Fri, 24 Jul 2020

New package xROI with initial version 0.9.17
Package: xROI
Title: Delineate Region of Interests (ROI's) and Extract Time-Series Data from Digital Repeat Photography Images
Version: 0.9.17
Date: 2020-07-24
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Depends: R (>= 3.4.0)
Imports: colourpicker, data.table, graphics, jpeg, lubridate, methods, moments, RCurl, raster, rgdal, rjson, sp, stats, stringr, tiff, utils, shiny, shinyjs,
Suggests: knitr, testthat, rmarkdown, shinyBS, shinyAce, shinyTime, shinyFiles, shinydashboard, shinythemes, plotly
License: AGPL-3
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/bnasr/xROI/issues
RoxygenNote: 7.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-24 18:56:34 UTC; bijan
Repository: CRAN
Date/Publication: 2020-07-24 23:20:02 UTC

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New package GermaParl with initial version 1.5.0
Package: GermaParl
Type: Package
Title: Download and Augment the Corpus of Plenary Protocols of the German Bundestag
Version: 1.5.0
Date: 2020-07-24
Authors@R: c( person(given = "Andreas", family = "Blaette", role = c("aut", "cre"), email = "andreas.blaette@uni-due.de"), person("Christoph", "Leonhardt", role = "ctb") )
Depends: R (>= 3.5.0)
Imports: cwbtools (>= 0.3.0), RcppCWB, zen4R
Suggests: topicmodels, knitr, rmarkdown, testthat
LazyData: yes
Description: Data package to disseminate the 'GermaParl' corpus of parliamentary debates of the German Bundestag prepared in the 'PolMine Project'. The package includes a small subset of the corpus for demonstration and testing purposes. The package includes functionality to download the full corpus and supplementary data from the open science repository 'Zenodo'.
URL: https://github.com/polmine/GermaParl
BugReports: https://github.com/polmine/GermaParl/issues
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
Collate: 'GermaParl.R' 'download.R' 'lda.R'
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-24 16:42:56 UTC; andreasblaette
Author: Andreas Blaette [aut, cre], Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Repository: CRAN
Date/Publication: 2020-07-24 23:32:05 UTC

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Package tidyUSDA updated to version 0.2.9 with previous version 0.2.8 dated 2020-06-30

Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for Analysis and Visualization
Description: Provides a consistent API to pull United States Department of Agriculture census and survey data from the National Agricultural Statistics Service (NASS) QuickStats service <https://quickstats.nass.usda.gov>.
Author: Brad Lindblad [aut, cre], Michael Thomas [ctb], Alex Mindeman [ctb]
Maintainer: Brad Lindblad <bradley.lindblad@gmail.com>

Diff between tidyUSDA versions 0.2.8 dated 2020-06-30 and 0.2.9 dated 2020-07-24

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More information about tidyUSDA at CRAN
Permanent link

Package radsafer updated to version 2.2.2 with previous version 2.2.1 dated 2020-06-10

Title: Radiation Safety
Description: Provides functions for radiation safety, also known as "radiation protection" and "radiological control". The science of radiation protection is called "health physics" and its engineering functions are called "radiological engineering". Functions in this package cover many of the computations needed by radiation safety professionals. Examples include: obtaining updated calibration and source check values for radiation monitors to account for radioactive decay in a reference source, simulating instrument readings to better understand measurement uncertainty, correcting instrument readings for geometry and ambient atmospheric conditions. Many of these functions are described in Johnson and Kirby (2011, ISBN-13: 978-1609134198). Utilities are also included for developing inputs and processing outputs with radiation transport codes, such as MCNP, a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport (Werner et. al. (2018) <doi:10.2172/1419730>).
Author: Mark Hogue <mark.hogue.chp@gmail.com>
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>

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Package AMCP updated to version 1.0.1 with previous version 1.0.0 dated 2020-02-13

Title: A Model Comparison Perspective
Description: Accompanies "Designing experiments and analyzing data: A model comparison perspective" (3rd ed.) by Maxwell, Delaney, & Kelley (2018; Routledge). Contains all of the data sets in the book's chapters and end-of-chapter exercises. Information about the book is available at <http://www.DesigningExperiments.com>.
Author: Scott Maxwell [aut], Harold Delaney [aut], Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>

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Package replicateBE updated to version 1.0.15 with previous version 1.0.14 dated 2020-04-09

Title: Average Bioequivalence with Expanding Limits (ABEL)
Description: Performs comparative bioavailability calculations for Average Bioequivalence with Expanding Limits (ABEL). Implemented are 'Method A' and 'Method B' and the detection of outliers. If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to control the consumer risk. Average Bioequivalence - optionally with a tighter (narrow therapeutic index drugs) or wider acceptance range (Gulf Cooperation Council, South Africa: Cmax) - is implemented as well.
Author: Helmut Schütz [aut, cre] (<https://orcid.org/0000-0002-1167-7880>), Michael Tomashevskiy [ctb], Detlew Labes [ctb] (<https://orcid.org/0000-0003-2169-426X>)
Maintainer: Helmut Schütz <helmut.schuetz@bebac.at>

