository: CRAN
Date/Publication: 2018-11-26 19:40:07 UTC

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New package GENEAsphere with initial version 1.5.0
Package: GENEAsphere
Type: Package
Title: Visualisation of Raw or Segmented Accelerometer Data
Version: 1.5.0
Date: 2018-11-23
Author: Mango Solutions [aut, cre], Joss Langford [aut, cre], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@Sweetland-solutions.co.uk>
Description: Creates visualisations in two and three dimensions of simulated data based on detected segments or raw accelerometer data.
License: GPL-3 | file LICENSE
LazyData: yes
Depends: ggplot2, rgl, MASS, misc3d, GENEAread
Suggests: knitr, rmarkdown
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-11-26 13:56:21 UTC; CharlesSweetland
Repository: CRAN
Date/Publication: 2018-11-26 14:50:02 UTC

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New package FlexParamCurve with initial version 1.5-5
Package: FlexParamCurve
Title: Tools to Fit Flexible Parametric Curves
Version: 1.5-5
Date: 2018-11-19
Authors@R: c(person("Stephen", "Oswald", role = c("aut", "cre"), email = "steve.oswald@psu.edu"))
Author: Stephen Oswald [aut, cre]
Description: Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
License: GPL-2
Encoding: UTF-8
URL: http://pennstate.academia.edu/SteveOswald
Depends: nlme
Imports: stats, utils
LazyData: true
NeedsCompilation: no
RoxygenNote: 6.1.1
Packaged: 2018-11-26 05:24:05 UTC; Admin
Maintainer: Stephen Oswald <steve.oswald@psu.edu>
Repository: CRAN
Date/Publication: 2018-11-26 11:00:14 UTC

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Thu, 22 Nov 2018

New package SIfEK with initial version 0.1.0
Package: SIfEK
Type: Package
Title: Statistical Inference for Enzyme Kinetics
Version: 0.1.0
Author: Donghyun Ra, Kyunghoon Kim, Boseung Choi
Maintainer: Donghyun Ra <dongcle72@gmail.com>
Description: Functions for estimating catalytic constant and Michaelis-Menten constant (MM constant) of stochastic Michaelis-Menten enzyme kinetics model are provided. The likelihood functions based on stochastic simulation approximation (SSA), diffusion approximation (DA), and Gaussian processes (GP) are provided to construct posterior functions for the Bayesian estimation. All functions utilize Markov Chain Monte Carlo (MCMC) methods with Metropolis- Hastings algorithm with random walk chain and robust adaptive Metropolis-Hastings algorithm based on Bayesian framework.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: R(>= 2.10.0)
Imports: MASS, ramcmc, smfsb, numDeriv
NeedsCompilation: no
Packaged: 2018-11-15 06:57:50 UTC; Ra
Repository: CRAN
Date/Publication: 2018-11-22 14:20:03 UTC

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Tue, 20 Nov 2018

New package rsppfp with initial version 1.0.3
Package: rsppfp
Title: R's Shortest Path Problem with Forbidden Subpaths
Version: 1.0.3
Authors@R: c(person("Melina", "Vidoni", email = "melinavidoni@santafe-conicet.gov.ar", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4099-1430")), person("Aldo", "Vecchietti", email = "aldovec@santafe-conicet.gov.ar", role = "aut"))
Maintainer: Melina Vidoni <melinavidoni@santafe-conicet.gov.ar>
Description: An implementation of functionalities to transform directed graphs that are bound to a set of known forbidden paths. There are several transformations, following the rules provided by Villeneuve and Desaulniers (2005) <doi: 10.1016/j.ejor.2004.01.032>, and Hsu et al. (2009) <doi: 10.1007/978-3-642-03095-6_60>. The resulting graph is generated in a data-frame format. See rsppfp website for more information, documentation an examples.
Depends: R (>= 3.4.0)
Imports: dplyr, foreach, doParallel, igraph, tidyr, stringr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat, covr, ggplot2
VignetteBuilder: knitr
URL: https://github.com/melvidoni/rsppfp
BugReports: https://github.com/melvidoni/rsppfp/issues
NeedsCompilation: no
Packaged: 2018-11-14 14:51:45 UTC; melina
Author: Melina Vidoni [aut, cre] (<https://orcid.org/0000-0002-4099-1430>), Aldo Vecchietti [aut]
Repository: CRAN
Date/Publication: 2018-11-20 15:50:03 UTC

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New package whiboclustering with initial version 0.1.2
Package: whiboclustering
Type: Package
Title: White Box Clustering Algorithm Design
Version: 0.1.2
Author: Sandro Radovanovic <sandro.radovanovic@gmail.com>, Milan Vukicevic <vucko83@gmail.com>
Maintainer: Sandro Radovanovic <sandro.radovanovic@gmail.com>
Description: White Box Cluster Algorithm Design allows you to create Representative based cluster algorithm by using reusable components. This way one can recreate already available cluster algorithms (i.e. K-Means, K-Means++, PAM) but also create new cluster algorithms not available in the literature or any other software. For more information see papers <doi:10.1007/s10462-009-9133-6> and <doi:10.1016/j.datak.2012.03.005>.
License: GPL-3
Depends: graphics, stats, clusterCrit, cluster
Suggests: methods, testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-14 19:22:15 UTC; UFBG
Repository: CRAN
Date/Publication: 2018-11-20 13:10:03 UTC

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New package modi with initial version 0.1.0
Package: modi
Type: Package
Title: Multivariate Outlier Detection and Imputation for Incomplete Survey Data
Version: 0.1.0
Authors@R: c( person("Beat", "Hulliger", email = "beat.hulliger@fhnw.ch", role = "aut"), person("Martin", "Sterchi", email = "martin.sterchi@fhnw.ch", role = "cre"))
Description: Algorithms for multivariate outlier detection when missing values occur. Algorithms are based on Mahalanobis distance or data depth. Imputation is based on the multivariate normal model or uses nearest neighbour donors. The algorithms take sample designs, in particular weighting, into account. The methods are described in Bill and Hulliger (2016) <doi:10.17713/ajs.v45i1.86>.
License: MIT + file LICENSE
URL: https://github.com/martinSter/modi
BugReports: https://github.com/martinSter/modi/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: MASS (>= 7.3-50), norm (>= 1.0-9.5), stats, graphics, utils
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-14 08:29:00 UTC; martin.sterchi
Author: Beat Hulliger [aut], Martin Sterchi [cre]
Maintainer: Martin Sterchi <martin.sterchi@fhnw.ch>
Repository: CRAN
Date/Publication: 2018-11-20 13:10:07 UTC

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New package GenEst with initial version 1.1.0
Package: GenEst
Title: Generalized Mortality Estimator
Version: 1.1.0
Date: 2018-11-13
Authors@R: c( person("Daniel", "Dalthorp", , "ddalthorp@usgs.gov", c("aut", "cre")), person("Juniper", "Simonis", , "simonis@dapperstats.com", "aut"), person("Lisa", "Madsen", , "madsenl@oregonstate.edu", "aut"), person("Manuela", "Huso", , "mhuso@usgs.gov", "aut"), person("Paul", "Rabie", , "prabie@west-inc.com", "aut"), person("Jeffrey", "Mintz", , "mintzj@oregonstate.edu", "aut"), person("Robert", "Wolpert", , "wolpert@stat.duke.edu", "aut"), person("Jared", "Studyvin", , "jstudyvin@west-inc.com", "aut"), person("Franzi", "Korner-Nievergelt", , "fraenzi.korner@oikostat.ch", "aut"))
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <https://pubs.usgs.gov/tm/7a2/tm7a2.pdf>.
Depends: R (>= 3.5.0)
License: CC0
Encoding: UTF-8
LazyData: true
Imports: cbinom (>= 1.3), corpus, DT, gsl, gtools, htmltools, lubridate, matrixStats, mvtnorm, Rcpp, shiny, shinyjs, sticky, survival
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-11-14 15:01:19 UTC; ddalthorp
Author: Daniel Dalthorp [aut, cre], Juniper Simonis [aut], Lisa Madsen [aut], Manuela Huso [aut], Paul Rabie [aut], Jeffrey Mintz [aut], Robert Wolpert [aut], Jared Studyvin [aut], Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Repository: CRAN
Date/Publication: 2018-11-20 13:10:11 UTC

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Mon, 19 Nov 2018

New package LindleyPowerSeries with initial version 0.1.0
Package: LindleyPowerSeries
Type: Package
Title: Lindley Power Series Distribution
Version: 0.1.0
Author: Saralees Nadarajah & Yuancheng Si, Peihao Wang
Maintainer: Yuancheng Si <yuancheng.si@manchester.ac.uk>
Description: Computes the probability density function, the cumulative distribution function, the hazard rate function, the quantile function and random generation for Lindley Power Series distributions, see Nadarajah and Si (2018) <doi:10.1007/s13171-018-0150-x>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: stats, lamW(>= 1.3.0)
NeedsCompilation: no
Packaged: 2018-11-19 19:36:41 UTC; Lenovo
Repository: CRAN
Date/Publication: 2018-11-19 23:20:11 UTC

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New package spreadr with initial version 0.1.0
Package: spreadr
Type: Package
Title: Simulating Spreading Activation in a Network
Version: 0.1.0
Authors@R: c( person("Cynthia","Siew", email = "cynsiewsq@gmail.com", role = c("aut", "cre")), person(c("Dirk","U."), "Wulff", role = "ctb", email = "dirk.wulff@gmail.com") )
Description: The notion of spreading activation is a prevalent metaphor in the cognitive sciences. This package provides the tools for cognitive scientists and psychologists to conduct computer simulations that implement spreading activation in a network representation. The algorithmic method implemented in 'spreadr' subroutines follows the approach described in Vitevitch, Ercal, and Adagarla (2011, Frontiers), who viewed activation as a fixed cognitive resource that could spread among nodes that were connected to each other via edges or connections (i.e., a network). See Vitevitch, M. S., Ercal, G., & Adagarla, B. (2011). Simulating retrieval from a highly clustered network: Implications for spoken word recognition. Frontiers in Psychology, 2, 369. <doi:10.3389/fpsyg.2011.00369>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: Rcpp (>= 0.12.5)
RoxygenNote: 6.1.0
Imports: igraph, extrafont, ggplot2
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-11-13 17:45:18 UTC; csqsiew
Author: Cynthia Siew [aut, cre], Dirk U. Wulff [ctb]
Maintainer: Cynthia Siew <cynsiewsq@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 19:20:03 UTC

