Mon, 26 Oct 2020

New package tdaunif with initial version 0.1.0
Package: tdaunif
Title: Uniform Manifold Samplers for Topological Data Analysis
Version: 0.1.0
Authors@R: c( person("Jason Cory", "Brunson", email = "cornelioid@gmail.com", role = c("aut", "cre")), person("Brandon", "Demkowicz", email = "brandondemkowicz@gmail.com", role = "aut"), person("Sanmati", "Choudhary", email = "20choudharysa@fpsct.org", role = "aut") )
Description: Uniform random samples from simple manifolds, sometimes with noise, are commonly used to test topological data analytic (TDA) tools. This package includes samplers powered by two techniques: analytic volume-preserving parameterizations, as employed by Arvo (1995) <doi:10.1145/218380.218500>, and rejection sampling, as employed by Diaconis, Holmes, and Shahshahani (2013) <doi:10.1214/12-IMSCOLL1006>.
Depends: R (>= 3.3.0)
Suggests: knitr, rmarkdown, testthat, vdiffr (>= 0.2)
License: GPL-3
Encoding: UTF-8
URL: https://corybrunson.github.io/tdaunif/
BugReports: https://github.com/corybrunson/tdaunif/issues
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-17 14:50:33 UTC; corybrunson
Author: Jason Cory Brunson [aut, cre], Brandon Demkowicz [aut], Sanmati Choudhary [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-26 09:20:02 UTC

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New package r3dmol with initial version 0.1.0
Package: r3dmol
Title: Create Interactive 3D Visualizations of Molecular Data
Version: 0.1.0
Authors@R: person(given = "Wei", family = "Su", role = c("aut", "cre"), email = "swsoyee@gmail.com")
Maintainer: Wei Su <swsoyee@gmail.com>
Description: Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: htmlwidgets, magrittr, methods
Suggests: knitr, rmarkdown, shiny, colourpicker, covr, testthat
VignetteBuilder: knitr
Depends: R (>= 2.10)
URL: https://github.com/swsoyee/r3dmol
BugReports: https://github.com/swsoyee/r3dmol/issues
NeedsCompilation: no
Packaged: 2020-10-17 16:51:58 UTC; wsu
Author: Wei Su [aut, cre]
Repository: CRAN
Date/Publication: 2020-10-26 09:20:06 UTC

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New package linne with initial version 0.0.2
Package: linne
Title: Convenient 'CSS'
Version: 0.0.2
Authors@R: person(given = "John", family = "Coene", role = c("aut", "cre"), email = "jcoenep@gmail.com")
Description: Conveniently generate 'CSS' using R code.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
Imports: R6, rlang, purrr, cli, shiny, magrittr
Suggests: htmltools, knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
URL: https://linne.john-coene.com/
BugReports: https://github.com/JohnCoene/linne/issues
NeedsCompilation: no
Packaged: 2020-10-17 14:28:05 UTC; jp
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-26 09:20:10 UTC

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New package imbibe with initial version 0.1.0
Package: imbibe
Version: 0.1.0
Date: 2020-10-17
Title: A Pipe-Friendly Image Calculator
Authors@R: c(person("Jon", "Clayden", email="code@clayden.org", role=c("aut","cre"), comment=c(ORCID="0000-0002-6608-0619")), person("Chris", "Rorden", role="aut", comment=c(ORCID="0000-0002-7554-6142")), person("John", "Muschelli", role="ctb", comment=c(ORCID="0000-0001-6469-1750")), person("Exstrom Laboratories LLC", role="cph"))
Maintainer: Jon Clayden <code@clayden.org>
Imports: Rcpp, RNifti, magrittr
LinkingTo: Rcpp, RNifti
Suggests: mmand, tinytest, covr
Description: Provides a set of fast, chainable image-processing operations which are applicable to images of two, three or four dimensions, particularly medical images.
License: BSD_3_clause + file LICENCE
URL: https://github.com/jonclayden/imbibe
BugReports: https://github.com/jonclayden/imbibe/issues
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-10-17 17:32:28 UTC; jon
Author: Jon Clayden [aut, cre] (<https://orcid.org/0000-0002-6608-0619>), Chris Rorden [aut] (<https://orcid.org/0000-0002-7554-6142>), John Muschelli [ctb] (<https://orcid.org/0000-0001-6469-1750>), Exstrom Laboratories LLC [cph]
Repository: CRAN
Date/Publication: 2020-10-26 09:30:02 UTC

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New package DIDmultiplegt with initial version 0.1.0
Package: DIDmultiplegt
Type: Package
Title: Estimation in DID with Multiple Groups and Periods
Version: 0.1.0
Authors@R: c(person("Shuo", "Zhang", role = c("aut", "cre"), email = "shuo_zhang@ucsb.edu"), person("Clément", "de Chaisemartin", role = "aut", email = "clementdechaisemartin@ucsb.edu"))
Maintainer: Shuo Zhang <shuo_zhang@ucsb.edu>
Description: Estimate the effect of a treatment on an outcome in sharp Difference-in-Difference designs with multiple groups and periods. It computes the DIDM estimator introduced in Section 4 of "Two-Way Fixed Effects Estimators with Heterogeneous Treatment Effects" (Chaisemartin, D'Haultfoeuille (2020) <doi:10.1257/aer.20181169>), which generalizes the standard DID estimator with two groups, two periods and a binary treatment to situations with many groups,many periods and a potentially non-binary treatment. For each pair of consecutive time periods t-1 and t and for each value of the treatment d, the package computes a DID estimator comparing the outcome evolution among the switchers, the groups whose treatment changes from d to some other value between t-1 and t, to the same evolution among control groups whose treatment is equal to d both in t-1 and t. Then the DIDM estimator is equal to the average of those DIDs across all pairs of consecutive time periods and across all values of the treatment. Under a parallel trends assumption, DIDM is an unbiased and consistent estimator of the average treatment effect among switchers, at the time period when they switch. The package can also compute placebo estimators that can be used to test the parallel trends assumption. Finally, in staggered adoption designs where each group's treatment is weakly increasing over time, it can compute estimators of switchers' dynamic treatment effects, one time period or more after they have started receiving the treatment.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R(>= 3.4.0)
Imports: dplyr (>= 1.0.0), fixest (>= 0.6.0), plotrix, stringr, sampling, stats, parallel, assertthat
Suggests: wooldridge
NeedsCompilation: no
Packaged: 2020-10-18 04:53:09 UTC; sicongfeng
Author: Shuo Zhang [aut, cre], Clément de Chaisemartin [aut]
Repository: CRAN
Date/Publication: 2020-10-26 09:50:02 UTC

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Sun, 25 Oct 2020

New package swissdd with initial version 1.0.4
Package: swissdd
Type: Package
Title: Get Swiss Federal and Cantonal Vote Results from Opendata.swiss
Version: 1.0.4
Authors@R: c( person("Thomas", "Lo Russo", email = "th.lorusso@gmail.com", role = c("cre","aut")), person("Thomas", "Willi", email = "thomas.willi@uzh.ch", role = "aut"))
Description: Builds upon the real time data service as well as the archive for national votes <https://opendata.swiss/api/3/action/package_show?id=echtzeitdaten-am-abstimmungstag-zu-eidgenoessischen-abstimmungsvorlagen> and cantonal votes <https://opendata.swiss/api/3/action/package_show?id=echtzeitdaten-am-abstimmungstag-zu-kantonalen-abstimmungsvorlagen>. It brings the results of Swiss popular votes, aggregated at the geographical level of choice, into R. Additionally, it allows to retrieve data from the Swissvotes-Database, one of the most comprehensive data platforms on Swiss referendums and initiatives <https://swissvotes.ch/page/dataset/swissvotes_dataset.csv>.
Imports: purrr, dplyr, tidyr (>= 1.0.0), jsonlite, magrittr, tibble, curl
URL: https://github.com/politanch/swissdd
BugReports: https://github.com/politanch/swissdd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2020-10-20 19:16:37 UTC; tlo1
Author: Thomas Lo Russo [cre, aut], Thomas Willi [aut]
Maintainer: Thomas Lo Russo <th.lorusso@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-25 16:20:02 UTC

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New package PRIMME with initial version 3.1-3
Package: PRIMME
Type: Package
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Version: 3.1-3
Date: 2020-10-20
Authors@R: c(person("Eloy", "Romero", role=c("aut", "cre"), email="eloy@cs.wm.edu"), person("Andreas", "Stathopoulos", role="aut", email="andreas@cs.wm.edu"), person("Lingfei", "Wu", role="aut", email="wuli@us.ibm.com"), person("College of William & Mary", role="cph"))
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software/>, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute singular values and vectors of a square or rectangular matrix. 'PRIMME' finds largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence. General description of the methods are provided in the papers Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>). See 'citation("PRIMME")' for details.
URL: http://www.cs.wm.edu/~andreas/software/ https://github.com/primme/primme
BugReports: https://github.com/primme/primme/issues
Imports: Rcpp
LinkingTo: Rcpp, Matrix
Suggests: Matrix
SystemRequirements: A POSIX system. Currently Linux and OS X are known to work. GNU make.
NeedsCompilation: yes
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Packaged: 2020-10-22 03:31:03 UTC; eloy
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], Lingfei Wu [aut], College of William & Mary [cph]
Repository: CRAN
Date/Publication: 2020-10-25 16:20:15 UTC

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New package mastif with initial version 1.0.1
Package: mastif
Type: Package
Title: Mast Inference and Forecasting
Version: 1.0.1
Date: 2020-10-19
Author: James S. Clark
Maintainer: James S. Clark <jimclark@duke.edu>
Description: Analyzes production and dispersal of seeds dispersed from trees and recovered in seed traps. Motivated by long-term inventory plots where seed collections are used to infer seed production by each individual plant.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.5), RANN, corrplot, xtable, repmis
Depends: R (>= 2.10)
LinkingTo: Rcpp, RcppArmadillo
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-10-19 16:08:49 UTC; jimclark
Repository: CRAN
Date/Publication: 2020-10-25 16:30:02 UTC

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Sat, 24 Oct 2020

New package visualpred with initial version 0.1.0
Package: visualpred
Title: Visualization 2D of Binary Classification Models
Version: 0.1.0
Authors@R: person(given = "Javier", family = "Portela", role = c("aut", "cre"), email = "javipgm@gmail.com")
Description: Visual 2D point and contour plots for binary classification modeling under algorithms such as glm(), randomForest(), gbm(), nnet() and svm(), presented over two dimensions generated by FAMD and MCA methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: gbm, randomForest, nnet (>= 7.3.12), e1071, MASS (>= 7.3.51.4), magrittr, FactoMineR (>= 2.3), ggplot2 (>= 3.3.0), mltools, dplyr, data.table, MBA, pROC, ggrepel
Suggests: knitr, markdown,egg
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2020-10-17 05:51:45 UTC; Usuario
Author: Javier Portela [aut, cre]
Maintainer: Javier Portela <javipgm@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:40:02 UTC

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New package Snake with initial version 1.0
Package: Snake
Title: Game of Snake
Version: 1.0
Date: 2020-10-08
Authors@R: person("Carsten", "Croonenbroeck", email = "carsten.croonenbroeck@uni-rostock.de", role = c("aut", "cre"))
Description: Implements snake in R as a programming example, see <https://en.wikipedia.org/wiki/Snake_(video_game_genre)>.
Depends: R (>= 3.5.0)
Imports: tcltk, grid
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-10-17 11:59:56 UTC; ccroo
Author: Carsten Croonenbroeck [aut, cre]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Repository: CRAN
Date/Publication: 2020-10-24 09:50:08 UTC

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New package MGDrivE2 with initial version 1.0.1
Package: MGDrivE2
Type: Package
Title: Mosquito Gene Drive Explorer 2
Version: 1.0.1
Authors@R: c( person("Sean L.", "Wu", email = "slwood89@gmail.com", role = c("aut","cre")), person("Jared B.", "Bennett", email = "jared_bennett@berkeley.edu ", role = "aut"), person("Héctor Manuel", "Sánchez Castellanos", email = "sanchez.hmsc@berkeley.edu", role = "ctb"), person("Tomás M.", "León", email = "tomas.leon@berkeley.edu", role = "ctb"), person("Andrew J.", "Dolgert", email = "adolgert@uw.edu", role = "ctb"), person("John M.", "Marshall", email = "john.marshall@berkeley.edu", role = "aut") )
Maintainer: Sean L. Wu <slwood89@gmail.com>
URL: https://marshalllab.github.io/MGDrivE/, https://www.marshalllab.com/
BugReports: https://github.com/MarshallLab/MGDrivE/issues
Description: A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.
License: GPL-3
Encoding: UTF-8
ByteCompile: true
LazyData: true
Depends: R (>= 3.1.0)
Imports: Matrix, deSolve
Suggests: MGDrivE, knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 21:06:45 UTC; slwu89
Author: Sean L. Wu [aut, cre], Jared B. Bennett [aut], Héctor Manuel Sánchez Castellanos [ctb], Tomás M. León [ctb], Andrew J. Dolgert [ctb], John M. Marshall [aut]
Repository: CRAN
Date/Publication: 2020-10-24 09:30:03 UTC

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New package hetu with initial version 1.0.1
Package: hetu
Type: Package
Title: Structural Handling of Finnish Personal Identity Numbers
Version: 1.0.1
Encoding: UTF-8
Date: 2020-10-15
Authors@R: c( person("Pyry", "Kantanen", email = "pyry.kantanen@gmail.com", role = c("aut", "cre")), person("Mans", "Magnusson", role = "aut"), person("Jussi", "Paananen", role = "aut"), person("Leo", "Lahti", role = "aut") )
MailingList: rOpenGov <ropengov-forum@googlegroups.com>
Description: Structural handling of Finnish identity numbers (persons and companies); extract information, check ID validity and diagnostics.
License: BSD_2_clause + file LICENSE
VignetteBuilder: knitr
BugReports: https://github.com/ropengov/hetu/issues
URL: https://github.com/ropengov/hetu
Depends: R (>= 4.0.0)
Suggests: Cairo, checkmate, lubridate, dplyr, knitr, testthat, rmarkdown, covr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 07:51:07 UTC; pyrykantanen
Author: Pyry Kantanen [aut, cre], Mans Magnusson [aut], Jussi Paananen [aut], Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:10:02 UTC

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New package flipdownr with initial version 0.1.0
Package: flipdownr
Type: Package
Title: Implement a Countdown in 'RMarkdown' Documents and 'shiny' Applications
Version: 0.1.0
Authors@R: c( person("Mohamed El Fodil", "Ihaddaden", email = "ihaddaden.fodeil@gmail.com", role = c("aut", "cre")), person("Butcher", "Peter", role = c("ctb", "cph"), comment = "flipdown.js library developer"))
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Description: Allows the user to create a countdown in 'RMarkdown' documents and 'shiny' applications. The package is a wrapper of the 'JavaScript' library 'flipdown.js'. See <https://pbutcher.uk/flipdown/> for more info.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: htmltools, glue, jsonlite
URL: https://github.com/feddelegrand7/flipdownr
BugReports: https://github.com/feddelegrand7/flipdownr/issues
NeedsCompilation: no
Packaged: 2020-10-16 15:01:25 UTC; Administrateur
Author: Mohamed El Fodil Ihaddaden [aut, cre], Butcher Peter [ctb, cph] (flipdown.js library developer)
Repository: CRAN
Date/Publication: 2020-10-24 09:20:02 UTC

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New package APML with initial version 0.0.1
Package: APML
Type: Package
Title: An Approach for Machine-Learning Modelling
Version: 0.0.1
Authors@R: c(person("Xinlei","Deng",role=c("aut","cre","cph"),email="xdeng3@albany.edu"), person("Wangjian","Zhang",role="aut"), person("Shao","Lin",role="aut"))
Description: We include 1) data cleaning including variable scaling, missing values and unbalanced variables identification and removing, and strategies for variable balance improving; 2) modeling based on random forest and gradient boosted model including feature selection, model training, cross-validation and external testing. For more information, please see H2O.ai (Oct. 2016). R Interface for H2O, R package version 3.10.0.8. <https://github.com/h2oai/h2o-3>; Zhang W (2016). <doi:10.1016/j.scitotenv.2016.02.023>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: tidyverse,h2o,DMwR,dummies,dplyr,ggplot2,pROC,survival
NeedsCompilation: no
Packaged: 2020-10-08 15:51:07 UTC; xd129664
Author: Xinlei Deng [aut, cre, cph], Wangjian Zhang [aut], Shao Lin [aut]
Maintainer: Xinlei Deng <xdeng3@albany.edu>
Repository: CRAN
Date/Publication: 2020-10-24 09:20:05 UTC

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New package healthfinance with initial version 0.1.0
Package: healthfinance
Title: Financial Projections and Planning for Health Care Practices
Version: 0.1.0
Authors@R: c( person(given = "Raoul", family = "Wadhwa", role = c("aut", "cre"), email = "raoulwadhwa@gmail.com"), person(given = "Vigneshwar", family = "Subramanian", role = "aut", email = "vs347@cornell.edu"), person(given = "Milind", family = "Desai", role = "aut"))
Description: Provides a shiny interface for a free, open-source managerial accounting-like system for health care practices. This package allows health care administrators to project revenue with monthly adjustments and procedure-specific boosts up to a 3-year period. Granular data (patient-level) to aggregated data (department- or hospital-level) can all be used as valid inputs provided historical volume and revenue data is available. For more details on managerial accounting techniques, see Brewer et al. (2015, ISBN:9780078025792).
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: ggplot2 (>= 3.3), lubridate (>= 1.7), readr (>= 1.3), scales (>= 1.1), shiny (>= 1.4), tibble (>= 3.0)
RoxygenNote: 7.1.1
URL: https://rrrlw.github.io/healthfinance/
BugReports: https://github.com/rrrlw/healthfinance/issues
Suggests: testthat (>= 2.3)
NeedsCompilation: no
Packaged: 2020-10-15 20:13:27 UTC; appveyor
Author: Raoul Wadhwa [aut, cre], Vigneshwar Subramanian [aut], Milind Desai [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:00:02 UTC

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New package drought with initial version 1.0
Package: drought
Type: Package
Title: Statistical Modeling and Assessment of Drought
Version: 1.0
Date: 2020-10-10
Author: Zengchao Hao
Maintainer: Zengchao Hao <z.hao4univ@gmail.com>
Description: Provide tools for drought monitoring based on univariate and multivariate drought indicators.Statistical drought prediction based on Ensemble Streamflow Prediction (ESP) and drought risk assessments are also provided. Please see Hao Zengchao et al. (2017) <doi:10.1016/j.envsoft.2017.02.008>.
Depends: R (>= 3.5.0)
Imports: stats,copula
Suggests: MASS
License: GPL-3
LazyData: true
Repository: CRAN
RoxygenNote: 7.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-10-15 00:44:34 UTC; HAO
Date/Publication: 2020-10-24 08:30:02 UTC

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New package assert with initial version 1.0.0
Package: assert
Title: Validate Function Arguments
Version: 1.0.0
Authors@R: person(given = "Olivier", family = "Binette", role = c("aut", "cre", "cph"), email = "olivier.binette@gmail.com")
Description: Lightweight validation tool for checking function arguments and validating data analysis scripts. This is an alternative to stopifnot() from the 'base' package and to assert_that() from the 'assertthat' package. It provides more informative error messages and facilitates debugging.
Imports: rlang
URL: https://github.com/OlivierBinette/assert
BugReports: https://github.com/OlivierBinette/assert/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-15 14:09:04 UTC; olivierbinette
Author: Olivier Binette [aut, cre, cph]
Maintainer: Olivier Binette <olivier.binette@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 08:50:02 UTC

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New package anovir with initial version 0.1.0
Package: anovir
Type: Package
Title: Analysis of Virulence
Version: 0.1.0
Authors@R: c(person("Philip", "Agnew", email = "philip.agnew@ird.fr", role = c("aut", "cre")), person("Jimmy","Lopez", email = "jimmy.lopez@ird.fr", role = c("aut")))
Maintainer: Philip Agnew <philip.agnew@ird.fr>
Description: Epidemiological population dynamics models traditionally define a pathogen's virulence as the increase in the per capita rate of mortality of infected hosts due to infection. This package provides functions allowing virulence to be estimated by maximum likelihood techniques. The approach is based on the analysis of relative survival comparing survival in matching cohorts of infected vs. uninfected hosts (Agnew 2019) <doi:10.1101/530709>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: bbmle, R (>= 2.10), stats4
Suggests: knitr, rmarkdown, stats, testthat
Collate: 'anovir-package.R' 'private_functions.R' 'nll_recovery.R' 'nll_recovery_II.R' 'data_descriptions.R' 'main.R' 'play_file.R' 'nll_functions.R' 'nll_frailty_correlated.R'
VignetteBuilder: knitr
URL: https://www.biorxiv.org/content/10.1101/530709v1
NeedsCompilation: no
Packaged: 2020-10-15 16:10:52 UTC; philipagnew
Author: Philip Agnew [aut, cre], Jimmy Lopez [aut]
Repository: CRAN
Date/Publication: 2020-10-24 08:50:05 UTC

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New package acled.api with initial version 1.0.7
Package: acled.api
Title: Automated Retrieval of ACLED Conflict Event Data
Version: 1.0.7
Date: 2020-10-14
Authors@R: person(given = "Christoph", family = "Dworschak", role = c("aut", "cre"), email = "c.dworschak@essex.ac.uk", comment = c(ORCID = "0000-0003-0196-9545"))
Author: Christoph Dworschak [aut, cre] (<https://orcid.org/0000-0003-0196-9545>)
Maintainer: Christoph Dworschak <c.dworschak@essex.ac.uk>
Description: Access and manage the application programming interface (API) of the Armed Conflict Location & Event Data Project (ACLED) at <https://acleddata.com/>. It makes it easy to retrieve a user-defined sample (or all of the available data) of ACLED, enabling a seamless integration of regular data updates into the research work flow. When using this package, you acknowledge that you have read ACLED's terms and conditions of use, and that you agree with their attribution requirements.
License: CC BY-NC 4.0
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.1.1
Imports: httr, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-15 12:35:11 UTC; root
Repository: CRAN
Date/Publication: 2020-10-24 08:40:02 UTC

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Fri, 23 Oct 2020

New package MPGE with initial version 1.0.0
Package: MPGE
Type: Package
Title: A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes
Version: 1.0.0
Date: 2020-10-14
Authors@R: c(person("Arunabha", "Majumdar", email = "statgen.arunabha@gmail.com", role = c("aut", "cre")), person("Tanushree", "Haldar", email = "tanushree.haldar@gmail.com", role = "aut"))
Description: Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1101/2020.07.06.190256>.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/ArunabhaCodes/MPGE
BugReports: https://github.com/ArunabhaCodes/MPGE/issues
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: car, purrr, stats, utils
NeedsCompilation: no
Packaged: 2020-10-14 20:45:02 UTC; arunmacpro13
Author: Arunabha Majumdar [aut, cre], Tanushree Haldar [aut]
Maintainer: Arunabha Majumdar <statgen.arunabha@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-23 15:40:07 UTC

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New package EnvExpInd with initial version 0.1.0
Package: EnvExpInd
Type: Package
Title: Environmental Exposure on the Individual Level
Imports: gstat,RCurl,dplyr,stringi,sp,maptools,zoo
Version: 0.1.0
Depends: R(>= 3.5.0)
Authors@R: person("Bing","Zhang", role = c("aut", "cre"), email = "zhangb269@mail2.sysu.edu.cn")
Description: Tools for the assessment of the environmental exposure. The package provides three methods (nearest monitoring site, inverse distance weighted as described in Li Wu (2017) <doi:10.1016/j.envint.2016.11.013>,and ordinary kriging) to calculate the environmental exposure (e.g. air pollution) on the individual level.
URL: https://github.com/Spatial-R/EnvExpInd
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-15 00:26:49 UTC; spatialr
Author: Bing Zhang [aut, cre]
Maintainer: Bing Zhang <zhangb269@mail2.sysu.edu.cn>
Repository: CRAN
Date/Publication: 2020-10-23 15:50:02 UTC

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New package scoringTools with initial version 0.1.0
Package: scoringTools
Type: Package
Title: Credit Scoring Tools
Version: 0.1.0
Date: 2020-10-06
Authors@R: c(person("Adrien", "Ehrhardt", email = "adrien.ehrhardt@centraliens-lille.org", role = c("aut", "cre")))
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@centraliens-lille.org>
Description: Grouping essential tools for credit scoring. These statistical tools may be useful for other use-cases as well but were primarily designed for it. First, there are Reject Inference methods (Ehrhardt et al. (2017) <arXiv:1903.10855>). Second, we build upon the already CRAN-available package 'discretization' to automate discretization of continuous features.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: discretization, sqldf, magrittr, dplyr, methods
Suggests: MASS, rpart, Rmixmod, mvtnorm, ggplot2, speedglm, knitr, rmarkdown, plotly, pROC, shiny, testthat, covr
URL: https://adimajo.github.io/scoringTools/
BugReports: https://github.com/adimajo/scoringTools/issues
VignetteBuilder: knitr
Collate: 'allClasses.R' 'allMethods.R' 'augmentation.R' 'check_consistency.R' 'chi2.R' 'chiM.R' 'cut.dataset.R' 'data.R' 'discretize.cutp.R' 'echi2.R' 'fuzzyAugmentation.R' 'get_cutp.R' 'mdlp.R' 'modChi2.R' 'model_f.R' 'normalizedGini.R' 'parcelling.R' 'reclassification.R' 'runDemo.R' 'scoring.R' 'topdown.R' 'twins.R'
NeedsCompilation: no
Packaged: 2020-10-14 14:20:14 UTC; adimajo
Author: Adrien Ehrhardt [aut, cre]
Repository: CRAN
Date/Publication: 2020-10-23 10:30:02 UTC

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New package deepredeff with initial version 0.1.0
Package: deepredeff
Title: Deep Learning Prediction of Effectors
Version: 0.1.0
Authors@R: person(given = "Ruth", family = "Kristianingsih", role = c("aut", "cre", "cph"), email = "ruth.kristianingsih30@gmail.com", comment = c(ORCID = "0000-0003-1873-6203"))
Description: A tool that contains trained deep learning models for predicting effector proteins. 'deepredeff' has been trained to identify effector proteins using a set of known experimentally validated effectors from either bacteria, fungi, or oomycetes. Documentation is available via several vignettes, and the paper by Kristianingsih and MacLean (2020) <doi:10.1101/2020.07.08.193250>.
License: MIT + file LICENSE
URL: https://github.com/ruthkr/deepredeff/
BugReports: https://github.com/ruthkr/deepredeff/issues/
Depends: R (>= 2.10)
Imports: Biostrings, dplyr, ggplot2, ggthemes, keras, magrittr, purrr, reticulate, rlang, seqinr, tensorflow
Suggests: covr, kableExtra, knitr, rmarkdown, stringr, testthat
VignetteBuilder: knitr
biocViews:
Config/reticulate: list( packages = list( list(package = "tensorflow", version = "2.0.0", pip = FALSE) ) )
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-14 15:23:40 UTC; ruth
Author: Ruth Kristianingsih [aut, cre, cph] (<https://orcid.org/0000-0003-1873-6203>)
Maintainer: Ruth Kristianingsih <ruth.kristianingsih30@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-23 10:30:06 UTC

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Thu, 22 Oct 2020

New package labstatR with initial version 1.0.11
Package: labstatR
Version: 1.0.11
Date: 2020-10-22
Title: Libreria Del Laboratorio Di Statistica Con R
Author: Stefano M.Iacus <stefano.iacus@unimi.it> and Guido Masarotto <guido@sirio.stat.unipd.it>
Maintainer: Stefano M.Iacus <stefano.iacus@unimi.it>
Description: Insieme di funzioni di supporto al volume "Laboratorio di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006. This package contains sets of functions defined in "Laboratorio di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006. Function names and docs are in italian as well.
License: GPL (>= 2)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-10-22 21:24:15 UTC; jago
Repository: CRAN
Date/Publication: 2020-10-22 21:40:02 UTC

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New package eefAnalytics with initial version 1.0.8
Package: eefAnalytics
Version: 1.0.8
Date: 2020-10-14
Title: Robust Analytical Methods for Evaluating Educational Interventions using Randomised Controlled Trials Designs
Description: The eefAnalytics provides tools for analysing data from evaluations of educational interventions using a randomised controlled trial designs. It provides analytical tools to perform sensitivity analysis using different methods(e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The functions contained in this package can be used for simple individual randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other interventions designs using Frequentist and Bayesian multilevel models.
Author: Germaine Uwimpuhwe, Akansha Singh, Steve Higgins, ZhiMin Xiao, Ewoud De Troyer and Adetayo Kasim
Maintainer: Germaine Uwimpuhwe <germaine.uwimpuhwe@durham.ac.uk>
Imports: lme4, mvtnorm, metafor, graphics, stats, rstanarm
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/germaine86/eefAnalytics
BugReports: https://github.com/germaine86/eefAnalytics/issues
NeedsCompilation: no
Packaged: 2020-10-20 16:44:20 UTC; germu
Repository: CRAN
Date/Publication: 2020-10-22 21:40:05 UTC

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New package abn with initial version 2.3-0
Package: abn
Version: 2.3-0
Date: 2020-10-20
Title: Modelling Multivariate Data with Additive Bayesian Networks
Authors@R: c(person(given = "Gilles", family = "Kratzer", role = c("aut", "cre"), email = "gilles.kratzer@gmail.com", comment = c(ORCID = "0000-0002-5929-8935")), person(given = "Fraser Ian", family = "Lewis", role = "aut", email = "fraseriain.lewis@uzh.ch"), person(given = "Reinhard", family = "Furrer", role = "ctb", email = "reinhard.furrer@math.uzh.ch", comment = c(ORCID = "0000-0002-6319-2332")), person(given = "Marta", family = "Pittavino", role = "ctb", email = "marta.pittavino@math.uzh.ch", comment = c(ORCID = "0000-0002-1232-1034")))
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>), Fraser Ian Lewis [aut], Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>), Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@gmail.com>
Imports: methods, rjags
LinkingTo: Rcpp, RcppArmadillo
Depends: nnet, lme4, R (>= 4.0.0)
Suggests: INLA, Rgraphviz, knitr, R.rsp, testthat, entropy, moments, boot, brglm
VignetteBuilder: R.rsp
Additional_repositories: https://inla.r-inla-download.org/R/stable/
SystemRequirements: Gnu Scientific Library version >= 1.12
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. The computing library JAGS <http://mcmc-jags.sourceforge.net/> is used to simulate 'abn'-like data. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website <http://r-bayesian-networks.org>.
License: GPL (>= 2)
LazyData: true
URL: http://r-bayesian-networks.org
BugReports: https://git.math.uzh.ch/reinhard.furrer/abn/-/issues
NeedsCompilation: yes
Packaged: 2020-10-20 12:36:42 UTC; furrer
Repository: CRAN
Date/Publication: 2020-10-22 21:30:02 UTC

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New package not with initial version 1.2
Package: not
Type: Package
Title: Narrowest-Over-Threshold Change-Point Detection
Version: 1.2
Date: 2019-06-30
Author: Rafal Baranowski, Yining Chen, Piotr Fryzlewicz
Maintainer: Rafal Baranowski <package_maintenance@rbaranowski.com>
Depends: graphics, stats, splines
Description: Provides efficient implementation of the Narrowest-Over-Threshold methodology for detecting an unknown number of change-points occurring at unknown locations in one-dimensional data following deterministic signal + noise model, see R. Baranowski, Y. Chen and P. Fryzlewicz (2019) <doi:10.1111/rssb.12322>. Currently implemented scenarios are: piecewise-constant signal, piecewise-constant signal with a heavy-tailed noise, piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal and with piecewise-constant variance of the noise.
License: GPL-2
NeedsCompilation: yes
Packaged: 2019-06-30 21:16:47 UTC; rafal
Repository: CRAN
Date/Publication: 2019-07-04 22:20:09

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New package klsh with initial version 0.1.0
Package: klsh
Type: Package
Title: Blocking for Record Linkage
Version: 0.1.0
Authors@R: person("Rebecca", "Steorts", email = "beka@stat.duke.edu", role = c("aut", "cre"))
Depends: R (>= 3.0.2), blink, stats, utils, plyr
Imports: Rcpp, stringi, SnowballC
Suggests: knitr, ggplot2, rmarkdown
VignetteBuilder: knitr
Description: An implementation of the blocking algorithm KLSH in Steorts, Ventura, Sadinle, Fienberg (2014) <DOI:10.1007/978-3-319-11257-2_20>, which is a k-means variant of locality sensitive hashing. The method is illustrated with examples and a vignette.
Encoding: UTF-8
LazyData: true
License: GPL-3
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-10-14 10:06:18 UTC; rebeccasteorts
Author: Rebecca Steorts [aut, cre]
Maintainer: Rebecca Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-22 15:20:02 UTC

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New package comsimitv with initial version 0.1.4
Package: comsimitv
Type: Package
Title: Flexible Framework for Simulating Community Assembly
Version: 0.1.4
Author: Zoltan Botta-Dukat
Maintainer: Zoltan Botta-Dukat <botta-dukat.zoltan@okologia.mta.hu>
Description: Flexible framework for trait-based simulation of community assembly, where components could be replaced by user-defined function and that allows variation of traits within species.
Imports: MASS, vegan
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat, bookdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-14 12:25:32 UTC; xy
Repository: CRAN
Date/Publication: 2020-10-22 15:30:02 UTC

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New package BlackCarbon with initial version 0.1.0
Package: BlackCarbon
Type: Package
Title: Processing Raw Black Carbon Concentration
Version: 0.1.0
Author: Sanjeev Bista <sanjeev.bista1@gmail.com>
Maintainer: Sanjeev Bista <sanjeev.bista1@gmail.com>
Description: The functions in this package are designed to be used in the processing of black carbon concentration collected by a specific type of a personal monitor. The package includes functions for processing of the data by applying Optimized noise reduction averaging algorithm along with filter loading correction and with an option of filter change adjustment.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-10-14 08:15:07 UTC; Sanjeev
Repository: CRAN
Date/Publication: 2020-10-22 15:10:02 UTC