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Package parameters updated to version 0.8.2 with previous version 0.8.0 dated 2020-06-08

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>), Søren Højsgaard [aut], Zen J. Lau [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between parameters versions 0.8.0 dated 2020-06-08 and 0.8.2 dated 2020-07-24

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 parameters-0.8.2/parameters/tests/testthat/test-panelr.R                         |only
 parameters-0.8.2/parameters/tests/testthat/test-pca.R                            |    2 
 parameters-0.8.2/parameters/tests/testthat/test-plm.R                            |   37 +
 parameters-0.8.2/parameters/tests/testthat/test-quantreg.R                       |only
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Package BIGL updated to version 1.5.2 with previous version 1.5.1 dated 2020-07-07

Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>

Diff between BIGL versions 1.5.1 dated 2020-07-07 and 1.5.2 dated 2020-07-24

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Package BGGM updated to version 2.0.2 with previous version 2.0.1 dated 2020-07-23

Title: Bayesian Gaussian Graphical Models
Description: Fit Bayesian Gaussian graphical models. The methods are separated into two Bayesian approaches for inference: hypothesis testing and estimation. There are extensions for confirmatory hypothesis testing, comparing Gaussian graphical models, and node wise predictability. These methods were recently introduced in the Gaussian graphical model literature, including Williams (2019) <doi:10.31234/osf.io/x8dpr>, Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>, Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.
Author: Donald Williams [aut, cre], Joris Mulder [aut]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>

Diff between BGGM versions 2.0.1 dated 2020-07-23 and 2.0.2 dated 2020-07-24

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Package lcsm updated to version 0.1.2 with previous version 0.1.1 dated 2020-06-05

Title: Univariate and Bivariate Latent Change Score Modeling
Description: Helper functions to implement univariate and bivariate latent change score models in R using the 'lavaan' package. For details about Latent Change Score Modeling (LCSM) see McArdle (2009) <doi:10.1146/annurev.psych.60.110707.163612> and Grimm, An, McArdle, Zonderman and Resnick (2012) <doi:10.1080/10705511.2012.659627>. The package automatically generates 'lavaan' syntax for different model specifications and varying timepoints. The 'lavaan' syntax generated by this package can be returned and further specifications can be added manually. Longitudinal plots as well as simplified path diagrams can be created to visualise data and model specifications. Estimated model parameters and fit statistics can be extracted as data frames. Data for different univariate and bivariate LCSM can be simulated by specifying estimates for model parameters to explore their effects. This package combines the strengths of other R packages like 'lavaan', 'broom', and 'semPlot' by generating 'lavaan' syntax that helps these packages work together.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>), Anke Ehlers [ths] (<https://orcid.org/0000-0002-8742-0192>), Mental Health Research UK [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

Diff between lcsm versions 0.1.1 dated 2020-06-05 and 0.1.2 dated 2020-07-24

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New package ztpln with initial version 0.1.0
Type: Package
Package: ztpln
Title: Zero-Truncated Poisson Lognormal Distribution
Version: 0.1.0
Date: 2020-07-17
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>
Description: Functions for obtaining the density, random variates and maximum likelihood estimates of the Zero-truncated Poisson lognormal distribution and their mixture distribution.
License: MIT + file LICENSE
URL: https://github.com/mattocci27/ztpln
BugReports: https://github.com/mattocci27/ztpln/issues
Depends: R (>= 3.5)
Imports: DBI, DistributionUtils, Rcpp (>= 0.12.0), colorspace, lubridate, mixtools, stats
Suggests: knitr, dplyr, ggplot2, rmarkdown, testthat, tidyr(>= 1.0.0)
LinkingTo: Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppNumerical (>= 0.3-2)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-07-20 11:29:01 UTC; rstudio
Repository: CRAN
Date/Publication: 2020-07-24 17:40:02 UTC

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New package waspr with initial version 1.0.0
Package: waspr
Type: Package
Title: Wasserstein Barycenters of Subset Posteriors
Version: 1.0.0
Authors@R: person("Jolien", "Cremers", email = "joliencremers@gmail.com", role = c("aut", "cre"))
Description: Functions to compute Wasserstein barycenters of subset posteriors using the swapping algorithm developed by Puccetti, Rüschendorf and Vanduffel (2020) <doi:10.1016/j.jmaa.2017.02.003>. The Wasserstein barycenter is a geometric approach for combining subset posteriors. It allows for parallel and distributed computation of the posterior in case of complex models and/or big datasets, thereby increasing computational speed tremendously.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 1.0.4.6), methods
LinkingTo: BH, Rcpp, RcppArmadillo,
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown, testthat, spelling
VignetteBuilder: knitr
Language: en-US
Biarch: true
Depends: R (>= 3.5.0)
NeedsCompilation: yes
Packaged: 2020-07-20 10:51:59 UTC; bsj777
Author: Jolien Cremers [aut, cre]
Maintainer: Jolien Cremers <joliencremers@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-24 17:30:02 UTC