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New package R.temis with initial version 0.1.0
Package: R.temis
Type: Package
Title: Integrated Text Mining Solution
Version: 0.1.0
Authors@R: c(person("Milan", "Bouchet-Valat", email="nalimilan@club.fr", role=c("aut", "cre")), person("Gilles", "Bastin", email="gilles.bastin@sciencespo-grenoble.fr", role="aut"), person("Antoine", "Chollet", email="antoine.chollet@eleve.ensai.fr", role="aut"))
Imports: stats, utils, graphics, testthat, wordcloud, igraph, stringi, crayon, SnowballC, tm.plugin.factiva, tm.plugin.lexisnexis, tm.plugin.europresse, tm.plugin.alceste
Depends: tm (>= 0.6), NLP, slam, FactoMineR, explor
Description: An integrated solution to perform a series of text mining tasks such as importing and cleaning a corpus, and analyses like terms and documents counts, lexical summary, terms co-occurrences and documents similarity measures, graphs of terms, correspondence analysis and hierarchical clustering. Corpora can be imported from spreadsheet-like files, directories of raw text files, as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-13 08:51:43 UTC; milan
Author: Milan Bouchet-Valat [aut, cre], Gilles Bastin [aut], Antoine Chollet [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Repository: CRAN
Date/Publication: 2018-11-19 19:10:03 UTC

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New package metR with initial version 0.2.0
Type: Package
Package: metR
Title: Tools for Easier Analysis of Meteorological Fields
Version: 0.2.0
Date: 2018-11-02
Authors@R: person(given = "Elio", family = "Campitelli", role = c("cre", "aut"), email = "elio.campitelli@cima.fcen.uba.ar", comment = c(ORCID = "0000-0002-7742-9230"))
Description: Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.
License: GPL-3
URL: https://github.com/eliocamp/metR
BugReports: https://github.com/eliocamp/metR/issues
Depends: R (>= 2.10)
Imports: checkmate, curl, data.table, digest, dplyr, fields, Formula, formula.tools, ggplot2, grid, gridExtra, gtable, lubridate, maps, maptools, Matrix, memoise, plyr, RCurl, scales, sp, stringr
Suggests: covr, irlba, knitr, ncdf4, pkgdown, reshape2, rmarkdown, testthat, udunits2, vdiffr, viridis
ByteCompile: yes
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-03 15:43:03 UTC; elio
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Repository: CRAN
Date/Publication: 2018-11-19 19:30:02 UTC

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New package hillR with initial version 0.4.0
Package: hillR
Type: Package
Title: Diversity Through Hill Numbers
Version: 0.4.0
Date: 2018-11-13
Author: Daijiang Li
Maintainer: Daijiang Li <daijianglee@gmail.com>
Description: Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.1)
Imports: FD, plyr, ade4, ape, tibble
RoxygenNote: 6.1.0
Suggests: testthat, vegetarian, covr
URL: https://github.com/daijiang/hillR
BugReports: https://github.com/daijiang/hillR/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-11-14 03:58:44 UTC; dli
Repository: CRAN
Date/Publication: 2018-11-19 19:20:05 UTC

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New package DiPs with initial version 0.1.1
Package: DiPs
Type: Package
Title: Directional Penalties for Optimal Matching in Observational Studies
Version: 0.1.1
Author: Ruoqi Yu
Maintainer: Ruoqi Yu <ruoqiyu@wharton.upenn.edu>
Description: Improves the balance of optimal matching with near-fine balance by giving penalties on the unbalanced covariates with the unbalanced directions. Many directional penalties can also be viewed as Lagrange multipliers, pushing a matched sample in the direction of satisfying a linear constraint that would not be satisfied without penalization. Rosenbaum, P.R. (1989). <DOI:10.1080/01621459.1989.10478868>. Yang, D., Small, D. S., Silber, J. H., and Rosenbaum, P. R. (2012). <DOI:10.1111/j.1541-0420.2011.01691.x>.
License: MIT+file LICENSE
Encoding: UTF-8
LazyData: true
Imports: rcbalance, stats, liqueueR, plyr, mvnfast, methods
Suggests: optmatch
Note: One minimum cost flow problem may have several or many solutions that are equivalent in providing the same minimum total or mean cost. Minor differences between computers or implementations may have the minor consequence of altering which equivalent solution is produced.
NeedsCompilation: no
Packaged: 2018-11-17 21:03:16 UTC; Ruoqi Yu
Repository: CRAN
Date/Publication: 2018-11-19 19:20:18 UTC

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New package dabestr with initial version 0.1.0
Package: dabestr
Type: Package
Title: Data Analysis using Bootstrap-Coupled Estimation
Version: 0.1.0
Authors@R: c( person("Joses W.", "Ho", email = "joseshowh@gmail.com", role = c("cre", "aut")), person("Tayfun", "Tumkaya", role = c("aut")) )
Maintainer: Joses W. Ho <joseshowh@gmail.com>
Description: Data Analysis using Bootstrap-Coupled ESTimation. Estimation statistics is a simple framework that avoids the pitfalls of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by P values. An estimation plot has two key features: 1. It presents all datapoints as a swarmplot, which orders each point to display the underlying distribution. 2. It presents the effect size as a bootstrap 95% confidence interval on a separate but aligned axes. Estimation plots are introduced in Ho et al (2018) <doi:10.1101/377978>.
License: file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), boot, magrittr
Imports: cowplot, dplyr, ggplot2 (>= 3.0), grid, forcats, ggforce, ggbeeswarm, rlang, simpleboot, stringr, tibble, tidyr
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, tufte, testthat, vdiffr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-13 14:19:53 UTC; joseshowh
Author: Joses W. Ho [cre, aut], Tayfun Tumkaya [aut]
Repository: CRAN
Date/Publication: 2018-11-19 19:20:10 UTC

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New package uavRst with initial version 0.5-0
Package: uavRst
Type: Package
Title: Unmanned Aerial Vehicle Remote Sensing Tools
Version: 0.5-0
Date: 2018-11-11
Authors@R: c(person("Florian", "Detsch", role = c("ctb")), person("Hanna", "Meyer", email = "hanna.meyer@uni-marburg.de", role = c("aut")), person("Thomas", "Nauss", email = "nauss@uni-marburg.de", role = c("ctb")), person("Lars", "Opgenoorth", email = "opgenoorth@uni-marburg.de", role = c("ctb")), person("Chris", "Reudenbach", email = "reudenbach@uni-marburg.de", role = c("cre","aut")), person("Environmental Informatics Marburg", role = c("ctb")) )
Encoding: UTF-8
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Description: Support the analysis of drone derived imagery and point clouds as a cheap and easy to use alternative/complement to light detection and ranging data. It provides functionality to analyze poor quality digital aerial images as taken by low budget ready to fly drones. This includes supported machine learning based classification functions, comprehensive texture analysis, segmentation algorithms as well as forest relevant analyzes of metrics and measures on the derived products.
License: GPL (>= 3) | file LICENSE
Depends: R (>= 3.1.0)
Imports: raster, foreach
Suggests: knitr, stringr, sp, sf, htmlwidgets, htmltools, Rcpp, rgdal, rgeos, gdalUtils, tools, caret, zoo, data.table, parallel, spatial.tools, velox, link2GI, doParallel, CAST, glcm, crayon, ForestTools, itcSegment, pROC, methods, RSAGA, reshape2, rgrass7, randomForest, rLiDAR, rlas, lidR, rmarkdown, mapview
LinkingTo: Rcpp
RoxygenNote: 6.1.1
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2018-11-13 00:39:19 UTC; creu
Author: Florian Detsch [ctb], Hanna Meyer [aut], Thomas Nauss [ctb], Lars Opgenoorth [ctb], Chris Reudenbach [cre, aut], Environmental Informatics Marburg [ctb]
Repository: CRAN
Date/Publication: 2018-11-19 19:00:03 UTC

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New package stevedore with initial version 0.9.0
Package: stevedore
Title: Docker Client
Version: 0.9.0
Description: Work with containers over the Docker API. Rather than using system calls to interact with a docker client, using the API directly means that we can receive richer information from docker. The interface in the package is automatically generated using the 'OpenAPI' (a.k.a., 'swagger') specification, and all return values are checked in order to make them type stable.
License: MIT + file LICENSE
Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"), email = "rich.fitzjohn@gmail.com"))
URL: https://github.com/richfitz/stevedore
BugReports: https://github.com/richfitz/stevedore/issues
Imports: crayon, curl (>= 2.3.0), jsonlite, yaml (>= 2.1.18)
Suggests: knitr, openssl, redux, reticulate, rmarkdown, testthat, withr
SystemRequirements: docker
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Encoding: UTF-8
ByteCompile: TRUE
Language: en-GB
NeedsCompilation: no
Packaged: 2018-11-12 08:32:15 UTC; rich
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:30:02 UTC

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New package similr with initial version 1.0.0
Package: similr
Type: Package
Title: Text Similarity
Version: 1.0.0
Date: 2018-11-04
Author: Michael Holmes
Maintainer: Michael Holmes <mepstudies@gmail.com>
Description: Using brute-force string comparator algorithms, this package facilitates finding a particular string's closest match amongst a target vector of strings.
License: GPL (>= 2)
Imports: Rcpp, R6, stringr
LinkingTo: Rcpp
SystemRequirements: C++11
ByteCompile: true
NeedsCompilation: yes
RoxygenNote: 6.1.1
Encoding: UTF-8
Packaged: 2018-11-13 01:27:28 UTC; micha
Repository: CRAN
Date/Publication: 2018-11-19 19:00:08 UTC