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New package aceEditor with initial version 0.1.0
Package: aceEditor
Title: The 'Ace' Editor as a HTML Widget
Version: 0.1.0
Authors@R: c( person( "Stéphane", "Laurent", role = c("aut", "cre"), email = "laurent_step@outlook.fr" ), person( "James", "Hrisho", role = c("ctb", "cph"), comment = "'react-ace' library" ), person( "James Long and contributors", role = c("ctb", "cph"), comment = "'Prettier' library" ), person( "Zeb", "Zhao", role = c("ctb","cph"), comment = "'indent.js' library" ), person( "jQuery contributors", role = c("ctb", "cph"), comment = "'jQuery' library" ), person( list("Tristan", "Limon"), list("Edwards", "Monte"), role = c("ctb", "cph"), comment = "'sweetalert2' library" ) )
Description: Wraps the 'Ace' editor in a HTML widget. The 'Ace' editor has support for many languages. It can be opened in the viewer pane of 'RStudio', and this provides a second source editor.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: htmltools, htmlwidgets, reactR, rstudioapi, tools
URL: https://github.com/stla/aceEditor
BugReports: https://github.com/stla/aceEditor/issues
NeedsCompilation: no
Packaged: 2020-10-14 08:37:29 UTC; stla
Author: Stéphane Laurent [aut, cre], James Hrisho [ctb, cph] ('react-ace' library), James Long and contributors [ctb, cph] ('Prettier' library), Zeb Zhao [ctb, cph] ('indent.js' library), jQuery contributors [ctb, cph] ('jQuery' library), Tristan Edwards [ctb, cph] ('sweetalert2' library), Limon Monte [ctb, cph] ('sweetalert2' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2020-10-22 15:20:05 UTC

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New package wsjplot with initial version 0.1.0
Package: wsjplot
Version: 0.1.0
Title: Style Time Series Plots Like the Wall Street Journal
Description: Easily override the default visual choices in 'ggplot2' to make your time series plots look more like the Wall Street Journal. Specific theme design choices include omitting x-axis grid lines and displaying sparse light grey y-axis grid lines. Additionally, this allows to label the y-axis scales with your units only displayed on the top-most number, while also removing the bottom most number (unless specifically overridden). The goal is visual simplicity, because who has time to waste looking at a cluttered graph?
Authors@R: person("Stephen", "Lee", email = "smlee.981@gmail.com", role = c("aut", "cre") )
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: ggplot2, magrittr, stringr, scales, dplyr
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-13 15:56:14 UTC; smlee
Author: Stephen Lee [aut, cre]
Maintainer: Stephen Lee <smlee.981@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-22 09:10:02 UTC

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New package thorn with initial version 0.1.0
Package: thorn
Type: Package
Title: 'HTMLwidgets' Displaying Some 'WebGL' Shaders
Version: 0.1.0
Authors@R: c( person( "Stéphane", "Laurent", role = c("aut", "cre"), email = "laurent_step@outlook.fr" ), person( "Scott", "Boyle", role = c("ctb", "cph"), comment = "'Hamster.js' library" ), person( list("Mathew", "Chad"), list("Groves", "Engler"), role = c("ctb", "cph"), comment = "'PixiJS' library" ) )
Description: Creates some 'WebGL' shaders. They can be used as the background of a 'Shiny' app. They also can be visualized in the 'RStudio' viewer pane or included in 'Rmd' documents, but this is pretty useless, besides contemplating them.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: htmlwidgets
Suggests: shiny, htmltools
URL: https://github.com/stla/thorn
BugReports: https://github.com/stla/thorn/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-13 20:15:49 UTC; stla
Author: Stéphane Laurent [aut, cre], Scott Boyle [ctb, cph] ('Hamster.js' library), Mathew Groves [ctb, cph] ('PixiJS' library), Chad Engler [ctb, cph] ('PixiJS' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2020-10-22 09:30:02 UTC

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New package smd with initial version 0.6.6
Package: smd
Type: Package
Title: Compute Standardized Mean Differences
Version: 0.6.6
Authors@R: c(person("Bradley", "Saul", role = c("aut", "cre"), email = "bsaul@novisci.com"), person("Alex", "Breskin", role = c("ctb"), email = "abreskin@novisci.com"), person("Catie", "Wiener", role = c("ctb"), email = "cwiener@novisci.com"), person("Matt", "Phelan", role = c("ctb"), email = "mphelan@novisci.com"))
Description: Computes standardized mean differences and confidence intervals for multiple data types based on Yang, D., & Dalton, J. E. (2012) <http://www.lerner.ccf.org/qhs/software/lib/stddiff.pdf>.
Imports: MASS (>= 7.3-50), methods (>= 3.5.1)
Suggests: testthat, stddiff, tableone, knitr, dplyr, purrr, markdown, rmarkdown
License: MIT + file LICENSE
URL: https://docs.novisci.com/smd/
BugReports: https://gitlab.novisci.com/nsstat/smd/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Repository: CRAN
NeedsCompilation: no
Packaged: 2020-10-13 20:13:52 UTC; bsaul
Author: Bradley Saul [aut, cre], Alex Breskin [ctb], Catie Wiener [ctb], Matt Phelan [ctb]
Maintainer: Bradley Saul <bsaul@novisci.com>
Date/Publication: 2020-10-22 09:20:02 UTC

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New package mbmixture with initial version 0.2-5
Package: mbmixture
Version: 0.2-5
Date: 2020-10-13
Title: Microbiome Mixture Analysis
Description: Evaluate whether a microbiome sample is a mixture of two samples, by fitting a model for the number of read counts as a function of single nucleotide polymorphism (SNP) allele and the genotypes of two potential source samples. Lobo et al. (2019) <doi:10.1101/529040>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl W Broman <broman@wisc.edu>
Authors@R: c(person("Karl W", "Broman", role=c("aut", "cre"), email="broman@wisc.edu", comment=c(ORCID = "0000-0002-4914-6671")))
Depends: R (>= 3.1.0)
Imports: stats, parallel, numDeriv
Suggests: knitr, rmarkdown, testthat, devtools, roxygen2
License: MIT + file LICENSE
URL: https://github.com/kbroman/mbmixture
BugReports: https://github.com/kbroman/mbmixture/issues
VignetteBuilder: knitr
LazyData: true
Encoding: UTF-8
ByteCompile: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-13 15:07:06 UTC; kbroman
Repository: CRAN
Date/Publication: 2020-10-22 09:10:05 UTC

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New package inti with initial version 0.1.0
Package: inti
Type: Package
Version: 0.1.0
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and technical writing (rtciles()). Learn more about the 'inkaverse' project at <https://inkaverse.com/apps/>.
Date: 2020-09-30
Authors@R: person("Flavio", "Lozano-Isla", email = "flavjack@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0714-669X"))
URL: https://github.com/flavjack/inti/
BugReports: https://github.com/flavjack/inti/issues
Depends: shiny, ggplot2, dplyr, tidyr, tibble
biocViews:
Imports: lme4, agricolae, FactoMineR, purrr, stringr, DT, emmeans, multtest
Suggests: agridat, googlesheets4, corrplot, knitr, rmarkdown, testthat
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-30 18:43:17 UTC; User
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-22 09:40:06 UTC

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New package gaussplotR with initial version 0.1.4
Package: gaussplotR
Type: Package
Title: Predict and Plot 2D Gaussians
Version: 0.1.4
Authors@R: person(given = "Vikram B.", family = "Baliga", role = c("aut", "cre", "cph"), email = "vbaliga87@gmail.com", comment = c(ORCID = "0000-0002-9367-8974") )
Description: Functions to predict values from a two-dimensional Gaussian function and produce plots of predicted data via either 'ggplot2' or base R plotting.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
Imports: ggplot2 (>= 3.3.0), metR (>= 0.7.0)
Suggests: lattice, knitr, rmarkdown
Depends: R (>= 2.10)
URL: https://github.com/vbaliga/gaussplotR
BugReports: https://github.com/vbaliga/gaussplotR/issues
NeedsCompilation: no
Packaged: 2020-10-14 02:24:20 UTC; thalassoma
Author: Vikram B. Baliga [aut, cre, cph] (<https://orcid.org/0000-0002-9367-8974>)
Maintainer: Vikram B. Baliga <vbaliga87@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-22 09:40:10 UTC

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New package findInFiles with initial version 0.1.0
Package: findInFiles
Type: Package
Title: Find Pattern in Files
Version: 0.1.0
Authors@R: c( person( "Stéphane", "Laurent", role = c("aut", "cre"), email = "laurent_step@outlook.fr" ), person( "Rob", "Burns", role = c("ctb", "cph"), comment = "'ansi-to-html' library" ) )
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given folder. The results can be viewed in the 'RStudio' viewer pane, included in a 'R Markdown' document or in a 'Shiny' app.
License: GPL-3
Encoding: UTF-8
LazyData: true
SystemRequirements: grep
Imports: htmlwidgets
Suggests: shiny
URL: https://github.com/stla/findInFiles
BugReports: https://github.com/stla/findInFiles/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-13 20:21:01 UTC; stla
Author: Stéphane Laurent [aut, cre], Rob Burns [ctb, cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2020-10-22 09:30:05 UTC

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New package bggAnalytics with initial version 0.1.1
Package: bggAnalytics
Type: Package
Title: BoardGameGeek's Board Game Data Analysis Tools
Description: Tools for analysing board game data. Mainly focused on providing an interface for BoardGameGeek's XML API2 through R6 class system objects. More details about the BoardGameGeek's API can be obtained here <https://boardgamegeek.com/wiki/page/BGG_XML_API2>.
Version: 0.1.1
Author: Jakub Bujnowicz [aut, cre]
Maintainer: Jakub Bujnowicz <bujnowiczgithub@gmail.com>
URL: https://github.com/JakubBujnowicz/bggAnalytics
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Language: en-GB
Imports: assertthat, pryr, rvest, stringr, utils, xml2
Depends: R (>= 4.0.0), data.table, R6
Collate: 'assertions.R' 'class_utils.R' 'bggAPI.R' 'bggAnalytics-package.R' 'bggCollection.R' 'bggGames.R' 'bggSearch.R' 'bgg_tools.R' 'custom_fetches.R' 'data.R' 'h_index.R' 'html_utils.R' 'params_utils.R' 'squeeze.R' 'utils.R' 'zzz.R'
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-13 16:50:15 UTC; User
Repository: CRAN
Date/Publication: 2020-10-22 09:20:05 UTC

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New package restaurant with initial version 0.1.0
Package: restaurant
Title: Restaurant Data for Entity Resolution
Version: 0.1.0
Authors@R: c(person("Rebecca", "Steorts", email= "beka@stat.duke.edu", role=c("aut", "cre")), person("Andee", "Kaplan", email= "andrea.kaplan@duke.edu", role="aut"), person("Srini", "Sunil", email="srinivas.sunil@duke.edu", role="aut"))
Description: Duplicated restaurant data (pre-processed and formatted) for entity resolution. This package contains formatted data from a data set that contains information about different restaurants, with the Zagats portion containing 331 records and the Fodors portion containing 533 records. The following variables are included in the data set: id, name, address, city, phone, type. The data set has a respective gold data set that provides information on which records match based on id.
URL: https://github.com/resteorts/restaurant
BugReports: https://github.com/resteorts/restaurant/issues
Depends: R (>= 3.4.0)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-10-13 13:56:58 UTC; rebeccasteorts
Author: Rebecca Steorts [aut, cre], Andee Kaplan [aut], Srini Sunil [aut]
Maintainer: Rebecca Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-22 08:50:02 UTC

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New package PAMmisc with initial version 1.6.3
Package: PAMmisc
Title: Miscellaneous Functions for Passive Acoustic Analysis
Version: 1.6.3
Authors@R: c( TS = person("Taiki", "Sakai", email = "taiki.sakai@noaa.gov", role = c("aut", "cre")), JB = person("Jay", "Barlow", role = c("ctb")), JO = person("Julie", "Oswald", role = c("ctb")))
Description: A collection of miscellaneous functions for passive acoustics. Much of the content here is adapted to R from code written by other people. If you have any ideas of functions to add, please contact Taiki Sakai.
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: ggplot2, tuneR, seewave, dplyr, magrittr, RcppRoll, PamBinaries, RSQLite, lubridate, rerddap, ncdf4, httr, purrr, plotKML, hoardr, methods, geosphere, tcltk
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-13 14:08:51 UTC; Taiki.Sakai
Author: Taiki Sakai [aut, cre], Jay Barlow [ctb], Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2020-10-22 09:00:05 UTC

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New package cd with initial version 0.1.0
Package: cd
Title: CD Data for Entity Resolution
Version: 0.1.0
Authors@R: c(person("Rebecca", "Steorts", email= "beka@stat.duke.edu", role=c("aut", "cre")), person("Andee", "Kaplan", email= "andrea.kaplan@duke.edu", role="aut"), person("Srini.", "Sunil", email="srinivas.sunil@duke.edu", role="aut"))
Description: Duplicated music data (pre-processed and formatted) for entity resolution. The total size of the data set is 9763. There are respective gold standard records that are labeled and can be considered as a unique identifier.
URL: https://github.com/resteorts/cd
BugReports: https://github.com/resteorts/cd/issues
Depends: R (>= 3.4.0)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-10-13 13:54:30 UTC; rebeccasteorts
Author: Rebecca Steorts [aut, cre], Andee Kaplan [aut], Srini. Sunil [aut]
Maintainer: Rebecca Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-22 08:40:02 UTC

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New package biogrowth with initial version 0.1.0
Package: biogrowth
Type: Package
Title: Modelling of Microbial Growth
Version: 0.1.0
Authors@R: c(person("Alberto", "Garre", email = "garre.alberto@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4404-3550")), person("Jeroen", "Koomen", email = "jeroen.koomen@wur.nl", role = "aut"), person("Heidy", "den Besten", email = "heidy.denbesten@wur.nl", role = "aut"), person("Marcel", "Zwietering", email = "marcel.zwietering@wur.nl", role = "aut") )
Description: Modelling of microbial growth under isothermal and dynamic conditions. Includes functions for model fitting and making prediction under isothermal and dynamic conditions using methods (algorithms & models) common in predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: deSolve (>= 1.28), tibble (>= 3.0.3), dplyr (>= 0.8.5), FME (>= 1.3.6), MASS (>= 7.3), rlang (>= 0.4.7), purrr (>= 0.3.4), ggplot2 (>= 3.3.2), cowplot (>= 1.0.0)
Suggests: knitr, rmarkdown, tidyverse (>= 1.3.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-10-13 14:29:21 UTC; alberto
Author: Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>), Jeroen Koomen [aut], Heidy den Besten [aut], Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-22 08:50:04 UTC

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New package asymptor with initial version 0.2
Package: asymptor
Title: Estimate Asymptomatic Cases via Capture/Recapture Methods
Version: 0.2
Authors@R: person(given = "Hugo", family = "Gruson", role = c("cre", "aut", "cph"), email = "hugo.gruson+R@normalesup.org", comment = c(ORCID = "0000-0002-4094-1476"))
Description: Estimate the lower and upper bound of asymptomatic cases in an epidemic using the capture/recapture methods from Böhning et al. (2020) <doi:10.1016/j.ijid.2020.06.009> and Rocchetti et al. (2020) <doi:10.1101/2020.07.14.20153445>.
License: GPL-3
URL: https://bisaloo.github.io/asymptor/, https://github.com/bisaloo/asymptor
BugReports: https://github.com/bisaloo/asymptor/issues
Depends: R (>= 3.5)
Suggests: covr, ggplot2, knitr, rmarkdown, spelling, testthat
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-13 14:48:52 UTC; hugo
Author: Hugo Gruson [cre, aut, cph] (<https://orcid.org/0000-0002-4094-1476>)
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Repository: CRAN
Date/Publication: 2020-10-22 09:00:02 UTC

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Tue, 20 Oct 2020

New package ripserr with initial version 0.1.1
Package: ripserr
Title: Calculate Persistent Homology with Ripser-Based Engines
Version: 0.1.1
Authors@R: c(person(given = "Raoul", family = "Wadhwa", role = c("aut", "cre"), email = "raoulwadhwa@gmail.com", comment = c(ORCID = "0000-0003-0503-9580")), person(given = "Matt", family = "Piekenbrock", role = "aut", email = "matt.piekenbrock@gmail.com"), person(given = "Jacob", family = "Scott", role = "aut", comment = c(ORCID = "0000-0003-2971-7673")), person(given = "Takeki", family = "Sudo", role = c("cph", "ctb"), comment = paste("Takeki Sudo is a copyright holder for Cubical", "Ripser (GPL-3 license), which was refactored", "prior to inclusion in ripserr.")), person(given = "Kazushi", family = "Ahara", role = c("cph", "ctb"), comment = paste("Kazushi Ahara is a copyright holder for Cubical", "Ripser (GPL-3 license), which was refactored", "prior to inclusion in ripserr.")), person(given = "Ulrich", family = "Bauer", role = c("cph", "ctb"), comment = paste("Ulrich Bauer holds the copyright to Ripser", "(MIT license), which was refactored prior", "to inclusion in ripserr.")))
Description: Ports the Ripser <arXiv:1908.02518> and Cubical Ripser <arXiv:2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://rrrlw.github.io/ripserr/
BugReports: https://github.com/rrrlw/ripserr/issues
LinkingTo: Rcpp
Depends: R (>= 3.5.0)
Imports: methods (>= 3.0), Rcpp (>= 1.0), stats (>= 3.0)
SystemRequirements: C++11
Suggests: testthat (>= 2.3), covr (>= 3.5), knitr (>= 1.29), rmarkdown (>= 2.3)
NeedsCompilation: yes
Packaged: 2020-10-15 10:51:01 UTC; appveyor
Author: Raoul Wadhwa [aut, cre] (<https://orcid.org/0000-0003-0503-9580>), Matt Piekenbrock [aut], Jacob Scott [aut] (<https://orcid.org/0000-0003-2971-7673>), Takeki Sudo [cph, ctb] (Takeki Sudo is a copyright holder for Cubical Ripser (GPL-3 license), which was refactored prior to inclusion in ripserr.), Kazushi Ahara [cph, ctb] (Kazushi Ahara is a copyright holder for Cubical Ripser (GPL-3 license), which was refactored prior to inclusion in ripserr.), Ulrich Bauer [cph, ctb] (Ulrich Bauer holds the copyright to Ripser (MIT license), which was refactored prior to inclusion in ripserr.)
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 20:10:03 UTC

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New package animint2 with initial version 2020.9.18
Package: animint2
Title: Animated Interactive Grammar of Graphics
Version: 2020.9.18
URL: https://github.com/tdhock/animint2
BugReports: https://github.com/tdhock/animint2/issues
Authors@R: c( person("Toby", "Hocking", email="toby.hocking@r-project.org", role=c("aut", "cre"), comment="Original animint code"), person("Hadley", "Wickham", role=c("aut"), comment="Forked ggplot2 code"), person("Winston", "Chang", role="aut", comment="Forked ggplot2 code"), person("RStudio", role = c("cph"), comment="Forked ggplot2 code"), person("Nicholas", "Lewin-Koh", role="aut", comment="hexGrob"), person("Martin", "Maechler", role="aut", comment="hexGrob"), person("Randall", "Prium", role="aut", comment="cut_width"), person("Susan", "VanderPlas", role="aut", comment="Animint GSOC 2013"), person("Carson", "Sievert", role="aut", comment="Animint GSOC 2014"), person("Kevin", "Ferris", role="aut", comment="Animint GSOC 2015"), person("Jun", "Cai", role="aut", comment="Animint GSOC 2015"), person("Faizan", "Khan", role="aut", comment="Animint GSOC 2016-2017"), person("Vivek", "Kumar", role="aut", comment="Animint GSOC 2018"), person("Himanshu", "Singh", role="aut", comment="Animint2 GSoC 2020"))
Description: Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Depends: R (>= 3.4.0)
Imports: digest, RJSONIO, grid, gtable (>= 0.1.1), MASS, plyr (>= 1.7.1), reshape2, scales (>= 0.4.1), stats, tibble, lazyeval, knitr (>= 1.5.33)
Suggests: servr, gistr (>= 0.2), shiny, htmltools, rmarkdown, testthat, devtools, httr, maps, ggplot2movies, hexbin, Hmisc, lattice, mapproj, maptools, mgcv, nlme, quantreg, rpart, svglite
Enhances: sp
License: GPL-3
Encoding: UTF-8
LazyData: true
Collate: 'gganimintproto.r' 'aaa-.r' 'aes-calculated.r' 'aes-colour-fill-alpha.r' 'aes-group-order.r' 'aes-linetype-size-shape.r' 'aes-position.r' 'utilities.r' 'aes.r' 'legend-draw.r' 'geom-.r' 'annotation-custom.r' 'annotation-logticks.r' 'geom-polygon.r' 'geom-map.r' 'annotation-map.r' 'geom-raster.r' 'annotation-raster.r' 'annotation.r' 'autoplot.r' 'bench.r' 'bin.R' 'coord-.r' 'coord-cartesian-.r' 'coord-fixed.r' 'coord-flip.r' 'coord-map.r' 'coord-munch.r' 'coord-polar.r' 'coord-quickmap.R' 'coord-transform.r' 'data.R' 'facet-.r' 'facet-grid-.r' 'facet-labels.r' 'facet-layout.r' 'facet-locate.r' 'facet-null.r' 'facet-viewports.r' 'facet-wrap.r' 'fortify-lm.r' 'fortify-map.r' 'fortify-spatial.r' 'fortify.r' 'stat-.r' 'geom-abline.r' 'geom-rect.r' 'geom-bar.r' 'geom-bin2d.r' 'geom-blank.r' 'geom-boxplot.r' 'geom-path.r' 'geom-contour.r' 'geom-count.r' 'geom-crossbar.r' 'geom-segment.r' 'geom-curve.r' 'geom-defaults.r' 'geom-ribbon.r' 'geom-density.r' 'geom-density2d.r' 'geom-dotplot.r' 'geom-errorbar.r' 'geom-errorbarh.r' 'geom-freqpoly.r' 'geom-hex.r' 'geom-histogram.r' 'geom-hline.r' 'geom-jitter.r' 'geom-label.R' 'geom-linerange.r' 'geom-point.r' 'geom-pointrange.r' 'geom-quantile.r' 'geom-rug.r' 'geom-smooth.r' 'geom-spoke.r' 'geom-text.r' 'geom-tile.r' 'geom-violin.r' 'geom-vline.r' 'ggplot2.r' 'grob-absolute.r' 'grob-dotstack.r' 'grob-null.r' 'grouping.r' 'guide-colorbar.r' 'guide-legend.r' 'guides-.r' 'guides-axis.r' 'guides-grid.r' 'hexbin.R' 'labels.r' 'layer.r' 'limits.r' 'margins.R' 'panel.r' 'plot-build.r' 'plot-construction.r' 'plot-last.r' 'plot.r' 'position-.r' 'position-collide.r' 'position-dodge.r' 'position-fill.r' 'position-identity.r' 'position-jitter.r' 'position-jitterdodge.R' 'position-nudge.R' 'position-stack.r' 'quick-plot.r' 'range.r' 'save.r' 'scale-.r' 'scale-alpha.r' 'scale-brewer.r' 'scale-continuous.r' 'scale-date.r' 'scale-discrete-.r' 'scale-gradient.r' 'scale-grey.r' 'scale-hue.r' 'scale-identity.r' 'scale-linetype.r' 'scale-manual.r' 'scale-shape.r' 'scale-size.r' 'scale-type.R' 'scales-.r' 'stat-bin.r' 'stat-bin2d.r' 'stat-bindot.r' 'stat-binhex.r' 'stat-boxplot.r' 'stat-contour.r' 'stat-count.r' 'stat-density-2d.r' 'stat-density.r' 'stat-ecdf.r' 'stat-ellipse.R' 'stat-function.r' 'stat-identity.r' 'stat-qq.r' 'stat-quantile.r' 'stat-smooth-methods.r' 'stat-smooth.r' 'stat-sum.r' 'stat-summary-2d.r' 'stat-summary-bin.R' 'stat-summary-hex.r' 'stat-summary.r' 'stat-unique.r' 'stat-ydensity.r' 'summary.r' 'theme-defaults.r' 'theme-elements.r' 'theme.r' 'translate-qplot-ggplot.r' 'translate-qplot-lattice.r' 'utilities-break.r' 'utilities-grid.r' 'utilities-help.r' 'utilities-matrix.r' 'utilities-resolution.r' 'utilities-table.r' 'uu_zxx.r' 'uu_zzz.r' 'z_animint.R' 'z_animintHelpers.R' 'z_facets.R' 'z_geoms.R' 'z_gist.R' 'z_helperFunctions.R' 'z_knitr.R' 'z_print.R' 'z_scales.R' 'z_theme_animint.R' 'z_transformShape.R'
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-19 22:51:31 UTC; tdhock
Author: Toby Hocking [aut, cre] (Original animint code), Hadley Wickham [aut] (Forked ggplot2 code), Winston Chang [aut] (Forked ggplot2 code), RStudio [cph] (Forked ggplot2 code), Nicholas Lewin-Koh [aut] (hexGrob), Martin Maechler [aut] (hexGrob), Randall Prium [aut] (cut_width), Susan VanderPlas [aut] (Animint GSOC 2013), Carson Sievert [aut] (Animint GSOC 2014), Kevin Ferris [aut] (Animint GSOC 2015), Jun Cai [aut] (Animint GSOC 2015), Faizan Khan [aut] (Animint GSOC 2016-2017), Vivek Kumar [aut] (Animint GSOC 2018), Himanshu Singh [aut] (Animint2 GSoC 2020)
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Repository: CRAN
Date/Publication: 2020-10-20 20:00:19 UTC

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New package r5r with initial version 0.2-0
Type: Package
Package: r5r
Title: Rapid Realistic Routing with 'R5'
Version: 0.2-0
Authors@R: c( person(given="Marcus", family="Saraiva", email="marcus.saraiva@gmail.com", role="aut", comment = c(ORCID = "0000-0001-6218-2338")), person(given="Rafael H. M.", family="Pereira", email="rafa.pereira.br@gmail.com", role=c("aut", "cre"), comment = c(ORCID = "0000-0003-2125-7465")), person(given="Daniel", family="Herszenhut", email="dhersz@gmail.com", role="aut", comment = c(ORCID = "0000-0001-8066-1105")), person(given="Carlos Kaue Vieira", family="Braga", email="kaue@kauebraga.dev", role="aut", comment = c(ORCID = "0000-0002-6104-7297")), person("Ipea - Institue for Applied Economic Research", role = c("cph", "fnd")) )
Description: Rapid realistic routing on multimodal transport networks (walk, bike, public transport and car) using 'R5', the Rapid Realistic Routing on Real-world and Reimagined networks <https://github.com/conveyal/r5>. The package allows users to generate detailed routing analysis or calculate travel time matrices using seamless parallel computing on top of the R5 Java machine.
Date: 2020-10-04
URL: https://github.com/ipeaGIT/r5r
BugReports: https://github.com/ipeaGIT/r5r/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.6)
Suggests: covr, ggplot2 (>= 3.3.1), knitr, mapview, rmarkdown, testthat
Imports: checkmate, data.table, methods, jdx (>= 0.1.4), rJava (>= 0.9-10), sf (>= 0.9-3), sfheaders, utils
SystemRequirements: Java JDK (>= 11.0)
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-20 14:54:00 UTC; user
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>), Rafael H. M. Pereira [aut, cre] (<https://orcid.org/0000-0003-2125-7465>), Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>), Carlos Kaue Vieira Braga [aut] (<https://orcid.org/0000-0002-6104-7297>), Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 15:40:02 UTC

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New package singcar with initial version 0.1.0
Package: singcar
Title: Comparing Single Cases to Small Samples
Version: 0.1.0
Authors@R: c(person(given = "Jonathan", family = "Rittmo", role = c("aut", "cre"), email = "j.rittmo@gmail.com", comment = c(ORCID = "0000-0001-5075-0166")), person(given = "Robert", family = "McIntosh", role = c("aut"), email = "r.d.mcintosh@ed.ac.uk", comment = c(ORCID = "0000-0002-7615-6699")))
Description: When comparing single cases to control populations and no parameters are known researchers and clinicians must estimate these with a control sample. This is often done when testing a case's abnormality on some variable or testing abnormality of the discrepancy between two variables. Appropriate frequentist and Bayesian methods for doing this are here implemented, including tests allowing for the inclusion of covariates. These have been developed first and foremost by John Crawford and Paul Garthwaite, e.g. in Crawford and Howell (1998) <doi:10.1076/clin.12.4.482.7241>, Crawford and Garthwaite (2005) <doi:10.1037/0894-4105.19.3.318>, Crawford and Garthwaite (2007) <doi:10.1080/02643290701290146> and Crawford, Garthwaite and Ryan (2011) <doi:10.1016/j.cortex.2011.02.017>. The package is also equipped with power calculators for each method.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
Imports: stats, CholWishart, MASS, withr
Suggests: knitr, rmarkdown, bookdown, testthat (>= 2.1.0)
VignetteBuilder: knitr
URL: https://github.com/jorittmo/singcar
BugReports: https://github.com/jorittmo/singcar/issues
NeedsCompilation: no
Packaged: 2020-10-13 08:36:34 UTC; jritt
Author: Jonathan Rittmo [aut, cre] (<https://orcid.org/0000-0001-5075-0166>), Robert McIntosh [aut] (<https://orcid.org/0000-0002-7615-6699>)
Maintainer: Jonathan Rittmo <j.rittmo@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 15:00:02 UTC

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New package parallelly with initial version 1.20.0
Package: parallelly
Version: 1.20.0
Title: Enhancing the 'parallel' Package
Imports: parallel, tools, utils
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), email = "henrikb@braju.com"))
Description: Utility functions that enhances the 'parallel' packages and that are used for the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by relevant R options and environment variables including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up a remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
License: LGPL (>= 2.1)
LazyLoad: TRUE
ByteCompile: TRUE
URL: https://github.com/HenrikBengtsson/parallelly
BugReports: https://github.com/HenrikBengtsson/parallelly/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-10 21:27:10 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2020-10-20 14:20:02 UTC

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New package packer with initial version 0.0.6
Package: packer
Title: An Opinionated Framework for Using 'JavaScript'
Date: 2020-10-11
Version: 0.0.6
Authors@R: person(given = "John", family = "Coene", role = c("aut", "cre"), email = "jcoenep@gmail.com", comment = c(ORCID = "0000-0002-6637-4107"))
Description: Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM' and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' packages, and much more.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
Imports: fs, usethis, jsonlite, htmlwidgets, cli, assertthat, rprojroot, rstudioapi
URL: https://github.com/JohnCoene/packer, https://packer.john-coene.com
BugReports: https://github.com/JohnCoene/packer/issues
Suggests: testthat, covr, golem
NeedsCompilation: no
Packaged: 2020-10-12 20:19:34 UTC; jp
Author: John Coene [aut, cre] (<https://orcid.org/0000-0002-6637-4107>)
Maintainer: John Coene <jcoenep@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 14:30:02 UTC

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New package SimSurvNMarker with initial version 0.1.1
Package: SimSurvNMarker
Type: Package
Title: Simulate Survival Time and Markers
Version: 0.1.1
Authors@R: c(person("Benjamin", "Christoffersen", email = "boennecd@gmail.com", role = c("cre", "aut")), person("Mark", "Clements", role = "cph"), person("Ignace", "Bogaert", role = "cph"))
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Description: Provides functions to simulate from joint survival and marker models. The user can specific all basis functions of time, random or deterministic covariates, random or deterministic left-truncation and right-censoring times, and model parameters.
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 2.1.0), splines, R.rsp, Matrix
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
SystemRequirements: C++11
VignetteBuilder: R.rsp
NeedsCompilation: yes
Packaged: 2020-10-19 17:18:14 UTC; boennecd
Author: Benjamin Christoffersen [cre, aut], Mark Clements [cph], Ignace Bogaert [cph]
Repository: CRAN
Date/Publication: 2020-10-20 07:00:38 UTC

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New package PortalHacienda with initial version 0.1.5
Package: PortalHacienda
Type: Package
Title: Acceder Con R a Los Datos Del Portal De Hacienda
Version: 0.1.5
Authors@R: person("Fernando", "Garcia Diaz", email = "fmgarciadiaz78@gmail.com", role = c("aut", "cre"))
Description: Obtener listado de datos, acceder y extender series del Portal de Datos de Hacienda.Las proyecciones se realizan con 'forecast', Hyndman RJ, Khandakar Y (2008) <doi:10.18637/jss.v027.i03>. Search, download and forecast time-series from the Ministry of Economy of Argentina. Forecasts are built with the 'forecast' package, Hyndman RJ, Khandakar Y (2008) <doi:10.18637/jss.v027.i03>.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/fmgarciadiaz/PortalHacienda-CRAN
Imports: dplyr (>= 0.8.5), forecast (>= 8.12), timetk (>= 2.0), lubridate (>= 1.7.8), xts (>= 0.12-0), httr, tibble (>= 3.0.1), magrittr (>= 1.5), zoo (>= 1.8-8), curl
RoxygenNote: 7.1.1
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-10 22:47:49 UTC; fernandogarciadiaz
Author: Fernando Garcia Diaz [aut, cre]
Maintainer: Fernando Garcia Diaz <fmgarciadiaz78@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 07:00:41 UTC