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New package l1ball with initial version 0.1.0
Package: l1ball
Type: Package
Title: L1-Ball Prior for Sparse Regression
Version: 0.1.0
Author: Maoran Xu and Leo L. Duan
Maintainer: Maoran Xu <maoranxu@ufl.edu>
Description: Provides function for the l1-ball prior on high-dimensional regression. The main function, l1ball(), yields posterior samples for linear regression, as introduced by Xu and Duan (2020) <arXiv:2006.01340>.
License: GPL (>= 2)
Depends: R (>= 3.1.0)
Imports: VGAM, stats
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-07-20 01:52:51 UTC; maoran
Repository: CRAN
Date/Publication: 2020-07-24 17:10:02 UTC

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Package broomExtra updated to version 4.0.4 with previous version 4.0.3 dated 2020-06-19

Title: Enhancements for 'broom' and 'easystats' Package Families
Description: Provides helper functions that assist in data analysis workflows involving regression analyses. The goal is to combine the functionality offered by different set of packages ('broom', 'broom.mixed', 'parameters', and 'performance') through a common syntax to return tidy dataframes containing model parameters and performance measure summaries. The 'grouped_' variants of the generics provides a convenient way to execute functions across a combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, cph] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between broomExtra versions 4.0.3 dated 2020-06-19 and 4.0.4 dated 2020-07-24

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Package BeyondBenford updated to version 1.4 with previous version 1.3 dated 2020-04-11

Title: Compare the Goodness of Fit of Benford's and Blondeau Da Silva's Digit Distributions to a Given Dataset
Description: Allows to compare the goodness of fit of Benford's and Blondeau Da Silva's digit distributions in a dataset. It is used to check whether the data distribution is consistent with theoretical distributions highlighted by Blondeau Da Silva or not (through the dat.distr() function): this ideal theoretical distribution must be at least approximately followed by the data for the use of Blondeau Da Silva's model to be well-founded. It also enables to plot histograms of digit distributions, both observed in the dataset and given by the two theoretical approaches (with the digit.ditr() function). Finally, it proposes to quantify the goodness of fit via Pearson's chi-squared test (with the chi2() function).
Author: Blondeau Da Silva Stephane
Maintainer: Blondeau Da Silva Stephane <Stephane.Blondeau-Da-Silva@ac-limoges.fr>

Diff between BeyondBenford versions 1.3 dated 2020-04-11 and 1.4 dated 2020-07-24

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New package bbotk with initial version 0.2.0
Package: bbotk
Title: Black-Box Optimization Toolkit
Version: 0.2.0
Authors@R: c(person(given = "Marc", family = "Becker", role = c("cre", "aut"), email = "marcbecker@posteo.de", comment = c(ORCID = "0000-0002-8115-0400")), person(given = "Jakob", family = "Richter", role = "aut", email = "jakob1richter@gmail.com", comment = c(ORCID = "0000-0003-4481-5554")), person(given = "Michel", family = "Lang", role = "aut", email = "michellang@gmail.com", comment = c(ORCID = "0000-0001-9754-0393")), person(given = "Bernd", family = "Bischl", role = "aut", email = "bernd_bischl@gmx.net", comment = c(ORCID = "0000-0001-6002-6980")), person(given = "Martin", family = "Binder", role = "aut", email = "martin.binder@mail.com"), person(given = "Olaf", family = "Mersmann", role = "ctb", email = "olafm@statistik.tu-dortmund.de"))
Description: Provides a common framework for optimization of black-box functions for other packages, e.g. 'mlr3'. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing.
License: LGPL-3
URL: https://bbotk.mlr-org.com, https://github.com/mlr-org/bbotk
BugReports: https://github.com/mlr-org/bbotk/issues
Depends: R (>= 3.1.0)
Imports: checkmate (>= 2.0.0), data.table, lgr, mlr3misc (>= 0.3.0), paradox (>= 0.3), R6
Suggests: bibtex, GenSA, knitr, nloptr, rmarkdown, testthat
VignetteBuilder: knitr
RdMacros: mlr3misc
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
RoxygenNote: 7.1.1
Collate: 'Archive.R' 'Objective.R' 'ObjectiveRFun.R' 'ObjectiveRFunDt.R' 'OptimInstance.R' 'OptimInstanceMultiCrit.R' 'OptimInstanceSingleCrit.R' 'mlr_optimizers.R' 'Optimizer.R' 'OptimizerDesignPoints.R' 'OptimizerGenSA.R' 'OptimizerGridSearch.R' 'OptimizerNLoptr.R' 'OptimizerRandomSearch.R' 'mlr_terminators.R' 'Terminator.R' 'TerminatorClockTime.R' 'TerminatorCombo.R' 'TerminatorEvals.R' 'TerminatorNone.R' 'TerminatorPerfReached.R' 'TerminatorRunTime.R' 'TerminatorStagnation.R' 'TerminatorStagnationBatch.R' 'assertions.R' 'bbotk_reflections.R' 'helper.R' 'sugar.R' 'zzz.R'
Packaged: 2020-07-20 09:41:37 UTC; marc
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Martin Binder [aut], Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Repository: CRAN
Date/Publication: 2020-07-24 17:20:02 UTC