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New package QuantumOps with initial version 1.0
Package: QuantumOps
Title: Performs Common Linear Algebra Operations Used in Quantum Computing
Version: 1.0
Date: 2018-11-11
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of kets, bras, matrices and implements quantum gates, inner products, and tensor products.
Depends: R (>= 3.1.0)
License: GPL-3
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2018-11-11 18:53:45 UTC; mike
Repository: CRAN
Date/Publication: 2018-11-19 18:10:11 UTC

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New package psica with initial version 1.0.0
Package: psica
Type: Package
Title: Decision Tree Analysis for Probabilistic Subgroup Identification with Multiple Treatments
Version: 1.0.0
Author: Oleg Sysoev, Krzysztof Bartoszek, Katarina Ekholm Selling and Lotta Ekstrom
Maintainer: Oleg Sysoev <Oleg.Sysoev@liu.se>
Description: In the situation when multiple alternative treatments or interventions available, different population groups may respond differently to different treatments. This package implements a method that discovers the population subgroups in which a certain treatment has a better effect than the other alternative treatments. This is done by first estimating the treatment effect for a given treatment and its uncertainty by computing random forests, and the resulting model is summarized by a decision tree in which the probabilities that the given treatment is best for a given subgroup is shown in the corresponding terminal node of the tree.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: grid, gridBase, randomForest, rpart, partykit, party, BayesTree
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-12 10:13:30 UTC; olesy12
Repository: CRAN
Date/Publication: 2018-11-19 18:30:05 UTC

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New package pivmet with initial version 0.1.0
Package: pivmet
Type: Package
Title: Pivotal Methods for Bayesian Relabelling and k-Means Clustering
Version: 0.1.0
Date: 2018-11-08
Author: Leonardo Egidi[aut, cre], Roberta Pappadà[aut], Francesco Pauli[aut], Nicola Torelli[aut]
Maintainer: Leonardo Egidi <legidi@units.it>
License: GPL-2
Description: Collection of pivotal algorithms for: relabelling the MCMC chains in order to undo the label switching problem in Bayesian mixture models; initializing the centers of the classical k-means algorithm in order to obtain a better clustering solution.
URL: https://github.com/leoegidi/pivmet
Encoding: UTF-8
LazyData: true
LazyLoad: yes
Depends: bayesmix, rjags, runjags, mvtnorm, RcmdrMisc
Imports: cluster, mclust, MASS
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.1.0
BuildManual: yes
NeedsCompilation: no
Packaged: 2018-11-12 11:20:17 UTC; leoeg
Repository: CRAN
Date/Publication: 2018-11-19 18:50:06 UTC

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New package npordtests with initial version 1.0
Package: npordtests
Type: Package
Title: Nonparametric Tests for Equality of Location Against Ordered Alternatives
Version: 1.0
Date: 2018-10-26
Depends: R (>= 2.15.0)
Author: Bulent Altunkaynak [aut, cre], Hamza Gamgam [aut]
Maintainer: Bulent Altunkaynak <bulenta@gazi.edu.tr>
Description: Performs nonparametric tests for equality of location against ordered alternatives.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-12 22:50:55 UTC; bulent
Repository: CRAN
RoxygenNote: 6.1.1
Encoding: UTF-8
Date/Publication: 2018-11-19 18:50:09 UTC

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New package NBDesign with initial version 1.0.0
Package: NBDesign
Type: Package
Version: 1.0.0
Date: 2018-11-11
Title: Design and Monitoring of Clinical Trials with Negative Binomial Endpoint
Description: Calculates various functions needed for design and monitoring clinical trials with negative binomial endpoint with variable follow-up.
Authors@R: c( person(given="Xiaodong", family="Luo", email = "Xiaodong.Luo@sanofi.com", role =c("aut", "cre")), person("Sanofi", role = "cph"))
Depends: R (>= 3.1.2)
Imports: stats,PWEALL,MASS
License: GPL (>= 2)
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-11 17:43:55 UTC; Administrator
Author: Xiaodong Luo [aut, cre], Sanofi [cph]
Maintainer: Xiaodong Luo <Xiaodong.Luo@sanofi.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:10:14 UTC

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New package MPTmultiverse with initial version 0.1
Package: MPTmultiverse
Title: Multiverse Analysis of Multinomial Processing Tree Models
Version: 0.1
Description: Statistical or cognitive modeling usually requires a number of more or less arbitrary choices creating one specific path through a 'garden of forking paths'. The multiverse approach (Steegen, Tuerlinckx, Gelman, & Vanpaemel, 2016, <doi:10.1177/1745691616658637>) offers a principled alternative in which results for all possible combinations of reasonable modeling choices are reported. MPTmultiverse performs a multiverse analysis for multinomial processing tree (MPT, Riefer & Batchelder, 1988, <doi:10.1037/0033-295X.95.3.318>) models combining maximum-likelihood/frequentist and Bayesian estimation approaches with different levels of pooling (i.e., data aggregation). For the frequentist approaches, no pooling (with and without parametric or nonparametric bootstrap) and complete pooling are implemented using MPTinR <https://cran.r-project.org/package=MPTinR>. For the Bayesian approaches, no pooling, complete pooling, and three different variants of partial pooling are implemented using TreeBUGS <https://cran.r-project.org/package=TreeBUGS>. The main function is fit_mpt() who performs the multiverse analysis in one call.
Authors@R: c( person("Henrik", "Singmann", role = c("aut", "cre"), email="singmann@gmail.com", comment=c(ORCID="0000-0002-4842-3657")) , person(c("Daniel", "W."), "Heck", email = "heck@uni-mannheim.de", role = c("aut")) , person("Marius", "Barth", email = "marius.barth@uni-koeln.de", role = c("aut")) , person("Frederik", "Aust", email = "frederik.aust@uni-koeln.de", role = c("ctb"), comment = c(ORCID = "0000-0003-4900-788X")) )
URL: https://github.com/mpt-network/MPTmultiverse
BugReports: https://github.com/mpt-network/MPTmultiverse/issues
Depends: R (>= 2.11.1),
Imports: parallel, magrittr, tidyr, dplyr, tibble, rlang, reshape2, ggplot2, MPTinR, TreeBUGS, runjags, coda, purrr, broom, readr
Suggests: knitr, rmarkdown, testthat
LazyData: yes
VignetteBuilder: knitr
RoxygenNote: 6.1.0
License: GPL-2
NeedsCompilation: no
Packaged: 2018-11-11 22:31:44 UTC; henrik
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>), Daniel W. Heck [aut], Marius Barth [aut], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Henrik Singmann <singmann@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:20:11 UTC

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New package irteQ with initial version 1.0.0
Package: irteQ
Type: Package
Title: Linking and Equating Methods in Unidimensional Item Response Theory
Version: 1.0.0
Description: IRT-based methods are used to estimate IRT linking coefficients and to perform IRT equating under the common item non-equivalent group design. For the IRT linking procedure, the Mean/Mean, Mean/Sigma, Haebara, and Stocking-Lord methods are available. For IRT test score equating, the true score equating and observed score equating methods are available. This package supports both dichotomous IRT models (1PL, 2PL and 3PL) and polytomous IRT models (graded response model, partial credit model, and generalized partial credit model). In addition to IRT linking and equating capabilities, there are several useful functions such as importing item and/or ability parameters from IRT software, generating simulated data, estimating the standard error of equating due to the random selection of common items, computing the conditional distribution of observed scores using the Lord-Wingersky recursion formula, computing item and test information functions, computing item and test characteristic curve functions, and plotting item and test characteristic curves and item and test information functions as well as scatter plots.
Depends: R (>= 3.4)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: stats, statmod, utils, reshape2, dplyr, tidyr, purrr, ggplot2, ggrepel, rlang
Authors@R: c(person("Hwanggyu", "Lim", email="hglim83@gmail.com", role=c("aut", "cre")), person("Francis", "O'Donnell", email="francisrick@me.com ", rol="ctb"), person("Craig S.", "Wells", email="cswells@educ.umass.edu ", rol="ctb") )
RoxygenNote: 6.1.0
Suggests: mirt
URL: https://github.com/hwangQ/irteQ
BugReports: https://github.com/hwangQ/irteQ/issues
NeedsCompilation: no
Packaged: 2018-11-12 06:18:29 UTC; kijja
Author: Hwanggyu Lim [aut, cre], Francis O'Donnell [ctb], Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:30:08 UTC

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New package GLSE with initial version 0.1.0
Package: GLSE
Type: Package
Title: Graphical Least Square Estimation
Version: 0.1.0
Author: Saeed Aldahmani
Maintainer: Saeed Aldahmani <saldahmani@uaeu.ac.ae>
Description: The Graphical Least Square Estimation 'GLSE' package consists of several functions. The first function (called GLSE()), which is the main function in this package, is for estimating linear regression via graphical models, especially when the number of observations is smaller than the number of variables. This function gives unbiased estimated regression models under some conditions on the predictors. Moreover, this function aims to deal with studies where all covariates need to be kept in the model (such as portfolio optimisation). The second function provides an estimation of the bootstrap standard errors of the 'GLSE' parameters. The third function generates data from multivariate normal distribution for regression purposes, and the fourth function generates data from multivariate t-distribution for the same purpose. Generating an undirected decomposable graph is carried out by the fifth function and its decomposability is tested in the sixth function. The seventh function gives a perfect sequence of the cliques and separators of the given decomposable graph. Finally, the last function gives the plot of the decomposale graph. The package supports both serial and parallel computations for estimating the graph.The 'GLSE' package is an implementation of the method introduced in Aldahmani, S., and Dai, H. (2015) <doi:10.5539/ijsp.v4n3p61>.
License: GPL-2
Imports: gRbase, igraph, mvtnorm, parallel, stats
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-12 12:48:37 UTC; saldahmani
Repository: CRAN
Date/Publication: 2018-11-19 18:50:18 UTC