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New package MixSIAR with initial version 3.1.12
Package: MixSIAR
Title: Bayesian Mixing Models in R
Version: 3.1.12
Authors@R: c( person("Brian", "Stock", email = "bstock09@gmail.com", role = c("cre","aut")), person("Brice", "Semmens", email = "semmens@ucsd.edu", role = "aut"), person("Eric", "Ward", role = "ctb"), person("Andrew", "Parnell", role = "ctb"), person("Andrew", "Jackson", role = "ctb"), person("Donald", "Phillips", role = "ctb"))
Description: Creates and runs Bayesian mixing models to analyze biological tracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR'.
Depends: R (>= 3.6.0)
Imports: ggplot2 (>= 3.3.0), R2jags (>= 0.5-7), MASS (>= 7.3), RColorBrewer (>= 1.1), reshape (>= 0.8.7), reshape2 (>= 1.4.3), lattice (>= 0.20-35), MCMCpack (>= 1.4-2), ggmcmc (>= 1.1), coda (>= 0.19-1), loo (>= 2.0.0), bayesplot (>= 1.4.0), splancs (>= 2.01-40)
Suggests: knitr, rmarkdown, testthat
SystemRequirements: JAGS (>= 4.3)
URL: https://github.com/brianstock/MixSIAR
BugReports: https://github.com/brianstock/MixSIAR/issues
Encoding: UTF-8
License: GPL-3
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 19:46:39 UTC; brian
Author: Brian Stock [cre, aut], Brice Semmens [aut], Eric Ward [ctb], Andrew Parnell [ctb], Andrew Jackson [ctb], Donald Phillips [ctb]
Maintainer: Brian Stock <bstock09@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-20 07:00:44 UTC

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New package eicm with initial version 1.0.1
Package: eicm
Version: 1.0.1
Date: 2020-10-02
Title: Explicit Interaction Community Models
Authors@R: c(person(given="Miguel", family="Porto", email="mpbertolo@gmail.com", comment = c(ORCID="0000-0001-7640-0623"), role=c("aut", "cre")), person(given="Pedro", family="Beja", comment = c(ORCID="0000-0001-8164-0760"), role="aut"))
Maintainer: Miguel Porto <mpbertolo@gmail.com>
Depends: R (>= 3.5.0)
Imports: methods, parallel, GA (>= 3.1.1), snow, doSNOW, iterators, pso, ucminf, foreach, graphics, optimParallel
Suggests: igraph, knitr, rmarkdown
VignetteBuilder: knitr
Description: Model fitting and species biotic interaction network topology selection for explicit interaction community models. Explicit interaction community models are an extension of binomial linear models for joint modelling of species communities, that incorporate both the effects of species biotic interactions and the effects of missing covariates. Species interactions are modelled as direct effects of each species on each of the others, and are estimated alongside the effects of missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood fitting function, and a genetic algorithm for selecting the most parsimonious species interaction network topology.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/miguel-porto/eicm
BugReports: https://github.com/miguel-porto/eicm
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-10-16 18:22:33 UTC; miguel
Author: Miguel Porto [aut, cre] (<https://orcid.org/0000-0001-7640-0623>), Pedro Beja [aut] (<https://orcid.org/0000-0001-8164-0760>)
Repository: CRAN
Date/Publication: 2020-10-20 07:00:20 UTC

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Mon, 19 Oct 2020

New package YPmodel with initial version 1.4
Package: YPmodel
Type: Package
Title: The Short-Term and Long-Term Hazard Ratio Model for Survival Data
Version: 1.4
Date: 2020-10-15
Author: Junlong Sun and Song Yang
Maintainer: Junlong Sun <junlong.sun@gmail.com>
Description: Inference procedures accommodate a flexible range of hazard ratio patterns with a two-sample semi-parametric model. This model contains the proportional hazards model and the proportional odds model as sub-models, and accommodates non-proportional hazards situations to the extreme of having crossing hazards and crossing survivor functions. Overall, this package has four major functions: 1) the parameter estimation, namely short-term and long-term hazard ratio parameters; 2) 95 percent and 90 percent point-wise confidence intervals and simultaneous confidence bands for the hazard ratio function; 3) p-value of the adaptive weighted log-rank test; 4) p-values of two lack-of-fit tests for the model. See the included "read_me_first.pdf" for brief instructions. In this version (1.1), there is no need to sort the data before applying this package.
License: GPL (>= 3)
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2020-10-18 01:51:03 UTC; junlongsun
Repository: CRAN
Date/Publication: 2020-10-19 23:10:16 UTC

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New package tablaxlsx with initial version 1.2.4
Package: tablaxlsx
Title: Write Formatted Tables in Excel Workbooks
Version: 1.2.4
Date: 2020-10-01
Author: Jesus Maria Rodríguez Rodríguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@gmail.com>
Description: For writing tables with custom formats in a Excel file ready to be distributed.
Depends: R (>= 3.2),openxlsx
License: GPL-3
LazyData: true
Encoding: latin1
NeedsCompilation: no
Packaged: 2020-10-18 18:12:25 UTC; jesus
Repository: CRAN
Date/Publication: 2020-10-19 23:10:02 UTC

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New package semantic.dashboard with initial version 0.1.8
Package: semantic.dashboard
Type: Package
Title: Dashboard with Fomantic UI Support for Shiny
Version: 0.1.8
Authors@R: c(person("Filip", "Stachura", email = "filip@appsilon.com", role = "aut"), person("Dominik", "Krzeminski", email = "dominik@appsilon.com", role = "cre"), person("Krystian", "Igras", role = "aut"), person("Michał", "Maj", role = "ctb"), person(family = "Appsilon Data Science", role = "cph"))
Description: It offers functions for creating dashboard with Fomantic UI.
BugReports: https://github.com/Appsilon/semantic.dashboard/issues
Encoding: UTF-8
LazyData: TRUE
License: MIT + file LICENSE
Imports: utils, shiny (>= 0.12.1), shiny.semantic (>= 0.3.3), htmltools, glue
Suggests: testthat, lintr, shinydashboard, covr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 11:53:31 UTC; dominik
Author: Filip Stachura [aut], Dominik Krzeminski [cre], Krystian Igras [aut], Michał Maj [ctb], Appsilon Data Science [cph]
Maintainer: Dominik Krzeminski <dominik@appsilon.com>
Repository: CRAN
Date/Publication: 2020-10-19 23:20:02 UTC

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New package nlnet with initial version 1.4
Package: nlnet
Type: Package
Title: Nonlinear Network, Clustering, and Variable Selection Based on DCOL
Version: 1.4
Date: 2020-10-16
Author: Tianwei Yu, Haodong Liu
Maintainer: Tianwei Yu<yutianwei@cuhk.edu.cn>
Description: It includes four methods: DCOL-based K-profiles clustering, non-linear network reconstruction, non-linear hierarchical clustering, and variable selection for generalized additive model. References: Tianwei Yu (2018)<DOI: 10.1002/sam.11381>; Haodong Liu and others (2016)<DOI: 10.1371/journal.pone.0158247>; Kai Wang and others (2015)<DOI: 10.1155/2015/918954>; Tianwei Yu and others (2010)<DOI: 10.1109/TCBB.2010.73>.
License: GPL (>= 2)
Imports: ROCR, TSP, igraph, fdrtool, coin, methods, graphics, stats, earth, randomForest, e1071
NeedsCompilation: no
Packaged: 2020-10-17 04:39:26 UTC; tyu8
Repository: CRAN
Date/Publication: 2020-10-19 23:10:05 UTC

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New package icesTAF with initial version 3.6.0
Package: icesTAF
Version: 3.6.0
Date: 2020-10-19
Title: Functions to Support the ICES Transparent Assessment Framework
Authors@R: c( person("Arni", "Magnusson", role = "aut"), person("Colin", "Millar", role = c("aut", "cre"), email="colin.millar@ices.dk"), person("Alexandros", "Kokkalis", role = "ctb"), person("Iago", "Mosqueira", role = "ctb"), person("Ibrahim", "Umar", role = "ctb"), person("Hjalte", "Parner", role = "ctb") )
Imports: grDevices, lattice, stats, tools, utils, purrr, roxygen2, glue, jsonlite
LazyData: yes
Description: Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.
License: GPL-3
URL: https://taf.ices.dk
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-19 16:21:44 UTC; colin
Author: Arni Magnusson [aut], Colin Millar [aut, cre], Alexandros Kokkalis [ctb], Iago Mosqueira [ctb], Ibrahim Umar [ctb], Hjalte Parner [ctb]
Maintainer: Colin Millar <colin.millar@ices.dk>
Repository: CRAN
Date/Publication: 2020-10-19 23:10:08 UTC

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New package i2dash with initial version 0.2.2
Package: i2dash
Type: Package
Title: Iterative and Interactive Dashboards
Version: 0.2.2
Authors@R: c( person(given = "Arsenij", family = "Ustjanzew", email = "arsenij.ustjanzew@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-1014-4521")), person(given = "Jens", family = "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1927-3458")), person(given = "Mario", family = "Looso", email = "mario.looso@mpi-bn.mpg.de", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1495-9530")))
Description: Create customized, web-based dashboards for data presentation, exploration and sharing. 'i2dash' integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Imports: magrittr, knitr, flexdashboard, yaml, assertive.sets, assertive.types, rmarkdown, stringr, stringi, glue, ymlthis, methods, stats, utils
Suggests: switchr, plotly, BiocStyle, xfun, htmltools, testthat, ComplexHeatmap, digest, ggplot2, gt, kableExtra, forcats, leaflet
Collate: 'i2dashboard.R' 'AllGenerics.R' 'assemble.R' 'components.R' 'colormap.R' 'get_set.R' 'pages.R' 'reexports.R' 'sidebar.R' 'vis_objects.R'
NeedsCompilation: no
Packaged: 2020-10-19 08:06:09 UTC; austjanz
Author: Arsenij Ustjanzew [aut, cre, cph] (<https://orcid.org/0000-0002-1014-4521>), Jens Preussner [aut, cph] (<https://orcid.org/0000-0003-1927-3458>), Mario Looso [aut, cph] (<https://orcid.org/0000-0003-1495-9530>)
Maintainer: Arsenij Ustjanzew <arsenij.ustjanzew@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-19 23:10:13 UTC

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New package tidycwl with initial version 1.0.5
Package: tidycwl
Type: Package
Title: Tidy Common Workflow Language Tools and Workflows
Version: 1.0.5
Authors@R: c( person("Soner", "Koc", email = "soner.koc@sevenbridges.com", role = c("aut", "cre")), person("Nan", "Xiao", role = c("aut")), person("Dennis", "Dean", email = "dennis.dean@sevenbridges.com", role = c("aut"), comment = c(ORCID = "0000-0002-7621-9717")), person("Seven Bridges Genomics", role = c("cph", "fnd")) )
Maintainer: Soner Koc <soner.koc@sevenbridges.com>
Description: The Common Workflow Language <https://www.commonwl.org/> is an open standard for describing data analysis workflows. This package takes the raw Common Workflow Language workflows encoded in JSON or 'YAML' and turns the workflow elements into tidy data frames or lists. A graph representation for the workflow can be constructed and visualized with the parsed workflow inputs, outputs, and steps. Users can embed the visualizations in their 'Shiny' applications, and export them as HTML files or static images.
License: AGPL-3
SystemRequirements: PhantomJS (https://phantomjs.org), pandoc (>= 1.12.3) - https://pandoc.org.
VignetteBuilder: knitr
URL: https://sbg.github.io/tidycwl/, https://github.com/sbg/tidycwl
BugReports: https://github.com/sbg/tidycwl/issues
Encoding: UTF-8
LazyData: true
Imports: jsonlite, yaml, dplyr, magrittr, visNetwork, htmlwidgets, webshot
Suggests: knitr, rmarkdown, shiny
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-15 05:26:34 UTC; c02sn03cfvh6
Author: Soner Koc [aut, cre], Nan Xiao [aut], Dennis Dean [aut] (<https://orcid.org/0000-0002-7621-9717>), Seven Bridges Genomics [cph, fnd]
Repository: CRAN
Date/Publication: 2020-10-19 23:00:02 UTC

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New package superpc with initial version 1.12
Package: superpc
Type: Package
Title: Supervised Principal Components
Version: 1.12
Date: 2020-10-19
Authors@R: c(person("Eric", "Bair", role = "aut", email = "ebair@email.unc.edu"), person("Jean-Eudes", "Dazard", role = c("cre", "ctb"), email = "jean-eudes.dazard@case.edu"), person("Rob", "Tibshirani", role = "ctb", email = "tibs@stanford.edu"))
Author: Eric Bair [aut], Jean-Eudes Dazard [cre, ctb], Rob Tibshirani [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Description: Does prediction in the case of a censored survival outcome, or a regression outcome, using the "supervised principal component" approach. 'Superpc' is especially useful for high-dimensional data when the number of features p dominates the number of samples n (p >> n paradigm), as generated, for instance, by high-throughput technologies.
Depends: R (>= 3.5.0)
Imports: survival, stats, graphics, grDevices
NeedsCompilation: no
URL: http://www-stat.stanford.edu/~tibs/superpc, https://github.com/jedazard/superpc
Repository: CRAN
Date/Publication: 2020-10-19 22:10:03 UTC
License: GPL (>= 3) | file LICENSE
Archs: i386, x64
Packaged: 2020-10-19 18:31:57 UTC; JE D

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New package PressPurt with initial version 1.0.2
Package: PressPurt
Title: Indeterminacy of Networks via Press Perturbations
Version: 1.0.2
Authors@R: c(person(given = "David", family = "Koslicki", role = c("aut", "cre"), email = "dmk333@psu.edu"), person(given = "Dana", family = "Gibbon", role = c("aut", "trl")), person(given = "Mark", family = "Novak", role = "aut"))
Description: This is a computational package designed to identify the most sensitive interactions within a network which must be estimated most accurately in order to produce qualitatively robust predictions to a press perturbation. This is accomplished by enumerating the number of sign switches (and their magnitude) in the net effects matrix when an edge experiences uncertainty. The package produces data and visualizations when uncertainty is associated to one or more edges in the network and according to a variety of distributions. The software requires the network to be described by a system of differential equations but only requires as input a numerical Jacobian matrix evaluated at an equilibrium point. This package is based on Koslicki, D., & Novak, M. (2017) <doi:10.1007/s00285-017-1163-0>.
URL: https://github.com/dkoslicki/PressPurt
BugReports: https://github.com/dkoslicki/PressPurt/issues
Depends: R (>= 3.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: data.table, ggplot2, grid, gridExtra, reticulate (>= 1.11), utils
Suggests: knitr, rmarkdown, R.rsp, qpdf
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2020-10-08 18:12:24 UTC; danag
Author: David Koslicki [aut, cre], Dana Gibbon [aut, trl], Mark Novak [aut]
Maintainer: David Koslicki <dmk333@psu.edu>
Repository: CRAN
Date/Publication: 2020-10-19 22:10:13 UTC

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New package growthcurver with initial version 0.3.1
Package: growthcurver
Type: Package
Title: Simple Metrics to Summarize Growth Curves
Version: 0.3.1
Date: 2020-10-3
Authors@R: person("Kathleen", "Sprouffske", email = "sprouffske@gmail.com", role = c("aut", "cre"))
Description: Fits the logistic equation to microbial growth curve data (e.g., repeated absorbance measurements taken from a plate reader over time). From this fit, a variety of metrics are provided, including the maximum growth rate, the doubling time, the carrying capacity, the area under the logistic curve, and the time to the inflection point. Method described in Sprouffske and Wagner (2016) <doi:10.1186/s12859-016-1016-7>.
LazyData: TRUE
Depends: R (>= 4.0)
Imports: minpack.lm (>= 1.2), stats (>= 4.0), graphics (>= 4.0), grDevices (>= 4.0)
URL: https://github.com/sprouffske/growthcurver
BugReports: https://github.com/sprouffske/growthcurver/issues
License: GPL (>= 2)
Suggests: testthat, knitr, dplyr, ggplot2, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-15 15:17:34 UTC; sprouffske
Author: Kathleen Sprouffske [aut, cre]
Maintainer: Kathleen Sprouffske <sprouffske@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-19 23:00:06 UTC

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New package trending with initial version 0.0.1.0
Package: trending
Title: Model Temporal Trends
Version: 0.0.1.0
Authors@R: c( person( given = "Dirk", family = "Schumacher", role = c("aut"), email = "mail@dirk-schumacher.net" ), person( given = "Thibaut", family = "Jombart", role = c("aut"), email = "thibautjombart@gmail.com" ), person( given = "Tim", family = "Taylor", role = c("ctb", "cre"), email = "tim.taylor@hiddenelephants.co.uk", comment = c(ORCID = "0000-0002-8587-7113") ) )
Description: Provides a coherent interface to multiple modelling tools for fitting trends along with a standardised approach for generating confidence and prediction intervals.
URL: https://github.com/reconhub/trending
BugReports: https://github.com/reconhub/trending/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: MASS, stats, utils
Suggests: brms, ciTools, covr, dplyr, ggplot2, knitr, outbreaks, patchwork, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-12 11:49:57 UTC; tim
Author: Dirk Schumacher [aut], Thibaut Jombart [aut], Tim Taylor [ctb, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Repository: CRAN
Date/Publication: 2020-10-19 14:10:02 UTC

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New package LimnoPalettes with initial version 0.1.0
Package: LimnoPalettes
Title: A Limnology Themed Palette Generator
Description: Palettes generated from limnology based field and laboratory photos. Palettes can be used to generate color values to be used in any functions that calls for a color (i.e. ggplot(), plot(), flextable(), etc.).
Date: 2020-10-12
Version: 0.1.0
Authors@R: c(person("Paul", "Julian", role = c("aut", "cre"), email = "pauljulianphd@gmail.com", comment = c(ORCID = "0000-0002-7617-1354")))
Depends: R (>= 3.0)
License: GPL-3
LazyData: true
URL: https://github.com/SwampThingPaul/LimnoPalettes
BugReports: https://github.com/SwampThingPaul/LimnoPalettes/issues
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-12 12:46:39 UTC; Julian_P
Author: Paul Julian [aut, cre] (<https://orcid.org/0000-0002-7617-1354>)
Maintainer: Paul Julian <pauljulianphd@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-19 14:30:02 UTC

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New package BET with initial version 0.1.0
Package: BET
Type: Package
Title: Binary Expansion Testing
Version: 0.1.0
Authors@R: c(person("Wan", "Zhang", role = c("aut", "cre"), email = "wanz63@live.unc.edu"), person("Zhigen", "Zhao", role = "aut", email = "zhaozhg@temple.edu"), person("Michael", "Baiocchi", role = "aut", email = "baiocchi@stanford.edu"), person("Kai", "Zhang", role = "aut", email = "zhangk@email.unc.edu"))
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Depends: R (>= 3.5.0)
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
License: GPL
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.3)
LinkingTo: Rcpp
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-10-11 19:08:05 UTC; zhangwan
Author: Wan Zhang [aut, cre], Zhigen Zhao [aut], Michael Baiocchi [aut], Kai Zhang [aut]
Repository: CRAN
Date/Publication: 2020-10-19 14:10:05 UTC

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New package keys with initial version 0.1.0
Package: keys
Title: Keyboard Shortcuts for 'shiny'
Version: 0.1.0
Authors@R: c( person(given = "Tyler", family = "Littlefield", role = c("aut", "cre"), email = "tylerlittlefield@hey.com", comment = "Author of Javascript wrapper"), person(given = "Colin", family = "Fay", role = "aut", email = "contact@colinfay.me", comment = c(ORCID = "0000-0001-7343-1846")), person(given = "Craig", family = "Campbell", role = c("cph"), comment = "Author of JavaScript code"))
Description: Assign and listen to keyboard shortcuts in 'shiny' using the 'Mousetrap' Javascript library.
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: htmltools, shiny, jsonlite
URL: https://github.com/r4fun/keys
BugReports: https://github.com/r4fun/keys/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-10 16:34:23 UTC; tlittlef
Author: Tyler Littlefield [aut, cre] (Author of Javascript wrapper), Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>), Craig Campbell [cph] (Author of JavaScript code)
Maintainer: Tyler Littlefield <tylerlittlefield@hey.com>
Repository: CRAN
Date/Publication: 2020-10-19 13:40:03 UTC

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Sun, 18 Oct 2020

New package rock with initial version 0.1.1
Package: rock
Title: Reproducible Open Coding Kit
Version: 0.1.1
Authors@R: c(person(given = "Gjalt-Jorn Ygram", family = "Peters", role = c("aut", "cre"), email = "gjalt-jorn@behaviorchange.eu", comment = c(ORCID = "0000-0002-0336-9589")), person(given = "Szilvia", family = "Zorgo", role = c("ctb"), comment = c(ORCID = "0000-0002-6916-2097")))
Maintainer: Gjalt-Jorn Ygram Peters <gjalt-jorn@behaviorchange.eu>
Description: The Reproducible Open Coding Kit ('ROCK', and this package, 'rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. Although it is a general-purpose toolkit, three specific applications have been implemented, specifically an interface to the 'rENA' package that implements Epistemic Network Analysis ('ENA'), means to process notes from Cognitive Interviews ('CIs'), and means to work with decentralized construct taxonomies ('DCTs').
BugReports: https://gitlab.com/r-packages/rock/-/issues
URL: https://r-packages.gitlab.io/rock
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.0.0)
Imports: data.tree (>= 0.7.8), dplyr (>= 0.7.8), DiagrammeR (>= 1.0.0), glue (>= 1.3.0), graphics (>= 3.0.0), purrr (>= 0.2.5), stats (>= 3.0.0), utils (>= 3.5.0), yum (>= 0.0.1)
Suggests: covr, knitr, rENA (>= 0.1.6), rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Author: Gjalt-Jorn Ygram Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>), Szilvia Zorgo [ctb] (<https://orcid.org/0000-0002-6916-2097>)
Packaged: 2020-10-16 13:00:00 UTC; micro
Repository: CRAN
Date/Publication: 2020-10-18 22:10:02 UTC

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Sat, 17 Oct 2020

New package representr with initial version 0.1.0
Package: representr
Type: Package
Title: Create Representative Records After Entity Resolution
Version: 0.1.0
Authors@R: c(person("Andee", "Kaplan", email = "andee.kaplan@colostate.edu", role = c("aut", "cre")), person("Brenda", "Betancourt", role = "aut"), person("Rebecca C.", "Steorts", email = "beka@stat.duke.edu", role = c("aut")))
Description: An implementation of Kaplan, Betancourt, Steorts (2020) <arXiv:1810.01538> that creates representative records for use in downstream tasks after entity resolution is performed. Multiple methods for creating the representative records (data sets) are provided.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: doParallel, foreach, dplyr
Suggests: knitr, rmarkdown, blink, ggplot2, stringdist
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-09 23:40:05 UTC; andeek
Author: Andee Kaplan [aut, cre], Brenda Betancourt [aut], Rebecca C. Steorts [aut]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>
Repository: CRAN
Date/Publication: 2020-10-17 12:40:02 UTC

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New package provExplainR with initial version 1.0
Package: provExplainR
Title: Compare Provenance Collections to Explain Changed Script Outputs
Version: 1.0
Date: 2020-10-09
Authors@R: c( person("Barbara", "Lerner", role = "cre", email = "blerner@mtholyoke.edu"), person("Emery", "Boose", role = "aut", email = "boose@fas.harvard.edu"), person("Khanh", "Ngo", role = "aut", email = "ngo22k@mtholyoke.edu") )
Copyright: President and Fellows of Harvard College, Trustees of Mount Holyoke College
Description: Inspects provenance collected by the 'rdt' or 'rdtLite' packages, or other tools providing compatible PROV JSON output created by the execution of a script, and find differences between two provenance collections. Factors under examination included the hardware and software used to execute the script, versions of attached libraries, use of global variables, modified inputs and outputs, and changes in main and sourced scripts. Based on detected changes, 'provExplainR' can be used to study how these factors affect the behavior of the script and generate a promising diagnosis of the causes of different script results. More information about 'rdtLite' and associated tools is available at <https://github.com/End-to-end-provenance/> and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect Provenance in R, Informatics, <doi:10.3390/informatics5010012>.
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, provParseR (>= 0.1.2), diffobj, digest, stringr
Suggests: testthat
URL: https://github.com/End-to-end-provenance
BugReports: https://github.com/End-to-end-provenance/provExplainR/issues
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-10-09 20:08:23 UTC; blerner
Author: Barbara Lerner [cre], Emery Boose [aut], Khanh Ngo [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Repository: CRAN
Date/Publication: 2020-10-17 12:30:02 UTC

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New package mcmcensemble with initial version 2.0
Package: mcmcensemble
Title: Ensemble Sampler for Affine-Invariant MCMC
Version: 2.0
Authors@R: c(person(given = "Hugo", family = "Gruson", role = c("cre", "aut", "cph"), email = "hugo.gruson+R@normalesup.org", comment = c(ORCID = "0000-0002-4094-1476")), person(given = "Sanda", family = "Dejanic", role = c("aut", "cph")), person(given = "Andreas", family = "Scheidegger", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-2575-2172")))
Description: Provides ensemble samplers for affine-invariant Monte Carlo Markov Chain, which allow a faster convergence for badly scaled estimation problems. Two samplers are proposed: the 'differential.evolution' sampler from ter Braak and Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.
License: GPL-2
URL: https://github.com/Bisaloo/mcmcensemble, https://bisaloo.github.io/mcmcensemble/
BugReports: https://github.com/Bisaloo/mcmcensemble/issues
Suggests: coda, mockery, testthat
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-09 14:08:44 UTC; hugo
Author: Hugo Gruson [cre, aut, cph] (<https://orcid.org/0000-0002-4094-1476>), Sanda Dejanic [aut, cph], Andreas Scheidegger [aut, cph] (<https://orcid.org/0000-0003-2575-2172>)
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Repository: CRAN
Date/Publication: 2020-10-17 12:20:02 UTC

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New package lucas with initial version 1.0
Package: lucas
Type: Package
Title: Package to Download and Create the DB of LUCAS Data Harmonized
Version: 1.0
Date: 2020-09-28
Authors@R: c(person("Momchil", "Yordanov", email = "momchilyordanov@abv.bg", role = "cre"), person("Laura", "Martinez", email = "lmartisa@gmail.com", role = "aut"), person("Raphael", "dAndrimont", email = "raphael.dandrimont@ec.europa.eu", role = "aut"))
Description: Reproduces the harmonized DB of the ESTAT survey of the same name. The survey data is served as separate spreadsheets with noticeable differences in the collected attributes. The tool here presented carries out a series of instructions that harmonize the attributes in terms of name, meaning, and occurrence, while also introducing a series of new variables, instrumental to adding value to the product. Outputs include one harmonized table with all the years, and three separate geometries, corresponding to the theoretical point, the gps location where the measurement was made and the 250m east-facing transect.
Depends: R (>= 3.4)
Imports: RPostgreSQL, rpostgis, plyr, utils, DBI
License: GPL (>= 3)
LazyData: TRUE
RoxygenNote: 7.0.2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-10-09 17:38:38 UTC; momut1
Author: Momchil Yordanov [cre], Laura Martinez [aut], Raphael dAndrimont [aut]
Maintainer: Momchil Yordanov <momchilyordanov@abv.bg>
Repository: CRAN
Date/Publication: 2020-10-17 12:20:05 UTC

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New package hkdatasets with initial version 0.0.3
Package: hkdatasets
Title: Datasets Related to Hong Kong
Version: 0.0.3
Authors@R: c(person(given = "Martin", family = "Chan", role = c("aut", "cre"), email = "martinchan53@gmail.com"), person(given = "Avision", family = "Ho", role = c("ctb"), email = "hkdistricts.info@gmail.com"), person(given = "Ocean", family = "Cheung", role = c("ctb")), person(given = "Justin", family = "Yim", role = c("ctb")), person(given = "Gabriel", family = "Tam", role = c("ctb")))
Description: Datasets related to Hong Kong, including information on the 2019 elected District Councillors (<https://www.districtcouncils.gov.hk> and <https://dce2019.hk01.com/>) and traffic collision data from the Hong Kong Department of Transport (<https://www.td.gov.hk/>). All of the data in this package is available in the public domain.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://hong-kong-districts-info.github.io/hkdatasets/
BugReports: https://github.com/Hong-Kong-Districts-Info/hkdatasets/issues
Maintainer: Martin Chan <martinchan53@gmail.com>
Depends: R (>= 3.5.0)
Suggests: dplyr, tidyr, here, showtext
NeedsCompilation: no
Packaged: 2020-10-03 11:52:53 UTC; Martin Chan
Author: Martin Chan [aut, cre], Avision Ho [ctb], Ocean Cheung [ctb], Justin Yim [ctb], Gabriel Tam [ctb]
Repository: CRAN
Date/Publication: 2020-10-17 12:10:02 UTC

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New package IBMPopSim with initial version 0.3.0
Package: IBMPopSim
Type: Package
Title: Individual Based Model Population Simulation
Version: 0.3.0
Date: 2020-10-09
Authors@R: c( person('Daphné', 'Giorgi', role = c('aut', 'cre'), email = 'daphne.giorgi@sorbonne-universite.fr'), person('Sarah', 'Kaakai', role = 'aut', email = 'sarah.kaakai@univ-lemans.fr'), person('Vincent', 'Lemaire', role = 'aut', email = 'vincent.lemaire@sorbonne-universite.fr') )
Maintainer: Daphné Giorgi <daphne.giorgi@sorbonne-universite.fr>
Description: Simulation of the random evolution of structured population dynamics, called stochastic Individual Based Models (IBMs) (see e.g. Ferrière and Tran (2009) <doi:10.1051/proc/2009033>, Bansaye and Méléard (2015) <doi:10.1007/978-3-319-21711-6>, Boumezoued (2016)). The package allows users to simulate the random evolution of a population in which individuals are characterised by their date of birth, a set of attributes, and their potential date of death.
URL: https://github.com/DaphneGiorgi/IBMPopSim, https://DaphneGiorgi.github.io/IBMPopSim/
BugReports: https://github.com/DaphneGiorgi/IBMPopSim/issues
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12), checkmate, stats, utils, readr, rlang, tidyr, dplyr (>= 0.8.0), reshape, purrr, ggplot2
Suggests: RcppArmadillo, knitr, rmarkdown, bookdown, ggfortify, magick, colorspace, gridExtra
LazyData: true
SystemRequirements: C++11
NeedsCompilation: no
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Encoding: UTF-8
Packaged: 2020-10-09 10:56:02 UTC; giorgi
Author: Daphné Giorgi [aut, cre], Sarah Kaakai [aut], Vincent Lemaire [aut]
Repository: CRAN
Date/Publication: 2020-10-17 12:00:02 UTC

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Fri, 16 Oct 2020

New package rxivistr with initial version 0.1.1
Package: rxivistr
Type: Package
Title: Tool for the 'Rxivist' API
Version: 0.1.1
Authors@R: c(person(given = "Ivan", family = "Kodvanj", role = c("aut", "cre"), email = "ikodvanj@gmail.com", comment = c(ORCID = "0000-0002-1359-3701")))
Maintainer: Ivan Kodvanj <ikodvanj@gmail.com>
Description: Client for Rxivist API <https://rxivist.org/docs>, used for accessing information about preprints and their authors. Rxivist indexes preprints from bioRxiv, a free online archive for preprints in biology and life sciences, by Cold Spring Harbor Laboratory.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, curl, httr, jsonlite
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
URL: https://github.com/ikodvanj/rxivistr
BugReports: https://github.com/ikodvanj/rxivistr/issues
NeedsCompilation: no
Packaged: 2020-09-28 11:24:44 UTC; ivan
Author: Ivan Kodvanj [aut, cre] (<https://orcid.org/0000-0002-1359-3701>)
Repository: CRAN
Date/Publication: 2020-10-17 00:10:05 UTC

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New package bayesmove with initial version 0.1.0
Package: bayesmove
Type: Package
Title: Non-Parametric Bayesian Analyses of Animal Movement
Version: 0.1.0
Authors@R: c(person(given = "Joshua", family = "Cullen", role = c("aut", "cre", "cph"), email = "joshcullen10@gmail.com", comment = c(ORCID = "0000-0002-6935-9340")), person(given = "Denis", family = "Valle", role = c("aut", "cph")))
Description: Methods for assessing animal movement from telemetry and biologging data using non-parametric Bayesian methods. This includes features for pre- processing and analysis of data, as well as the visualization of results from the models. This framework does not rely on standard parametric density functions, which provides flexibility during model fitting.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: dplyr (>= 0.8.3), furrr (>= 0.1.0), ggplot2 (>= 3.3.0), lubridate (>= 1.7.4), MCMCpack (>= 1.4.5), progress (>= 1.2.2), purrr (>= 0.3.3), Rcpp, rlang, tictoc (>= 1.0), tidyr (>= 1.0.0), magrittr, future (>= 1.15.1)
URL: https://github.com/joshcullen/bayesmove, https://joshcullen.github.io/bayesmove/
BugReports: https://github.com/joshcullen/bayesmove/issues
Suggests: covr, testthat, spelling, knitr, rmarkdown, ggforce, RcppArmadillo
Language: en-US
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2020-10-09 01:32:23 UTC; joshcullen
Author: Joshua Cullen [aut, cre, cph] (<https://orcid.org/0000-0002-6935-9340>), Denis Valle [aut, cph]
Maintainer: Joshua Cullen <joshcullen10@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-16 14:10:02 UTC

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New package shinypanel with initial version 0.1.2
Package: shinypanel
Type: Package
Title: Shiny Control Panel
Version: 0.1.2
Author: Alex Pickering
Maintainer: Alex Pickering <alexvpickering@gmail.com>
Description: Add shiny inputs with one or more inline buttons that grow and shrink with inputs. Also add tool tips to input buttons and styling and messages for input validation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: shinyjs, shiny, shinyBS, htmltools, jsonlite
NeedsCompilation: no
Packaged: 2020-10-08 20:00:55 UTC; alex
Repository: CRAN
Date/Publication: 2020-10-16 14:00:02 UTC

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New package pould with initial version 1.0.1
Package: pould
Title: Phased or Unphased Linkage Disequilibrium
Version: 1.0.1
Authors@R: person("Steven", "Mack", email = "steven.mack@ucsf.edu", role = c("aut", "cre"))
Description: Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) <doi:10.1016/j.humimm.2019.01.010>, and Osoegawa et. al. (2019b) <doi:10.1016/j.humimm.2019.05.018>.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: haplo.stats,gap,stats,utils,ggplot2,reshape2,BIGDAWG,graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-08 17:34:11 UTC; sjmack
Author: Steven Mack [aut, cre]
Maintainer: Steven Mack <steven.mack@ucsf.edu>
Repository: CRAN
Date/Publication: 2020-10-16 13:50:03 UTC