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New package owd with initial version 1.0.4
Package: owd
Version: 1.0.4
Date: 2020-07-19
Title: Open Working Directory
Authors@R: c(person(c("Benjamin", "G."), "Feakins", role = c("aut", "cre"), email = "benjamin.feakins@ndph.ox.ac.uk", comment = c(ORCID = "0000-0002-3928-6750")), person(c("Benjamin", "J."), "Cairns", role = "ctb", email = "ben.cairns@ndph.ox.ac.uk", comment = c(ORCID = "0000-0001-7994-8213")), person("University of Oxford", role = c("cph", "sht")))
Description: Open the current working directory (or a given directory path) in your computer's file manager.
Depends: R (>= 2.13)
License: MIT + file LICENSE
URL: https://github.com/Feakster/owd
BugReports: https://github.com/Feakster/owd/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-07-19 08:10:18 UTC; benjamin
Author: Benjamin G. Feakins [aut, cre] (<https://orcid.org/0000-0002-3928-6750>), Benjamin J. Cairns [ctb] (<https://orcid.org/0000-0001-7994-8213>), University of Oxford [cph, sht]
Maintainer: Benjamin G. Feakins <benjamin.feakins@ndph.ox.ac.uk>
Repository: CRAN
Date/Publication: 2020-07-24 16:40:03 UTC

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New package dittodb with initial version 0.1.0
Package: dittodb
Title: A Test Environment for Database Requests
Version: 0.1.0
Authors@R: c( person(given = "Jonathan", family = "Keane", role = c("aut", "cre"), email = "jkeane@gmail.com", comment = c(ORCID = "0000-0001-7087-9776")), person(given = "Mauricio", family = "Vargas", role = "aut", email = "mvargas@dcc.uchile.cl", comment = c(ORCID = "0000-0003-1017-7574")), person(given = "Helen", family = "Miller", role = "rev", comment = "reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/366"), person(given = "Etienne", family = "Racine", role = "rev", comment = "reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/366") )
URL: https://dittodb.jonkeane.com/, https://github.com/ropensci/dittodb
BugReports: https://github.com/ropensci/dittodb/issues
Description: Testing and documenting code that communicates with remote databases can be painful. Although the interaction with R is usually relatively simple (e.g. data(frames) passed to and from a database), because they rely on a separate service and the data there, testing them can be difficult to set up, unsustainable in a continuous integration environment, or impossible without replicating an entire production cluster. This package addresses that by allowing you to make recordings from your database interactions and then play them back while testing (or in other contexts) all without needing to spin up or have access to the database your code would typically connect to.
License: Apache License (>= 2.0)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0), DBI
Imports: digest, glue, methods, testthat, utils
Suggests: callr, covr, dplyr, dbplyr, knitr, nycflights13, odbc, RMariaDB, RPostgres, RPostgreSQL, RSQLite, spelling, withr, rmarkdown, lintr
RoxygenNote: 7.1.1
Language: en-US
VignetteBuilder: knitr
Collate: 'capture-requests.R' 'connection.R' 'dbExistsTable.R' 'dbListTables-Fields.R' 'driver-specific-connections.R' 'dbQueries-Results.R' 'dbMisc.R' 'mock-paths.R' 'dittodb-env.R' 'mock-db.R' 'nycflights13-sql.R' 'paths.R' 'quote.R' 'redact.R' 'use-dittodb.R' 'utils.R'
NeedsCompilation: yes
Packaged: 2020-07-19 05:49:40 UTC; jkeane
Author: Jonathan Keane [aut, cre] (<https://orcid.org/0000-0001-7087-9776>), Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>), Helen Miller [rev] (reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/366), Etienne Racine [rev] (reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/366)
Maintainer: Jonathan Keane <jkeane@gmail.com>
Repository: CRAN
Date/Publication: 2020-07-24 16:40:06 UTC