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New package gginference with initial version 0.1.0
Package: gginference
Type: Package
Title: Visualise the Results of Inferential Statistics using 'ggplot2'
Version: 0.1.0
Date: 2018-10-24
Description: Visualise the results of F test to compare two variances, Student's t-test, test of equal or given proportions, Pearson's chi-squared test for count data and test for association/correlation between paired samples.
Authors@R: c( person("Charalampos", "Bratsas", , "cbratsas@math.auth.gr", role = "aut"), person("Anastasia", "Foudouli", , "anastasiafoudouli@gmail.com", role = "aut"), person("Kleanthis", "Koupidis", , "koupidis@okfn.gr", role = c("aut", "cre")) )
Maintainer: Kleanthis Koupidis <koupidis@okfn.gr>
URL: https://github.com/okgreece/gginference
BugReports: https://github.com/okgreece/gginference/issues
Depends: R (>= 3.4.0)
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, rlang, stats
RoxygenNote: 6.1.0.9000
Suggests: knitr, MASS, rmarkdown
NeedsCompilation: no
Packaged: 2018-11-05 13:23:02 UTC; akis_
Author: Charalampos Bratsas [aut], Anastasia Foudouli [aut], Kleanthis Koupidis [aut, cre]
Repository: CRAN
Date/Publication: 2018-11-19 18:10:03 UTC

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New package FlexScan with initial version 0.1.0
Package: FlexScan
Type: Package
Title: Flexible Scan Statistics
Version: 0.1.0
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du <dgdzc@hotmail.com>
Depends: R (>= 2.10)
Description: An easy way to conduct flexible scan. Monte-Carlo method is used to test the spatial clusters given the cases, population, and shapefile. A table with formal style and a map with clusters are included in the result report. The method can be referenced at: Toshiro Tango and Kunihiko Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
License: GPL-3
Imports: smerc, sp, spdep, methods, graphics
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-11-04 17:50:22 UTC; dgdzc
Repository: CRAN
Date/Publication: 2018-11-19 18:10:17 UTC

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New package ffmetadata with initial version 1.0.0
Package: ffmetadata
Type: Package
Title: Access to Fragile Families Metadata
Version: 1.0.0
Authors@R: c( person("Ryan", "Vinh", email = "rvinh@princeton.edu", role = c("aut", "cre")), person("Ian", "Fellows", email = "ian@fellstat.com", role = "aut"), person("Will", "Lowe", email = "wlowe@princeton.edu", role = "ctb"))
Description: A collection of functions that allows users to retrieve metadata for the Fragile Families challenge via a Web API (<http://api.metadata.fragilefamilies.princeton.edu>). Users can select and search metadata for relevant variables by filtering on different attribute names.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: jsonlite, httr
RoxygenNote: 6.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/fragilefamilieschallenge/ffmetadata
BugReports: https://github.com/fragilefamilieschallenge/ffmetadata/issues
NeedsCompilation: no
Packaged: 2018-11-13 01:25:26 UTC; ryanvinh
Author: Ryan Vinh [aut, cre], Ian Fellows [aut], Will Lowe [ctb]
Maintainer: Ryan Vinh <rvinh@princeton.edu>
Repository: CRAN
Date/Publication: 2018-11-19 19:00:11 UTC

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New package dqshiny with initial version 0.0.1
Package: dqshiny
Type: Package
Title: Enhance Shiny Apps with Customizable Modules
Version: 0.0.1
Author: Richard Kunze, Mirjam Rehr
Maintainer: Richard Kunze <richard.kunze@daqana.com>
Description: Provides highly customizable modules to enhance your shiny apps. Includes layout independent collapsible boxes and value boxes, a very fast autocomplete input, rhandsontable extensions for filtering and paging and much more.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: shiny, htmltools
Suggests: testthat, extrafont, ggplot2, jsonlite, rhandsontable, V8, htmlwidgets, shinytest
URL: https://github.com/daqana/dqshiny
BugReports: https://github.com/daqana/dqshiny/issues
NeedsCompilation: no
Packaged: 2018-11-12 14:50:28 UTC; richardkunze
Repository: CRAN
Date/Publication: 2018-11-19 18:50:13 UTC

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New package deckgl with initial version 0.1.8
Package: deckgl
Title: An R Interface to 'deck.gl'
Version: 0.1.8
Date: 2018-11-10
Authors@R: person("Stefan", "Kuethe", email = "crazycapivara@gmail.com", role = c("aut", "cre"))
Maintainer: Stefan Kuethe <crazycapivara@gmail.com>
Description: Makes 'deck.gl' <https://deck.gl/>, a WebGL-powered open-source JavaScript framework for visual exploratory data analysis of large datasets, available within R via the 'htmlwidgets' package. Furthermore, it supports basemaps from 'mapbox' <https://www.mapbox.com/> via 'mapbox-gl-js' <https://github.com/mapbox/mapbox-gl-js>.
URL: https://github.com/crazycapivara/deckgl/, https://crazycapivara.github.io/deckgl/
BugReports: https://github.com/crazycapivara/deckgl/issues/
Depends: R (>= 3.3)
Imports: htmlwidgets, htmltools, magrittr, base64enc, yaml, jsonlite, readr, tibble
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat, rprojroot
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-10 20:53:42 UTC; gabbo
Author: Stefan Kuethe [aut, cre]
Repository: CRAN
Date/Publication: 2018-11-19 18:10:06 UTC

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New package BHSBVAR with initial version 1.0.0
Encoding: UTF-8
Package: BHSBVAR
Type: Package
Title: Structural Bayesian Vector Autoregression Models
Version: 1.0.0
Date: 2018-11-01
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Description: Provides a function for running Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
License: GPL (>= 3)
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.19)
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.1.1
Suggests: knitr
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2018-11-12 02:35:59 UTC; prich
Repository: CRAN
Date/Publication: 2018-11-19 18:30:13 UTC

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New package rphylopic with initial version 0.2.0
Package: rphylopic
Title: Get 'Silhouettes' of 'Organisms' from 'Phylopic'
Description: Work with 'Phylopic' web service (<http://phylopic.org/api/>) to get 'silhouette' images of 'organisms', search names, and more. Includes functions for adding 'silhouettes' to both base plots and ggplot2 plots.
Version: 0.2.0
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com", comment = c(ORCID = "0000-0003-1444-9135")), person("David", "Miller", role = "ctb", email = "dave@ninepointeightone.net") )
License: MIT + file LICENSE
URL: https://github.com/sckott/rphylopic
BugReports: https://github.com/sckott/rphylopic/issues
Encoding: UTF-8
Language: en-US
Imports: ggplot2, crul (>= 0.5.2), jsonlite, grid, gridBase, graphics, png
Suggests: testthat, vcr (>= 0.2.0)
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-09 23:32:34 UTC; sckott
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), David Miller [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:00:03 UTC

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New package ref.ICAR with initial version 1.0
Package: ref.ICAR
Title: Objective Bayes Intrinsic Conditional Autoregressive Model for Areal Data
Version: 1.0
Author: Erica M. Porter, Matthew J. Keefe, Christopher T. Franck, and Marco A.R. Ferreira
Maintainer: Erica M. Porter <ericamp@vt.edu>
Depends: R (>= 3.1.0)
Description: Implements an objective Bayes intrinsic conditional autoregressive prior. This model provides an objective Bayesian approach for modeling spatially correlated areal data using an intrinsic conditional autoregressive prior on a vector of spatial random effects.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: rgdal, spdep, mvtnorm, coda, MCMCglmm, Rdpack, graphics
RdMacros: Rdpack
Suggests: maptools, maps, MASS, sp, knitr, rmarkdown, RColorBrewer, captioner, rcrossref
VignetteBuilder: knitr
BuildManual: yes
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-09 23:46:50 UTC; EricaPorter
Repository: CRAN
Date/Publication: 2018-11-19 18:00:06 UTC

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New package rcosmo with initial version 1.0.0
Package: rcosmo
URL: https://github.com/VidaliLama/rcosmo
BugReports: https://github.com/VidaliLama/rcosmo/issues
Title: Cosmic Microwave Background Data Analysis
Version: 1.0.0
Authors@R: c(person("Daniel", "Fryer", role = c("aut", "cre"), email = "d.fryer@latrobe.edu.au", comment = c(ORCID = "0000-0001-6032-0522")), person("Andriy", "Olenko", role = "aut", email = "a.olenko@latrobe.edu.au", comment = c(ORCID = "0000-0002-0917-7000")), person("Ming", "Li", role = "aut", comment = c(ORCID = "0000-0002-1218-2804")), person("Yuguang", "Wang", role = "aut"))
Description: Handling and Analysing Spherical, HEALPix and Cosmic Microwave Background data on a HEALPix grid.
Depends: R (>= 3.4.0)
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: FITSio (>= 2.1-0), Rcpp (>= 0.12.11), mmap (>= 0.6-17), tibble (>= 1.4.2), rgl (>= 0.99.16), cli (>= 1.0.0), entropy (>= 1.2.1), geoR (>= 1.7-5.2.1), nnls (>= 1.4)
Suggests: knitr, rmarkdown, testthat, R.rsp, gsl
LinkingTo: Rcpp
RoxygenNote: 6.1.0
NeedsCompilation: yes
Packaged: 2018-11-10 00:05:13 UTC; danie
Author: Daniel Fryer [aut, cre] (<https://orcid.org/0000-0001-6032-0522>), Andriy Olenko [aut] (<https://orcid.org/0000-0002-0917-7000>), Ming Li [aut] (<https://orcid.org/0000-0002-1218-2804>), Yuguang Wang [aut]
Maintainer: Daniel Fryer <d.fryer@latrobe.edu.au>
Repository: CRAN
Date/Publication: 2018-11-19 18:00:09 UTC