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New package GARCOM with initial version 1.2.0
Package: GARCOM
Type: Package
Title: Gene and Region Counting of Mutations ("GARCOM")
Version: 1.2.0
Authors@R: c(person("Sanjeev","Sariya", role = c("aut", "cre","cph"),email = "ss5505@cumc.columbia.edu"),person("Giuseppe","Tosto", role =c("aut","cph")))
Description: Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: data.table (>= 1.12.8), stats, vcfR (>= 1.12.0)
Suggests: testthat
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-09-23 14:26:54 UTC; ss5505
Author: Sanjeev Sariya [aut, cre, cph], Giuseppe Tosto [aut, cph]
Maintainer: Sanjeev Sariya <ss5505@cumc.columbia.edu>
Repository: CRAN
Date/Publication: 2020-10-16 13:40:02 UTC

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New package CTD with initial version 0.99.8
Package: CTD
Title: A Method for 'Connecting The Dots' in Weighted Graphs
Version: 0.99.8
Date: 2020-09-12
Authors@R: person("Lillian", "Thistlethwaite", email="lillian.thistlethwaite@bcm.edu", role=c("aut", "cre"))
Description: A method for pattern discovery in weighted graphs. Two use cases are achieved: 1) Given a weighted graph and a subset of its nodes, do the nodes show significant connectedness? 2) Given a weighted graph and two subsets of its nodes, are the subsets close neighbors or distant?
Depends: R (>= 4.0), gmp, igraph, stats, grDevices, graphics
Suggests: knitr, rmarkdown, huge, ggplot2, gplots, RColorBrewer, testthat
SystemRequirements: gmp (>=5.0)
VignetteBuilder: knitr
biocViews: BiomedicalInformatics, Metabolomics, SystemsBiology, GraphAndNetwork
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-08 18:52:06 UTC; lillian.rosa
Author: Lillian Thistlethwaite [aut, cre]
Maintainer: Lillian Thistlethwaite <lillian.thistlethwaite@bcm.edu>
Repository: CRAN
Date/Publication: 2020-10-16 14:00:09 UTC

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Thu, 15 Oct 2020

New package survivalmodels with initial version 0.1.0
Package: survivalmodels
Title: Models for Survival Analysis
Version: 0.1.0
Authors@R: person(given = "Raphael", family = "Sonabend", role = c("aut", "cre"), email = "raphael.sonabend.15@ucl.ac.uk", comment = c(ORCID = "0000-0001-9225-4654"))
Description: Implementations of classical and machine learning models for survival analysis, including deep neural networks via 'keras' and 'tensorflow'. Each model includes a separated fit and predict interface with consistent prediction types for predicting risk, survival probabilities, or survival distributions with 'distr6' <https://CRAN.R-project.org/package=distr6>. Models are either implemented from 'Python' via 'reticulate' <https://CRAN.R-project.org/package=reticulate>, from code in GitHub packages, or novel implementations using 'Rcpp' <https://CRAN.R-project.org/package=Rcpp>. Novel machine learning survival models wil be included in the package in near-future updates. Neural networks are implemented from the 'Python' package 'pycox' <https://github.com/havakv/pycox> and are detailed by Kvamme et al. (2019) <https://jmlr.org/papers/v20/18-424.html>. The 'Akritas' estimator is defined in Akritas (1994) <doi:10.1214/aos/1176325630>. 'DNNSurv' is defined in Zhao and Feng (2020) <arXiv:1908.02337>.
License: MIT + file LICENSE
URL: https://github.com/RaphaelS1/survivalmodels/
BugReports: https://github.com/RaphaelS1/survivalmodels/issues
Imports: Rcpp (>= 1.0.5)
Suggests: distr6 (>= 1.4.4), keras, pseudo, reticulate, survival, testthat
LinkingTo: Rcpp
Encoding: UTF-8
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-10-08 10:48:04 UTC; raphael
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2020-10-15 13:30:02 UTC

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New package sparta with initial version 0.5.0
Package: sparta
Type: Package
Title: Sparse Tables
Version: 0.5.0
Date: 2020-10-08
Authors@R: c(person(given = "Mads", family = "Lindskou", email = "mads@math.aau.dk", role = c("aut", "cre")))
Description: Fast Multiplication and Division of Sparse Tables.
Encoding: UTF-8
LazyData: true
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.5)
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11
RoxygenNote: 7.1.1
Suggests: tinytest
URL: https://github.com/mlindsk/sparta
BugReports: https://github.com/mlindsk/sparta/issues
NeedsCompilation: yes
Packaged: 2020-10-08 12:51:23 UTC; mads
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Repository: CRAN
Date/Publication: 2020-10-15 13:40:02 UTC

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New package rameritrade with initial version 0.1.4
Package: rameritrade
Title: 'TD Ameritrade' API Interface for R
Version: 0.1.4
Author: Tony Trevisan [aut, cre]
Authors@R: person(given = "Tony", family = "Trevisan", role = c("aut", "cre"), email = "anthonytrevisan@gmail.com")
Maintainer: Tony Trevisan <anthonytrevisan@gmail.com>
URL: https://github.com/tonytrevisan/rameritrade/, https://developer.tdameritrade.com/
BugReports: https://github.com/tonytrevisan/rameritrade/issues
Description: Use R to interface with the 'TD Ameritrade' API, including authentication, trading, price requests, account information, and option chains. A user will need a TD brokerage account and TD Ameritrade developer app. See README for authentication process and examples.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: httr, urltools (>= 1.7.3), lubridate, dplyr, jsonlite, magrittr
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-08 00:30:44 UTC; rstudio
Repository: CRAN
Date/Publication: 2020-10-15 13:20:02 UTC

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New package JSconsole with initial version 0.1.0
Package: JSconsole
Type: Package
Title: A 'RStudio' Addin to Send 'JavaScript' Code to the 'V8' Console
Version: 0.1.0
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Description: Provides a 'RStudio' addin to send some 'JavaScript' code to the 'V8' console. The user can send an entire 'JavaScript' file or only some selected lines. This is useful to test the code.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: V8, rstudioapi
URL: https://github.com/stla/JSconsole
BugReports: https://github.com/stla/JSconsole/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-08 06:47:57 UTC; stla
Repository: CRAN
Date/Publication: 2020-10-15 13:30:06 UTC

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New package RxODE with initial version 0.9.2-1
Package: RxODE
Version: 0.9.2-1
Title: Facilities for Simulating from ODE-Based Models
Authors@R: c( person("Matthew L.","Fidler", role = c("aut"), email = "matthew.fidler@gmail.com", comment=c(ORCID="0000-0001-8538-6691")), person("Melissa", "Hallow", role = "aut", email = "hallowkm@uga.edu"), person("Wenping", "Wang", role = c("aut", "cre"), email = "wwang8198@gmail.com"), person("Zufar", "Mulyukov", role="ctb", email="zufar.mulyukov@novartis.com"), person("Justin", "Wilkins", role = "ctb", email = "justin.wilkins@occams.com", comment=c(ORCID="0000-0002-7099-9396")), person("Simon", "Frost", role="ctb"), person("Goro", "Fuji", role="ctb", email="gfuji@cpan.org"), person("Morwenn","", role="ctb"), person("Heng", "Li", role="ctb"), person("Yu", "Feng", role="ctb"), person("Alan", "Hindmarsh",role="ctb"), person("Linda", "Petzold", role="ctb"), person("Ernst", "Hairer", role="ctb"), person("Gerhard", "Wanner", role="ctb"), person("J", "Colinge", role="ctb"), person("Hadley", "Wickham", role="ctb"), person("G", "Grothendieck", role="ctb"), person("Robert", "Gentleman",role="ctb"), person("Daniel C.", "Dillon", role="ctb"), person("Ross", "Ihaka", role="ctb"), person("Cleve", "Moler", role="ctb"), person("Jack", "Dongarra", role="ctb"), person("R core team", role="cph") )
Maintainer: Wenping Wang <wwang8198@gmail.com>
Depends: R (>= 3.6.0)
Suggests: DT, data.table (>= 1.12.4), nlme, shiny, tcltk, testthat, usethis, devtools, covr, rmarkdown, SnakeCharmR, dplyr (>= 0.8.0), tidyr, tibble, curl, gridExtra, microbenchmark, scales, stringi, htmltools, reticulate, rlang, installr, learnr, remotes, crayon, xgxr, digest, vdiffr, ggrepel
Imports: knitr, Matrix, PreciseSums (>= 0.3), Rcpp (>= 0.12.3), brew, cli, dparser (>= 0.1.8), ggplot2, inline, magrittr, memoise, methods, mvnfast, pillar, rex, sys, units(>= 0.6-0), utils, assertthat, lotri
Description: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS. You can also obtain the archived SnakeCharmR for python integration from CRAN archives <https://cran.r-project.org/src/contrib/Archive/SnakeCharmR/> or <https://github.com/nlmixrdevelopment/SnakeCharmR>.
BugReports: https://github.com/nlmixrdevelopment/RxODE/issues
NeedsCompilation: yes
VignetteBuilder: knitr
License: GPL (>= 3)
URL: https://nlmixrdevelopment.github.io/RxODE/
RoxygenNote: 7.1.1
Biarch: true
LinkingTo: dparser(>= 0.1.8), Rcpp (>= 0.12.3), RcppArmadillo(>= 0.9.300.2.0), PreciseSums (>= 0.3)
Encoding: UTF-8
LazyData: true
Language: en-US
Packaged: 2020-10-12 12:55:12 UTC; wangwez
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>), Melissa Hallow [aut], Wenping Wang [aut, cre], Zufar Mulyukov [ctb], Justin Wilkins [ctb] (<https://orcid.org/0000-0002-7099-9396>), Simon Frost [ctb], Goro Fuji [ctb], Morwenn [ctb], Heng Li [ctb], Yu Feng [ctb], Alan Hindmarsh [ctb], Linda Petzold [ctb], Ernst Hairer [ctb], Gerhard Wanner [ctb], J Colinge [ctb], Hadley Wickham [ctb], G Grothendieck [ctb], Robert Gentleman [ctb], Daniel C. Dillon [ctb], Ross Ihaka [ctb], Cleve Moler [ctb], Jack Dongarra [ctb], R core team [cph]
Repository: CRAN
Date/Publication: 2020-10-15 12:10:13 UTC

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New package acumos with initial version 0.4-1
Package: acumos
Title: 'Acumos' R Interface
Version: 0.4-1
Authors@R: c(person("Simon", "Urbanek", role = c("aut"), email = "simon.urbanek@R-project.org"), person("Alassane", "Samba", role = c("aut","cre"), email = "alassane.samba@orange.com"), person("AT&T", role = c("cph")), person("Tech Mahindra", role = c("cph")), person("Orange", role = c("cph")))
Description: Create, upload and run 'Acumos' R models. 'Acumos' (<https://www.acumos.org>) is a platform and open source framework intended to make it easy to build, share, and deploy AI apps. 'Acumos' is part of the 'LF AI Foundation', an umbrella organization within The Linux Foundation. With this package, user can create a component, and push it to an 'Acumos' platform.
License: Apache License (== 2.0)
Imports: httr, jsonlite, RProtoBuf, Rserve, RestRserve, yaml
Suggests: randomForest, testthat, callr
BugReports: https://jira.acumos.org/projects/ACUMOS/issues
URL: https://www.acumos.org (Acumos project website) https://gerrit.acumos.org/r/gitweb?p=acumos-r-client.git (code repository) https://github.com/acumos/acumos-r-client (mirror repository) https://docs.acumos.org/en/latest/submodules/acumos-r-client/docs (docs)
RoxygenNote: 7.0.2
NeedsCompilation: no
Packaged: 2020-10-02 14:33:29 UTC; alassane
Author: Simon Urbanek [aut], Alassane Samba [aut, cre], AT&T [cph], Tech Mahindra [cph], Orange [cph]
Maintainer: Alassane Samba <alassane.samba@orange.com>
Repository: CRAN
Date/Publication: 2020-10-15 12:00:02 UTC

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Wed, 14 Oct 2020

New package rfacts with initial version 0.0.2
Package: rfacts
Title: R Interface to 'FACTS' on Unix-Like Systems
Description: The 'rfacts' package is an R interface to the Fixed and Adaptive Clinical Trial Simulator ('FACTS') on Unix-like systems. It programmatically invokes 'FACTS' to run clinical trial simulations, and it aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation workflows, and they enhance computational reproducibility. For more information on 'FACTS' itself, please visit <https://www.berryconsultants.com/software/>.
Version: 0.0.2
License: MIT + file LICENSE
URL: https://elilillyco.github.io/rfacts/, https://github.com/EliLillyCo/rfacts
BugReports: https://github.com/EliLillyCo/rfacts/issues
Authors@R: c( person( family = "Landau", given = c("William", "Michael"), email = "will.landau@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1878-3253") ), person( family = "Eli Lilly and Company", role = "cph" ))
SystemRequirements: FACTS Linux engines (>= 6.2.4), FLFLL (>= 6.2.4), Mono (>= 5.20.1.19)
Depends: R (>= 3.6.0)
Imports: tibble (>= 2.1.3), utils, xml2 (>= 1.2.2)
Suggests: dplyr (>= 0.8.4), fs (>= 1.3.1), knitr (>= 1.28), rmarkdown (>= 2.1), testthat (>= 2.1.0), withr (>= 2.2.0)
VignetteBuilder: knitr
Language: en-US
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-10-07 13:45:00 UTC; c240390
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-14 12:30:02 UTC

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New package qqr with initial version 0.0.1
Package: qqr
Title: Data from Brazilian Soccer Championship
Version: 0.0.1
Authors@R: c(person(given = "Jeferson", family = "Andrade", role = c("aut", "cre"), email = "jefersonandrafee@gmail.com"), person(given = "Joao", family = "Melo", role = "aut"), person(given = "Maisa", family = "Andrade", role = "aut"), person(given = "Andre", family = "Kalinovski", role = "aut"))
Description: Get data about the Brazilian soccer championship since 2014. Official data can be found at <https://www.cbf.com.br/futebol-brasileiro/competicoes/campeonato-brasileiro-serie-a/>.
License: GPL-2
Depends: xml2, rvest, tidyverse, dplyr, stringr, R (>= 2.10)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Author: Jeferson Andrade [aut, cre], Joao Melo [aut], Maisa Andrade [aut], Andre Kalinovski [aut]
Maintainer: Jeferson Andrade <jefersonandrafee@gmail.com>
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-06 17:18:35 UTC; Jeferson
Repository: CRAN
Date/Publication: 2020-10-14 12:10:02 UTC

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New package MCPtests with initial version 1.0
Package: MCPtests
Type: Package
Title: Multiples Comparisons Procedures
Version: 1.0
Date: 2020-10-07
Authors@R: c( person("Ben", "Deivide", email = "ben.deivide@ufsj.edu.br", role = c("aut", "cre")), person("Daniel", "Furtado", email = "danielff@dex.ufla.br", role = "aut"), person("Diego", "Arthur", email = "digo.arthur@hotmail.com", role = "aut"), person("Matheus", "Fernando", email = "matheusfers3500@gmail.com", role = "ctb"))
Description: Performs the execution of the main procedures of multiple comparisons in the literature, Scott-Knott (1974) <http://www.jstor.org/stable/2529204>, Batista (2016) <http://repositorio.ufla.br/jspui/handle/1/11466>, including graphic representations and export to different extensions of its results. An additional part of the package is the presence of the performance evaluation of the tests (Type I error per experiment and the power). This will assist the user in making the decision for the chosen test.
Imports: stats, base, utils, graphics, grDevices, SMR, writexl, xtable, tcltk, tkrplot, foreach, doParallel, parallel
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-10-07 13:10:17 UTC; MABENLA
Author: Ben Deivide [aut, cre], Daniel Furtado [aut], Diego Arthur [aut], Matheus Fernando [ctb]
Maintainer: Ben Deivide <ben.deivide@ufsj.edu.br>
Repository: CRAN
Date/Publication: 2020-10-14 12:20:02 UTC

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New package groupr with initial version 0.1.0
Package: groupr
Title: Groups with Inapplicable Values
Version: 0.1.0
Authors@R: person(given = "Nicholas", family = "Griffiths", role = c("aut", "cre"), email = "ngriffiths21@gmail.com", comment = c(ORCID = "0000-0001-8166-9045"))
Description: The 'groupr' package provides a more powerful version of grouped tibbles from 'dplyr'. It allows groups to be marked inapplicable, which is a simple but widely useful way to express structure in a dataset. It also provides powerful pivoting and other group manipulation functions.
License: MIT + file LICENSE
URL: https://github.com/ngriffiths21/groupr
BugReports: https://github.com/ngriffiths21/groupr/issues
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown, covr
RoxygenNote: 7.1.1
Imports: dplyr, rlang, vctrs, purrr, tidyr, tibble
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-07 13:56:10 UTC; nick
Author: Nicholas Griffiths [aut, cre] (<https://orcid.org/0000-0001-8166-9045>)
Maintainer: Nicholas Griffiths <ngriffiths21@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-14 12:30:06 UTC

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New package rinat with initial version 0.1.6
Package: rinat
Type: Package
Title: Access 'iNaturalist' Data Through APIs
Version: 0.1.6
Date: 2020-10-13
Authors@R: c( person("Vijay", "Barve", role = "aut", email = "vijay.barve@gmail.com", comment = c(ORCID = "0000-0002-4852-2567")), person("Edmund", "Hart", role = "aut", email = "edmund.m.hart@gmail.com"), person("Stéphane", "Guillou", role = "cre", email = "stephane.guillou@member.fsf.org", comment = c(ORCID = "0000-0001-8992-0951")) )
Description: A programmatic interface to the API provided by the 'iNaturalist' website <https://www.inaturalist.org/> to download species occurrence data submitted by citizen scientists.
License: MIT + file LICENSE
Imports: httr, plyr, jsonlite, ggplot2, maps, sp
RoxygenNote: 7.1.1
URL: https://docs.ropensci.org/rinat/ (website) https://github.com/ropensci/rinat (devel)
Suggests: knitr, rmarkdown, testthat, sf
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-10-13 14:06:15 UTC; stragu
Author: Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Edmund Hart [aut], Stéphane Guillou [cre] (<https://orcid.org/0000-0001-8992-0951>)
Maintainer: Stéphane Guillou <stephane.guillou@member.fsf.org>
Repository: CRAN
Date/Publication: 2020-10-14 09:10:03 UTC

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New package fishflux with initial version 0.0.1.3
Package: fishflux
Title: Model Elemental Fluxes in Fishes
Version: 0.0.1.3
Authors@R: c( person("Nina M. D.", "Schiettekatte", , "nina.schiettekatte@gmail.com", c("aut", "cre")), person("Diego", "Barneche", , "d.barneche@aims.gov.au", "aut") )
Description: Model fluxes of carbon, nitrogen, and phosphorus with the use of a coupled bioenergetics and stoichiometric model that incorporates flexible elemental limitation. Additional functions to help the user to find parameters are included. Finally, functions to extract and visualize results are available as well. For an introduction, see vignette. For more information on the theoretical background of this model, see Schiettekatte et al. (2020) <doi:10.1111/1365-2435.13618>.
URL: https://nschiett.github.io/fishflux/
BugReports: https://github.com/nschiett/fishflux/issues
License: MIT + file LICENSE
Encoding: UTF-8
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.0.0), parallel, dplyr, fishualize, ggplot2, plyr, rfishbase, tidybayes, tidyr, httr, curl
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown, testthat, covr
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.4.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
LazyData: true
RoxygenNote: 7.1.0
VignetteBuilder: knitr
Biarch: true
NeedsCompilation: yes
Packaged: 2020-10-13 14:08:30 UTC; nschiettekatte
Author: Nina M. D. Schiettekatte [aut, cre], Diego Barneche [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-14 09:10:06 UTC

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New package CoordinateCleaner with initial version 2.0-18
Package: CoordinateCleaner
Type: Package
Title: Automated Cleaning of Occurrence Records from Biological Collections
Version: 2.0-18
Authors@R: c(person(given = "Alexander", family = "Zizka", email = "alexander.zizka@idiv.de", role = c("aut", "cre")), person(given = "Daniele", family = "Silvestro", role = "ctb"), person(given = "Tobias", family = "Andermann", role = "ctb"), person(given = "Josue", family = "Azevedo", role = "ctb"), person(given = "Camila", family = "Duarte Ritter", role = "ctb"), person(given = "Daniel", family = "Edler", role = "ctb"), person(given = "Harith", family = "Farooq", role = "ctb"), person(given = "Andrei", family = "Herdean", role = "ctb"), person(given = "Maria", family = "Ariza", role = "ctb"), person(given = "Ruud", family = "Scharn", role = "ctb"), person(given = "Sten", family = "Svanteson", role = "ctb"), person(given = "Niklas", family = "Wengstrom", role = "ctb"), person(given = "Vera", family = "Zizka", role = "ctb"), person(given = "Alexandre", family ="Antonelli", role = "ctb"), person("Irene", "Steves", role = "rev", comment = "Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>"), person("Francisco", "Rodriguez-Sanchez", role = "rev", comment = "Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>"))
Description: Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Language: en-gb
Encoding: UTF-8
License: GPL-3
URL: https://ropensci.github.io/CoordinateCleaner/
BugReports: https://github.com/ropensci/CoordinateCleaner/issues
Depends: R (>= 3.5.0)
Imports: dplyr, geosphere, ggplot2, graphics, grDevices, methods, raster, rgbif, rgeos, rgdal, rnaturalearth, stats, sp, tidyselect, utils
LazyData: true
RoxygenNote: 7.1.1
Suggests: covr, countrycode, knitr, maps, magrittr, paleobioDB, rmarkdown, rnaturalearthdata, testthat, viridis
SystemRequirements: GDAL (>= 2.0.1)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-13 16:23:40 UTC; az64mycy
Author: Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)
Maintainer: Alexander Zizka <alexander.zizka@idiv.de>
Repository: CRAN
Date/Publication: 2020-10-14 09:10:09 UTC

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New package frailtypack with initial version 3.3.2
Package: frailtypack
Version: 3.3.2
Date: 2020-10-07
Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction; Evaluation of Failure-Time Surrogate Endpoints
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Amadou Diakite, Alexandre Laurent, Myriam Lopez, Agnieszka Krol, Casimir L. Sofeu, Julien Dumerc, Denis Rustand
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Depends: R (>= 2.10.0), survival, boot, MASS, survC1, doBy
Imports: statmod, nlme,rootSolve, shiny
LazyLoad: no
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. 10) Joint frailty models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints 11) Conditional and Marginal two-part joint models for longitudinal semicontinuous data and a terminal event. 12) Joint frailty-copula models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints. Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models. Moreover, the package can be used with its shiny application, in a local mode or by following the link below.
License: GPL (>= 2.0)
URL: https://virginie1rondeau.wixsite.com/virginierondeau/software-frailtypack https://frailtypack-pkg.shinyapps.io/shiny_frailtypack
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2020-10-14 09:00:02 UTC
Packaged: 2020-10-07 11:44:19 UTC; cs10
NeedsCompilation: yes
RoxygenNote: 6.0.1

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Tue, 13 Oct 2020

New package vein with initial version 0.9.0.1
Package: vein
Type: Package
Title: Vehicular Emissions Inventories
Version: 0.9.0.1
Date: 2020-09-23
Authors@R: c( person(given = "Sergio", family = "Ibarra-Espinosa", role = c("aut", "cre", "wdc"), email = "sergio.ibarra@usp.br", comment = c(ORCID = "0000-0002-3162-1905")))
Description: Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.
License: MIT + file LICENSE
URL: https://gitlab.com/ibarraespinosa/vein
BugReports: https://gitlab.com/ibarraespinosa/vein/-/issues
LazyData: no
Depends: R (>= 3.5.0)
Imports: sf, data.table, units, graphics, stats
Suggests: knitr, rmarkdown, testthat, covr, lwgeom, cptcity
RoxygenNote: 7.1.1
Encoding: UTF-8
NeedsCompilation: yes
Config/testthat/parallel: true
Packaged: 2020-10-07 18:00:38 UTC; sergio
VignetteBuilder: knitr
Author: Sergio Ibarra-Espinosa [aut, cre, wdc] (<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Repository: CRAN
Date/Publication: 2020-10-13 23:50:02 UTC

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New package redist with initial version 2.0.2
Package: redist
Version: 2.0.2
Date: 2020-10-03
Title: Simulation Methods for Legislative Redistricting
Authors@R: c( person("Ben", "Fifield", email = "benfifield@gmail.com", role = c("aut", "cre")), person("Christopher T.", "Kenny", email = "christopherkenny@fas.harvard.edu", role = "aut"), person("Cory", "McCartan", email = "cmccartan@g.harvard.edu", role = "aut"), person("Alexander", "Tarr", email = "atarr@princeton.edu", role = "aut"), person("Michael", "Higgins", email = "mikehiggins@k-state.edu", role = "ctb"), person("Jun", "Kawahara", email = "jkawahara@i.kyoto-u.ac.jp", role = "aut"), person("Kosuke", "Imai", email = "imai@harvard.edu", role = "aut"))
Maintainer: Ben Fifield <benfifield@gmail.com>
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo algorithms. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. Tools for analysis such as computation of various summary statistics and plotting functionality are also included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2020) <doi: 10.1080/10618600.2020.1739532>, Fifield, Imai, Kawahara, and Kenny (2020) <doi: 10.1080/2330443X.2020.1791773>, and McCartan and Imai (2020) <arXiv: 2008.06131>.
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.11.0), spdep, sp, sf, coda, parallel, doParallel, foreach, lwgeom, dplyr, ggplot2, magrittr, readr, servr, sys, tibble, stringr
Suggests: testthat, Rmpi, knitr, rmarkdown, igraph
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH
License: GPL (>= 2)
SystemRequirements: gmp, libxml2, python
Packaged: 2020-10-04 16:33:44 UTC; benfifield
NeedsCompilation: yes
BugReports: https://github.com/kosukeimai/redist/issues
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Encoding: UTF-8
Author: Ben Fifield [aut, cre], Christopher T. Kenny [aut], Cory McCartan [aut], Alexander Tarr [aut], Michael Higgins [ctb], Jun Kawahara [aut], Kosuke Imai [aut]
Repository: CRAN
Date/Publication: 2020-10-13 23:50:07 UTC

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New package miic with initial version 1.5.3
Package: miic
Title: Learning Causal or Non-Causal Graphical Models Using Information Theory
Version: 1.5.3
Authors@R: c(person(given = "Vincent", family = "Cabeli", role = c("aut", "cre"), email = "vincent.cabeli@curie.fr"), person(given = "Honghao", family = "Li", role = "aut", email = "honghao.li@curie.fr"), person(given = "Marcel", family = "Ribeiro Dantas", role = "aut", email = "marcel.ribeiro-dantas@curie.fr"), person(given = "Nadir", family = "Sella", role = "aut", email = "nadir.sella@curie.fr"), person(given = "Louis", family = "Verny", role = "aut"), person(given = "Severine", family = "Affeldt", role = "aut"), person(given = "Hervé", family = "Isambert", role = "aut", email = "Herve.Isambert@curie.fr"))
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>, Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
License: GPL (>= 2)
URL: https://github.com/miicTeam/miic_R_package
BugReports: https://github.com/miicTeam/miic_R_package/issues
Imports: ppcor, Rcpp, scales, stats,
Suggests: igraph, grDevices, ggplot2 (>= 3.3.0), gridExtra
LinkingTo: Rcpp
SystemRequirements: C++14
LazyData: true
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-10-09 13:30:22 UTC; vcabeli
Author: Vincent Cabeli [aut, cre], Honghao Li [aut], Marcel Ribeiro Dantas [aut], Nadir Sella [aut], Louis Verny [aut], Severine Affeldt [aut], Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>
Repository: CRAN
Date/Publication: 2020-10-13 23:50:11 UTC

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New package hutilscpp with initial version 0.5.1
Package: hutilscpp
Title: Miscellaneous Functions in C++
Version: 0.5.1
Authors@R: person(given = "Hugh", family = "Parsonage", role = c("aut", "cre"), email = "hugh.parsonage@gmail.com")
Description: Provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for 'reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package 'hutils' by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and 'Rcpp'.
URL: https://github.com/hughparsonage/hutilscpp
BugReports: https://github.com/hughparsonage/hutilscpp/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp, data.table, glue, hutils, magrittr, utils
RoxygenNote: 7.1.1
Suggests: bench, parallel, testthat (>= 2.1.0), TeXCheckR, withr, covr
NeedsCompilation: yes
Packaged: 2020-10-04 06:37:26 UTC; hughp
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-13 23:50:21 UTC

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New package agtboost with initial version 0.9.1
Package: agtboost
Type: Package
Title: Adaptive and Automatic Gradient Boosting Computations
Version: 0.9.1
Date: 2020-09-06
Author: Berent Ånund Strømnes Lunde
Maintainer: Berent Ånund Strømnes Lunde <lundeberent@gmail.com>
Description: Fast and automatic gradient tree boosting designed to avoid manual tuning and cross-validation by utilizing an information theoretic approach. This makes the algorithm adaptive to the dataset at hand; it is completely automatic, and with minimal worries of overfitting. Consequently, the speed-ups relative to state-of-the-art implementations can be in the thousands while mathematical and technical knowledge required on the user are minimized.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: methods, Rcpp (>= 1.0.1)
LinkingTo: Rcpp, RcppEigen
RcppModules: aGTBModule
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2020-10-04 16:29:20 UTC; lunde
Repository: CRAN
Date/Publication: 2020-10-13 23:50:34 UTC

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New package vfinputs with initial version 0.1.0
Package: vfinputs
Type: Package
Title: Visual Filter Inputs for Shiny
Version: 0.1.0
Date: 2020-09-28
Authors@R: c( person("Rafael", "Henkin", email = "r.henkin@qmul.ac.uk", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-5511-5230")), person("Mike", "Bostock", role = c("cph"), comment = "D3.js library, https://d3js.org") )
Depends: R (>= 3.0.2)
Imports: shiny, htmltools, jsonlite, scales
Suggests: RColorBrewer, testthat
Maintainer: Rafael Henkin <r.henkin@qmul.ac.uk>
Description: A set of visual input controls for Shiny apps to facilitate filtering across multiple outputs.
License: GPL-3
LazyData: TRUE
RoxygenNote: 7.1.1
Encoding: UTF-8
URL: https://github.com/rhenkin/vfinputs
BugReports: https://github.com/rhenkin/vfinputs/issues
NeedsCompilation: no
Packaged: 2020-10-02 09:42:34 UTC; rafael
Author: Rafael Henkin [cre, aut] (<https://orcid.org/0000-0002-5511-5230>), Mike Bostock [cph] (D3.js library, https://d3js.org)
Repository: CRAN
Date/Publication: 2020-10-13 15:20:03 UTC

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New package survivalMPLdc with initial version 0.1.0
Package: survivalMPLdc
Type: Package
Title: Penalised Likelihood for Survival Analysis with Dependent Censoring
Version: 0.1.0
Authors@R: c(person("Jing", "Xu", role = c("aut", "cre"), email = "kenny.xu@duke-nus.edu.sg"), person("Jun", "Ma", role = c("aut"), email = "jun.ma@mq.edu.au"), person("Thomas", "Fung", role = c("aut"), email = "thomas.fung.dr@gmail.com", comment =c(ORCID = "0000-0003-2601-0728")))
Description: Fitting Cox proportional hazard model under dependent right censoring using copula and maximum penalised likelihood methods.
Depends: R (>= 3.5)
License: GPL-3
Imports: copula, stats, methods, splines2, survival, graphics, matrixcalc
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-07 07:02:31 UTC; kennyxu1983hotmail.com
Author: Jing Xu [aut, cre], Jun Ma [aut], Thomas Fung [aut] (<https://orcid.org/0000-0003-2601-0728>)
Maintainer: Jing Xu <kenny.xu@duke-nus.edu.sg>
Repository: CRAN
Date/Publication: 2020-10-13 15:10:02 UTC

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New package SE.EQ with initial version 1.0
Package: SE.EQ
Type: Package
Title: SE-Test for Equivalence
Version: 1.0
Date: 2020-10-06
Author: Thomas Hoffelder
Maintainer: Thomas Hoffelder <thomas.hoffelder@boehringer-ingelheim.com>
Description: Implements the SE-test for equivalence according to Hoffelder et al. (2015) <DOI:10.1080/10543406.2014.920344>. The SE-test for equivalence is a multivariate two-sample equivalence test. Distance measure of the test is the sum of standardized differences between the expected values or in other words: the sum of effect sizes (SE) of all components of the two multivariate samples. The test is an asymptotically valid test for normally distributed data (see Hoffelder et al.,2015). The function SE.EQ() implements the SE-test for equivalence according to Hoffelder et al. (2015). The function SE.EQ.dissolution.profiles() implements a variant of the SE-test for equivalence for similarity analyses of dissolution profiles as mentioned in Suarez-Sharp et al.(2020) <DOI:10.1208/s12248-020-00458-9>). The equivalence margin used in SE.EQ.dissolution.profiles() is analogically defined as for the T2EQ approach according to Hoffelder (2019) <DOI:10.1002/bimj.201700257>) by means of a systematic shift in location of 10 [\% of label claim] of both dissolution profile populations. SE.EQ.dissolution.profiles() checks whether the weighted mean of the differences of the expected values of both dissolution profile populations is statistically significantly smaller than 10 [\% of label claim]. The weights are built up by the inverse variances.
Imports: MASS
License: GPL-3
NeedsCompilation: no
Packaged: 2020-10-06 11:04:08 UTC; hoffelde
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2020-10-13 14:10:05 UTC