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New package covidregionaldata with initial version 0.5.0
Package: covidregionaldata
Title: Subnational Data for the Covid-19 Outbreak
Version: 0.5.0
Authors@R: c(person(given = "Sam Abbott", role = c("aut", "cre"), email = "sam.abbott@lshtm.ac.uk", comment = c(ORCID = "0000-0001-8057-8037")), person("Katharine", "Sherratt", email = "katharine.sherratt@lshtm.ac.uk", role = c("aut"), comment = c(ORCID = "0000-0003-4413-453X")), person("Jonnie", "Bevan", email = "jonnie.bevan@tessella.com", role = c("aut")), person("Hamish", "Gibbs", email = "Hamish.Gibbs@lshtm.ac.uk", role = c("aut"), comment = c(ORCID = "0000-0003-4413-453X")), person("Joel", "Hellewell", email = "joel.hellewell@lshtm.ac.uk", role = c("aut"), comment = c(ORCID = "0000-0003-2683-0849")), person("James", "Munday", email = "james.munday@lshtm.ac.uk", role = c("aut")), person("Patrick", "Barks", email = "patrick.barks@epicentre.msf.org", role = c("ctb")), person("Paul", "Campbell", email = " paul.campbell@epicentre.msf.org", role = c("aut")), person("Flavio", "Finger", email = "flavio.finger@epicentre.msf.org", role = c("ctb"), comment = c(ORCID = "0000-0002-8613-5170")), person("Sebastian", "Funk", email = "sebastian.funk@lshtm.ac.uk", role = c("aut")))
Description: An interface to subnational and national level Covid-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisations, and tests. National level data is also supported using a range of data sources as well as linelist data and links to intervention data sets. Data sources included: WHO <https://dashboards-dev.sprinklr.com/data/9043/global-covid19-who-gis.json>, <https://covid19.who.in>; ACAPS interventions <https://data.humdata.org/dataset/acaps-covid19-government-measures-dataset>; patient linelist: <https://github.com/beoutbreakprepared/nCoV2019>), regional data (Afghanistan: <https://data.humdata.org/dataset/afghanistan-covid-19-statistics-per-province>; Belgium: <https://epistat.wiv-isp.be/covid>; Brazil: <https://github.com/wcota/covid19br>; Canada: <https://health-infobase.canada.ca/>; Colombia: <https://github.com/danielcs88/colombia_covid-19>; Germany: <https://npgeo-corona-npgeo-de.hub.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0>; India: <https://api.covid19india.org/>; Italy: <https://github.com/pcm-dpc/COVID-19>; Russia: <https://github.com/grwlf/COVID-19_plus_Russia>; UK: <https://coronavirus.data.gov.uk>, <https://github.com/tomwhite/covid-19-uk-data>; USA: <https://github.com/nytimes/covid-19-data>), and geocoding data (Colombia: <https://en.wikipedia.org/wiki/ISO_3166-2:CO>; Russia: <https://en.wikipedia.org/wiki/ISO_3166-2:RU>).
Language: en-gb
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: readr, dplyr, tibble, purrr, stringr, magrittr, memoise, lubridate, tidyr, httr, yaml, readxl, xml2, rvest, jsonlite, countrycode
Suggests: data.table, pkgdown, testthat, spelling
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-24 13:28:43 UTC; seabbs
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>), Katharine Sherratt [aut] (<https://orcid.org/0000-0003-4413-453X>), Jonnie Bevan [aut], Hamish Gibbs [aut] (<https://orcid.org/0000-0003-4413-453X>), Joel Hellewell [aut] (<https://orcid.org/0000-0003-2683-0849>), James Munday [aut], Patrick Barks [ctb], Paul Campbell [aut], Flavio Finger [ctb] (<https://orcid.org/0000-0002-8613-5170>), Sebastian Funk [aut]
Maintainer: Sam Abbott <sam.abbott@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2020-07-24 14:00:02 UTC

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Package bootUR updated to version 0.2.0 with previous version 0.1.0 dated 2020-06-25

Title: Bootstrap Unit Root Tests
Description: Set of functions to perform various bootstrap unit root tests for both individual time series (including augmented Dickey-Fuller test and union tests), multiple time series and panel data; see Palm, Smeekes and Urbain (2008) <doi:10.1111/j.1467-9892.2007.00565.x>, Palm, Smeekes and Urbain (2011) <doi:10.1016/j.jeconom.2010.11.010>, Moon and Perron (2012) <doi:10.1016/j.jeconom.2012.01.008>, Smeekes and Taylor (2012) <doi:10.1017/S0266466611000387> and Smeekes (2015) <doi:10.1111/jtsa.12110> for key references.
Author: Stephan Smeekes [cre, aut] (<https://orcid.org/0000-0002-0157-639X>), Ines Wilms [aut]
Maintainer: Stephan Smeekes <s.smeekes@maastrichtuniversity.nl>

Diff between bootUR versions 0.1.0 dated 2020-06-25 and 0.2.0 dated 2020-07-24

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Package betadiv updated to version 1.0.1 with previous version 1.0.0 dated 2020-06-05

Title: Estimators of Multiple-Site Dissimilarity Indices for the Assessment of Beta Diversity
Description: Implement the multiple-site dissimilarity indices of Simpson, Sorensen and nestedness, which can be used to assess the beta diversity of a population. These indices were adapted from those developed by Baselga (2010) <doi:10.1111/j.1466-8238.2009.00490.x> in order to have them population size-independent. All the details behind the calculation and estimation of these adapted indices can be found in Fortin et al. (2020) <doi:10.1111/geb.13080>.
Author: Mathieu Fortin, Anna Kondratyeva, Rosalinde Van Couwenberghe
Maintainer: Mathieu Fortin <mathieu.fortin.re@gmail.com>