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New package phylocomr with initial version 0.1.0
Package: phylocomr
Type: Package
Title: Interface to 'Phylocom'
Description: Interface to 'Phylocom' (<http://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
Version: 0.1.0
Authors@R: c( person("Jeroen", "Ooms", role = "aut", email = "jeroen@berkeley.edu"), person("Scott", "Chamberlain", role = c("aut", "cre"), email = "sckott@protonmail.com", comment = c(ORCID="0000-0003-1444-9135")), person("Cam", "Webb", role = "cph", comment = "Author of libphylocom (see AUTHORS and COPYRIGHT files for details)"), person("David", "Ackerly", role = "cph", comment = "Author of libphylocom (see AUTHORS and COPYRIGHT files for details)"), person("Steven", "Kembel", role = "cph", comment = "Author of libphylocom (see AUTHORS and COPYRIGHT files for details)") )
URL: https://github.com/ropensci/phylocomr
BugReports: https://github.com/ropensci/phylocomr/issues
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
Language: en-US
LazyData: true
VignetteBuilder: knitr
Imports: tibble, sys (>= 1.1)
Suggests: testthat, knitr, rmarkdown, ape
RoxygenNote: 6.1.1
X-schema.org-applicationCategory: Biodiversity
X-schema.org-keywords: phylogeny, Phylocom, phylodiversity, community structure, character evolution, species
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: yes
Packaged: 2018-11-10 00:17:50 UTC; sckott
Author: Jeroen Ooms [aut], Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Cam Webb [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT files for details)), David Ackerly [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT files for details)), Steven Kembel [cph] (Author of libphylocom (see AUTHORS and COPYRIGHT files for details))
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Repository: CRAN
Date/Publication: 2018-11-19 18:00:16 UTC

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New package ordering with initial version 0.7.0
Package: ordering
Type: Package
Title: Test, Check, Verify, Investigate the Monotonic Properties of Vectors
Version: 0.7.0
Date: 2018-11-09
Authors@R: c( person("Christopher", "Brown", , "chris.brown@decisionpatterns.com", c("aut", "cre") ), person("Decision Patterns", role = "cph") )
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Description: Functions to test/check/verify/investigate the ordering of vectors. The 'is_[strictly_]*' family of functions test vectors for 'sorted', 'monotonic', 'increasing', 'decreasing' order; 'is_constant' and 'is_incremental' test for the degree of ordering. `ordering` provides a numeric indication of ordering -2 (strictly decreasing) to 2 (strictly increasing).
Suggests: testthat, na.tools(>= 0.3.0)
License: GPL (>= 2)
URL: https://github.com/decisionpatterns/ordering
BugReports: https://github.com/decisionpatterns/ordering/issues
RoxygenNote: 6.1.1
Repository: CRAN
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-11-09 23:29:18 UTC; cbrown
Author: Christopher Brown [aut, cre], Decision Patterns [cph]
Date/Publication: 2018-11-19 18:00:20 UTC

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New package ODS with initial version 0.2.0
Package: ODS
Type: Package
Title: Statistical Methods for Outcome-Dependent Sampling Designs
Version: 0.2.0
Authors@R: c(person("Yinghao", "Pan", role = c("aut", "cre"), email = "ypan8@uncc.edu"), person("Haibo", "Zhou", role = "aut", email = "zhou@bios.unc.edu"), person("Mark", "Weaver", role = "aut"), person("Guoyou", "Qin", role = "aut"), person("Jianwen", "Cai", role = "aut"))
Author: Yinghao Pan [aut, cre], Haibo Zhou [aut], Mark Weaver [aut], Guoyou Qin [aut], Jianwen Cai [aut]
Maintainer: Yinghao Pan <ypan8@uncc.edu>
Description: Outcome-dependent sampling (ODS) schemes are cost-effective ways to enhance study efficiency. In ODS designs, one observes the exposure/covariates with a probability that depends on the outcome variable. Popular ODS designs include case-control for binary outcome, case-cohort for time-to-event outcome, and continuous outcome ODS design (Zhou et al. 2002) <doi: 10.1111/j.0006-341X.2002.00413.x>. Because ODS data has biased sampling nature, standard statistical analysis such as linear regression will lead to biases estimates of the population parameters. This package implements four statistical methods related to ODS designs: (1) An empirical likelihood method analyzing the primary continuous outcome with respect to exposure variables in continuous ODS design (Zhou et al., 2002). (2) A partial linear model analyzing the primary outcome in continuous ODS design (Zhou, Qin and Longnecker, 2011) <doi: 10.1111/j.1541-0420.2010.01500.x>. (3) Analyze a secondary outcome in continuous ODS design (Pan et al. 2018) <doi: 10.1002/sim.7672>. (4) An estimated likelihood method analyzing a secondary outcome in case-cohort data (Pan et al. 2017) <doi: 10.1111/biom.12838>.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: cubature (>= 1.4-1), survival (>= 2.42-3), utils, stats
URL: https://github.com/Yinghao-Pan/ODS
BugReports: https://github.com/Yinghao-Pan/ODS/issues
NeedsCompilation: no
Packaged: 2018-11-18 23:43:39 UTC; yinghaopan
Repository: CRAN
Date/Publication: 2018-11-19 17:50:03 UTC

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New package fdq with initial version 0.11
Package: fdq
Type: Package
Title: Forest Data Quality
Date: 2018-11-19
Version: 0.11
Authors@R: c(person("Caíque", "de Oliveira de Souza", email = "forestgrowthsoftware@gmail.com", role = c("aut", "cre")), person("Clayton", "Vieira Fraga Filho", email = "claytonfraga@gmail.com", role = c("ctb", "dtc")), person("Miquéias", "Fernandes", email = "contatomiqueiasfernandes@gmail.com", role = c("ctb")))
Maintainer: Caíque de Oliveira de Souza <forestgrowthsoftware@gmail.com>
Description: Forest data quality is a package that contains methods of analysis of forest databases, the purpose of the analyzes is to evaluate the quality of the data present in the databases focusing on the dimensions of consistency, pountuality and completeness. Databases can range from forest inventory data to growth model data. The package has methods to work with large volumes of data quickly, in addition in certain analyzes it is possible to generate the graphs for a better understanding of the analysis and reporting of the analyzed analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: testthat
Depends: R(>= 3.0), Fgmutils
Imports: data.table, sqldf, randomcoloR, ggplot2, plyr, utils, stats
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-19 16:01:37 UTC; Clayton
Author: Caíque de Oliveira de Souza [aut, cre], Clayton Vieira Fraga Filho [ctb, dtc], Miquéias Fernandes [ctb]
Repository: CRAN
Date/Publication: 2018-11-19 17:10:03 UTC

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New package collateral with initial version 0.4.2
Package: collateral
Title: Quickly Evaluate Captured Side Effects
Version: 0.4.2
Authors@R: person("James", "Goldie", email = "me@rensa.co", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5024-6207"))
Description: The purrr package allows you to capture the side effects (errors, warning, messages and other output) of functions using safely() and quietly(). Using collateral, you can quickly see which elements of a list (or list-column) returned results, which threw errors and which returned warnings or other output.
URL: https://rensa.co/collateral/index.html, https://github.com/rensa/collateral
Depends: R (>= 3.1.0)
Imports: purrr, crayon, methods, pillar
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
BugReports: https://github.com/rensa/collateral/issues
Suggests: dplyr, knitr, magrittr, rmarkdown, tidyverse
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-09 08:05:14 UTC; rensa
Author: James Goldie [aut, cre] (<https://orcid.org/0000-0002-5024-6207>)
Maintainer: James Goldie <me@rensa.co>
Repository: CRAN
Date/Publication: 2018-11-19 18:00:23 UTC

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New package ITGM with initial version 0.41
Package: ITGM
Type: Package
Title: Individual Tree Growth Modeling
Version: 0.41
Author: Clayton Vieira Fraga Filho, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Description: Individual tree model is an instrument to support the decision with regard to forest management. This package provides functions that let you work with data for this model. Also other support functions and extension related to this model are available.
License: GPL-2
LazyData: TRUE
Depends: Fgmutils (>= 0.8), R (>= 3.0)
Imports: gsubfn, data.table, sqldf, plyr
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-11-19 12:25:43 UTC; Clayton
Repository: CRAN
Date/Publication: 2018-11-19 13:10:03 UTC

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Sun, 18 Nov 2018

New package TSMCP with initial version 1.0
Package: TSMCP
Type: Package
Title: Fast Two Stage Multiple Change Point Detection
Version: 1.0
Author: Yaguang Li [aut, cre], Baisuo Jin [aut]
Maintainer: Yaguang Li <liyg@mail.ustc.edu.cn>
Depends: R (>= 3.3.0), plus, lars
Suggests: MASS
Description: A novel and fast two stage method for simultaneous multiple change point detection and variable selection for piecewise stationary autoregressive (PSAR) processes and linear regression model. It also simultaneously performs variable selection for each autoregressive model and hence the order selection.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-09 06:36:29 UTC; ustcr7
Repository: CRAN
Date/Publication: 2018-11-18 19:00:09 UTC

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New package shinyEffects with initial version 0.1.0
Package: shinyEffects
Type: Package
Title: Customize Your Web Apps with Fancy Effects
Version: 0.1.0
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com", role = c("aut", "cre")))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: Add fancy CSS effects to your 'shinydashboards' or 'shiny' apps. 100% compatible with 'shinydashboardPlus' and 'bs4Dash'.
License: GPL-2
Imports: htmltools, shiny, shinydashboard
Suggests: shinydashboardPlus, bs4Dash, knitr
URL: https://github.com/DivadNojnarg/shinyEffects, https://divadnojnarg.github.io/shinyEffects/
BugReports: https://github.com/DivadNojnarg/shinyEffects/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-09 14:38:28 UTC; macdavidgranjon
Author: David Granjon [aut, cre]
Repository: CRAN
Date/Publication: 2018-11-18 18:40:03 UTC