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New package giscoR with initial version 0.1.0
Package: giscoR
Type: Package
Title: Download Geospatial Data from GISCO API - Eurostat
Version: 0.1.0
Authors@R: c( person("Diego", "Hernangómez", role=c("aut", "cre"), email="diego.hernangomezherrero@gmail.com", comment=c(ORCID="0000-0001-8457-4658")))
Description: Tools to download data from the GISCO (Geographic Information System of the Commission) Eurostat database <https://ec.europa.eu/eurostat/web/gisco>. This package is in no way officially related to or endorsed by Eurostat.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
BugReports: https://github.com/dieghernan/giscoR/issues
URL: https://dieghernan.github.io/giscoR/, https://github.com/dieghernan/giscoR
Depends: R (>= 3.3.0)
Imports: sf (>= 0.9), countrycode (>= 1.2.0), geojsonsf (>= 2.0)
Suggests: cartography (>= 2.0.0), colorspace, eurostat, lwgeom, tinytest, knitr, rmarkdown
Date: 2020-10-05
VignetteBuilder: knitr
SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ.4 (>= 4.8.0)
NeedsCompilation: no
Packaged: 2020-10-06 12:02:04 UTC; rstudio-user
Author: Diego Hernangómez [aut, cre] (<https://orcid.org/0000-0001-8457-4658>)
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-13 14:30:02 UTC

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New package fxTWAPLS with initial version 0.0.2
Package: fxTWAPLS
Title: An Improved Version of WA-PLS
Version: 0.0.2
Authors@R: c( person(given = "Mengmeng", family = "Liu", role = c("aut"), email = "m.liu18@imperial.ac.uk", comment = c(ORCID = "0000-0001-6250-0148")), person(given = "Roberto", family = "Villegas-Diaz", role = c("aut", "cre"), email = "r.villegas-diaz@reading.ac.uk", comment = c(ORCID = "0000-0001-5036-8661")), person("SPECIAL Research Group @ University of Reading", role = c("cph")))
Description: The goal of this package is to provide an improved version of WA-PLS (Weighted Averaging Partial Least Squares) by including the tolerances of taxa and the frequency of the sampled climate variable. This package also provides a way of leave-out cross-validation that removes both the test site and sites that are both geographically close and climatically close for each cycle, to avoid the risk of pseudo-replication.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/special-uor/fxTWAPLS, https://special-uor.github.io/fxTWAPLS/, https://research.reading.ac.uk/palaeoclimate/
BugReports: https://github.com/special-uor/fxTWAPLS/issues
Imports: doParallel, foreach, geosphere, ggplot2, MASS, matrixStats, parallel, tictoc
Suggests: badger, hexSticker, knitr, kableExtra, pkgdown, rmarkdown, scales, testthat
Depends: R (>= 3.6)
RoxygenNote: 7.1.1
Language: en-GB
NeedsCompilation: no
Packaged: 2020-10-06 14:05:41 UTC; roberto.villegas-diaz
Author: Mengmeng Liu [aut] (<https://orcid.org/0000-0001-6250-0148>), Roberto Villegas-Diaz [aut, cre] (<https://orcid.org/0000-0001-5036-8661>), SPECIAL Research Group @ University of Reading [cph]
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@reading.ac.uk>
Repository: CRAN
Date/Publication: 2020-10-13 14:50:03 UTC

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New package ecochange with initial version 1.3
Package: ecochange
Type: Package
Title: Integrating Ecological Remote Sensing Data to Derive EBV Metrics
Version: 1.3
Date: 2020-10-06
Authors@R: c(person(given = "Wilson", family = "Lara Henao", role = c("aut", "cre"), email = "wilarhen@temple.edu"), person(given = "Victor", family = "Gutierrez-Velez", role = "aut"))
Maintainer: Wilson Lara Henao <wilarhen@temple.edu>
Description: Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that can document biodiversity change. Freely available remote sensing products (RSP) are downloaded and integrated with data for national or regional domains to derive EBV metrics related to horizontal ecosystem extent, forest fragmentation, species distribution ranges, among others. To process the spatial data, the users must provide at least a region of interest (polygon or geographic administrative unit). Downloadable RSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
License: GPL-3
Depends: R (>= 3.5.0), raster, rgeos
Imports: readr,rgdal,parallel,curl,gdalUtils,ggplot2,graphics,rvest,stats,landscapemetrics,sp,tibble,utils,xml2,dplyr,sf,R.utils,httr,getPass,methods,rasterVis,viridis,rlang,forcats,lattice
Encoding: latin1
LazyData: TRUE
NeedsCompilation: no
Packaged: 2020-10-06 22:13:33 UTC; wilar
Author: Wilson Lara Henao [aut, cre], Victor Gutierrez-Velez [aut]
Repository: CRAN
Date/Publication: 2020-10-13 15:00:02 UTC

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New package RRBoost with initial version 0.1
Package: RRBoost
Type: Package
Title: A Robust Boosting Algorithm
Version: 0.1
Date: 2020-09-28
Authors@R: c(person("Xiaomeng", "Ju", role=c("aut", "cre"), email="xiaomeng.ju@stat.ubc.ca"), person("Matias", "Salibian-Barrera", role = c("aut"), email = "matias@stat.ubc.ca") )
Description: An implementation of robust boosting algorithms for regression in R. This includes the RRBoost method proposed in the paper "Robust Boosting for Regression Problems" (Ju X and Salibian-Barrera M. 2020) <doi:10.1016/j.csda.2020.107065> (to appear in Computational Statistics and Data Science). It also implements previously proposed boosting algorithms in the simulation section of the paper: L2Boost, LADBoost, MBoost (Friedman, J. H. (2001) <doi:10.1214/aos/1013203451>) and Robloss (Lutz et al. (2008) <doi:10.1016/j.csda.2007.11.006>).
Depends: R (>= 3.5.0)
Imports: stats, rpart, RobStatTM
License: GPL (>= 3)
LazyData: True
RoxygenNote: 7.1.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-10-05 16:10:45 UTC; JasmineJu
Author: Xiaomeng Ju [aut, cre], Matias Salibian-Barrera [aut]
Maintainer: Xiaomeng Ju <xiaomeng.ju@stat.ubc.ca>
Repository: CRAN
Date/Publication: 2020-10-13 13:10:06 UTC

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New package rapsimng with initial version 0.1.0
Package: rapsimng
Type: Package
Title: APSIM Next Generation
Version: 0.1.0
Authors@R: person("Bangyou", "Zheng", email = "bangyou.zheng@csiro.au", role = c("aut", "cre"))
Description: The Agricultural Production Systems sIMulator ('APSIM') is a widely used to simulate the agricultural systems for multiple crops. This package is designed to create, modify and run 'apsimx' files in the 'APSIM' Next Generation <https://www.apsim.info/>.
License: MIT + file LICENSE
URL: https://rapsimng.bangyou.me/, https://github.com/byzheng/rapsimng
BugReports: https://github.com/byzheng/rapsimng/issues
Encoding: UTF-8
LazyData: true
Imports: jsonlite, xml2, tibble, magrittr, tidyr, dplyr, rlang
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-06 04:52:56 UTC; zhe00a
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Repository: CRAN
Date/Publication: 2020-10-13 14:00:02 UTC

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New package MMDCopula with initial version 0.1.0
Package: MMDCopula
Type: Package
Title: Robust Estimation of Copulas by Maximum Mean Discrepancy
Version: 0.1.0
Description: Provides functions for the robust estimation of parametric families of copulas using minimization of the Maximum Mean Discrepancy, following the article Alquier, Chérief-Abdellatif, Derumigny and Fermanian (2020) <arXiv:2010.00408>.
Authors@R: c( person("Alexis", "Derumigny",, email = "a.f.f.derumigny@utwente.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6163-8097")), person("Pierre", "Alquier",, email = "pierre.alquier.stat@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-4249-7337")), person("Jean-David", "Fermanian",, email = "Jean-David.Fermanian@ensae.fr", role = "aut", comment = c(ORCID = "0000-0001-5960-5555")), person("Badr-Eddine", "Chérief-Abdellatif",, email = "badr.eddine.cherief.abdellatif@gmail.com", role = "aut") )
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 3.6.0)
Imports: VineCopula, cubature, pcaPP, randtoolbox,
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/AlexisDerumigny/MMDCopula/issues
NeedsCompilation: no
Packaged: 2020-10-06 07:36:00 UTC; Alexis
Author: Alexis Derumigny [aut, cre] (<https://orcid.org/0000-0002-6163-8097>), Pierre Alquier [aut] (<https://orcid.org/0000-0003-4249-7337>), Jean-David Fermanian [aut] (<https://orcid.org/0000-0001-5960-5555>), Badr-Eddine Chérief-Abdellatif [aut]
Maintainer: Alexis Derumigny <a.f.f.derumigny@utwente.nl>
Repository: CRAN
Date/Publication: 2020-10-13 14:00:06 UTC

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New package gsisdecoder with initial version 0.0.1
Package: gsisdecoder
Title: High Efficient Functions to Decode NFL Player IDs
Version: 0.0.1
Authors@R: person(given = "Sebastian", family = "Carl", role = c("aut", "cre"), email = "mrcaseb@gmail.com")
Description: A set of high efficient functions to decode identifiers of National Football League players.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
LinkingTo: Rcpp
Imports: Rcpp
URL: https://github.com/mrcaseb/gsisdecoder
BugReports: https://github.com/mrcaseb/gsisdecoder/issues
Suggests: testthat, covr
NeedsCompilation: yes
Packaged: 2020-10-05 20:07:29 UTC; S.Carl
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-13 13:50:03 UTC

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New package dadjoke with initial version 1.0
Package: dadjoke
Title: Displays a Dad Joke
Version: 1.0
Authors@R: person("Shambhavi", "Priyam", email = "priyam@coll.mpg.de", role = c("aut", "cre"))
Maintainer: Shambhavi Priyam <priyam@coll.mpg.de>
Description: Displays a terrible joke, the kind only dads crack.
Depends: R (>= 3.0.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-06 00:36:26 UTC; priyam
Author: Shambhavi Priyam [aut, cre]
Repository: CRAN
Date/Publication: 2020-10-13 13:50:06 UTC

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New package CompModels with initial version 0.1.0
Package: CompModels
Title: Pseudo Computer Models for Optimization
Version: 0.1.0
Authors@R: person(given = "Tony", family = "Pourmohamad", role = c("aut", "cre"), email = "tpourmohamad@gmail.com")
Description: A suite of computer model test functions that can be used to test and evaluate algorithms for Bayesian (also known as sequential) optimization. Some of the functions have known functional forms, however, most are intended to serve as black-box functions where evaluation requires running computer code that reveals little about the functional forms of the objective and/or constraints. The primary goal of the package is to provide users (especially those who do not have access to real computer models) a source of reproducible and shareable examples that can be used for benchmarking algorithms. The package is a living repository, and so more functions will be added over time. For function suggestions, please do contact the author of the package.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-10-06 06:11:52 UTC; pourmoht
Author: Tony Pourmohamad [aut, cre]
Maintainer: Tony Pourmohamad <tpourmohamad@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-13 14:00:09 UTC

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New package BeastJar with initial version 1.10.5
Package: BeastJar
Type: Package
Title: JAR Dependency for MCMC Using 'BEAST'
Version: 1.10.5
Authors@R: c( person("Marc A.", "Suchard", email = "msuchard@ucla.edu", role = c("aut","cre","cph")), person("Andrew", "Rambaut", role = "cph"), person("Alexei J.", "Drummond", role = "cph") )
Description: Provides JAR to perform Markov chain Monte Carlo (MCMC) inference using the popular Bayesian Evolutionary Analysis by Sampling Trees 'BEAST' software library of Suchard et al (2018) <doi:10.1093/ve/vey016>. 'BEAST' supports auto-tuning Metropolis-Hastings, slice, Hamiltonian Monte Carlo and Sequential Monte Carlo sampling for a large variety of composable standard and phylogenetic statistical models using high performance computing. By placing the 'BEAST' JAR in this package, we offer an efficient distribution system for 'BEAST' use by other R packages using CRAN.
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
Imports: rJava
URL: https://github.com/beast-dev/BeastJar
Copyright: See file COPYRIGHTS
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-06 01:03:35 UTC; msuchard
Author: Marc A. Suchard [aut, cre, cph], Andrew Rambaut [cph], Alexei J. Drummond [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Repository: CRAN
Date/Publication: 2020-10-13 13:50:08 UTC

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New package sdmpredictors with initial version 0.2.9
Package: sdmpredictors
Type: Package
Title: Species Distribution Modelling Predictor Datasets
Version: 0.2.9
Date: 2020-10-09
Depends: R (>= 3.2.5), raster (>= 2.5-8), rgdal (>= 1.1-10)
Imports: R.utils (>= 2.4.0), stats, utils, RCurl
Authors@R: c( person("Samuel", "Bosch", email = "mail@samuelbosch.com", role = c("aut")), person("Lennert", "Tyberghein", email = "lennert.tyberghein@vliz.be", role = c("ctb")), person("Olivier", "De Clerck", email = "olivier.declerck@ugent.be", role = c("ctb")), person("Salvador", "Fernandez", email = "salvador.fernandez@vliz.be", role = c("ctb", "cre")), person("Lennert", "Schepers", email = "lennert.schepers@vliz.be", role = c("ctb")))
Description: Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <https://www.worldclim.org/>,, ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/> and MARSPEC <http://www.marspec.org/>.
License: MIT + file LICENSE
URL: https://www.samuelbosch.com/p/sdmpredictors.html
BugReports: https://github.com/lifewatch/sdmpredictors/issues
LazyData: true
Suggests: ggplot2, reshape2, testthat, knitr, rmarkdown
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-09 14:59:23 UTC; salvadorf
Author: Samuel Bosch [aut], Lennert Tyberghein [ctb], Olivier De Clerck [ctb], Salvador Fernandez [ctb, cre], Lennert Schepers [ctb]
Maintainer: Salvador Fernandez <salvador.fernandez@vliz.be>
Repository: CRAN
Date/Publication: 2020-10-13 12:50:02 UTC

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New package rmangal with initial version 2.0.2
Package: rmangal
Type: Package
Title: 'Mangal' Client
Version: 2.0.2
Authors@R: c( person(given = "Steve", family = "Vissault", comment = c(ORCID = "0000-0002-0866-4376"), email = "s.vissault@yahoo.fr", role = c("aut", "cre")), person(given = "Kevin", family = "Cazelles", comment = c(ORCID = "0000-0001-6619-9874"), email = "kcazelle@uoguelph.ca", role = c("aut","ctb")), person(given = "Gabriel", family = "Bergeron", email = "gabriel.bergeron3@usherbrooke.ca", role = c("aut","ctb")), person(given = "Benjamin", family = "Mercier", email = "Benjamin.B.Mercier@usherbrooke.ca", role = c("aut","ctb")), person(given = "Clément", family = "Violet", email = "Clement.Violet@etudiant.univ-brest.fr", role = c("aut","ctb")), person(given = "Dominique", family = "Gravel", email = "dominique.gravel@usherbrooke.ca", role = c("aut")), person(given = "Timothée", family = "Poisot", email = "timothee.poisot@umontreal.ca", role = c("aut")), person(given = "Thomas Lin", family = "Pedersen", role = "rev", comment = c(ORCID = "0000-0002-5147-4711")), person(given = "Anna Willoughby", role = "rev", comment = c(ORCID = "0000-0002-0504-0605")) )
Description: An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal.io/doc/api/>).
URL: https://docs.ropensci.org/rmangal/, https://mangal.io, https://github.com/ropensci/rmangal
BugReports: https://github.com/ropensci/rmangal/issues
License: MIT + file LICENSE
Encoding: UTF-8
Imports: httr (>= 1.3.1), igraph, jsonlite (>= 1.5), memoise, purrr
RoxygenNote: 7.1.1
Suggests: ggraph (>= 2.0.0), knitr, magrittr, mapview, rmarkdown, sf, spelling, taxize, tidygraph, testthat, tibble, USAboundaries, webshot,
VignetteBuilder: knitr
X-schema.org-applicationCategory: ecologicalNetworks
X-schema.org-keywords: ecology, networks, food webs, interactions, data publications, open access
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2020-10-12 16:25:20 UTC; steve
Author: Steve Vissault [aut, cre] (<https://orcid.org/0000-0002-0866-4376>), Kevin Cazelles [aut, ctb] (<https://orcid.org/0000-0001-6619-9874>), Gabriel Bergeron [aut, ctb], Benjamin Mercier [aut, ctb], Clément Violet [aut, ctb], Dominique Gravel [aut], Timothée Poisot [aut], Thomas Lin Pedersen [rev] (<https://orcid.org/0000-0002-5147-4711>), Anna Willoughby [rev] (<https://orcid.org/0000-0002-0504-0605>)
Maintainer: Steve Vissault <s.vissault@yahoo.fr>
Repository: CRAN
Date/Publication: 2020-10-13 12:30:02 UTC

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New package MODIStsp with initial version 2.0.4
Package: MODIStsp
Title: A Tool for Automating Download and Preprocessing of MODIS Land Products Data
Type: Package
Version: 2.0.4
Authors@R: c(person("Lorenzo", "Busetto", email = "lbusett@gmail.com", role = c("aut", "cre"), comment = c(ORCID = '0000-0001-9634-6038')), person("Luigi", "Ranghetti", email = "ranghetti.l@irea.cnr.it", role = c("aut"), comment = c(ORCID = '0000-0001-6207-5188')), person("Leah", "Wasser", role = "rev", comment = "Leah Wasser reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/184"), person("Jeff", "Hanson", role = "rev", comment = "Jeff Hanson reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/184"))
Description: Allows automating the creation of time series of rasters derived from MODIS Satellite Land Products data. It performs several typical preprocessing steps such as download, mosaicking, reprojection and resize of data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional Quality Indicators should be extracted from aggregated MODIS Quality Assurance layers and, in the case of Surface Reflectance products , which Spectral Indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing to automatically update time series related to a MODIS product whenever a new image is available.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: assertthat, bitops (>= 1.0-6), data.table (>= 1.9.6), gdalUtilities, httr (>= 1.4.2), jsonlite, geojsonio, parallel, raster (>= 3.3.13), sf (>= 0.9.3), stringr (>= 1.0.0), xts (>= 0.9-7), xml2 (>= 1.2.0),
Suggests: testthat, spelling, knitr, rmarkdown, png, grid, httptest, geojsonlint, leaflet, shiny, shinydashboard, shinyFiles, shinyalert, shinyjs, rappdirs, leafem (>= 0.1.3), mapedit (>= 0.6.0), rgdal, magrittr, formatR
SystemRequirements:
URL: https://github.com/ropensci/MODIStsp/, https://docs.ropensci.org/MODIStsp/
BugReports: https://github.com/ropensci/MODIStsp/issues
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2020-10-12 15:55:52 UTC; LB_laptop
Author: Lorenzo Busetto [aut, cre] (<https://orcid.org/0000-0001-9634-6038>), Luigi Ranghetti [aut] (<https://orcid.org/0000-0001-6207-5188>), Leah Wasser [rev] (Leah Wasser reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/184), Jeff Hanson [rev] (Jeff Hanson reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/184)
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-13 12:40:07 UTC

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New package easyr with initial version 0.5-2
Package: easyr
Type: Package
Title: Helpful Functions from Oliver Wyman Actuarial Consulting
Version: 0.5-2
Authors@R: c( person( "Oliver Wyman", "Actuarial Consulting", email = "rajesh.sahasrabuddhe@oliverwyman.com", role = c("aut", "cph") ), person( "Bryce", "Chamberlain", email = "bryce.chamberlain@oliverwyman.com", role = c("aut", "cre") ), person( "Scott", "Sobel", email = "scott.sobel@oliverwyman.com", role = c("ctb") ), person( "Rajesh", "Sahasrabuddhe", email = "rajesh.sahasrabuddhe@oliverwyman.com", role = c("ctb") ) )
Maintainer: Bryce Chamberlain <bryce.chamberlain@oliverwyman.com>
Description: Makes difficult operations easy. Includes these types of functions: shorthand, type conversion, data wrangling, and work flow. Also includes some helpful data objects: NA strings, U.S. state list, color blind charting colors. Built and shared by Oliver Wyman Actuarial Consulting. Accepting proposed contributions through GitHub.
License: GPL (>= 2)
LazyData: true
URL: https://github.com/oliver-wyman-actuarial/easyr
BugReports: https://github.com/oliver-wyman-actuarial/easyr/issues
Depends: R (>= 3.4.0)
Imports: data.table, digest, dplyr, foreign, glue, Hmisc, lubridate, stringr, openssl, readxl, rlang, rprojroot, XML
RoxygenNote: 6.1.1
Suggests: pdftools, qs, rstudioapi, testthat
NeedsCompilation: no
Packaged: 2020-10-09 15:24:51 UTC; bryce.chamberlain
Author: Oliver Wyman Actuarial Consulting [aut, cph], Bryce Chamberlain [aut, cre], Scott Sobel [ctb], Rajesh Sahasrabuddhe [ctb]
Repository: CRAN
Date/Publication: 2020-10-13 12:40:02 UTC

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New package cora with initial version 0.1.0
Package: cora
Title: Cora Data for Entity Resolution
Version: 0.1.0
Authors@R: c(person("Rebecca", "Steorts", email= "beka@stat.duke.edu", role=c("aut", "cre")), person("Andee", "Kaplan", email= "andrea.kaplan@duke.edu", role="aut"), person("Srini", "Sunil", email="srinivas.sunil@duke.edu", role="aut"))
Description: Duplicated publication data (pre-processed and formatted) for entity resolution. This data set contains a total of 1879 records. The following variables are included in the data set: id, title, book title, authors, address, date, year, editor, journal, volume, pages, publisher, institution, type, tech, note. The data set has a respective gold data set that provides information on which records match based on id.
URL: https://github.com/resteorts/cora
BugReports: https://github.com/resteorts/cora/issues
Depends: R (>= 3.4.0)
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-10-05 10:57:07 UTC; rebeccasteorts
Author: Rebecca Steorts [aut, cre], Andee Kaplan [aut], Srini Sunil [aut]
Maintainer: Rebecca Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-13 12:50:06 UTC

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New package bRacatus with initial version 1.0.0
Package: bRacatus
Title: Estimating the Accuracy and the Status of Point Occurrence Records
Version: 1.0.0
Language: en-GB
Authors@R: c(person("Eduardo", "Arlé", email = "eduardo.arle@idiv.de", role = c("aut", "cre")), person("Alexander","Zizka",email = "alexaner.zizka@idiv.de", role = "ctb"))
Description: Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Depends: R (>= 3.5.0)
Imports: data.table, geojsonio, graphics, grDevices, jsonlite, maptools, methods, plotfunctions, raster, rgbif, rgeos, rworldmap, sp, stats, testthat
License: GPL (>= 2)
Encoding: UTF-8
URL: https://github.com/EduardoArle/bRacatus
BugReports: https://github.com/EduardoArle/bRacatus/issues
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-05 12:25:04 UTC; ca13kute
Author: Eduardo Arlé [aut, cre], Alexander Zizka [ctb]
Maintainer: Eduardo Arlé <eduardo.arle@idiv.de>
Repository: CRAN
Date/Publication: 2020-10-13 13:00:14 UTC

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Sun, 11 Oct 2020

New package anscombiser with initial version 1.0.0
Package: anscombiser
Title: Create Datasets with Identical Summary Statistics
Version: 1.0.0
Date: 2020-10-10
Authors@R: person(c("Paul", "J."), "Northrop", email = "p.northrop@ucl.ac.uk", role = c("aut", "cre", "cph"))
Description: Anscombe's quartet are a set of four two-variable datasets that have several common summary statistics but which have very different joint distributions. This becomes apparent when the data are plotted, which illustrates the importance of using graphical displays in Statistics. This package enables the creation of datasets that have identical marginal sample means and sample variances, sample correlation, least squares regression coefficients and coefficient of determination. The user supplies an initial dataset, which is shifted, scaled and rotated in order to achieve target summary statistics. The general shape of the initial dataset is retained. The target statistics can be supplied directly or calculated based on a user-supplied dataset. The 'datasauRus' package <https://cran.r-project.org/package=datasauRus> provides further examples of datasets that have markedly different scatter plots but share many sample summary statistics.
Imports: datasets, graphics, stats
License: GPL (>= 2)
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.3.0)
RoxygenNote: 7.1.0
Suggests: datasauRus, maps, testthat, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://paulnorthrop.github.io/anscombiser/, https://github.com/paulnorthrop/anscombiser
BugReports: https://github.com/paulnorthrop/anscombiser/issues
NeedsCompilation: no
Packaged: 2020-10-10 11:17:25 UTC; paul
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2020-10-11 23:40:05 UTC

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Sat, 10 Oct 2020

New package MKclass with initial version 0.3
Package: MKclass
Version: 0.3
Date: 2020-10-04
Title: Statistical Classification
Authors@R: person("Matthias", "Kohl", role = c("aut", "cre"), email = "Matthias.Kohl@stamats.de", comment = c(ORCID = "0000-0001-9514-8910"))
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Depends: R(>= 4.0.0)
Imports: stats
Suggests: knitr, rmarkdown, foreach, parallel, doParallel
VignetteBuilder: knitr
Description: Performance measures and scores for statistical classification such as accuracy, sensitivity, specificity, recall, similarity coefficients, AUC, GINI index, Brier score and many more. Calculation of optimal cut-offs and decision stumps (Iba and Langley (1991), <doi:10.1016/B978-1-55860-247-2.50035-8>) for all implemented performance measures. Hosmer-Lemeshow goodness of fit tests (Lemeshow and Hosmer (1982), <doi:10.1093/oxfordjournals.aje.a113284>; Hosmer et al (1997), <doi:10.1002/(SICI)1097-0258(19970515)16:9%3C965::AID-SIM509%3E3.0.CO;2-O>). Statistical and epidemiological risk measures such as relative risk, odds ratio, number needed to treat (Porta (2014), <doi:10.1093%2Facref%2F9780199976720.001.0001>).
License: LGPL-3
URL: http://www.stamats.de/
NeedsCompilation: no
Packaged: 2020-10-04 12:57:19 UTC; kohlm
Repository: CRAN
Date/Publication: 2020-10-10 12:50:02 UTC

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New package vasicek with initial version 0.0.1
Package: vasicek
Title: Miscellaneous Functions for Vasicek Distribution
Version: 0.0.1
Description: Provide a collection of miscellaneous R functions related to the Vasicek distribution with the intent to make the lives of risk modelers easier.
License: GPL (>= 2)
URL: https://github.com/statcompute/vasicek
Author: WenSui Liu
Maintainer: WenSui Liu <liuwensui@gmail.com>
Depends: R (>= 3.3.3)
Imports: stats
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-05 00:11:02 UTC; liuwensui
Repository: CRAN
Date/Publication: 2020-10-10 10:10:02 UTC

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New package discoverableresearch with initial version 0.0.1
Package: discoverableresearch
Title: Checks Title, Abstract and Keywords to Optimise Discoverability
Version: 0.0.1
Authors@R: person(given = "Neal", family = "Haddaway", role = c("aut", "cre"), email = "nealhaddaway@gmail.com", comment = c(ORCID = "0000-0003-3902-2234"))
Description: A suite of tools are provided here to support authors in making their research more discoverable. check_keywords() - this function checks the keywords to assess whether they are already represented in the title and abstract. check_fields() - this function compares terminology used across the title, abstract and keywords to assess where terminological diversity (i.e. the use of synonyms) could increase the likelihood of the record being identified in a search. The function looks for terms in the title and abstract that also exist in other fields and highlights these as needing attention. suggest_keywords() - this function takes a full text document and produces a list of unigrams, bigrams and trigrams (1-, 2- or 2-word phrases) present in the full text after removing stop words (words with a low utility in natural language processing) that do not occur in the title or abstract that may be suitable candidates for keywords. suggest_title() - this function takes a full text document and produces a list of the most frequently used unigrams, bigrams and trigrams after removing stop words that do not occur in the abstract or keywords that may be suitable candidates for title words. check_title() - this function carries out a number of sub tasks: 1) it compares the length (number of words) of the title with the mean length of titles in major bibliographic databases to assess whether the title is likely to be too short; 2) it assesses the proportion of stop words in the title to highlight titles with low utility in search engines that strip out stop words; 3) it compares the title with a given sample of record titles from an .ris import and calculates a similarity score based on phrase overlap. This highlights the level of uniqueness of the title. This version of the package also contains functions currently in a non-CRAN package called 'litsearchr' <https://github.com/elizagrames/litsearchr>.
License: GPL-3
Imports: dplyr, graphics, magrittr, ngram, readr, stats, stringdist, stringi, stopwords, synthesisr, tm
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2020-10-05 06:04:53 UTC; nealhaddaway
Author: Neal Haddaway [aut, cre] (<https://orcid.org/0000-0003-3902-2234>)
Maintainer: Neal Haddaway <nealhaddaway@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-10 10:10:05 UTC

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New package tidyCpp with initial version 0.0.1
Package: tidyCpp
Type: Package
Title: Tidy C++ Header-Only Definitions for Parts of the C API of R
Version: 0.0.1
Date: 2020-10-04
Authors@R: c( person("Dirk", "Eddelbuettel", role = c("aut", "cre", "cph"), email = "edd@debian.org"), person("Romain", "Francois", role = c("ctb", "cph"), comment="Via included file Shield.h"), person("Kevin", "Ushey", role = c("ctb", "cph"), comment="Via included file Shield.h"))
Description: Core parts of the C API of R are wrapped in a C++ namespace via a set of inline functions giving a tidier representation of the underlying data structures and functionality using a header-only implementation without additional dependencies.
Suggests: Rcpp, knitr, rmarkdown, minidown
VignetteBuilder: knitr
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2020-10-04 14:14:55.907454 UTC; edd
Author: Dirk Eddelbuettel [aut, cre, cph], Romain Francois [ctb, cph] (Via included file Shield.h), Kevin Ushey [ctb, cph] (Via included file Shield.h)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Repository: CRAN
Date/Publication: 2020-10-10 09:50:02 UTC

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New package mappoly with initial version 0.2.0
Package: mappoly
Type: Package
Title: Genetic Linkage Maps in Autopolyploids
Version: 0.2.0
Authors@R: c(person(given = "Marcelo", family = "Mollinari", role = c("aut", "cre"), email = "mmollin@ncsu.edu", comment = c(ORCID="0000-0002-7001-8498")), person(given = "Gabriel", family = "Gesteira", role = "aut", email = "gabrielgesteira@usp.br", comment = c(ORCID="0000-0002-4106-7346")), person(given = "Guilhereme", family = "Pereira", role = "ctb", comment = c(ORCID="0000-0002-7106-8630")), person(given = "Augusto", family = "Garcia", role = "ctb", comment = c(ORCID="0000-0003-0634-3277")), person(given = "Zhao-Bang", family = "Zeng", role = "ctb", comment = c(ORCID="0000-0002-3115-1149")), person(given = "Katharine", family = "Preedy", role = c("ctb", "cph"), comment = "MDS ordering algorithm"), person(given = "Robert", family = "Gentleman", role = "cph", comment = "C code for MLE optimization in src/pairwise_estimation.cpp"), person(given = "Ross", family = "Ihaka", role = "cph", comment = "C code for MLE optimization in src/pairwise_estimation.cpp"), person(given = "R Foundation", role = "cph", comment = "C code for MLE optimization in src/pairwise_estimation.cpp"), person(given = "R-core", role = "cph", comment = "C code for MLE optimization in src/pairwise_estimation.cpp"))
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Description: Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologs. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.6), RCurl, plotly, fields, ggpubr, ggsci, rstudioapi, plot3D, memuse, dplyr, crayon, cli, magrittr, reshape2, ggplot2, smacof, princurve, dendextend, vcfR
LinkingTo: Rcpp
RoxygenNote: 7.1.1
SystemRequirements: C++11
Encoding: UTF-8
Suggests: testthat, RColorBrewer, updog, covr, polymapR
URL: https://github.com/mmollina/MAPpoly
BugReports: https://github.com/mmollina/MAPpoly/issues
NeedsCompilation: yes
Packaged: 2020-10-04 22:38:05 UTC; marcelo
Author: Marcelo Mollinari [aut, cre] (<https://orcid.org/0000-0002-7001-8498>), Gabriel Gesteira [aut] (<https://orcid.org/0000-0002-4106-7346>), Guilhereme Pereira [ctb] (<https://orcid.org/0000-0002-7106-8630>), Augusto Garcia [ctb] (<https://orcid.org/0000-0003-0634-3277>), Zhao-Bang Zeng [ctb] (<https://orcid.org/0000-0002-3115-1149>), Katharine Preedy [ctb, cph] (MDS ordering algorithm), Robert Gentleman [cph] (C code for MLE optimization in src/pairwise_estimation.cpp), Ross Ihaka [cph] (C code for MLE optimization in src/pairwise_estimation.cpp), R Foundation [cph] (C code for MLE optimization in src/pairwise_estimation.cpp), R-core [cph] (C code for MLE optimization in src/pairwise_estimation.cpp)
Repository: CRAN
Date/Publication: 2020-10-10 10:00:05 UTC

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New package cmdfun with initial version 1.0.2
Package: cmdfun
Type: Package
Title: Framework for Building Interfaces to Shell Commands
Version: 1.0.2
Authors@R: person("Spencer", "Nystrom", email = "nystromdev@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1000-1579"))
Description: Writing interfaces to command line software is cumbersome. 'cmdfun' provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. 'cmdfun' also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: magrittr, purrr, R.utils, rlang, testthat, usethis, utils
RoxygenNote: 7.0.2
Suggests: cli, covr, knitr, processx, rmarkdown
VignetteBuilder: knitr
URL: https://snystrom.github.io/cmdfun/, https://github.com/snystrom/cmdfun
BugReports: https://github.com/snystrom/cmdfun
NeedsCompilation: no
Packaged: 2020-10-02 14:16:21 UTC; snystrom
Author: Spencer Nystrom [aut, cre, cph] (<https://orcid.org/0000-0003-1000-1579>)
Maintainer: Spencer Nystrom <nystromdev@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-10 09:30:03 UTC