Diff between betadiv versions 1.0.0 dated 2020-06-05 and 1.0.1 dated 2020-07-24

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Package Jdmbs updated to version 1.4 with previous version 1.3 dated 2018-05-01

Title: Monte Carlo Option Pricing Algorithms for Jump Diffusion Models with Correlational Companies
Description: Option is a one of the financial derivatives and its pricing is an important problem in practice. The process of stock prices are represented as Geometric Brownian motion [Black (1973) <doi:10.1086/260062>] or jump diffusion processes [Kou (2002) <doi:10.1287/mnsc.48.8.1086.166>]. In this package, algorithms and visualizations are implemented by Monte Carlo method in order to calculate European option price for three equations by Geometric Brownian motion and jump diffusion processes and furthermore a model that presents jumps among companies affect each other.
Author: Masashi Okada [aut, cre]
Maintainer: Masashi Okada <okadaalgorithm@gmail.com>

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Package ijtiff updated to version 2.1.2 with previous version 2.1.1 dated 2020-07-05

Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Kent Johnson [aut], Simon Urbanek [ctb], Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>), Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>), Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package RcppEnsmallen updated to version 0.2.13.0.1 with previous version 0.2.12.1.1 dated 2020-04-24

Title: Header-Only C++ Mathematical Optimization Library for 'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library (by the 'MLPACK' team) that provides a simple set of abstractions for writing an objective function to optimize. Provided within are various standard and cutting-edge optimizers that include full-batch gradient descent techniques, small-batch techniques, gradient-free optimizers, and constrained optimization. The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library and pairs the appropriate header files from 'armadillo' through the 'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor 'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under 3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2, 'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under similar terms. Note that 'Ensmallen' requires a compiler that supports 'C++11' and 'Armadillo' 8.400 or later.
Author: James Joseph Balamuta [aut, cre, cph] (<https://orcid.org/0000-0003-2826-8458>), Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package incidence updated to version 1.7.2 with previous version 1.7.1 dated 2020-03-25

Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut], Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Rich FitzJohn [aut], Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>), Sangeeta Bhatia [ctb], Jakob Schumacher [ctb], Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

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Package goffda updated to version 0.0.7 with previous version 0.0.6 dated 2019-12-17

Title: Goodness-of-Fit Tests for Functional Data
Description: Implementation of several goodness-of-fit tests for functional data. Currently, mostly related with the functional linear model with functional/scalar response and functional/scalar predictor. The package allows for the replication of the data applications considered in García-Portugués, Álvarez-Liébana, Álvarez-Pérez and González-Manteiga (2019) <arXiv:1909.07686>.
Author: Eduardo García-Portugués [aut, cre], Javier Álvarez-Liébana [aut], Gonzalo Álvarez-Pérez [ctb], Manuel Febrero-Bande [ctb]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>

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Package altmeta updated to version 3.1 with previous version 3.0 dated 2020-04-24

Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including: - new heterogeneity tests and measures that are robust to outliers (Lin et al., 2017 <doi:10.1111/biom.12543>); - measures, tests, and visualization tools for publication bias or small-study effects (Lin and Chu, 2018 <doi:10.1111/biom.12817>; Lin, 2019 <doi:10.1002/jrsm.1340>; Lin, 2020 <doi:10.1177/0962280220910172>; Shi et al., 2020 <doi:10.1002/jrsm.1415>); - meta-analysis methods for synthesizing proportions (Lin and Chu, 2020 <doi:10.1097/ede.0000000000001232>); - models for multivariate meta-analysis (Lin and Chu, 2018 <doi:10.1002/jrsm.1293>).
Author: Lifeng Lin [aut, cre] (<https://orcid.org/0000-0002-3562-9816>), Linyu Shi [ctb], Haitao Chu [aut] (<https://orcid.org/0000-0003-0932-598X>)
Maintainer: Lifeng Lin <linl@stat.fsu.edu>

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Package mstDIF updated to version 0.1.6 with previous version 0.1.5 dated 2020-07-20

Title: A Collection of DIF Tests for Multistage Tests
Description: A collection of statistical tests for the detection of differential item functioning (DIF) in multistage tests. Methods entail logistic regression, an adaptation of the simultaneous item bias test (SIBTEST), and various score-based tests. The presented tests provide itemwise test for DIF along categorical, ordinal or metric covariates. Methods for uniform and non-uniform DIF effects are available depending on which method is used.
Author: Rudolf Debelak [aut, cre], Dries Debeer [aut], Sebastian Appelbaum [ctb], Mark J. Gierl [ctb]
Maintainer: Rudolf Debelak <rudolf.debelak@gmail.com>

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Package tsibble updated to version 0.9.2 with previous version 0.9.1 dated 2020-06-20

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>)
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package xfun updated to version 0.16 with previous version 0.15 dated 2020-06-21

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>)
Maintainer: Yihui Xie <xie@yihui.name>

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Package provSummarizeR updated to version 1.4.2 with previous version 1.4.1 dated 2020-07-16