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New package rfviz with initial version 1.0.0
Package: rfviz
Type: Package
Title: Interactive Visualization Tool for Random Forests
Version: 1.0.0
Authors@R: person("Chris", "Beckett", email = "chrisbeckett8@gmail.com", role = c("aut", "cre"))
Description: An interactive data visualization and exploration toolkit that implements Breiman and Cutler's original random forest Java based visualization tools in R, for supervised and unsupervised classification and regression within the algorithm random forest.
Depends: R (>= 3.5.0), randomForest, loon, tcltk
License: GPL (>= 2)
URL: https://www.stat.berkeley.edu/~breiman/RandomForests/cc_graphics.htm
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: stats, utils, base
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-11-08 17:28:53 UTC; chris
Author: Chris Beckett [aut, cre]
Maintainer: Chris Beckett <chrisbeckett8@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-18 18:30:03 UTC

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New package RFishBC with initial version 0.1.1
Package: RFishBC
Version: 0.1.1
Date: 2018-11-12
Title: Back-Calculation of Fish Length
Authors@R: person("Derek","Ogle", email="derek@derekogle.com", role=c("aut","cre"), comment=c(ORCID="0000-0002-0370-9299"))
Description: Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software.
URL: http://derekogle.com/RFishBC
BugReports: https://github.com/droglenc/RFishBC/issues
License: GPL-3
LazyData: true
Depends: R (>= 3.2.0)
Imports: graphics, grDevices, clisymbols, crayon, readbitmap, rlang, settings, stringr, tidyr, withr
Suggests: FSA, covr, pkgdown, testthat
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-12 14:06:13 UTC; dogle
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>
Repository: CRAN
Date/Publication: 2018-11-18 18:30:17 UTC

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New package RainfallErosivityFactor with initial version 0.1.0
Package: RainfallErosivityFactor
Type: Package
Title: The Rainfall-Runoff Erosivity Factor
Version: 0.1.0
Author: Edilson Marcelino Silva [aut], Dione Pereira Cardoso [aut, cre], Marx Leandro Naves Silva [ctb], Joel Augusto Muniz [ctb], Daniel Furtado Ferreira [ctb], Junior Cesar Avanzi [ctb]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Description: Determination of rainfall-runoff erosivity factor.
Depends: R (>= 2.10)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-08 17:11:14 UTC; UX303L
Repository: CRAN
Date/Publication: 2018-11-18 18:30:14 UTC

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New package NPBayesImputeCat with initial version 0.1
Package: NPBayesImputeCat
Type: Package
Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Version: 0.1
Date: 2018-11-09
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Jingchen Hu <jingchen.monika.hu@gmail.com>
Description: These routines create multiple imputations of missing at random categorical data, and create multiply imputed synthesis of categorical data, with or without structural zeros. Imputations and syntheses are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
License: GPL (>= 3)
Depends: methods, Rcpp (>= 0.10.2)
LinkingTo: Rcpp
RcppModules: clcm
NeedsCompilation: yes
Repository: CRAN
Packaged: 2018-11-09 18:15:56 UTC; jingchenmonikahu
Date/Publication: 2018-11-18 19:00:12 UTC

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New package lmviz with initial version 0.1.1
Package: lmviz
Type: Package
Title: A Package to Visualize Linear Models Features and Play with Them
Version: 0.1.1
Author: Francesco Pauli (see file LICENSEMEDIA for credits on sounds and images)
Maintainer: Francesco Pauli <francesco.pauli@deams.units.it>
Description: Contains three shiny applications. Two are meant to explore linear model inference feature through simulation. The third is a game to learn interpreting diagnostic plots.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinyjs, lmtest, mgcv, methods
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-08 21:56:51 UTC; Franz
Repository: CRAN
Date/Publication: 2018-11-18 18:30:10 UTC

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New package cusum with initial version 0.1.0
Package: cusum
Title: CUSUM Charts for Monitoring of Hospital Performance
Version: 0.1.0
Authors@R: c( person("Lena", "Hubig", email = "cs@lenahubig.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9454-1232")))
Description: Provides functions for constructing and evaluating CUSUM charts and RA-CUSUM charts with focus on false signal probability.
Depends: R (>= 3.5.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stats, graphics, checkmate
Suggests: testthat, knitr, rmarkdown
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-08 14:10:46 UTC; lena
Author: Lena Hubig [aut, cre] (<https://orcid.org/0000-0002-9454-1232>)
Maintainer: Lena Hubig <cs@lenahubig.de>
Repository: CRAN
Date/Publication: 2018-11-18 18:20:02 UTC

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New package bpbounds with initial version 0.1.0
Package: bpbounds
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions
Version: 0.1.0
Authors@R: c(person("Tom", "Palmer", email = "tom.palmer@lancaster.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4655-4511")), person("Roland", "Ramsahai", role = c("aut")), person("Vanessa", "Didelez", role = c("aut"), comment = c(ORCID = "0000-0001-8587-7706")), person("Nuala", "Sheehan", role = c("aut")))
Description: Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).
Depends: R (>= 3.5.0)
Imports: methods
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: dplyr, testthat, knitr, rmarkdown, tidyr
VignetteBuilder: knitr
RoxygenNote: 6.1.0
URL: https://github.com/remlapmot/bpbounds
BugReports: https://github.com/remlapmot/bpbounds/issues
NeedsCompilation: no
Packaged: 2018-11-09 17:42:31 UTC; remlapmot
Author: Tom Palmer [aut, cre] (<https://orcid.org/0000-0003-4655-4511>), Roland Ramsahai [aut], Vanessa Didelez [aut] (<https://orcid.org/0000-0001-8587-7706>), Nuala Sheehan [aut]
Maintainer: Tom Palmer <tom.palmer@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2018-11-18 19:00:06 UTC

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New package argonR with initial version 0.1.0
Package: argonR
Type: Package
Title: R Interface to Argon HTML Design
Version: 0.1.0
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com", role = c("aut", "cre")), person(family = "Creative Tim", role = c("ctb", "cph"), comment = "Argon theme for Bootstrap 4"), person("Winston", "Chang", role = c("ctb", "cph"), comment = "Unexported functions from htmltools"))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: R wrapper around the argon HTML library. More at <https://demos.creative-tim.com/argon-design-system/>.
URL: https://github.com/RinteRface/argonR
BugReports: https://github.com/RinteRface/argonR/issues
Imports: htmltools, utils
Suggests: magrittr, knitr, rmarkdown
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-11-09 14:44:34 UTC; macdavidgranjon
Author: David Granjon [aut, cre], Creative Tim [ctb, cph] (Argon theme for Bootstrap 4), Winston Chang [ctb, cph] (Unexported functions from htmltools)
Repository: CRAN
Date/Publication: 2018-11-18 18:40:06 UTC

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New package sctransform with initial version 0.1.0
Package: sctransform
Type: Package
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Version: 0.1.0
Authors@R: person(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-6365-8254'))
Description: A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction/denoising.
URL: https://github.com/ChristophH/sctransform
BugReports: https://github.com/ChristophH/sctransform/issues
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: MASS, Matrix, parallel, methods
Suggests: matrixStats, testthat
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-16 10:54:11 UTC; chafemeister
Author: Christoph Hafemeister [aut, cre] (<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <chafemeister@nygenome.org>
Repository: CRAN
Date/Publication: 2018-11-18 16:30:03 UTC

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Sat, 17 Nov 2018

New package PDFEstimator with initial version 0.1-1
Package: PDFEstimator
Version: 0.1-1
Date: 2018-11-7
Title: Nonparametric Probability Density Estimator
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>
Description: A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2018-11-16 23:47:56 UTC; jenny
Repository: CRAN
Date/Publication: 2018-11-18 00:50:19 UTC

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New package fungible with initial version 1.75
Package: fungible
Version: 1.75
Date: 2018-11-16
Title: Psychometric Functions from the Waller Lab
Author: c( person("Niels", "Waller", role = c("aut", "cre"), email="nwaller@umn.edu" ), person("Jeff","Jones", role = "ctb"))
Maintainer: Niels G. Waller <nwaller@umn.edu>
Depends: R (>= 3.0)
Imports: clue, e1071, GPArotation, lattice, MASS, methods, mvtnorm, nleqslv, psych, Rcsdp, RSpectra, stringr
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications: Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI10.1007/s11336-008-9066-z>. Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights. Psychometrika, 74(4), 589-602, <DOI10.1007/s11336-008-9087-7>. Waller, N. G. (2016). Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI10.1080/00273171.2016.1178566>. Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF) covariance matrix of standardized regression coefficients: theoretical extensions and finite sample behavior. Psychometrika, 80, 365-378, <DOI10.1007/s11336-013-9380-y>. Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI 10.1007/s11336-017-9599-0>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2018-11-16 20:34:46 UTC; nielswaller
Repository: CRAN
Date/Publication: 2018-11-18 00:50:14 UTC

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New package Fgmutils with initial version 0.9.5
Package: Fgmutils
Type: Package
Title: Forest Growth Model Utilities
Version: 0.9.5
Date: 2018-10-11
Author: Clayton Vieira Fraga Filho, Ana Paula Simiqueli, Gilson Fernandes da Silva, Miqueias Fernandes, Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
License: GPL-2
Depends: sqldf, stringr, plyr, R (>= 3.0)
Imports: data.table, tcltk, utils, stats, graphics, devEMF, png, grDevices, methods, ggplot2, gridExtra
LazyData: TRUE
Suggests: testthat
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-17 22:29:47 UTC; clayt
Repository: CRAN
Date/Publication: 2018-11-18 00:50:22 UTC