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Fri, 09 Oct 2020

New package SSHAARP with initial version 1.0.1
Package: SSHAARP
Version: 1.0.1
Date: 2020-10-08
Title: Searching Shared HLA Amino Acid Residue Prevalence
Authors@R: c(person("Livia", "Tran", role = c("aut", "cre"), email = "livia.tran@ucsf.edu"), person("Steven", "Mack", role= "aut", email = "steven.mack@ucsf.edu"), person("Josh", "Bredeweg", role= "ctb"), person("Dale", "Steinhardt", role= "ctb"))
Maintainer: Livia Tran <livia.tran@ucsf.edu>
Depends: R (>= 2.10)
Description: Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, and calculates the frequencies of those motifs based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: data.table, stringr, gtools, BIGDAWG, gmt, DescTools, dplyr, sessioninfo, filesstrings
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
SystemRequirements: GMT (5 or 6), Ghostscript (>=9.6)
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-08 20:36:02 UTC; tran.livia
Author: Livia Tran [aut, cre], Steven Mack [aut], Josh Bredeweg [ctb], Dale Steinhardt [ctb]
Repository: CRAN
Date/Publication: 2020-10-09 10:40:02 UTC

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New package T4transport with initial version 0.1.0
Package: T4transport
Type: Package
Title: Tools for Computational Optimal Transport
Version: 0.1.0
Authors@R: c(person("Kisung", "You", role = c("aut", "cre"),email = "kyoustat@gmail.com",comment=c(ORCID="0000-0002-8584-459X")))
Description: Transport theory has seen much success in many fields of statistics and machine learning. We provide a variety of algorithms to compute Wasserstein distance, barycenter, and others. See Peyré and Cuturi (2019) <doi:10.1561/2200000073> for the general exposition to the study of computational optimal transport.
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.5), Rdpack, lpSolve, stats, utils
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
RoxygenNote: 7.1.1
RdMacros: Rdpack
Suggests: ggplot2
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2020-10-02 01:47:05 UTC; kisung
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-09 08:10:03 UTC

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Thu, 08 Oct 2020

New package gglm with initial version 0.1.0
Package: gglm
Type: Package
Title: Grammar of Graphics for Linear Model Diagnostic Plots
Version: 0.1.0
Authors@R: c( person("Grayson", "White", email = "graysonwhite13@gmail.com", role = c("cre","aut")))
Description: Allows for easy creation of diagnostic plots for linear models using the Grammar of Graphics. Provides functionality for both individual diagnostic plots and an array of four standard diagnostic plots.
License: CC0
Encoding: UTF-8
LazyData: true
Imports: ggplot2, patchwork, rlang
URL: https://github.com/graysonwhite/gglm
BugReports: https://github.com/graysonwhite/gglm/issues
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-10-02 16:30:01 UTC; graysonwhite
Author: Grayson White [cre, aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-08 12:20:02 UTC

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New package AirSensor with initial version 1.0.2
Type: Package
Package: AirSensor
Version: 1.0.2
Title: Process and Display Data from Air Quality Sensors
Authors@R: c( person("Jonathan", "Callahan", email="jonathan.s.callahan@gmail.com", role=c("aut","cre")), person("Hans", "Martin", email="hans@mazamascience.com", role=c("aut")), person("Kayleigh", "Wilson", email="andrakayleigh@gmail.com", role=c("aut")), person("Tate", "Brasel", email="tatebrasel6@gmail.com", role=c("aut")), person("Helen", "Miller", email="helen@ohana.org", role=c("aut")), person("Vasileios", "Papapostolou", email="vpapapostolou@aqmd.gov", role=c("ctb")), person("Ashley", "Collier-Oxandale", email="Acollier-oxandale@aqmd.gov", role=c("ctb")), person("Brandon", "Feenstra", email="bfeenstra@aqmd.gov", role=c("ctb")) )
Author: Jonathan Callahan [aut, cre], Hans Martin [aut], Kayleigh Wilson [aut], Tate Brasel [aut], Helen Miller [aut], Vasileios Papapostolou [ctb], Ashley Collier-Oxandale [ctb], Brandon Feenstra [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Depends: R (>= 3.5.0)
Imports: countrycode, cowplot, dplyr (>= 1.0.0), dygraphs, geodist, geosphere, GGally, ggmap, ggplot2, gridExtra, httpcode, httr, jsonlite, leaflet, lubridate, magrittr, MazamaCoreUtils (>= 0.4.2), MazamaLocationUtils (>= 0.1.6), MazamaSpatialUtils (>= 0.6.3), openair, PWFSLSmoke (>= 1.2.100), readr, RColorBrewer, rlang, scales, seismicRoll, sp, stringr, tibble, tidyr, tidyselect, worldmet (>= 0.9.2), xts, zoo
Suggests: knitr, markdown, testthat (>= 2.1.0), rmarkdown, roxygen2
Description: Process and display data from air quality sensors. Initial focus is on PM2.5 measurements from sensors produced by 'PurpleAir' <https://www2.purpleair.com>.
License: GPL-3
URL: https://github.com/MazamaScience/AirSensor
BugReports: https://github.com/MazamaScience/AirSensor/issues
VignetteBuilder: knitr
Repository: CRAN
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2020-10-02 14:17:35 UTC; jonathan
Date/Publication: 2020-10-08 12:10:02 UTC

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New package spDates with initial version 1.0
Package: spDates
Title: Analysis of Spatial Gradients in Radiocarbon Dates
Version: 1.0
Authors@R: person(given = "Jonas", family = "Gregorio de Souza", role = c("aut", "cre"), email = "jonas.gregorio@gmail.com", comment = c(ORCID = "0000-0001-6032-4443"))
Description: Inspired by space-time regressions often performed to assess the expansion of the Neolithic from the Near East to Europe (Pinhasi et al. 2005 <doi:10.1371/journal.pbio.0030410>). Test for significant correlations between the (earliest) radiocarbon dates of archaeological sites and their respective distances from a hypothetical center of origin. Distances can be either great-circle or least-cost paths calculated from a friction surface. Both ordinary least squares (OLS) and reduced major axis (RMA) methods are supported (Russell et al. 2014 <doi:10.1371/journal.pone.0087854>). It is also possible to iterate over many sites to identify the most likely origin.
Depends: R (>= 3.5.0), rcarbon
Imports: data.table, dplyr, gdistance, ggplot2, parallel, raster, smatr, viridisLite, magrittr, rlang, sp, gstat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-02 09:49:18 UTC; jgregoriods
Author: Jonas Gregorio de Souza [aut, cre] (<https://orcid.org/0000-0001-6032-4443>)
Maintainer: Jonas Gregorio de Souza <jonas.gregorio@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-08 11:20:02 UTC

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New package quickerstats with initial version 0.0.1
Package: quickerstats
Type: Package
Title: An 'R' Client for the 'USDA NASS Quick Stats API'
Version: 0.0.1
Authors@R: person("Aaron", "Anderson", email = "aaronanderson.co@gmail.com", role = c("aut", "cre"))
Description: Provides several convenience functions for searching and pulling data from the 'USDA NASS Quick Stats API' <https://quickstats.nass.usda.gov/api>. Users can easily search for specific data items, and then download county-level or state-level Census of Agricultural data from a specified year.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: httr (>= 1.4.1), readr (>= 1.3.1), curl (>= 4.2.0), tibble (>= 2.1.3)
BugReports: https://github.com/anderaa/quickerstats/issues
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-02 14:21:35 UTC; ama
Author: Aaron Anderson [aut, cre]
Maintainer: Aaron Anderson <aaronanderson.co@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-08 12:00:07 UTC

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New package MSGARCHelm with initial version 0.1.0
Package: MSGARCHelm
Type: Package
Title: Hybridization of MS-GARCH and ELM Model
Version: 0.1.0
Authors@R: c(person(given = "Rajeev Ranjan", family = "Kumar", role = c("aut", "cre"), email = "rrk.uasd@gmail.com"), person(given = "Girish Kumar", family = "Jha", role = c("aut", "ths", "ctb")), person(given = "Neeraj", family = "Budhlakoti", role = "ctb"))
Description: Implements the three parallel forecast combinations of Markov Switching GARCH and extreme learning machine model along with the selection of appropriate model for volatility forecasting. For method details see Hsiao C, Wan SK (2014). <doi:10.1016/j.jeconom.2013.11.003>, Hansen BE (2007). <doi:10.1111/j.1468-0262.2007.00785.x>, Elliott G, Gargano A, Timmermann A (2013). <doi:10.1016/j.jeconom.2013.04.017>.
Depends: R (>= 3.6)
Imports: nnfor, MSGARCH, forecast
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2020-10-02 14:11:40 UTC; Neeraj
Author: Rajeev Ranjan Kumar [aut, cre], Girish Kumar Jha [aut, ths, ctb], Neeraj Budhlakoti [ctb]
Maintainer: Rajeev Ranjan Kumar <rrk.uasd@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-08 11:40:02 UTC

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New package dCUR with initial version 1.0.0
Package: dCUR
Type: Package
Title: Dimension Reduction with Dynamic CUR
Version: 1.0.0
Depends: R (>= 3.5.0)
Maintainer: Cesar Gamboa <info@cesargamboasanabria.com>
URL: https://www.cesargamboasanabria.com
Author: Cesar Gamboa-Sanabria [aut, mdc, cph, cre] (<https://orcid.org/0000-0001-6733-4759>), Stefani Matarrita-Munoz [aut] (<https://orcid.org/0000-0002-1222-1981>), Katherine Barquero-Mejias [aut] (<https://orcid.org/0000-0003-1760-9026>), Greibin Villegas-Barahona [aut] (<https://orcid.org/0000-0002-4380-0812>), Mercedes Sanchez-Barba [aqt] (<https://orcid.org/0000-0002-3324-5798>), Maria Purificacion Galindo-Villardon [aqt] (<https://orcid.org/0000-0001-6977-7545>)
Description: Dynamic CUR (dCUR) boosts the CUR decomposition (Mahoney MW., Drineas P. (2009) <doi:10.1073/pnas.0803205106>) varying the k, the number of columns and rows used, and its final purposes to help find the stage, which minimizes the relative error to reduce matrix dimension. The goal of CUR Decomposition is to give a better interpretation of the matrix decomposition employing proper variable selection in the data matrix, in a way that yields a simplified structure. Its origins come from analysis in genetics. The goal of this package is to show an alternative to variable selection (columns) or individuals (rows). The idea proposed consists of adjusting the probability distributions to the leverage scores and selecting the best columns and rows that minimize the reconstruction error of the matrix approximation ||A-CUR||. It also includes a method that recalibrates the relative importance of the leverage scores according to an external variable of the user's interest.
Imports: parallel, magrittr, stackoverflow, mclust, MASS, ppcor, ggplot2, dplyr, Rdpack
License: GPL-3
Encoding: UTF-8
LazyData: true
RdMacros: Rdpack
RoxygenNote: 7.1.1
Suggests: testthat, snow
NeedsCompilation: no
Packaged: 2020-10-02 13:52:15 UTC; Dell
Repository: CRAN
Date/Publication: 2020-10-08 11:30:02 UTC

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New package EHR with initial version 0.3-1
Package: EHR
Version: 0.3-1
Date: 2020-09-28
Title: Electronic Health Record (EHR) Data Processing and Analysis Tool
Maintainer: Leena Choi <naturechoi@gmail.com>
Authors@R: c(person("Leena", "Choi", role = c("aut", "cre"), email = "naturechoi@gmail.com", comment = c(ORCID = "0000-0002-2544-7090")), person("Cole", "Beck", role = "aut", email = "cole.beck@vumc.org", comment = c(ORCID = "0000-0002-6849-6255")), person("Hannah", "Weeks", role = "aut", email = "hannah.l.weeks@vanderbilt.edu"), person("Elizabeth", "McNeer", role = "aut", email = "elizabeth.mcneer@vumc.org"))
Description: Process and analyze Electronic Health Record (EHR) data. The 'EHR' package provides modules to perform diverse medication-related studies using data from EHR databases. Especially, the package includes modules to perform pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden, Stein, Bejan, Denny, and Van Driest (2020) <doi:10.1002/cpt.1787>. Additional modules will be added in future. In addition, this package provides various functions useful to perform Phenome Wide Association Study (PheWAS) to explore associations between drug exposure and phenotypes obtained from EHR data, as outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018) <doi:10.1093/bioinformatics/bty306>.
Depends: R (>= 2.10)
License: GPL (>= 3)
Imports: stats, utils, data.table, methods
Suggests: glmnet, logistf, medExtractR, knitr, rmarkdown, ggplot2, formula.tools
NeedsCompilation: no
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Packaged: 2020-10-05 16:34:36 UTC; beckca
Author: Leena Choi [aut, cre] (<https://orcid.org/0000-0002-2544-7090>), Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>), Hannah Weeks [aut], Elizabeth McNeer [aut]
Repository: CRAN
Date/Publication: 2020-10-08 10:40:02 UTC

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New package LDheatmap with initial version 1.0-4
Package: LDheatmap
Version: 1.0-4
Date: 2020-10-03
Title: Graphical Display of Pairwise Linkage Disequilibria Between SNPs
Authors@R: c(person("Ji-Hyung","Shin",email="shin@sfu.ca", role="aut"), person("Sigal","Blay", email="sblay@sfu.ca",role="aut"), person("Nicholas","Lewin-Koh",email="nikko@hailmail.net", role="ctb"), person("Brad","McNeney",email="mcneney@sfu.ca",role=c("aut","cre")), person("Gloria","Yang",email="xuefei_yang@sfu.ca",role="ctb"), person("Matthew","Reyers",email="matthew_reyers@sfu.ca",role="ctb"), person("Youwei","Yan",email="youweiy@sfu.ca",role="ctb"), person("Jinko","Graham",email="jgraham@sfu.ca",role="aut"))
Maintainer: Brad McNeney <mcneney@sfu.ca>
Depends: R (>= 4.0)
Imports: grid, genetics, snpStats, Rcpp
Suggests: rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, lattice, ggplot2, vcfR
Description: Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The methods are described in Shin et al. (2006) <doi:10.18637/jss.v016.c03>. Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages <https://bioconductor.org>.
License: GPL-3
URL: https://sfustatgen.github.io/LDheatmap/
Repository: CRAN
Date/Publication: 2020-10-08 10:00:02 UTC
RoxygenNote: 7.1.0
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2020-10-03 16:53:57 UTC; mcneney
Author: Ji-Hyung Shin [aut], Sigal Blay [aut], Nicholas Lewin-Koh [ctb], Brad McNeney [aut, cre], Gloria Yang [ctb], Matthew Reyers [ctb], Youwei Yan [ctb], Jinko Graham [aut]

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New package sketch with initial version 1.0.3
Package: sketch
Type: Package
Title: Interactive Sketches
Version: 1.0.3
Authors@R: c( person("Chun Fung","Kwok", role = c("aut", "cre"), email = "kwokcf@unimelb.edu.au"), person("Kate", "Saunders", role = "ctb") )
Description: Creates static / animated / interactive visualisations embeddable in R Markdown documents. It implements an R-to-JavaScript transpiler and enables users to write JavaScript applications using the syntax of R.
License: Apache License (>= 2.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: magrittr, rlang, purrr, rstudioapi, glue, htmltools, base64enc, jsonlite, shiny
Suggests: testthat, covr, knitr, rmarkdown,
BugReports: https://github.com/kcf-jackson/sketch
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-02 05:25:39 UTC; mac_ks
Author: Chun Fung Kwok [aut, cre], Kate Saunders [ctb]
Maintainer: Chun Fung Kwok <kwokcf@unimelb.edu.au>
Repository: CRAN
Date/Publication: 2020-10-08 07:40:03 UTC

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New package BIGDAWG with initial version 2.3.1
Package: BIGDAWG
Type: Package
Title: Case-Control Analysis of Multi-Allelic Loci
Version: 2.3.1
Date: 2020-10-07
Author: Derek Pappas <pappas.derek@gmail.com>, Steve Mack <steven.mack@ucsf.edu>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <steven.mack@ucsf.edu>
URL: http://tools.immunogenomics.org/, https://github.com/IgDAWG/BIGDAWG
BugReports: https://github.com/IgDAWG/BIGDAWG/issues
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: True
Depends: R (>= 3.5.0)
Imports: XML, httr, haplo.stats, parallel, knitr
Suggests: rmarkdown, qpdf
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-07 20:24:41 UTC; sjmack
Repository: CRAN
Date/Publication: 2020-10-08 07:50:02 UTC

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Wed, 07 Oct 2020

New package TVMM with initial version 3.2
Package: TVMM
Type: Package
Title: Multivariate Tests for the Vector of Means
Version: 3.2
Authors@R: c( person("Henrique", "Jose de Paula Alves", email = "jpahenrique@gmail.com", role= c("aut", "cre")), person("Ben", "Deivide de Oliveira Batista", email = "ben.deivide@gmail.com", role = "ctb"), person("Daniel", "Furtado Ferreira", email = "danielff@ufla.br", role= "aut"))
Author: Henrique Jose de Paula Alves [aut, cre], Ben Deivide de Oliveira Batista [ctb], Daniel Furtado Ferreira [aut]
Maintainer: Henrique Jose de Paula Alves <jpahenrique@gmail.com>
Description: This is a statistical tool interactive that provides multivariate statistical tests that are more powerful than traditional Hotelling T2 test and LRT (likelihood ratio test) for the vector of normal mean populations with and without contamination and non-normal populations (Henrique J. P. Alves & Daniel F. Ferreira (2019) <DOI: 10.1080/03610918.2019.1693596>).
Depends: R (>= 3.1.0)
Imports: tcltk, ggplot2, robustbase, tcltk2, tkrplot, gridExtra, stats, utils, MASS, grDevices, DescToolsAddIns
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-07 10:22:17 UTC; Henrique
Repository: CRAN
Date/Publication: 2020-10-07 12:40:10 UTC

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New package skynet with initial version 1.4.0
Type: Package
Package: skynet
Version: 1.4.0
Title: Generates Networks from BTS Data
Authors@R: person("Filipe", "Teixeira", email = "Filipe.MarquesTeixeira@Ugent.be", role = c("aut", "cre"))
Maintainer: Filipe Teixeira <Filipe.MarquesTeixeira@Ugent.be>
URL: https://github.com/ropensci/skynet
Description: A flexible tool that allows generating bespoke air transport statistics for urban studies based on publicly available data from the Bureau of Transport Statistics (BTS) in the United States <https://www.transtats.bts.gov/databases.asp?Mode_ID=1&Mode_Desc=Aviation&Subject_ID2=0>.
License: MIT + file LICENSE
BugReports: https://github.com/ropensci/skynet/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Collate: 'PowerLaw.R' 'createNodes.R' 'data_ODsample.R' 'data_airports.R' 'data_carriers.R' 'data_metro.R' 'disparityfilter.R' 'findAirport.R' 'fromto.R' 'netImport.R' 'netDir.R' 'netUnd.R' 'netInt.R' 'netPath.R' 'make_net_trip.R' 'skynet.R' 'nodeStats.R' 'import_t100.R' 'import_db1b.R' 'import_ontime.R' 'findCarrier.R' 'plotMap.R' 'skynet_example.R' 'bootnet.R' 'summary.R' 'download_db1b.R' 'download_t100.R' 'download_t100_int.R' 'download_ontime.R'
Depends: R (>= 3.1.2)
Imports: data.table, igraph, dplyr, ggplot2, ggrepel, stringr, maps, httr, geosphere, leaflet
Suggests: knitr, rmarkdown, testthat, kableExtra, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-05 11:32:17 UTC; Fil
Author: Filipe Teixeira [aut, cre]
Repository: CRAN
Date/Publication: 2020-10-07 12:40:03 UTC

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New package modeltime.ensemble with initial version 0.1.0
Package: modeltime.ensemble
Type: Package
Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Version: 0.1.0
Authors@R: c( person("Matt", "Dancho", email = "mdancho@business-science.io", role = c("aut", "cre")), person("Business Science", role = "cph") )
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging, weighted averaging, and stacking. These techniques are popular methods to improve forecast accuracy and stability. Refer to papers such as "Machine-Learning Models for Sales Time Series Forecasting" Pavlyshenko, B.M. (2019) <doi:10.3390>.
URL: https://github.com/business-science/modeltime.ensemble
BugReports: https://github.com/business-science/modeltime.ensemble/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: modeltime (>= 0.2.0), R (>= 3.5)
Imports: tune, rsample, yardstick, workflows, parsnip, recipes, dials, timetk (>= 2.3.0), tibble, dplyr, tidyr, purrr, glue, stringr, rlang (>= 0.1.2), cli, crayon, utils, generics, magrittr, glmnet, progressr, tictoc
Suggests: roxygen2, testthat, tidymodels, tidyverse, lubridate, knitr, rmarkdown, covr, remotes
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-01 18:51:13 UTC; mdancho
Author: Matt Dancho [aut, cre], Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Repository: CRAN
Date/Publication: 2020-10-07 12:30:06 UTC

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New package hdiVAR with initial version 1.0.1
Package: hdiVAR
Type: Package
Title: Statistical Inference for Noisy Vector Autoregression
Version: 1.0.1
Authors@R: c(person("Xiang", "Lyu", role = c("aut","cre"), email="xianglyu@berkeley.edu"), person("Jian", "Kang", role = c("aut")), person("Lexin", "Li", role = c("aut")))
Description: The model is high-dimensional vector autoregression with measurement error, also known as linear gaussian state-space model. Provable sparse expectation-maximization algorithm is provided for the estimation of transition matrix and noise variances. Global and simultaneous testings are implemented for transition matrix with false discovery rate control. For more information, see the accompanying paper: Lyu, X., Kang, J., & Li, L. (2020). "Statistical inference for high-dimensional vector autoregression with measurement error", arXiv preprint <arXiv:2009.08011>.
Imports: lpSolve, abind
License: GPL (>= 2)
Depends: R (>= 3.1)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Author: Xiang Lyu [aut, cre], Jian Kang [aut], Lexin Li [aut]
Maintainer: Xiang Lyu <xianglyu@berkeley.edu>
NeedsCompilation: no
Packaged: 2020-10-01 18:29:18 UTC; xianglyu
Repository: CRAN
Date/Publication: 2020-10-07 12:20:03 UTC

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New package fanovaGraph with initial version 1.5
Package: fanovaGraph
Type: Package
Title: Building Kriging Models from FANOVA Graphs
Version: 1.5
Date: 2020-10-01
Author: Jana Fruth, Thomas Muehlenstaedt, Olivier Roustant, Malte Jastrow, Sonja Kuhnt
Maintainer: Sonja Kuhnt <sonja.kuhnt@fh-dortmund.de>
Description: Estimation and plotting of a function's FANOVA graph to identify the interaction structure and fitting, prediction and simulation of a Kriging model modified by the identified structure. The interactive function plotManipulate() can only be run on the 'RStudio IDE' with 'RStudio' package 'manipulate' loaded. 'RStudio' is freely available (<https://rstudio.com/>), and includes package 'manipulate'. The equivalent function plotTk() bases on CRAN Repository packages only. For further information on the method see Fruth, J., Roustant, O., Kuhnt, S. (2014) <doi:10.1016/j.jspi.2013.11.007>.
License: GPL-3
LazyLoad: yes
Depends: sensitivity, igraph, DiceKriging (>= 1.4)
Suggests: manipulate, testthat
Packaged: 2020-10-06 15:30:48 UTC; Sonja
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2020-10-07 12:10:02 UTC

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New package satin with initial version 1.0
Package: satin
Type: Package
Title: Visualisation and Analysis of Ocean Data Derived from Satellites
Version: 1.0
Date: 2020-09-26
Encoding: UTF-8
Author: Héctor Villalobos and Eduardo González-Rodríguez <egonzale@cicese.mx>
Maintainer: Héctor Villalobos <hvillalo@ipn.mx>
Description: With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University <http://sites.science.oregonstate.edu/ocean.productivity/> can also be handled previous conversion from HDF4 to HDF5 format. Many other ocean variables can be processed by importing netCDF data files from two European Union's Copernicus Marine Service databases <https://marine.copernicus.eu/>, namely Global Ocean Physical Reanalysis and Global Ocean Biogeochemistry Hindcast.
Depends: R (>= 3.5.0)
License: GPL-3
URL: https://github.com/hvillalo/satin
BugReports: https://github.com/hvillalo/satin/issues
Collate: satin-class.R read.cmems.R read.ghrsst.R read.nasaoc.R read.osunpp.R fmainPos.R imageScale.R plot.satin.R satinPalette.R quiver.R verticalProfiles.R satinDataframe.R pixelate.R climatology.R crop.R extractPts.R isolines.R satinMean.R anomaly.R
Imports: ncdf4, maps, maptools, PBSmapping, grDevices, splancs, sp, geosphere, graphics, methods, lubridate
NeedsCompilation: no
Packaged: 2020-10-01 14:19:20 UTC; hecvi
Repository: CRAN
Date/Publication: 2020-10-07 12:00:02 UTC

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New package quantdr with initial version 1.0.0
Package: quantdr
Type: Package
Title: Dimension Reduction Techniques for Conditional Quantiles
Version: 1.0.0
Authors@R: person("Eliana", "Christou", email="echris15@uncc.edu", role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0001-5044-0969"))
Description: An implementation of dimension reduction techniques for conditional quantiles. Nonparametric estimation of conditional quantiles is also available.
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Imports: dr, KernSmooth, MTS, mvtnorm, quantreg
Depends: R (>= 3.1.0)
RoxygenNote: 7.1.1
Collate: 'bic_d.R' 'llqrcv.R' 'llqr.R' 'cqs.R'
Suggests: knitr, rmarkdown, testthat, pracma, MASS
VignetteBuilder: knitr
SystemRequirements: GNU make
URL: https://github.com/elianachristou/quantdr
BugReports: https://github.com/elianachristou/quantdr/issues
NeedsCompilation: no
Packaged: 2020-10-01 14:16:49 UTC; echris15
Author: Eliana Christou [aut, cre] (<https://orcid.org/0000-0001-5044-0969>)
Maintainer: Eliana Christou <echris15@uncc.edu>
Repository: CRAN
Date/Publication: 2020-10-07 11:50:03 UTC

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New package PVplr with initial version 0.1.0
Package: PVplr
Type: Package
Title: Performance Loss Rate Analysis Pipeline
Version: 0.1.0
Authors@R: c( person("Alan", "Curran", email = "alan.curran@case.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4505-8359")), person("Tyler", "Burleyson", email = "tyler.burleyson@case.edu", role = "aut", comment = c(ORCID = "0000-0002-6356-5354")), person("Sascha", "Lindig", email = "Sascha.Lindig@eurac.edu", role = "aut", comment = c(ORCID = "0000-0001-5421-8265")), person("David", "Moser", email = "david.moser@eurac.edu", role = "aut", comment = c(ORCID = "0000-0002-4895-8862")), person("Roger", "French", email = "roger.french@case.edu", role = "aut", comment = c(ORCID = "0000-0002-6162-0532")), person(given = "Solar Durability and Lifetime Extension research center", role = c("cph", "fnd")))
Description: The pipeline contained in this package provides tools used in the Solar Durability and Lifetime Extension Center (SDLE) for the analysis of Performance Loss Rates (PLR) in real world photovoltaic systems. Functions included allow for data cleaning, feature correction, power predictive modeling, PLR determination, and uncertainty bootstrapping through various methods <doi:10.1109/PVSC40753.2019.8980928>. The vignette "Pipeline Walkthrough" gives an explicit run through of typical package usage. This material is based upon work supported by the U.S Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) under Solar Energy Technologies Office (SETO) Agreement Number DE-EE-0008172. This work made use of the High Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University.
Depends: R (>= 2.10)
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr (>= 0.7.8), magrittr (>= 1.5), broom (>= 0.5.1), ggplot2 (>= 3.1.0), stlplus (>= 0.5.1), cluster (>= 2.0.7-1), purrr (>= 0.3.3), tidyr (>= 1.1.1), minpack.lm (>= 1.2-1), rlang (>= 0.3.1), segmented
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-01 15:05:14 UTC; Alan
Author: Alan Curran [aut, cre] (<https://orcid.org/0000-0002-4505-8359>), Tyler Burleyson [aut] (<https://orcid.org/0000-0002-6356-5354>), Sascha Lindig [aut] (<https://orcid.org/0000-0001-5421-8265>), David Moser [aut] (<https://orcid.org/0000-0002-4895-8862>), Roger French [aut] (<https://orcid.org/0000-0002-6162-0532>), Solar Durability and Lifetime Extension research center [cph, fnd]
Maintainer: Alan Curran <alan.curran@case.edu>
Repository: CRAN
Date/Publication: 2020-10-07 12:00:20 UTC

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Tue, 06 Oct 2020

New package Momocs with initial version 1.3.2
Package: Momocs
Title: Morphometrics using R
Version: 1.3.2
Date: 2020-10-05
Authors@R: c( person("Vincent", "Bonhomme", ,"bonhomme.vincent@gmail.com", c("aut", "cre")), person("Julien", "Claude", , , c("aut"), comment = "core functions in base R"))
Description: The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.
License: GPL-2 | GPL-3
Encoding: UTF-8
URL: https://github.com/MomX/Momocs/
BugReports: https://github.com/MomX/Momocs/issues
Depends: R(>= 3.2)
LazyData: true
Imports: cluster, dendextend, dplyr, magrittr, geometry, geomorph, ggplot2, graphics, grDevices, jpeg, MASS, progress, RColorBrewer, rgeos, sp, utils, vegan, tibble
Suggests: devtools, knitr, rmarkdown, testthat, covr, roxygen2
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-10-06 12:46:30 UTC; vbonhomme
Author: Vincent Bonhomme [aut, cre], Julien Claude [aut] (core functions in base R)
Maintainer: Vincent Bonhomme <bonhomme.vincent@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-06 15:20:11 UTC

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New package sivs with initial version 0.2.2
Package: sivs
Type: Package
Title: Seed Independent Variable Selection
Version: 0.2.2
Date: 2020-09-11
Authors@R: c(person(given = "Mehrad", family = "Mahmoudian", role = c("aut", "cre"), email = "mehrad.mahmoudian@utu.fi", comment = c(ORCID = "0000-0001-7650-1862")), person(given = "Mikko", family = "Venäläinen", role = c("aut", "rev"), email = "", comment = c(ORCID = "0000-0003-1777-4259")), person(given = "Riku", family = "Klèn", role = c("aut", "ths"), email = "", comment = c(ORCID = "0000-0002-0982-8360")), person(given = "Laura", family = "Elo", role = c("aut", "ths", "fnd"), email = "", comment = c(ORCID = "0000-0001-5648-4532")))
Imports: doParallel, parallel, foreach, glmnet, pROC, varhandle, utils
Suggests: knitr, rmarkdown, markdown
Description: An iterative feature selection method (manuscript submitted) that internally utilizes various Machine Learning methods that have embedded feature reduction in order to shrink down the feature space into a small and yet robust set.
License: GPL-3
URL: https://github.com/mmahmoudian/sivs
BugReports: https://github.com/mmahmoudian/sivs/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-01 09:34:45 UTC; mehrad
Author: Mehrad Mahmoudian [aut, cre] (<https://orcid.org/0000-0001-7650-1862>), Mikko Venäläinen [aut, rev] (<https://orcid.org/0000-0003-1777-4259>), Riku Klèn [aut, ths] (<https://orcid.org/0000-0002-0982-8360>), Laura Elo [aut, ths, fnd] (<https://orcid.org/0000-0001-5648-4532>)
Maintainer: Mehrad Mahmoudian <mehrad.mahmoudian@utu.fi>
Repository: CRAN
Date/Publication: 2020-10-06 12:40:03 UTC

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New package occCite with initial version 0.3.0
Package: occCite
Type: Package
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Version: 0.3.0
Authors@R: c( person(given = "Hannah L.", family = "Owens", ,"hannah.owens@gmail.com", role=c("aut","cre"), comment = c(ORCID = "0000-0003-0071-1745")), person(given = "Cory", family = "Merow",,,role="aut", comment = c(ORCID = "0000-0003-0561-053X")), person(given = "Brian", family = "Maitner", ,,,role="aut", comment = c(ORCID = "0000-0002-2118-9880")), person(given = "Jamie M.", family = "Kass", ,,,role="aut", comment = c(ORCID = "0000-0002-9432-895X")), person(given = "Vijay", family = "Barve",,"vijay.barve@gmail.com ",role="aut", comment = c(ORCID = "0000-0002-4852-2567")), person(given = "Robert P.", family = "Guralnick",,,role="aut", comment = c(ORCID = "0000-0001-6682-1504")) )
Author: Hannah L. Owens [aut, cre] (<https://orcid.org/0000-0003-0071-1745>), Cory Merow [aut] (<https://orcid.org/0000-0003-0561-053X>), Brian Maitner [aut] (<https://orcid.org/0000-0002-2118-9880>), Jamie M. Kass [aut] (<https://orcid.org/0000-0002-9432-895X>), Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Robert P. Guralnick [aut] (<https://orcid.org/0000-0001-6682-1504>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Description: Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
License: GPL (>= 2)
URL: https://github.com/hannahlowens/occCite
BugReports: https://github.com/hannahlowens/occCite/issues
Encoding: UTF-8
LazyData: true
Language: en-US
Depends: R (>= 3.5.0)
Suggests: rmarkdown, RColorBrewer, viridis, remotes
Imports: RefManageR, bib2df, BIEN, bit64, dplyr, ape, lubridate, methods, rgbif (>= 3.1), taxize, stringr, knitr, stats, leaflet, htmltools, ggplot2, rlang, magrittr, tidyr, RPostgreSQL, DBI, waffle
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-01 08:49:10 UTC; HannahOwens
Repository: CRAN
Date/Publication: 2020-10-06 12:30:02 UTC