Title: Summarizes Provenance Related to Inputs and Outputs of a Script or Console Commands
Description: Reads the provenance collected by the 'rdt' or 'rdtLite' packages, or other tools providing compatible PROV JSON output created by the execution of a script, and provides a human-readable summary identifying the input and output files, the script used (if any), errors and warnings produced, and the environment in which it was executed. It can also optionally package all the files into a zip file. The exact format of the JSON created by 'rdt' and 'rdtLite' is described in <https://github.com/End-to-end-provenance/ExtendedProvJson>. 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>.
Author: Barbara Lerner [cre], Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>

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Package kStatistics updated to version 2.0 with previous version 1.0 dated 2019-08-05

Title: Unbiased Estimators for Cumulant Products
Description: Tools for estimate (joint) cumulants and products of (joint) cumulants of a given population distribution using (multivariate) k-statistics and (multivariate) polykays, unbiased estimators with minimum variance. Tools for generating univariate and multivariate Faa di Bruno's formula and related polynomials, such as Bell polynomials, generalized complete Bell polynomials, partition polynomials, generalized partition polynomials. For more details see Di Nardo E., Guarino G., Senato D. (2009) <arXiv:0807.5008>, <arXiv:1012.6008>.
Author: Elvira Di Nardo <elvira.dinardo@unito.it>, Giuseppe Guarino <giuseppe.guarino@rete.basilicata.it>
Maintainer: Giuseppe Guarino <giuseppe.guarino@rete.basilicata.it>

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New package InformativeCensoring with initial version 0.3.5
Package: InformativeCensoring
Type: Package
Title: Multiple Imputation for Informative Censoring
Version: 0.3.5
Authors@R: c( person("David", "Ruau", email='davidruau@gmail.com', role=c("aut")), person("Nikolas", "Burkoff", role=c("aut")), person("Jonathan", "Bartlett", email='j.w.bartlett@bath.ac.uk', role=c("aut","cre")), person("Dan", "Jackson", email='daniel.jackson1@astrazeneca.com', role=c("aut")), person("Edmund", "Jones", email='epaj2@medschl.cam.ac.uk', role=c("aut")), person("Martin", "Law", email='martin.law@mrc-bsu.cam.ac.uk', role=c("aut")), person("Paul", "Metcalfe", email='paul.metcalfe@astrazeneca.com', role=c("aut")) )
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Author: David Ruau [aut], Nikolas Burkoff [aut], Jonathan Bartlett [aut, cre], Dan Jackson [aut], Edmund Jones [aut], Martin Law [aut], Paul Metcalfe [aut]
Description: Multiple Imputation for Informative Censoring. This package implements two methods. Gamma Imputation described in <DOI:10.1002/sim.6274> and Risk Score Imputation described in <DOI:10.1002/sim.3480>.
License: GPL (>= 2) | file LICENSE
LazyLoad: yes
Depends: R (>= 3.1.2), survival (>= 2.36-1)
Imports: boot, dplyr (>= 0.4.3), parallel
Suggests: knitr, testthat
VignetteBuilder: knitr
URL: https://github.com/jwb133/InformativeCensoring
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-07-23 16:42:21 UTC; JWB-beast
Repository: CRAN
Date/Publication: 2020-07-24 09:42:20 UTC

More information about InformativeCensoring at CRAN
Permanent link

Package IFC updated to version 0.0.9 with previous version 0.0.8 dated 2020-07-13

Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read, write and subset .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre], Gautier Stoll [ctb], Guido Kroemer [ldr], Jean-Pierre Marolleau [ldr], Loïc Garçon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>

Diff between IFC versions 0.0.8 dated 2020-07-13 and 0.0.9 dated 2020-07-24

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Permanent link

Package flatxml updated to version 0.1.0 with previous version 0.0.2 dated 2018-07-08

Title: Tools for Working with XML Files as R Dataframes
Description: On import, the XML information is converted to a dataframe that reflects the hierarchical XML structure. Intuitive functions allow to navigate within this transparent XML data structure (without any knowledge of 'XPath'). 'flatXML' also provides tools to extract data from the XML into a flat dataframe that can be used to perform statistical operations. It also supports converting dataframes to XML.
Author: Joachim Zuckarelli [aut, cre]
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>

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Package data.table updated to version 1.13.0 with previous version 1.12.8 dated 2019-12-09

Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre], Arun Srinivasan [aut], Jan Gorecki [ctb], Michael Chirico [ctb], Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Toby Hocking [ctb], Leonardo Silvestri [ctb], Tyson Barrett [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>

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Package chk updated to version 0.5.1 with previous version 0.5.0 dated 2020-05-29

Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package CB2 updated to version 1.3.4 with previous version 1.3.3 dated 2020-05-26

Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <jeong.hyunhwan@gmail.com>

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Package anytime updated to version 0.3.8 with previous version 0.3.7 dated 2020-01-20

Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor, or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package wrMisc updated to version 1.3.0 with previous version 1.2.4 dated 2020-07-03

Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>

Diff between wrMisc versions 1.2.4 dated 2020-07-03 and 1.3.0 dated 2020-07-24

 DESCRIPTION                   |    8 ++++----
 MD5                           |   40 ++++++++++++++++++++++------------------
 NAMESPACE                     |    2 ++
 R/asSepList.R                 |    2 +-
 R/combinatIntTable.R          |only
 R/conv01toColNa.R             |   20 ++++++++++----------
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 R/moderTest2grp.R             |    2 +-
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 R/pVal2lfdr.R                 |    4 ++--
 R/readVarColumns.R            |    2 +-
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 23 files changed, 95 insertions(+), 82 deletions(-)

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Package WebGestaltR updated to version 0.4.4 with previous version 0.4.3 dated 2020-01-16

Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut], Yuxing Liao [aut, cre], Eric Jaehnig [ctb], Zhiao Shi [ctb], Quanhu Sheng [ctb]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>

Diff between WebGestaltR versions 0.4.3 dated 2020-01-16 and 0.4.4 dated 2020-07-24

 DESCRIPTION                                 |    8 
 MD5                                         |  168 
 NAMESPACE                                   |  150 
 NEWS.md                                     |   34 
 R/RcppExports.R                             |   62 
 R/WebGestaltR.R                             |  480 
 R/WebGestaltRBatch.R                        |  120 
 R/WebGestaltRGsea.R                         |  298 
 R/WebGestaltRNta.R                          |  164 
 R/WebGestaltROra.R                          |  304 
 R/affinityPropagation.R                     |  206 
 R/cacheFile.R                               |  104 
 R/createNtaReport.R                         |  240 
 R/createReport.R                            |  270 
 R/dagUtils.R                                |  284 
 R/enrichResultSection.R                     |   70 
 R/errorMessage.R                            |  792 
 R/formatCheck.R                             |  162 
 R/goSlimReport.R                            |   12 
 R/goSlimSummary.R                           |  246 
 R/gseaEnrichment.R                          |  306 
 R/idMapping.R                               |  138 
 R/idMappingGene.R                           |  220 
 R/idMappingPhosphosite.R                    |  310 
 R/idMappingUtils.R                          |  146 
 R/idToSymbol.R                              |  208 
 R/linkModification.R                        |   96 
 R/listArchiveURL.R                          |   42 
 R/listGeneSet.R                             |  104 
 R/listIdType.R                              |   64 
 R/listOrganism.R                            |   50 
 R/listReferenceSet.R                        |   50 
 R/loadGeneList.R                            |  250 
 R/loadGeneSet.R                             |  428 
 R/oraEnrichment.R                           |  136 
 R/randomWalkEnrichment.R                    |  382 
 R/readGmt.R                                 |  168 
 R/reportUtils.R                             |  226 
 R/summaryDescription.R                      |  262 
 R/weightedSetCover.R                        |  252 
 README.md                                   |    6 
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 inst/extdata/GeneRankList.rnk               |23906 ++++++++++++++--------------
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 man/WebGestaltR.Rd                          |  596 
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 man/expandDag.Rd                            |   24 
 man/fillInputDataFrame.Rd                   |   50 
 man/formatCheck.Rd                          |   46 
 man/goSlimSummary.Rd                        |   86 
 man/gseaPermutation.Rd                      |   50 
 man/idMapping.Rd                            |  146 
 man/jaccardSim.Rd                           |   46 
 man/keepRep.Rd                              |   24 
 man/linkModification.Rd                     |   24 
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 man/listGeneSet.Rd                          |   60 
 man/listIdType.Rd                           |   62 
 man/listOrganism.Rd                         |   38 
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 man/prepareGseaInput.Rd                     |   38 
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 man/specificParameterSummaryGsea.Rd         |   52 
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 85 files changed, 30551 insertions(+), 30549 deletions(-)

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Package tinytex updated to version 0.25 with previous version 0.24 dated 2020-06-20

Title: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), RStudio, PBC [cph], Fernando Cagua [ctb], Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between tinytex versions 0.24 dated 2020-06-20 and 0.25 dated 2020-07-24

 DESCRIPTION  |   12 ++++++------
 MD5          |   10 +++++-----
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 man/tlmgr.Rd |    5 +++++
 6 files changed, 35 insertions(+), 15 deletions(-)

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Package ralger updated to version 2.0.1 with previous version 2.0.0 dated 2020-04-12

Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R. The user has the ability to extract a vector with scrap(), a tidy dataframe using tidy_scrap(), a table with table_scrap() and web links with weblink_scrap().
Author: Mohamed El Fodil Ihaddaden [aut, cre], Ezekiel Ogundepo [ctb]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>

Diff between ralger versions 2.0.0 dated 2020-04-12 and 2.0.1 dated 2020-07-24

 DESCRIPTION             |   14 ++-
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 13 files changed, 371 insertions(+), 296 deletions(-)

More information about ralger at CRAN
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