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Fri, 16 Nov 2018

New package pterrace with initial version 1.0
Package: pterrace
Type: Package
Title: Persistence Terrace for Topological Data Analysis
Version: 1.0
Author: Chul Moon
Maintainer: Chul Moon <chulm@smu.edu>
Description: Plot the summary graphic called the persistence terrace for topological inference. It also provides the aid tool called the terrace area plot for determining the number of significant topological features. Moon, C., Giansiracusa, N., and Lazar, N. A. (2018) <doi:10.1080/10618600.2017.1422432>.
Encoding: UTF-8
License: GPL-2
RoxygenNote: 6.0.1
Imports: TDA, doParallel, foreach, plotly, viridis
NeedsCompilation: no
Packaged: 2018-11-07 22:03:38 UTC; Chul
Repository: CRAN
Date/Publication: 2018-11-16 17:20:03 UTC

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New package psymonitor with initial version 0.0.1
Type: Package
Package: psymonitor
Title: Real Time Monitoring of Asset Markets: Bubbles and Crisis
Version: 0.0.1
Authors@R: c(person(given = "Peter", family = "C.B. Phillips", role = "aut"), person(given = "Shuping", family = "Shi", role = "aut"), person(given = "Itamar", family = "Caspi", role = c("aut", "cre"), email = "caspi.itamar@gmail.com"))
Description: Apply the popular real-time monitoring strategy proposed by Phillips, Shi and Yu (2015a,b;PSY) <doi:10.1111/iere.12132>, <doi:10.1111/iere.12131>, along with a new bootstrap procedure designed to mitigate the potential impact of heteroskedasticity and to effect family-wise size control in recursive testing algorithms (Phillips and Shi, forthcoming).
License: GPL-3
URL: https://github.com/itamarcaspi/psymonitor
BugReports: https://github.com/itamarcaspi/psymonitor/issues
Depends: R (>= 3.2.0)
Imports: doParallel, foreach, magrittr, parallel
Suggests: ggplot2, knitr, lubridate, rmarkdown, spelling, testthat,
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-07 14:33:37 UTC; user
Author: Peter C.B. Phillips [aut], Shuping Shi [aut], Itamar Caspi [aut, cre]
Maintainer: Itamar Caspi <caspi.itamar@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-16 17:20:06 UTC

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New package ipcwswitch with initial version 1.0.1
Package: ipcwswitch
Title: Inverse Probability of Censoring Weights to Deal with Treatment Switch in Randomized Clinical Trials
Version: 1.0.1
Authors@R: c(person("Nathalie", "Graffeo", email = "nathalie.graffeo@univ-amu.fr", role = c("aut", "cre")), person("Aurelien", "Latouche", role=c("aut")), person("Sylvie", "Chevret", role=c("aut")))
Maintainer: Nathalie Graffeo <nathalie.graffeo@univ-amu.fr>
Description: Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.
Depends: R (>= 2.10), survival (>= 2.42)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: stats
NeedsCompilation: no
Packaged: 2018-11-07 19:27:59 UTC; Nathalie
Author: Nathalie Graffeo [aut, cre], Aurelien Latouche [aut], Sylvie Chevret [aut]
Repository: CRAN
Date/Publication: 2018-11-16 17:20:10 UTC

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New package TGS with initial version 1.0.0
Package: TGS
Title: Rapid Reconstruction of Time-Varying Gene Regulatory Networks
Version: 1.0.0
Authors@R: c(person("Manan", "Gupta", , "guptamanan100@gmail.com", c("aut", "cre")),person("Saptarshi", "Pyne", ,"saptarshipyne01@gmail.com", role = "aut"),person("Alok", "Kumar", ,"alok4039@gmail.com", role = "aut"), person("Ashish", "Anand", , "anand.ashish@iitg.ac.in", role = "aut"))
Description: Rapid advancement in high-throughput gene expression measurement technologies has resulted in genome- scale time series datasets. Uncovering the underlying temporal sequence of gene regulatory events in the form of time-varying Gene Regulatory Networks (GRNs) demands computationally fast, accurate and highly scalable algorithms. To provide a flexible framework in a significantly time-efficient manner, a novel algorithm, namely TGS (Ashish Anand et al., 2018 <doi:10.1109/TCBB.2018.2861698>), is proposed here. TGS is shown to consume only 29 minutes for a microarray dataset with 4028 genes. Moreover, it provides the flexibility and time-efficiency, without losing the accuracy. Nevertheless, TGS’s main memory requirement grows exponentially with the number of genes, which it tackles by restricting the maximum number of regulators for each gene. Relaxing this restriction remains an important challenge as the true number of regulators is not known a prior.
License: CC BY-NC-SA 4.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
biocViews:
Imports: minet, stats, base, utils, bnstruct, ggm, foreach, doParallel, rjson
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2018-11-07 11:12:19 UTC; cse
Author: Manan Gupta [aut, cre], Saptarshi Pyne [aut], Alok Kumar [aut], Ashish Anand [aut]
Maintainer: Manan Gupta <guptamanan100@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-16 16:10:13 UTC

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New package survELtest with initial version 1.0.0
Package: survELtest
Title: Comparing Multiple Survival Functions via Empirical Likelihood (EL) Based Tests
Version: 1.0.0
Description: Contains routines for computing the one-sided/two-sided integrated/maximally selected EL statistics for simultaneous testing, the one-sided/two-sided EL tests for pointwise testing, and an initial test that precedes one-sided testing to exclude the possibility of crossings or alternative orderings.
Depends: R (>= 2.13.0)
Imports: Iso, nloptr, methods, plyr, survival, stats
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>
Archs: i386, x64
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-07 01:24:22 UTC; Wally
Repository: CRAN
Date/Publication: 2018-11-16 16:40:02 UTC

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New package qkerntool with initial version 1.17
Package: qkerntool
Title: Q-Kernel-Based and Conditionally Negative Definite Kernel-Based Machine Learning Tools
Version: 1.17
Authors@R: c(person("Yusen", "Zhang", role = c("aut", "cre"), email = "yusenzhang@126.com", comment = c(ORCID = "0000-0003-3842-1153")), person("Daolin","Pang", role = c("ctb")), person("Jinghao", "Wang", role = c("ctb")), person("Jialin", "Zhang", role = c("ctb")))
Description: Nonlinear machine learning tool for classification, clustering and dimensionality reduction. It integrates 12 q-kernel functions and 14 conditional negative definite kernel functions and includes the q-kernel and conditional negative definite kernel version of density-based spatial clustering of applications with noise, spectral clustering, generalized discriminant analysis, principal component analysis, multidimensional scaling, locally linear embedding, sammon's mapping and t-Distributed stochastic neighbor embedding.
Depends: R (>= 3.0.1)
Imports: stats, class, MASS, graphics, methods
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Maintainer: Yusen Zhang <yusenzhang@126.com>
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-07 07:53:00 UTC; Administrator
Author: Yusen Zhang [aut, cre] (<https://orcid.org/0000-0003-3842-1153>), Daolin Pang [ctb], Jinghao Wang [ctb], Jialin Zhang [ctb]
Repository: CRAN
Date/Publication: 2018-11-16 16:40:06 UTC

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New package pammtools with initial version 0.1.7
Package: pammtools
Title: Piece-Wise Exponential Additive Mixed Modeling Tools
Version: 0.1.7
Date: 2018-11-02
Authors@R: c( person("Andreas", "Bender", , "andreas.bender@stat.uni-muenchen.de", role = c("aut", "cre"), comment=c(ORCID = "0000-0001-5628-8611")), person("Fabian", "Scheipl", , "fabian.scheipl@stat.uni-muenchen.de", role = c("aut")))
Description: Functions that facilitate fitting piece-wise exponential (additive mixed) models (Bender and Scheipl (2018) <doi: 10.1177/1471082X17748083>). This includes restructuring the data to the needed format and various convenience functions, e.g., for plotting the results.
Depends: R (>= 3.3.0)
Imports: mgcv, survival (>= 2.39-5), checkmate, magrittr, rlang, tidyr (>= 0.7.0), ggplot2, dplyr (>= 0.7.0), purrr (>= 0.2.3), tibble, msm, lazyeval, Formula, mvtnorm
Suggests: RColorBrewer, scam, coxme, testthat, timereg, knitr, rmarkdown, grid, gridExtra, covr
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/adibender/pammtools
BugReports: https://github.com/adibender/pammtools/issues
RoxygenNote: 6.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-11-06 13:06:00 UTC; andreasb
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>), Fabian Scheipl [aut]
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>
Repository: CRAN
Date/Publication: 2018-11-16 16:10:03 UTC

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New package mltest with initial version 1.0.1
Package: mltest
Title: Classification Evaluation Metrics
Version: 1.0.1
Authors@R: person("G.", "Dudnik", email = "gl.dudnik@gmail.com", role = c("aut", "cre", "cph"))
Description: A fast, robust and easy-to-use calculation of multi-class classification evaluation metrics based on confusion matrix.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-07 14:07:48 UTC; fcku
Author: G. Dudnik [aut, cre, cph]
Maintainer: G. Dudnik <gl.dudnik@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-16 17:00:03 UTC

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New package instruments with initial version 0.1.0
Package: instruments
Type: Package
Title: Estimate Regression Models with Instrumental Variables
Version: 0.1.0
Author: Alex Pavlakis
Maintainer: Alex Pavlakis <alexpavlakis@gmail.com>
Description: A consistent API for estimating linear and generalized linear models with instrumental variables.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: testthat
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2018-11-06 17:10:10 UTC; alexpavlakis
Repository: CRAN
Date/Publication: 2018-11-16 16:10:09 UTC