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New package cmsafvis with initial version 1.0.0
Package: cmsafvis
Title: Visualize CM SAF NetCDF Data
Version: 1.0.0
Authors@R: person(given = "Steffen", family = "Kothe", role = c("aut", "cre"), email = "Steffen.Kothe@dwd.de")
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafvis' R-package provides a collection of R-operators for the analysis and visualization of CM SAF NetCDF data. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).
License: GPL (>= 3)
Depends: R (>= 3.6)
Imports: animation (>= 2.6), assertthat (>= 0.2.1), cmsafops (>= 1.0.0), colorspace (>= 1.4), countrycode (>= 1.1), fields (>= 10.3), mapproj (>= 1.2.7), maps (>= 3.3.0), maptools (>= 0.9), methods (>= 3.6), ncdf4 (>= 1.17), png (>= 0.1), progress (>= 1.2.2), raster (>= 3.0), rworldxtra (>= 1.01), sp (>= 1.4), yaml (>= 2.2)
NeedsCompilation: no
Repository: CRAN
LazyData: true
RoxygenNote: 7.1.1
Encoding: UTF-8
Language: en-US
Suggests: plotKML (>= 0.6), rgdal (>= 1.4), rnaturalearth (>= 0.1), spelling (>= 2.1), testthat (>= 2.3)
Packaged: 2020-10-01 07:33:13 UTC; stkothe
Author: Steffen Kothe [aut, cre]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Date/Publication: 2020-10-06 12:20:02 UTC

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New package suppdata with initial version 1.1-4
Package: suppdata
Type: Package
Title: Downloading Supplementary Data from Published Manuscripts
Version: 1.1-4
Authors@R: c(person("William D.", "Pearse", email = "will.pearse@gmail.com", role = c("aut", "cre"), comment=c(ORCID="0000-0002-6241-3164")), person("Scott", "Chamberlain", role = "aut", comment=c(ORCID="0000-0003-1444-9135")), person("Daniel", "Nuest", role = "aut", comment=c(ORCID="0000-0002-0024-5046")), person("Ross", "Mounce", role = c("rev"), comment = "Ross Mounce reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195"), person("Sarah", "Supp", role = c("rev"), comment = "Sarah Supp reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195"))
Maintainer: William D. Pearse <will.pearse@gmail.com>
Description: Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().
License: MIT + file LICENSE
URL: https://docs.ropensci.org/suppdata/, https://github.com/ropensci/suppdata/
BugReports: https://github.com/ropensci/suppdata/
VignetteBuilder: knitr
LazyLoad: yes
Suggests: knitr (>= 1.6), testthat (>= 2.0.0), covr (>= 3.0.1), fulltext (>= 0.1.4.9000)
Imports: httr (>= 1.0.0), xml2 (>= 1.2.0), jsonlite (>= 1.5), rcrossref (>= 0.8.0)
Encoding: UTF-8
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-05 12:41:47 UTC; will
Author: William D. Pearse [aut, cre] (<https://orcid.org/0000-0002-6241-3164>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Daniel Nuest [aut] (<https://orcid.org/0000-0002-0024-5046>), Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195), Sarah Supp [rev] (Sarah Supp reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195)
Repository: CRAN
Date/Publication: 2020-10-06 12:00:03 UTC

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New package blink with initial version 1.1.0
Package: blink
Type: Package
Title: Record Linkage for Empirically Motivated Priors
Version: 1.1.0
Authors@R: person("Rebecca", "Steorts", email = "beka@stat.duke.edu", role = c("aut", "cre"))
Depends: R (>= 3.0.2), stringdist, plyr
Imports: stats, utils
Suggests: knitr, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
Description: An implementation of the model in Steorts (2015) <DOI:10.1214/15-BA965SI>, which performs Bayesian entity resolution for categorical and text data, for any distance function defined by the user. In addition, the precision and recall are in the package to allow one to compare to any other comparable method such as logistic regression, Bayesian additive regression trees (BART), or random forests. The experiments are reproducible and illustrated using a simple vignette. LICENSE: GPL-3 + file license.
License: GPL-3
LazyData: TRUE
RoxygenNote: 7.1.1.9000
NeedsCompilation: no
Packaged: 2020-09-30 21:00:40 UTC; rebeccasteorts
Author: Rebecca Steorts [aut, cre]
Maintainer: Rebecca Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-06 09:50:02 UTC

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New package treeducken with initial version 1.0.0
Package: treeducken
Type: Package
Title: Nested Phylogenetic Tree Simulator
Version: 1.0.0
Authors@R: c(person("Wade", "Dismukes", email="wade.dismukes@gmail.com", role=c("aut","cre")), person(c("Tracy","A."), "Heath", role=c("aut")), person("Josh", "Justison", role=c("ctb")), person("Damien", "de Vienne", role=c("ctb")), person("Liam", "Revell", role=c("ctb")), person("Emmanuel", "Paradis", role=c("ctb")), person("Klaus", "Schliep", role=c("ctb")), person("Ben", "Bolker", role=c("ctb")), person(c("Luke","J."), "Harmon", role=c("ctb")), person(c("Joseph","W."), "Brown", role=c("ctb")))
Description: Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) <doi:10.1093/sysbio/syv082>, Rasmussen and Kellis (2012) <doi:10.1101/gr.123901.111>.
License: GPL-3
SystemRequirements: C++11
Imports: Rcpp (>= 1.0.2), apTreeshape, graphics, methods
Depends: ape
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 7.1.1
LazyData: true
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-09-30 15:45:29 UTC; waded
Author: Wade Dismukes [aut, cre], Tracy A. Heath [aut], Josh Justison [ctb], Damien de Vienne [ctb], Liam Revell [ctb], Emmanuel Paradis [ctb], Klaus Schliep [ctb], Ben Bolker [ctb], Luke J. Harmon [ctb], Joseph W. Brown [ctb]
Maintainer: Wade Dismukes <wade.dismukes@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-06 08:10:02 UTC

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Mon, 05 Oct 2020

New package FunWithNumbers with initial version 1.0
Package: FunWithNumbers
Type: Package
Title: Fun with Fractions and Number Sequences
Version: 1.0
Date: 2020-09-05
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>
Description: A collection of toys to do things like generate Collatz sequences, convert a fraction to "continued fraction" form, calculate a fraction which is a close approximation to some value (e.g., 22/7 or 355/113 or pi), and so on.
License: LGPL-3
LazyData: FALSE
Imports: Rmpfr, gmp
NeedsCompilation: no
Packaged: 2020-09-30 10:16:10 UTC; cgw
Repository: CRAN
Date/Publication: 2020-10-05 12:10:02 UTC

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New package CNAIM with initial version 1.0.0
Package: CNAIM
Type: Package
Title: Common Network Asset Indices Methodology (CNAIM)
Version: 1.0.0
Authors@R: c(person(given = "Emil", family = "Larsen", role = c("aut", "cre"), email = "mohsin@utiligize.com"), person(given = "Kalle", family = "Hansen", role = c("aut"), email = "kalle@utiligize.com"), person(given = "Peter", family = "Larsen", role = c("aut"), email = "peter@utiligize.com"))
Maintainer: Emil Larsen <mohsin@utiligize.com>
Description: Implementation of the CNAIM standard in R. Contains a series of algorithms which determine the probability of failure, consequences of failure and monetary risk associated with electricity distribution companies' assets such as transformers and cables. Results are visualized in an easy-to-understand risk matrix.
URL: https://www.cnaim.io/
BugReports: https://github.com/Utiligize/CNAIM/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: dplyr, htmltools, htmlwidgets (>= 1.2), jsonlite, magrittr, r2d3, readxl, stringr, testthat, tibble, widgetframe
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-30 13:22:13 UTC; mohsinvindhani
Author: Emil Larsen [aut, cre], Kalle Hansen [aut], Peter Larsen [aut]
Repository: CRAN
Date/Publication: 2020-10-05 12:10:05 UTC

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New package winch with initial version 0.0.1
Package: winch
Title: Portable Native and Joint Stack Traces
Version: 0.0.1
Date: 2020-09-26
Authors@R: c(person(given = "Kirill", family = "Müller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org", comment = c(ORCID = "0000-0002-1416-3412")), person(given = "R Consortium", role = "fnd"), person(given = "Ian Lance", family = "Taylor", role = "aut", comment = "Bundled libbacktrace library"), person(given = "Free Software Foundation", role = "cph", comment = "Bundled libbacktrace library"))
Description: Obtain the native stack trace and fuse it with R's stack trace for easier debugging of R packages with native code.
License: GPL-3
URL: https://r-prof.github.io/winch/, https://github.com/r-prof/winch
BugReports: https://github.com/r-prof/winch/issues
Imports: procmaps (>= 0.0.2)
Suggests: DBI, knitr, magrittr, purrr, rlang, rmarkdown, RSQLite, testthat, vctrs
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
NeedsCompilation: yes
Packaged: 2020-09-30 09:09:20 UTC; kirill
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd], Ian Lance Taylor [aut] (Bundled libbacktrace library), Free Software Foundation [cph] (Bundled libbacktrace library)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Repository: CRAN
Date/Publication: 2020-10-05 11:50:02 UTC

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New package REPPlabShiny with initial version 0.4.0
Package: REPPlabShiny
Type: Package
Title: 'REPPlab' via a Shiny Application
Version: 0.4.0
Date: 2020-09-30
Authors@R: c(person(given = "Thomas", family = "Janka", role = c("aut")), person(given = "Klaus", family = "Nordhausen", role = c("cre","ctb"), email = "klaus.nordhausen@tuwien.ac.at", comment = c(ORCID = "0000-0002-3758-8501")), person(given = "Anne", family = "Ruiz-Gazen", role = "ctb", comment = c(ORCID = "0000-0001-8970-8061")))
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>
Description: Performs exploratory projection pursuit via 'REPPlab' (Daniel Fischer, Alain Berro, Klaus Nordhausen & Anne Ruiz-Gazen (2019) <doi:10.1080/03610918.2019.1626880>) using a Shiny app.
License: GPL (>= 2)
Depends: shiny, DT, REPPlab
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
RoxygenNote: 7.1.1
Packaged: 2020-09-30 09:02:07 UTC; Klaus Nordhausen
Author: Thomas Janka [aut], Klaus Nordhausen [cre, ctb] (<https://orcid.org/0000-0002-3758-8501>), Anne Ruiz-Gazen [ctb] (<https://orcid.org/0000-0001-8970-8061>)
Repository: CRAN
Date/Publication: 2020-10-05 11:40:02 UTC

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New package pvldcurve with initial version 1.2.6
Package: pvldcurve
Type: Package
Title: Simplifies the Analysis of Pressure Volume and Leaf Drying Curves
Version: 1.2.6
Authors@R: person("Anna", "Raesch", email = "annaraesch@gmail.com", role = c("aut", "cre", "cph"))
Depends: ggplot2, R (>= 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Description: Simplifies the manufacturing, analysis and display of pressure volume and leaf drying curves. From the progression of the curves turgor loss point, osmotic potential, apoplastic fraction as well as minimum conductance and stomatal closure can be derived. Methods adapted from Bartlett, Scoffoni, Sack (2012) <doi:10.1111/j.1461-0248.2012.01751.x> and Sack, Scoffoni, PrometheusWikiContributors (2011) <http://prometheuswiki.org/tiki-index.php?page=Minimum+epidermal+conductance+%28gmin%2C+a.k.a.+cuticular+conductance%29>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2020-08-24 15:29:59 UTC; Anna
Author: Anna Raesch [aut, cre, cph]
Maintainer: Anna Raesch <annaraesch@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-05 11:30:02 UTC

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New package mapboxapi with initial version 0.2
Package: mapboxapi
Type: Package
Title: R Interface to 'Mapbox' Web Services
Date: 2020-09-29
Version: 0.2
Authors@R: c(person(given = "Kyle", family = "Walker", email = "kyle@walker-data.com", role = c("aut", "cre")))
Maintainer: Kyle Walker <kyle@walker-data.com>
Description: Includes support for 'Mapbox' Navigation APIs, including directions, isochrones, and route optimization; the Search API for forward and reverse geocoding; the Maps API for interacting with 'Mapbox' vector tilesets and visualizing 'Mapbox' maps in R; and the 'tippecanoe' tile-generation utility. See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Imports: httr, sf, jsonlite, purrr, curl, dplyr (>= 1.0.0), tidyr (>= 1.0.0), aws.s3, stringi, slippymath, protolite, rlang, geojsonsf, magick, leaflet
Suggests: mapdeck, tigris, tidycensus
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-29 10:15:09 UTC; kyle
Author: Kyle Walker [aut, cre]
Repository: CRAN
Date/Publication: 2020-10-05 11:20:02 UTC

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New package animalEKF with initial version 1.1
Package: animalEKF
Type: Package
Title: Extended Kalman Filters for Animal Movement
Version: 1.1
Date: 2020-09-21
Author: Samuel Ackerman
Maintainer: Samuel Ackerman <smackrmn@gmail.com>
Description: Synthetic generation of 1-D and 2-D correlated random walks (CRWs) for animal movement with behavioral switching, and particle filter estimation of movement parameters from observed trajectories using Extended Kalman Filter (EKF) model. See Ackerman (2018) <https://digital.library.temple.edu/digital/collection/p245801coll10/id/499150>.
Depends: R (>= 3.3.0), shiny, maptools, sp, rgeos (>= 0.5.2)
License: GPL (>= 2)
Imports: MCMCpack, ellipse, mvtnorm, deldir, colorspace, Matrix, MASS, png, grDevices, bezier, HDInterval, plyr, stats, methods, utils, ggplot2, rgdal
NeedsCompilation: no
Packaged: 2020-09-30 08:39:21 UTC; Sam Ackerman
Repository: CRAN
Date/Publication: 2020-10-05 11:50:06 UTC

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Sun, 04 Oct 2020

New package PairViz with initial version 1.3.3
Package: PairViz
Version: 1.3.3
Date: 2019-12-19
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Title: Visualization using Graph Traversal
Description: Improving graphics by ameliorating order effects, using Eulerian tours and Hamiltonian decompositions of graphs.
biocViews:
Depends: TSP,gtools, graph, methods
Suggests: knitr, rmarkdown, Sleuth3, colorspace,multcomp,igraph, scales,RColorBrewer,alr3,scagnostics
License: GPL-2
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-12-20 09:31:15 UTC; catherine
Repository: CRAN
Date/Publication: 2019-12-20 10:10:08 UTC

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Sat, 03 Oct 2020

New package gmGeostats with initial version 0.10-7
Package: gmGeostats
Version: 0.10-7
Date: 2020-09-28
Title: Geostatistics for Compositional Analysis
Authors@R: c(person(given = "Raimon", family = "Tolosana-Delgado", role = c("aut"), email = "r.tolosana@hzdr.de", comment = c(ORCID = "0000-0001-9847-0462")), person(given = "Ute", family = "Mueller", role = c("aut"), email = "u.mueller@ecu.edu.au"), person(given = "K. Gerald", family = "van den Boogaart", role = c("ctb", "cre"), email = "support@boogaart.de"), person(given = "Hassan", family = "Talebi", role = c("ctb", "cph"), email = "hassan.talebi@csiro.au"), person(given = "Helmholtz-Zentrum Dresden-Rossendorf", role = "cph"), person(given = "Edith Cowan University", role = "cph") )
Depends: R (>= 2.10)
Suggests: FNN, JADE, jointDiag, DescTools, knitr, rmarkdown (>= 2.3), magrittr, readxl
Imports: methods, gstat, compositions (>= 2.0), sp, boot, foreach, utils, RColorBrewer
Description: Support for geostatistical analysis of multivariate data, in particular data with restrictions, e.g. positive amounts data, compositional data, distributional data, microstructural data, etc. It includes descriptive analysis and modelling for such data, both from a two-point Gaussian perspective and multipoint perspective. The methods mainly follow Tolosana-Delgado, Mueller and van den Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
License: CC BY-SA 4.0 | GPL (>= 2)
URL: https://gitlab.hzdr.de/geomet/gmGeostats
Copyright: (C) 2020 by Helmholtz-Zentrum Dresden-Rossendorf and Edith Cowan University; gsi.DS code by Hassan Talebi
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
Collate: 'Anamorphosis.R' 'compositionsCompatibility.R' 'gstatCompatibility.R' 'variograms.R' 'gmValidationStrategy.R' 'gmAnisotropy.R' 'abstractClasses.R' 'accuracy.R' 'data.R' 'exploratools.R' 'genDiag.R' 'geostats.R' 'gmDataFrameStack.R' 'gmSimulation.R' 'gmSpatialMethodParameters.R' 'gmSpatialModel.R' 'grids.R' 'mask.R' 'spSupport.R' 'uncorrelationTest.R' 'zzz.R'
NeedsCompilation: yes
Packaged: 2020-10-02 12:47:34 UTC; tolosa53
Author: Raimon Tolosana-Delgado [aut] (<https://orcid.org/0000-0001-9847-0462>), Ute Mueller [aut], K. Gerald van den Boogaart [ctb, cre], Hassan Talebi [ctb, cph], Helmholtz-Zentrum Dresden-Rossendorf [cph], Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Repository: CRAN
Date/Publication: 2020-10-03 15:20:05 UTC

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New package zenplots with initial version 1.0.2
Package: zenplots
Version: 1.0.2
Encoding: UTF-8
Title: Zigzag Expanded Navigation Plots
Description: Graphical tools for visualizing high-dimensional data along a path of alternating one- and two-dimensional plots. Note that this includes interactive graphics plots based on 'loon' in turn based on 'tcltk' (included as part of the standard R distribution). It also requires 'graph' from Bioconductor. For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Authors@R: c(person(given = "Marius", family = "Hofert", role = "aut", email = "marius.hofert@uwaterloo.ca"), person(given = "Wayne", family = "Oldford", role = c("aut", "cre"), email = "rwoldford@uwaterloo.ca"))
Author: Marius Hofert [aut], Wayne Oldford [aut, cre]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>
URL: https://github.com/great-northern-diver/zenplots
Depends: R (>= 3.4.0)
Imports: grid, graphics, loon, stats, methods, MASS, graph, PairViz
Suggests: knitr, rmarkdown, Rgraphviz, ADGofTest, copula, Matrix, pcaPP, qqtest, qrmdata, qrmtools, rugarch, zoo, ggplot2, lattice, gridExtra, scagnostics
Enhances:
License: GPL-2 | GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr, rmarkdown
Repository: CRAN
Date: 2020-10-02
RoxygenNote: 7.1.0
Packaged: 2020-10-03 02:54:05 UTC; rwoldford
Date/Publication: 2020-10-03 06:00:02 UTC

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New package priceR with initial version 0.1.5
Package: priceR
Type: Package
Title: Economics and Pricing Tools
Version: 0.1.5
Imports: dplyr, gsubfn, stringr, purrr, jsonlite, stats, lubridate, curl, stringi
Author: Steve Condylios [aut, cre] (<https://orcid.org/0000-0003-0599-844X>)
Maintainer: Steve Condylios <steve.condylios@gmail.com>
BugReports: https://github.com/stevecondylios/priceR/issues
License: MIT + file LICENSE
URL: https://github.com/stevecondylios/priceR
Description: Functions to aid in micro and macro economic analysis and handling of price and currency data. Includes extraction of relevant inflation and exchange rate data from World Bank API, data cleaning/parsing, and standardisation. Inflation adjustment calculations as found in Principles of Macroeconomics by Gregory Mankiw et al (2014). Current and historical end of day exchange rates for 171 currencies from the European Central Bank Statistical Data Warehouse (2020) <https://sdw.ecb.europa.eu/curConverter.do>.
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-02 18:33:45 UTC; st
Repository: CRAN
Date/Publication: 2020-10-03 06:00:10 UTC

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New package collidr with initial version 0.1.3
Package: collidr
Type: Package
Title: Check for Namespace Collisions Across Packages and Functions on CRAN
Version: 0.1.3
Imports: dplyr, stringr, jsonlite, utils
Author: Steve Condylios [aut, cre] (<https://orcid.org/0000-0003-0599-844X>)
Maintainer: Steve Condylios <steve.condylios@gmail.com>
BugReports: https://github.com/collidrpackage/collidr/issues
License: MIT + file LICENSE
URL: https://github.com/collidrpackage/collidr
Description: Check for namespace collisions between a string input (your function or package name) and half a million packages and functions on CRAN.
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-10-02 20:15:00 UTC; st
Repository: CRAN
Date/Publication: 2020-10-03 06:00:13 UTC

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Fri, 02 Oct 2020

New package concreg with initial version 0.7
Package: concreg
Version: 0.7
Type: Package
Date: 2020-09-21
Title: Concordance Regression
Authors@R: c(person("Georg", "Heinze", role=c("aut", "cre"), email="georg.heinze@meduniwien.ac.at"), person("Meinhard", "Ploner", role=c("aut")), person("Daniela","Dunkler", role=c("aut")))
Depends: R (>= 3.0.0)
Imports: survival
Description: Implements concordance regression which can be used to estimate generalized odds of concordance. Can be used for non- and semi-parametric survival analysis with non-proportional hazards, for binary and for continuous outcome data. The method was introduced by Dunkler, Schemper and Heinze (2010) <doi:10.1093/bioinformatics/btq035>.
License: GPL
URL: https://cemsiis.meduniwien.ac.at/kb/wf/software/statistische-software/concreg/
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2020-10-02 08:48:40 UTC; Biometrikus
Author: Georg Heinze [aut, cre], Meinhard Ploner [aut], Daniela Dunkler [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Repository: CRAN
BugReports: https://github.com/georgheinze/concreg/issues/
Date/Publication: 2020-10-02 14:42:08 UTC

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New package tsibbletalk with initial version 0.1.0
Package: tsibbletalk
Title: Interactive Graphics for Tsibble Objects
Version: 0.1.0
Authors@R: c(person(given = "Earo", family = "Wang", role = c("aut", "cre"), email = "earo.wang@gmail.com", comment = c(ORCID = "0000-0001-6448-5260")), person(given = "Di", family = "Cook", role = "aut", comment = c(ORCID = "0000-0002-3813-7155")))
Description: A shared tsibble data easily communicates between htmlwidgets on both client and server sides, powered by 'crosstalk'. A shiny module is provided to visually explore periodic/aperiodic temporal patterns.
License: GPL-3
Depends: R (>= 2.10)
Imports: crosstalk (>= 1.1.0.1), dendextend (>= 1.13.4), dplyr (>= 1.0.0), glue (>= 1.4.1), lubridate (>= 1.7.9), plotly (>= 4.9.2.1), R6 (>= 2.4.1), rlang (>= 0.4.6), shiny (>= 1.5.0), tsibble (>= 0.9.1), vctrs (>= 0.3.1)
Suggests: fabletools (>= 0.2.0), ggplot2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-30 01:36:08 UTC; wany568
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>)
Maintainer: Earo Wang <earo.wang@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-02 08:40:02 UTC

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New package stfit with initial version 0.99.8
Package: stfit
Type: Package
Title: Spatio-Temporal Functional Imputation Tool
Version: 0.99.8
Date: 2020-09-29
Authors@R: person("Weicheng", "Zhu", email = "mingsnu@gmail.com", role = c("aut", "cre"))
Description: A general spatiotemporal satellite image imputation method based on sparse functional data analytic techniques. The imputation method applies and extends the Functional Principal Analysis by Conditional Estimation (PACE). The underlying idea for the proposed procedure is to impute a missing pixel by borrowing information from temporally and spatially contiguous pixels based on the best linear unbiased prediction.
BugReports: https://github.com/mingsnu/stfit/issues
License: GPL-3
LazyData: true
Depends: R (>= 3.5.0)
Imports: Rcpp, Matrix, doParallel, foreach, abind, fda, raster, rasterVis, RColorBrewer
LinkingTo: Rcpp
Suggests: testthat, dplyr
RoxygenNote: 7.1.0
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2020-09-30 01:08:11 UTC; Weicheng
Author: Weicheng Zhu [aut, cre]
Maintainer: Weicheng Zhu <mingsnu@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-02 08:30:02 UTC

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New package pmlbr with initial version 0.2.0
Package: pmlbr
Title: Interface to the Penn Machine Learning Benchmarks Data Repository
Description: Check available classification and regression data sets from the PMLB repository and download them. The PMLB repository (<https://github.com/EpistasisLab/pmlbr>) contains a curated collection of data sets for evaluating and comparing machine learning algorithms. These data sets cover a range of applications, and include binary/multi-class classification problems and regression problems, as well as combinations of categorical, ordinal, and continuous features. There are currently over 150 datasets included in the PMLB repository.
Version: 0.2.0
Authors@R: c( person("Trang", "Le", email = "grixor@gmail.com", role = c("aut", "cre"), comment = "https://trang.page/"), person("makeyourownmaker", email = "makeyourownmaker@gmx.com", role = "aut", comment = "https://github.com/makeyourownmaker"), person("Jason", "Moore", email = "jhmoore@upenn.edu", role = "aut", comment = "http://www.epistasisblog.org/"), person("University of Pennsylvania", role = "cph"))
BugReports: https://github.com/EpistasisLab/pmlbr/issues
Depends: R (>= 3.2.0)
Imports: utils, FNN, stats
License: GPL-2 | file LICENSE
URL: https://github.com/EpistasisLab/pmlbr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-09-29 21:59:17 UTC; trangle
Author: Trang Le [aut, cre] (https://trang.page/), makeyourownmaker [aut] (https://github.com/makeyourownmaker), Jason Moore [aut] (http://www.epistasisblog.org/), University of Pennsylvania [cph]
Maintainer: Trang Le <grixor@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-02 08:20:05 UTC

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Thu, 01 Oct 2020

New package statgenGxE with initial version 1.0.2
Package: statgenGxE
Type: Package
Title: Genotype by Environment (GxE) Analysis
Version: 1.0.2
Date: 2020-09-28
Authors@R: c(person(given = "Bart-Jan", family = "van Rossum", email = "bart-jan.vanrossum@wur.nl", role = c("aut", "cre")), person(given = "Fred", family = "van Eeuwijk", role = "ctb", comment = c(ORCID = "0000-0003-3672-2921")), person(given = "Martin", family = "Boer", role = "ctb"), person(given = "Marcos", family = "Malosetti", role = "ctb", comment = c(ORCID = "0000-0002-8150-1397")), person(given = "Daniela", family = "Bustos-Korts", role = "ctb", comment = c(ORCID = "0000-0003-3827-6726")), person(given = "Emilie J", family = "Millet", role = "ctb", comment = c(ORCID = "0000-0002-2913-4892")), person(given = "Joao", family = "Paulo", role = "ctb", comment = c(ORCID = "0000-0002-4180-0763")), person(given = "Maikel", family = "Verouden", role = "ctb", comment = c(ORCID = "0000-0002-4893-3323")), person(given = "Willem", family = "Kruijer", role = "ctb", comment = c(ORCID = "0000-0001-7179-1733")), person(given = "Ron", family = "Wehrens", role = "ctb", comment = c(ORCID = "0000-0002-8798-5599")), person(given = "Choazhi", family = "Zheng", role = "ctb", comment = c(ORCID = "0000-0001-6030-3933")) )
Description: Analysis of multi environment data of plant breeding experiments following the analyses described in Malosetti, Ribaut, and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<http://www.vsni.co.uk/software/asreml-r>).
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 3.3)
Imports: emmeans, ggplot2 (>= 3.3.0), gridExtra, knitr, lme4, methods, statgenSTA (>= 1.0.6), xtable
Suggests: asreml(>= 3.0), rmarkdown, testthat
SystemRequirements: pdflatex
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-29 06:13:07 UTC; rossu027
Author: Bart-Jan van Rossum [aut, cre], Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>), Martin Boer [ctb], Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>), Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>), Emilie J Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>), Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>), Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>), Willem Kruijer [ctb] (<https://orcid.org/0000-0001-7179-1733>), Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>), Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Repository: CRAN
Date/Publication: 2020-10-01 09:20:02 UTC

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New package mlr3cluster with initial version 0.1.0
Package: mlr3cluster
Title: Cluster Extension for 'mlr3'
Version: 0.1.0
Authors@R: c(person(given = "Damir", family = "Pulatov", role = c("cre", "aut"), email = "dpulatov@uwyo.edu"), person(given = "Michel", family = "Lang", role = "aut", email = "michellang@gmail.com", comment = c(ORCID = "0000-0001-9754-0393")))
Description: Extends the 'mlr3' package with cluster analysis.
License: LGPL-3
URL: https://mlr3cluster.mlr-org.com, https://github.com/mlr-org/mlr3cluster
BugReports: https://github.com/mlr-org/mlr3cluster/issues
Depends: R (>= 3.1.0)
Imports: backports (>= 1.1.10), checkmate, clue, clusterCrit, data.table, mlr3 (>= 0.5.0), mlr3misc (>= 0.4.0), paradox, R6
Suggests: bibtex, dbscan, e1071, mlbench, RWeka, testthat
Encoding: UTF-8
RoxygenNote: 7.1.1
Collate: 'LearnerClust.R' 'LearnerClustAgnes.R' 'LearnerClustCMeans.R' 'LearnerClustDBSCAN.R' 'LearnerClustDiana.R' 'LearnerClustFanny.R' 'LearnerClustFeatureless.R' 'LearnerClustKMeans.R' 'LearnerClustPAM.R' 'LearnerClustXMeans.R' 'MeasureClust.R' 'measures.R' 'MeasureClustInternal.R' 'PredictionClust.R' 'PredictionDataClust.R' 'TaskClust.R' 'TaskClust_usarrest.R' 'helper.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2020-09-29 01:55:05 UTC; damir
Author: Damir Pulatov [cre, aut], Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Damir Pulatov <dpulatov@uwyo.edu>
Repository: CRAN
Date/Publication: 2020-10-01 09:10:02 UTC

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New package lmkCHK with initial version 1.0.0
Package: lmkCHK
Title: Tools to Visualize and Screen 2D/3D Landmark Data
Version: 1.0.0
Authors@R: c(person(given = "Daniel", family = "Ehrlich", role = c("aut", "cre"), email = "dan.ehrlich.e@gmail.com"), person(given = "Michelle", family = "Singleton", role = "aut"))
Description: Provides visual and interactive tools to screen 2D/3D landmark data. Meant to supplement other geometric morphometric packages by making vibrant visuals easy/automatic.
Depends: R (>= 3.2.0), geomorph, rgl
Imports: Morpho, shiny
Suggests: psych
License: GPL (>= 3.0)
URL: <https://github.com/ehrlichd/lmkCHK>
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-29 17:28:20 UTC; camel
Author: Daniel Ehrlich [aut, cre], Michelle Singleton [aut]
Maintainer: Daniel Ehrlich <dan.ehrlich.e@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-01 09:40:07 UTC

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New package amapGeocode with initial version 0.3.1
Type: Package
Package: amapGeocode
Title: An Interface to the 'AutoNavi Maps' API Geocoding Services
Version: 0.3.1
Authors@R: c(person(given = "Han", family = "Chen", role = c("aut", "cre"), email = "chenhan28@gmail.com"), person(given = "Wanyanhan", family = "Jiang", role = "ctb", email = "243016042@qq.com"))
Description: Getting and parsing data of location geocode/reverse-geocode and administrative regions from 'AutoNavi Maps'<https://lbs.amap.com/api/webservice/summary> API.
License: MIT + file LICENSE
URL: https://github.com/womeimingzi11/amapGeocode
Imports: dplyr, httr, jsonlite, magrittr, sjmisc, stats, stringr, tibble, xml2, purrr, lifecycle
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
RdMacros: lifecycle
NeedsCompilation: no
Packaged: 2020-09-29 15:36:18 UTC; chenhan
Author: Han Chen [aut, cre], Wanyanhan Jiang [ctb]
Maintainer: Han Chen <chenhan28@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-01 09:30:03 UTC

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New package pkdata with initial version 0.1.0
Package: pkdata
Type: Package
Title: Creates Pharmacokinetic/Pharmacodynamic (PK/PD) Data
Version: 0.1.0
Date: 2020-09-28
Maintainer: Cole Beck <cole.beck@vumc.org>
Authors@R: c(person("Cole", "Beck", role = c("aut", "cre"), email = "cole.beck@vumc.org", comment = c(ORCID = "0000-0002-6849-6255")), person("Leena", "Choi", role = "aut", email = "naturechoi@gmail.com"))
Description: Prepare pharmacokinetic/pharmacodynamic (PK/PD) data for PK/PD analyses. This package provides functions to standardize infusion and bolus dose data while linking it to drug level or concentration data.
License: GPL (>= 3)
Depends: lubridate
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-28 23:00:57 UTC; beckca
Author: Cole Beck [aut, cre] (<https://orcid.org/0000-0002-6849-6255>), Leena Choi [aut]
Repository: CRAN
Date/Publication: 2020-10-01 09:00:02 UTC

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New package microclustr with initial version 0.1.0
Package: microclustr
Type: Package
Title: Entity Resolution with Random Partition Priors for Microclustering
Version: 0.1.0
Date: 2020-09-15
Authors@R: c( person(given=c("Rebecca", "C"), family="Steorts", role = c("aut","cre"), email="beka@stat.duke.edu"), person("Brenda", "Betancourt", email = "bbetancourt@ufl.edu", role = c("aut")), person("Giacomo", "Zanella", email = "zanella.gcm@gmail.com", role = c("aut")) )
Depends: R (>= 3.2.4)
Imports: Rcpp (>= 1.0.1), stats
Suggests: knitr, rmarkdown
Description: An implementation of the model in Betancourt, Zanella, Steorts (2020) <arXiv:2004.02008>, which performs microclustering models for categorical data. The package provides a vignette for two proposed methods in the paper as well as two standard Bayesian non-parametric clustering approaches for entity resolution. The experiments are reproducible and illustrated using a simple vignette. LICENSE: GPL-3 + file license.
VignetteBuilder: knitr
License: GPL-3
LinkingTo: Rcpp
RoxygenNote: 7.1.1.9000
NeedsCompilation: yes
Packaged: 2020-09-28 15:10:13 UTC; rebeccasteorts
Author: Rebecca C Steorts [aut, cre], Brenda Betancourt [aut], Giacomo Zanella [aut]
Maintainer: Rebecca C Steorts <beka@stat.duke.edu>
Repository: CRAN
Date/Publication: 2020-10-01 08:30:02 UTC

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New package IsoCorr with initial version 1.0
Package: IsoCorr
Type: Package
Title: Correcting Drift and Carry-over in Continuous Isotopic Measurements
Version: 1.0
Author: Jeroen D.M. Schreel
Maintainer: Jeroen D.M. Schreel <Jeroen.Schreel@gmail.com>
Description: A series of functions that allow an easy and fast correction for drift and carry-over in continuous isotopic measurements. This implementation provides queries allowing users to perform the implemented corrections according to their needs. These functions further enable the processing of large datasets and can provides apt visualizations of the corrections performed.
Depends: R (>= 3.5.0)
Imports: stats, graphics
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-09-28 13:48:02 UTC; UGent
Repository: CRAN
Date/Publication: 2020-10-01 08:30:12 UTC

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New package FoReco with initial version 0.1.0
Type: Package
Package: FoReco
Title: Point Forecast Reconciliation
Version: 0.1.0
Authors@R: c(person(given = "Daniele", family = "Girolimetto", role = c("aut", "cre", "fnd"), email = "daniele.girolimetto@studenti.unipd.it"), person(given = "Tommaso", family = "Di Fonzo", role = c("aut", "fnd")))
Description: Provides classical (bottom-up), optimal and heuristic combination forecast reconciliation procedures for cross-sectional, temporal, and cross-temporal linearly constrained time series.
License: GPL-3
URL: https://github.com/daniGiro/FoReco, https://danigiro.github.io/FoReco/
BugReports: https://github.com/daniGiro/FoReco/issues
Depends: R (>= 2.10), Matrix, osqp, stats
Imports: cli, corpcor, methods, pracma
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
RoxygenNote: 7.1.1
Packaged: 2020-09-28 13:45:10 UTC; daniele
Author: Daniele Girolimetto [aut, cre, fnd], Tommaso Di Fonzo [aut, fnd]
Maintainer: Daniele Girolimetto <daniele.girolimetto@studenti.unipd.it>
Repository: CRAN
Date/Publication: 2020-10-01 08:20:03 UTC

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New package epitweetr with initial version 0.1.20
Package: epitweetr
Title: Early Detection of Public Health Threats from Twitter Data
Version: 0.1.20
Authors@R: c( person(given = "Francisco", family = "Orchard", role = c("aut", "ctr"), email = "f.orchard@epiconcept.fr", comment = c(structure("0000-0001-5793-3301", .Names = "ORCID"), "Author of the package and original code")), person(given = "Laura", family = "Espinosa", role = c("aut", "cre", "fnd"), email = "laura.espinosa@ecdc.europa.eu", comment = "Project manager, author of the design and concept of the package, and package maintainer"), person(given = "Ariana", family = "Wijermans", role = "ctb", email = "ariana.wijermans@ecdc.europa.eu", comment = "Contributor to the design and concept of the package"), person(given = "Thomas", family = "Mollet", role = c("ctb", "fnd"), email = "thomas.mollet@ecdc.europa.eu", comment = "Business owner of the project, and contributor to the design and concept of the package"), person(given = "Adrian", family = "Prodan", role = "ctb", email = "adrian.prodan@ecdc.europa.eu"), person(given = "Thomas", family = "Czernichow", role = "ctb", email = "thomas.czernichow@epiconcept.fr"), person(given = "Maria", family = "Prieto Gonzalez", role = "ctb", email = "m.gonzalez@epiconcept.fr"), person(given = "Esther", family = "Kissling", role = "ctb", email = "e.kissling@epiconcept.fr"), person(given = "Michael", family = "Höhle", role = "ctb", email = "hoehle@math.su.se") )
Description: It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords.
License: EUPL
URL: https://github.com/EU-ECDC/epitweetr
BugReports: https://github.com/EU-ECDC/epitweetr/issues
Encoding: UTF-8
LazyData: true
Imports: bit64, dplyr, plyr, DT, httpuv, httr, jsonlite, keyring, emayili, ggplot2, magrittr, parallel, plotly, rtweet, readxl, rgeos, rgdal, rmarkdown, rnaturalearthdata, shiny, sp, stringr, stats, tidyverse, tidytext, tokenizers, tools, utils, xtable, xml2
RoxygenNote: 7.1.0
Suggests: knitr, taskscheduleR
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-28 13:02:04 UTC; fod
Author: Francisco Orchard [aut, ctr] (<https://orcid.org/0000-0001-5793-3301>, Author of the package and original code), Laura Espinosa [aut, cre, fnd] (Project manager, author of the design and concept of the package, and package maintainer), Ariana Wijermans [ctb] (Contributor to the design and concept of the package), Thomas Mollet [ctb, fnd] (Business owner of the project, and contributor to the design and concept of the package), Adrian Prodan [ctb], Thomas Czernichow [ctb], Maria Prieto Gonzalez [ctb], Esther Kissling [ctb], Michael Höhle [ctb]
Maintainer: Laura Espinosa <laura.espinosa@ecdc.europa.eu>
Repository: CRAN
Date/Publication: 2020-10-01 08:30:09 UTC

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New package DImodels with initial version 1.0
Package: DImodels
Type: Package
Title: Diversity-Interactions (DI) Models
Version: 1.0
Date: 2020-09-28
Authors@R: c(person("Rafael", "de Andrade Moral", role = c("aut", "cre"), email = "rafael.deandrademoral@mu.ie"), person("John", "Connolly", role = "aut"), person("Caroline", "Brophy", role = "aut"))
Author: Rafael de Andrade Moral [aut, cre], John Connolly [aut], Caroline Brophy [aut]
Maintainer: Rafael de Andrade Moral <rafael.deandrademoral@mu.ie>
Imports: methods, graphics, stats, utils, hnp, rootSolve
Suggests: ggplot2, knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.6.0)
Description: The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data_prepare() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2020-09-28 20:07:39 UTC; rafael
Repository: CRAN
Date/Publication: 2020-10-01 09:00:05 UTC

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New package bigSurvSGD with initial version 0.0.1
Package: bigSurvSGD
Type: Package
Title: Big Survival Analysis Using Stochastic Gradient Descent
Version: 0.0.1
Date: 2020-09-11
Authors@R: c(person(given = "Aliasghar", family = "Tarkhan", role = c("aut", "cre"), email = "atarkhan@uw.edu"), person(given = "Noah", family = "Simon", role = "aut", email = "nrsimon@uw.edu"))
Description: Fits Cox model via stochastic gradient descent. This implementation avoids computational instability of the standard Cox Model when dealing large datasets. Furthermore, it scales up with large datasets that do not fit the memory. It also handles large sparse datasets using proximal stochastic gradient descent algorithm. For more details about the method, please see Aliasghar Tarkhan and Noah Simon (2020) <arXiv:2003.00116v2>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.4), bigmemory, doParallel, survival
Depends: foreach, parallel, R (>= 3.5.0)
LinkingTo: Rcpp
Encoding: UTF-8
RoxygenNote: 7.1.0
BugReports: https://github.com/atarkhan/bigSurvSGD/issues
NeedsCompilation: yes
Packaged: 2020-09-28 16:59:42 UTC; arash
Author: Aliasghar Tarkhan [aut, cre], Noah Simon [aut]
Maintainer: Aliasghar Tarkhan <atarkhan@uw.edu>
Repository: CRAN
Date/Publication: 2020-10-01 08:40:02 UTC

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Wed, 30 Sep 2020

New package sccore with initial version 0.1.0
Package: sccore
Title: Core Utilities for Single-Cell RNA-Seq
Version: 0.1.0
Authors@R: c(person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Viktor","Petukhov", email="viktor.s.petuhov@ya.ru", role="aut"), person("Ramus","Rydbirk", email="rasmus.rydbirk@bric.ku.dk", role="aut"), person("Evan","Biederstedt", email="evan.biederstedt@gmail.com", role=c("aut", "cre")))
Description: Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, ggplot2, ggrepel, graphics, grDevices, igraph, magrittr, Matrix, methods, pROC, parallel, Rcpp, rlang, scales, tibble, utils, uwot, withr
Depends: R (>= 3.5.0)
Suggests: ggrastr (>= 0.1.7), pbapply, rmumps, testthat
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppEigen
NeedsCompilation: yes
URL: https://github.com/kharchenkolab/sccore
BugReports: https://github.com/kharchenkolab/sccore/issues
Author: Peter Kharchenko [aut], Viktor Petukhov [aut], Ramus Rydbirk [aut], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Packaged: 2020-09-28 13:24:22 UTC; evanbiederstedt
Repository: CRAN
Date/Publication: 2020-09-30 10:00:02 UTC

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New package rgenie with initial version 1.0.0
Package: rgenie
Title: Analysis of GenIE Experiments
Version: 1.0.0
Authors@R: person("Jeremy", "Schwartzentruber", email = "jeremy37@gmail.com", role = c("aut", "cre"))
Description: The R package for GenIE analysis is designed to analyze the next-generation sequencing output from a set of GenIE experimental replicates. GenIE (genome-editing interrogation of enhancers) is an experimental method to evaluate the effects of individual single-nucleotide polymorphisms (SNPs) on gene transcription. It is based on targeted CRISPR-Cas9 genome editing in cultured cells to produce indels at a target locus, optionally with a homology-dependent recombination (HDR) construct to create precisely defined genomic changes. Following this, both genomic DNA (gDNA) and RNA are extracted from the same pool of cells, then complementary DNA (cDNA) is generated from the RNA. Both gDNA and cDNA are amplified with locus-specific PCR primers, in multiple replicates, and libraries of the experimental replicates are prepared for next-generation sequencing. The sequencing data from each replicate for each region should be aligned to either the full reference genome or to a locus-specific (amplicon) reference genome for analysis by 'rgenie'.
License: MIT + file LICENSE
URL: https://github.com/jeremy37/rgenie
BugReports: https://github.com/jeremy37/rgenie/issues
Encoding: UTF-8
LazyData: true
biocViews:
Imports: dplyr (>= 1.0.2), ggplot2 (>= 3.3.2), magrittr (>= 1.5), stringr (>= 1.4.0), readr (>= 1.3.1), tidyr (>= 1.1.2), tibble (>= 3.0.3), forcats (>= 0.5.0), stats, cowplot (>= 0.9.4), egg (>= 0.4.2), ggdendro (>= 0.1-20), gridExtra (>= 2.3), FNN (>= 1.1.3), variancePartition (>= 1.14.0), Rsamtools (>= 2.0.0), IRanges (>= 2.18.1)
Suggests: knitr, rmarkdown, devtools
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Depends: R (>= 3.3)
NeedsCompilation: no
Packaged: 2020-09-28 10:28:51 UTC; jeremys
Author: Jeremy Schwartzentruber [aut, cre]
Maintainer: Jeremy Schwartzentruber <jeremy37@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-30 09:20:03 UTC

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New package LearnClust with initial version 1.0
Package: LearnClust
Type: Package
Date: 2020-09-04
Title: Learning Hierarchical Clustering Algorithms
Version: 1.0
Authors@R: c( person("Roberto","Alcantara", role = c("aut","cre"), email = "roberto.alcantara@edu.uah.es"), person("Juan Jose Cuadrado", role = c("aut"), email = "jjcg@uah.es"), person("Universidad de Alcala de Henares", role = c("aut")) )
Author: Roberto Alcantara [aut, cre], Juan Jose Cuadrado [aut], Universidad de Alcala de Henares [aut]
Maintainer: Roberto Alcantara <roberto.alcantara@edu.uah.es>
Description: Classical hierarchical clustering algorithms, agglomerative and divisive clustering. Algorithms are implemented as a theoretical way, step by step. It includes some detailed functions that explain each step. Every function allows options to get different results using different techniques. The package explains non expert users how hierarchical clustering algorithms work.
License: Unlimited
Depends: magick
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-28 11:23:12 UTC; Roberto
Repository: CRAN
Date/Publication: 2020-09-30 09:30:03 UTC

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New package h2o with initial version 3.30.1.3
Package: h2o
Version: 3.30.1.3
Type: Package
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Date: 2020-09-28
Authors@R: c( person("Erin", "LeDell", role = c("aut", "cre"), email = "erin@h2o.ai"), person("Navdeep", "Gill", role = c("aut")), person("Spencer", "Aiello", role = c("aut")), person("Anqi", "Fu", role = c("aut")), person("Arno", "Candel", role = c("aut")), person("Cliff", "Click", role = c("aut")), person("Tom", "Kraljevic", role = c("aut")), person("Tomas", "Nykodym", role = c("aut")), person("Patrick", "Aboyoun", role = c("aut")), person("Michal", "Kurka", role = c("aut")), person("Michal", "Malohlava", role = c("aut")), person("Ludi", "Rehak", role = c("ctb")), person("Eric", "Eckstrand", role = c("ctb")), person("Brandon", "Hill", role = c("ctb")), person("Sebastian", "Vidrio", role = c("ctb")), person("Surekha", "Jadhawani", role = c("ctb")), person("Amy", "Wang", role = c("ctb")), person("Raymond", "Peck", role = c("ctb")), person("Wendy", "Wong", role = c("ctb")), person("Jan", "Gorecki", role = c("ctb")), person("Matt", "Dowle", role = c("ctb")), person("Yuan", "Tang", role = c("ctb")), person("Lauren", "DiPerna", role = c("ctb")), person("H2O.ai", role = c("cph", "fnd")) )
Description: R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), Cox Proportional Hazards, K-Means, PCA, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
License: Apache License (== 2.0)
URL: https://github.com/h2oai/h2o-3
BugReports: https://0xdata.atlassian.net/projects/PUBDEV
NeedsCompilation: no
SystemRequirements: Java (>= 8)
Depends: R (>= 2.13.0), methods, stats
Imports: graphics, tools, utils, RCurl, jsonlite
Suggests: ggplot2, mlbench, Matrix, slam, bit64 (>= 0.9.7), data.table (>= 1.9.8), rgl (>= 0.100.19), plot3Drgl (>= 1.0.1), survival
Collate: 'aggregator.R' 'astfun.R' 'automl.R' 'classes.R' 'config.R' 'connection.R' 'constants.R' 'datasets.R' 'logging.R' 'communication.R' 'kvstore.R' 'frame.R' 'targetencoder_deprecated.R' 'targetencoder.R' 'import.R' 'isolationforest.R' 'parse.R' 'export.R' 'edicts.R' 'models.R' 'coxph.R' 'coxphutils.R' 'kmeans.R' 'gam.R' 'gbm.R' 'generic.R' 'glm.R' 'glrm.R' 'pca.R' 'svd.R' 'psvm.R' 'deeplearning.R' 'stackedensemble.R' 'xgboost.R' 'randomforest.R' 'naivebayes.R' 'word2vec.R' 'w2vutils.R' 'locate.R' 'grid.R' 'segment.R' 'predict.R' 'zzz.R' 'tf-idf.R'
RoxygenNote: 7.1.1
Packaged: 2020-09-28 15:32:55 UTC; jenkins
Author: Erin LeDell [aut, cre], Navdeep Gill [aut], Spencer Aiello [aut], Anqi Fu [aut], Arno Candel [aut], Cliff Click [aut], Tom Kraljevic [aut], Tomas Nykodym [aut], Patrick Aboyoun [aut], Michal Kurka [aut], Michal Malohlava [aut], Ludi Rehak [ctb], Eric Eckstrand [ctb], Brandon Hill [ctb], Sebastian Vidrio [ctb], Surekha Jadhawani [ctb], Amy Wang [ctb], Raymond Peck [ctb], Wendy Wong [ctb], Jan Gorecki [ctb], Matt Dowle [ctb], Yuan Tang [ctb], Lauren DiPerna [ctb], H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>
Repository: CRAN
Date/Publication: 2020-09-30 09:10:02 UTC

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New package composits with initial version 0.1.0
Package: composits
Type: Package
Title: Compositional, Multivariate and Univariate Time Series Outlier Ensemble
Version: 0.1.0
Authors@R: c( person("Sevvandi", "Kandanaarachchi", email = "sevvandik@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0337-0395")), person("Patricia", "Menendez", email = "Patricia.Menendez@monash.edu", role = c("aut"), comment = c(ORCID = "0000-0003-0701-6315")), person("Ursula", "Laa", email = "Ursula.Laa@monash.edu", role = c("aut"), comment = c(ORCID = "0000-0002-0249-6439")), person("Ruben", "Loaiza-Maya", email = "Ruben.LoaizaMaya@monash.edu", role = c("aut"), comment = c(ORCID = "0000-0003-4132-8355")) )
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Description: An ensemble of time series outlier detection methods that can be used for compositional, multivariate and univariate data. It uses the four R packages 'forecast', 'tsoutliers', 'otsad' and 'anomalize' to detect time series outliers.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: otsad, tsoutliers, forecast, anomalize, dplyr, tibble, rlang, pracma, dobin, ICS, fastICA, gridExtra, grid, ggplot2, tidyr, kableExtra
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, tourr, stringr, broom, rgdal
VignetteBuilder: knitr
Depends: R (>= 3.4.0)
URL: https://sevvandi.github.io/composits/
NeedsCompilation: no
Packaged: 2020-09-28 12:29:00 UTC; Sevvandi
Author: Sevvandi Kandanaarachchi [aut, cre] (<https://orcid.org/0000-0002-0337-0395>), Patricia Menendez [aut] (<https://orcid.org/0000-0003-0701-6315>), Ursula Laa [aut] (<https://orcid.org/0000-0002-0249-6439>), Ruben Loaiza-Maya [aut] (<https://orcid.org/0000-0003-4132-8355>)
Repository: CRAN
Date/Publication: 2020-09-30 09:50:02 UTC

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New package VoxR with initial version 1.0.0
Package: VoxR
Title: Trees Geometry and Morphology from Unstructured TLS Data
Version: 1.0.0
Authors@R: person(given = "Bastien", family = "Lecigne", role = c("aut", "cre"), email = "lecignebastien@gmail.com", comment = c(ORCID = "https://orcid.org/0000-0002-1496-202X"))
Description: Tools for 3D point cloud voxelisation, projection, geometrical and morphological description of trees (DBH, height, volume, crown diameter), analyses of temporal changes between different measurement times, distance based clustering and visualisation of 3D voxel clouds and 2D projection. Most analyses and algorithms provided in the package are based on the concept of space exploration and are described in Lecigne et al. (2018, <doi:10.1093/aob/mcx095>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: data.table, FNN, Rfast, circular, dplyr, fastcluster, geometry, raster, rgl, grDevices
URL: https://github.com/Blecigne/VoxR
BugReports: https://github.com/Blecigne/VoxR/issues
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-09-28 22:27:39 UTC; bastienlecigne
Author: Bastien Lecigne [aut, cre] (<https://orcid.org/0000-0002-1496-202X>)
Maintainer: Bastien Lecigne <lecignebastien@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-30 08:50:08 UTC

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New package treedata.table with initial version 0.1.0
Package: treedata.table
Title: Manipulation of Matched Phylogenies and Data using 'data.table'
Version: 0.1.0
Authors@R: c( person(given = "Josef", family = "Uyeda", role=c("aut"), email="juyeda@vt.edu", comment = c(ORCID="0000-0003-4624-9680") ), person(given = "Cristian", family = "Roman-Palacios", role = c("cre"), email = "cromanpa94@email.arizona.edu", comment = c(ORCID="0000-0003-4692-3225") ), person(given = "April", family = "Wright", role = c("aut"), email = "april.wright@southeastern.edu", comment = c(ORCID="0000-0003-4692-3225")), person(given = "Luke", family = "Harmon", role = c("ctb")), person(given = "Hugo", family = "Gruson", role = c("rev")), person(given = "Kari", family = "Norman", role = c("rev")) )
URL: https://docs.ropensci.org/treedata.table/ (website) https://github.com/ropensci/treedata.table/
BugReports: https://github.com/ropensci/treedata.table/issues
Description: An implementation that combines trait data and a phylogenetic tree (or trees) into a single object of class treedata.table. The resulting object can be easily manipulated to simultaneously change the trait- and tree-level sampling. Currently implemented functions allow users to use a 'data.table' syntax when performing operations on the trait dataset within the treedata.table object.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: lazyeval, ape, geiger, utils, data.table
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-09-27 13:09:41 UTC; cristianroman
Author: Josef Uyeda [aut] (<https://orcid.org/0000-0003-4624-9680>), Cristian Roman-Palacios [cre] (<https://orcid.org/0000-0003-4692-3225>), April Wright [aut] (<https://orcid.org/0000-0003-4692-3225>), Luke Harmon [ctb], Hugo Gruson [rev], Kari Norman [rev]
Maintainer: Cristian Roman-Palacios <cromanpa94@email.arizona.edu>
Repository: CRAN
Date/Publication: 2020-09-30 08:30:02 UTC

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New package table.glue with initial version 0.0.1
Package: table.glue
Title: Make and Apply Customized Rounding Specifications for Tables
Version: 0.0.1
Authors@R: c(person(given = "Byron", family = "Jaeger", role = c("aut", "cre"), email = "bcjaeger@uab.edu", comment = c(ORCID = "0000-0001-7399-2299")))
Description: Translate double and integer valued data into character values formatted for tabulation in manuscripts or other types of academic reports.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, covr, knitr, rmarkdown
Imports: glue, stringi
URL: https://github.com/bcjaeger/table.glue
BugReports: https://github.com/bcjaeger/table.glue/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-27 20:14:38 UTC; bcjaeger
Author: Byron Jaeger [aut, cre] (<https://orcid.org/0000-0001-7399-2299>)
Maintainer: Byron Jaeger <bcjaeger@uab.edu>
Repository: CRAN
Date/Publication: 2020-09-30 08:40:03 UTC

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New package svyVGAM with initial version 0.222-2
Package: svyVGAM
Title: Design-Based Inference in Vector Generalised Linear Models
Version: 0.222-2
Author: Thomas Lumley
Description: Provides design-based inference for the wide range of parametric models in the 'VGAM' package.
Imports: stats, methods
Depends: VGAM, survey, R (>= 3.5.0)
Suggests: pscl, knitr, markdown, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
License: GPL-3
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
NeedsCompilation: no
Packaged: 2020-09-27 20:46:56 UTC; tlum005
Repository: CRAN
Date/Publication: 2020-09-30 08:50:02 UTC

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New package robservable with initial version 0.2.0
Package: robservable
Type: Package
Title: Import an Observable Notebook as HTML Widget
Version: 0.2.0
Date: 2020-09-23
Authors@R: c( person( "Julien", "Barnier", email = "julien.barnier@cnrs.fr", role = c("aut", "cre") ), person( "Kenton", "Russell", email = "kent.russell@timelyportfolio.com", role = "aut" ))
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Description: Allows loading and displaying an Observable notebook (online JavaScript notebooks powered by <https://observablehq.com>) as an HTML Widget in an R session, 'shiny' application or 'rmarkdown' document.
VignetteBuilder: knitr
URL: https://juba.github.io/robservable/
BugReports: https://github.com/juba/robservable/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Enhances: shiny
Imports: htmlwidgets, jsonlite
Suggests: gapminder, knitr, rmarkdown, readr, dplyr, tidyr, lubridate, stringr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-28 07:25:38 UTC; julien
Author: Julien Barnier [aut, cre], Kenton Russell [aut]
Repository: CRAN
Date/Publication: 2020-09-30 09:00:02 UTC

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New package rintimg with initial version 0.1.0
Package: rintimg
Type: Package
Title: View Images on Full Screen in 'RMarkdown' Documents and 'shiny' Applications
Version: 0.1.0
Authors@R: c( person("Mohamed El Fodil", "Ihaddaden", email = "ihaddaden.fodeil@gmail.com", role = c("aut", "cre")), person("Tim", "Holman", role = c("ctb", "cph"), comment = "intense-images.js library developer"))
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Description: Allows the user to view an image in full screen when clicking on it in 'RMarkdown' documents and 'shiny' applications. The package relies on the 'JavaScript' library 'intense-images'. See <https://tholman.com/intense-images/> for more information.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: htmltools, glue
RoxygenNote: 7.1.1
URL: https://github.com/feddelegrand7/rintimg
BugReports: https://github.com/feddelegrand7/rintimg/issues
NeedsCompilation: no
Packaged: 2020-09-27 21:43:50 UTC; Administrateur
Author: Mohamed El Fodil Ihaddaden [aut, cre], Tim Holman [ctb, cph] (intense-images.js library developer)
Repository: CRAN
Date/Publication: 2020-09-30 08:40:06 UTC

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New package MLGdata with initial version 0.1.0
Package: MLGdata
Type: Package
Title: Datasets for Use with Salvan, Sartori and Pace (2020)
Version: 0.1.0
Author: Nicola Sartori, Alessandra Salvan, Luigi Pace
Maintainer: Nicola Sartori <nicola.sartori@unipd.it>
Description: Contains the datasets for use with the book Salvan, Sartori and Pace (2020, ISBN:978-88-470-4002-1) "Modelli Lineari Generalizzati".
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-28 07:10:45 UTC; nk
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2020-09-30 08:50:12 UTC

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New package localFDA with initial version 1.0.0
Package: localFDA
Type: Package
Title: Localization Processes for Functional Data Analysis
Version: 1.0.0
Date: 2020-09-24
Authors@R: c(person("Antonio", "Elías", email = "antonioefz91@gmail.com", role = c("aut", "cre")), person("Raul", "Jiménez", role = c("aut")), person("Joe", "Yukich", role = c("aut")))
Description: Implementation of a theoretically supported alternative to k-nearest neighbors for functional data to solve problems of estimating unobserved segments of a partially observed functional data sample, functional classification and outlier detection. The approximating neighbor curves are piecewise functions built from a functional sample. Instead of a distance on a function space we use a locally defined distance function that satisfies stabilization criteria. The package allows the implementation of the methodology and the replication of the results in Elías, A., Jiménez, R. and Yukich, J. (2020) <arXiv:2007.16059>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/aefdz/localFDA
BugReports: https://github.com/aefdz/localFDA
Imports: stats, graphics
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-09-27 14:10:55 UTC; anton
Author: Antonio Elías [aut, cre], Raul Jiménez [aut], Joe Yukich [aut]
Maintainer: Antonio Elías <antonioefz91@gmail.com>
Repository: CRAN
Date/Publication: 2020-09-30 08:30:09 UTC

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New package geomultistar with initial version 1.0.0
Package: geomultistar
Type: Package
Title: Multidimensional Queries Enriched with Geographic Data
Version: 1.0.0
Authors@R: person(given = "Jose", family = "Samos", role = c("aut", "cre", "cph"), email = "jsamos@ugr.es", comment = c(ORCID = "0000-0002-4457-3439"))
Description: Multidimensional systems allow complex queries to be carried out in an easy way. The geographical dimension, together with the temporal dimension, plays a fundamental role in multidimensional systems. Through this package, vector layers can be associated to the attributes of geographic dimensions, so that the results of multidimensional queries can be obtained directly as vector layers. The multidimensional structures on which we can define the queries can be created from a flat table or imported directly using functions from this package.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
LazyData: true
RoxygenNote: 7.1.1
Imports: dplyr, readr, tibble, tidyr, tidyselect, starschemar, generics, purrr, sf, magrittr, rlang, pander
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2020-09-27 21:50:24 UTC; jsamos
Author: Jose Samos [aut, cre, cph] (<https://orcid.org/0000-0002-4457-3439>)
Maintainer: Jose Samos <jsamos@ugr.es>
Repository: CRAN
Date/Publication: 2020-09-30 08:40:09 UTC

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New package densEstBayes with initial version 1.0-1
Package: densEstBayes
Version: 1.0-1
Date: 2020-09-28
Title: Density Estimation via Bayesian Inference Engines
Authors@R: person("Matt P.", "Wand", role = c("aut","cre"), email = "matt.wand@uts.edu.au", comment = c(ORCID = "0000-0003-2555-896X"))
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Description: Bayesian density estimates for univariate continuous random samples are provided using the Bayesian inference engine paradigm. The engine options are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field variational Bayes and slice sampling. The methodology is described in Wand and Yu (2020) <arXiv:2009.06182>.
License: GPL (>= 2)
LazyData: true
Biarch: true
Depends: R (>= 3.5.0)
Imports: MASS, nlme, Rcpp, methods, rstan
LinkingTo: BH, Rcpp, RcppArmadillo, RcppEigen, RcppParallel, StanHeaders, rstan
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2020-09-27 21:42:01 UTC; mwand
Author: Matt P. Wand [aut, cre] (<https://orcid.org/0000-0003-2555-896X>)
Repository: CRAN
Date/Publication: 2020-09-30 08:50:05 UTC

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Tue, 29 Sep 2020

New package prettifyAddins with initial version 0.1.0
Package: prettifyAddins
Type: Package
Title: 'RStudio' Addins to Prettify 'HTML', 'CSS', 'JavaScript', and More
Version: 0.1.0
Authors@R: c( person( "Stéphane", "Laurent", role = c("aut", "cre"), email = "laurent_step@outlook.fr" ), person( "James Long and contributors", role = c("ctb", "cph"), comment = "'Prettier' library" ), person( "Zeb", "Zhao", role = c("ctb","cph"), comment = "'indent.js' library" ), person( "Marijn", "Haverbeke", role = c("ctb", "cph"), comment = "'CodeMirror' library" ) )
Description: Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS', 'JavaScript', 'JSX', 'Markdown', and to format 'C', 'C++', 'Julia', 'Python', 'Shell' and 'SQL'. Two addins are provided: 'Prettify' and 'Indent'. The 'Indent' addin only reindents the code, while the 'Prettify' addin also modifies the code, e.g. it adds trailing semi-colons to 'JavaScript' code when they are missing.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinythemes, shinyAce, miniUI, rstudioapi, tools
URL: https://github.com/stla/prettifyAddins
BugReports: https://github.com/stla/prettifyAddins/issues
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-26 07:32:54 UTC; stla
Author: Stéphane Laurent [aut, cre], James Long and contributors [ctb, cph] ('Prettier' library), Zeb Zhao [ctb, cph] ('indent.js' library), Marijn Haverbeke [ctb, cph] ('CodeMirror' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2020-09-29 09:20:03 UTC

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New package covid19br with initial version 0.1.0
Package: covid19br
Type: Package
Title: Brazilian COVID-19 Pandemic Data
Version: 0.1.0
Authors@R: c(person(given = "Fabio", family = "Demarqui", email = "fndemarqui@est.ufmg.br", role = c("aut", "cre")), person(given = "Cristiano", family = "Santos", email = "ccsgaus@ufmg.br", role = "aut"), person(given = "Matheus", family = "Costa", email = "matheus_belo@id.uff.br", role = "ctb"))
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
URL: https://github.com/fndemarqui/covid19br
BugReports: https://github.com/fndemarqui/covid19br/issues
Encoding: UTF-8
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Imports: data.table, dplyr, httr, lubridate, openxlsx, rlang, R.utils, tidyr
Suggests: testthat, tidyverse
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-26 15:07:25 UTC; fndemarqui
Author: Fabio Demarqui [aut, cre], Cristiano Santos [aut], Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Repository: CRAN
Date/Publication: 2020-09-29 09:20:05 UTC

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New package clinmon with initial version 0.2.0
Type: Package
Package: clinmon
Title: Calculation of Hemodynamic Indexes from Clinical Monitoring
Version: 0.2.0
Authors@R: c( person("Markus Harboe", "Olsen", email = "oel@oelfam.com", role = c("cre","aut")), person("Christian", "Riberholt", role = "aut"))
Description: Every research team have their own script for calculation of hemodynamic indexes. This package makes it possible to insert a long-format dataframe, and add both periods of interest (trigger-periods), and delete artifacts with deleter-files. The calculation methods are based on Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>.
License: MIT + file LICENSE
URL: https://github.com/lilleoel/clinmon
BugReports: https://github.com/cosimameyer/overviewR/issues
Depends: R (>= 3.5.0)
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-09-26 10:57:33 UTC; MOLS0212
Author: Markus Harboe Olsen [cre, aut], Christian Riberholt [aut]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Repository: CRAN
Date/Publication: 2020-09-29 09:20:08 UTC

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New package BayesProject with initial version 1.0
Package: BayesProject
Type: Package
Title: Fast Projection Direction for Multivariate Changepoint Detection
Version: 1.0
Date: 2020-09-24
Author: Georg Hahn [aut,cre], Paul Fearnhead [ctb], Idris A. Eckley [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Description: Implementations in 'cpp' of the BayesProject algorithm (see G. Hahn, P. Fearnhead, I.A. Eckley (2020) <doi:10.1007/s11222-020-09966-2>) which implements a fast approach to compute a projection direction for multivariate changepoint detection, as well as the sum-cusum and max-cusum methods, and a wild binary segmentation wrapper for all algorithms.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.13), Rdpack
RdMacros: Rdpack
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-09-27 00:07:29 UTC; acer
Repository: CRAN
Date/Publication: 2020-09-29 09:30:16 UTC

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New package wordpressr with initial version 0.1.1
Package: wordpressr
Type: Package
Title: An API Wrapper for WordPress Site APIs
Version: 0.1.1
Authors@R: c(person("Simit", "Patel", email = "simit@sixjupiter.com", role = c("aut", "cre")), person(given = 'SixJupiter',role = c('cph','fnd')))
URL: https://sixjupiter.com/wordpressr/
BugReports: https://github.com/simitpatel/wordpressr/issues
Description: An API wrapper that helps R developers retrieve data from a WordPress site's API in tidy format, in addition to publishing content on the WordPress site (WordPress API documentation: <https://developer.wordpress.org/rest-api/>).
Imports: httr, tibble, dplyr, tidyr, magrittr, glue, purrr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown, testthat, stringi
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-09-25 21:22:34 UTC; simit.patel
Author: Simit Patel [aut, cre], SixJupiter [cph, fnd]
Maintainer: Simit Patel <simit@sixjupiter.com>
Repository: CRAN
Date/Publication: 2020-09-29 08:50:02 UTC

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