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New package evtclass with initial version 1.0
Package: evtclass
Title: Extreme Value Theory for Open Set Classification - GPD and GEV Classifiers
Version: 1.0
Authors@R: person("Edoardo", "Vignotto", email = "edoardo.vignotto@unige.ch", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9870-8020"))
Description: Two classifiers for open set recognition and novelty detection based on extreme value theory. The first classifier is based on the generalized Pareto distribution (GPD) and the second classifier is based on the generalized extreme value (GEV) distribution. For details, see Vignotto, E., & Engelke, S. (2018) <arXiv:1808.09902>.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0.9000
Imports: RANN, evd, fitdistrplus
NeedsCompilation: no
Packaged: 2018-11-07 10:28:50 UTC; vignotto
Author: Edoardo Vignotto [aut, cre] (<https://orcid.org/0000-0001-9870-8020>)
Maintainer: Edoardo Vignotto <edoardo.vignotto@unige.ch>
Repository: CRAN
Date/Publication: 2018-11-16 16:40:11 UTC

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New package BivRec with initial version 1.0.0
Package: BivRec
Type: Package
Title: Bivariate Alternating Recurrent Event Data Analysis
Date: 2018-10-31
Version: 1.0.0
Authors@R: c(person("Sandra", "Castro-Pearson", email= "cast0135@umn.edu", role = c("aut", "cre")), person("Chi-Hyun", "Lee", email = "chihyunlee@umass.edu", role ="aut"), person("Chiung-Yu", "Huang", email = "chiungyu.huang@ucsf.edu", role = "aut"), person("Xianghua", "Luo", email = "luox0054@umn.edu", role = "ctb"))
Author: Sandra Castro-Pearson [aut, cre], Chi-Hyun Lee [aut], Chiung-Yu Huang [aut], Xianghua Luo [ctb]
Maintainer: Sandra Castro-Pearson <cast0135@umn.edu>
Description: Alternating recurrent event data arise frequently in biomedical and social sciences where 2 types of events such as hospital admissions and discharge occur alternatively over time. As such we implement a collection of non-parametric and semiparametric methods to analyze such data. The main functions are biv.rec.fit() and biv.rec.np(). Use biv.rec.fit() for estimation of covariate effects on the two alternating event gap times (xij and yij) using semiparametric methods. The method options are "Lee.et.al" and "Chang". Use biv.rec.np() for estimation of the joint cumulative distribution function (cdf) for the two alternating events gap times (xij and yij) as well as the marginal survival function for type I gap times (xij) and the conditional cdf of the type II gap times (yij) given an interval of type I gap times (xij) in a non-parametric fashion. The package also provides options to simulate and visualize the data and results of analysis.
BugReports: https://github.com/SandraCastroPearson/BivRec/issues
Depends: R (>= 3.2.0), survival, stats
Imports: MASS, stringr, utils, knitr, rmarkdown, Rcpp, graphics, grDevices
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-11-06 17:33:18 UTC; pearsons0519
Repository: CRAN
Date/Publication: 2018-11-16 16:10:17 UTC

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New package randcorr with initial version 1.0
Package: randcorr
Type: Package
Title: Generate a Random p x p Correlation Matrix
Version: 1.0
Date: 2018-11-07
Author: Daniel F. Schmidt [aut, cph, cre], Enes Makalic [aut, cph]
Maintainer: Daniel F. Schmidt <daniel.schmidt@monash.edu>
Description: Implements the algorithm by Pourahmadi and Wang (2015) <doi:10.1016/j.spl.2015.06.015> for generating a random p x p correlation matrix. Briefly, the idea is to represent the correlation matrix using Cholesky factorization and p(p-1)/2 hyperspherical coordinates (i.e., angles), sample the angles from a particular distribution and then convert to the standard correlation matrix form. The angles are sampled from a distribution with pdf proportional to sin^k(theta) (0 < theta < pi, k >= 1) using the efficient sampling algorithm described in Enes Makalic and Daniel F. Schmidt (2018) <arXiv:1809.05212>.
License: GPL (>= 3)
Authors@R: c( person("Daniel F. Schmidt", email="daniel.schmidt@monash.edu", role = c("aut","cph","cre")), person("Enes Makalic", email="emakalic@unimelb.edu.au", role=c("aut","cph")) )
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-11-07 00:30:09 UTC; dschmidt
Repository: CRAN
Date/Publication: 2018-11-16 15:30:03 UTC

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New package pkgsearch with initial version 2.0.0
Package: pkgsearch
Title: Search CRAN R Packages
Version: 2.0.0
Authors@R: c(person("Gábor", "Csárdi", email = "csardi.gabor@gmail.com", role = c("aut", "cre")))
Description: Search CRAN R packages. Uses the 'METACRAN' search server, see <https://r-pkg.org>.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/metacran/pkgsearch#readme
BugReports: https://github.com/metacran/pkgsearch/issues
Imports: magrittr, httr, jsonlite, parsedate, prettyunits
Suggests: covr, testthat, tibble
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-07 11:20:26 UTC; gaborcsardi
Author: Gábor Csárdi [aut, cre]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-16 16:00:03 UTC

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New package lcc with initial version 1.0
Package: lcc
Type: Package
Title: Longitudinal Concordance Correlation
Version: 1.0
Authors@R: c(person("Thiago", "de Paula Oliveira", role=c("aut", "cre"), email = "thiago.paula.oliveira@usp.br"), person("Rafael","de Andrade Moral", role="aut"), person( "John","Hinde",role="aut"), person("Silvio", "Sandoval Zocchi", role=c("aut","ctb")), person("Clarice", "Garcia Borges Demetrio", role=c("aut", "ctb")))
Author: Thiago de Paula Oliveira [aut, cre], Rafael de Andrade Moral [aut], John Hinde [aut], Silvio Sandoval Zocchi [aut, ctb], Clarice Garcia Borges Demetrio [aut, ctb]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@usp.br>
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Date: 2018-11-05
Depends: R (>= 3.2.3), nlme (>= 3.1-124), ggplot2 (>= 2.2.1), grid (>= 3.2.3), gdata (>= 2.18.0)
Suggests: roxygen2 (>= 3.0.0)
License: GPL (>= 2)
Encoding: UTF-8
Repository: CRAN
NeedsCompilation: yes
LazyData: true
RoxygenNote: 6.1.0
Packaged: 2018-11-06 11:37:34 UTC; thiago
Date/Publication: 2018-11-16 16:00:07 UTC

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New package IRkernel with initial version 0.8.14
Package: IRkernel
Title: Native R Kernel for the 'Jupyter Notebook'
Description: The R kernel for the 'Jupyter' environment executes R code which the front-end ('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Version: 0.8.14
Authors@R: c( person('Thomas', 'Kluyver', role = c('aut', 'cph'), email = 'thomas@kluyver.me.uk'), person('Philipp', 'Angerer', role = c('aut', 'cph', 'cre'), email = 'phil.angerer@gmail.com'), person('Jan', 'Schulz', role = c('aut', 'cph'), email = 'jasc@gmx.net'), person('Karthik', 'Ram', role = c('aut', 'cph'), email = 'karthik.ram@gmail.com'))
Depends: R (>= 3.2.0)
Suggests: testthat, roxygen2
SystemRequirements: jupyter, jupyter_kernel_test (Python package for testing)
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
Imports: repr (>= 0.4.99), methods, evaluate (>= 0.10), IRdisplay (>= 0.3.0.9999), pbdZMQ (>= 0.2-1), crayon, jsonlite (>= 0.9.6), uuid, digest
Collate: 'class_unions.r' 'logging.r' 'comm_manager.r' 'compat.r' 'environment_runtime.r' 'environment_shadow.r' 'options.r' 'execution.r' 'handlers.r' 'help.r' 'installspec.r' 'utils.r' 'kernel.r' 'main.r' 'onload.r'
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-06 17:40:59 UTC; phil
Author: Thomas Kluyver [aut, cph], Philipp Angerer [aut, cph, cre], Jan Schulz [aut, cph], Karthik Ram [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Repository: CRAN
Date/Publication: 2018-11-16 15:30:06 UTC

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Thu, 15 Nov 2018

New package MultiJoin with initial version 0.1.1
Package: MultiJoin
Type: Package
Title: Enables Efficient Joining of Data File on Common Fields using the Unix Utility Join
Version: 0.1.1
Date: 2018-11-10
Depends: R (>= 2.10), graphics, stats, utils
Author: "Markus Loecher, Berlin School of Economics and Law (BSEL)" <markus.loecher@gmail.com>
Maintainer: "Markus Loecher" <markus.loecher@gmail.com>
Description: Wrapper around the Unix join facility which is more efficient than the built-in R routine merge(). The package enables the joining of multiple files on disk at once. The files can be compressed and various filters can be deployed before joining. Compiles only under Unix.
License: GPL
LazyLoad: yes
NeedsCompilation: no
Packaged: 2018-11-15 14:10:12 UTC; loecherm
Repository: CRAN
Date/Publication: 2018-11-15 22:10:07 UTC

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New package UncDecomp with initial version 0.0.4
Package: UncDecomp
Title: Uncertainty Decomposition
Version: 0.0.4
Authors@R: c(person("Seonghyeon", "Kim", email = "shkim93@snu.ac.kr", role = c("aut", "cre")), person("Yongdai", "Kim", role = "aut"), person("Ilsang", "Ohn", role = "aut"))
Author: Seonghyeon Kim [aut, cre], Yongdai Kim [aut], Ilsang Ohn [aut]
Maintainer: Seonghyeon Kim <shkim93@snu.ac.kr>
Description: If a procedure consists of several stages and there are several scenarios that can be selected for each stage, uncertainty of the procedure can be decomposed by stages or scenarios. cum_uncertainty() is used to decompose uncertainty based on the cumulative uncertainty. stage_uncertainty() and scenario_uncertainty() is used to decompose uncertainty based on the second order interaction ANOVA model. In stage_uncertainty() and scenario_uncertainty(), the uncertainty from interaction effect from two stages is distributed equally to each stage.
Depends: R (>= 3.3.2)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-11-06 09:37:21 UTC; ksh
Repository: CRAN
Date/Publication: 2018-11-15 17:40:12 UTC

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