Thu, 27 Aug 2020

Package vctrs updated to version 0.3.3 with previous version 0.3.2 dated 2020-07-15

Title: Vector Helpers
Description: Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut], Lionel Henry [aut, cre], Davis Vaughan [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between vctrs versions 0.3.2 dated 2020-07-15 and 0.3.3 dated 2020-08-27

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More information about vctrs at CRAN
Permanent link

Package photobiology updated to version 0.10.5 with previous version 0.10.4 dated 2020-06-07

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb], Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiology versions 0.10.4 dated 2020-06-07 and 0.10.5 dated 2020-08-27

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More information about photobiology at CRAN
Permanent link

Package vov updated to version 0.1.2 with previous version 0.1.1 dated 2020-08-02

Title: CSS Animations for 'shiny' Elements
Description: A wrapper around a CSS library called 'vov.css', intended for use in 'shiny' applications. Simply wrap a UI element in one of the animation functions to see it move.
Author: Tyler Littlefield [aut, cre] (Creator of Shiny Wrapper), Vaibhav Tandon [ctb, cph] (Author of included CSS code), Danube Huynhle [ctb]
Maintainer: Tyler Littlefield <tylerlittlefield@hey.com>

Diff between vov versions 0.1.1 dated 2020-08-02 and 0.1.2 dated 2020-08-27

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More information about vov at CRAN
Permanent link

Package MiRKAT updated to version 1.1.1 with previous version 1.1.0 dated 2020-04-14

Title: Microbiome Regression-Based Analysis Tests
Description: Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). The package can also use robust and quantile regression (Fu et al. (2020+), in preparation). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.
Author: Anna Plantinga [aut, cre], Nehemiah Wilson [aut, ctb], Haotian Zheng [aut, ctb], Xiang Zhan [aut, ctb], Michael Wu [aut], Ni Zhao [aut, ctb], Jun Chen [aut]
Maintainer: Anna Plantinga <amp9@williams.edu>

Diff between MiRKAT versions 1.1.0 dated 2020-04-14 and 1.1.1 dated 2020-08-27

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Package contentid updated to version 0.0.5 with previous version 0.0.4 dated 2020-08-12

Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based identifiers for data management. Content-based identifiers rely on the 'cryptographic' hashes to refer to the files they identify, thus, anyone possessing the file can compute the identifier using a well-known standard algorithm, such as 'SHA256'. By registering a URL at which the content is accessible to a public archive, such as <https://hash-archive.org>, the content identifier can serve many functions typically associated with A Digital Object Identifier ('DOI'). Unlike location-based identifiers like 'DOIs', content-based identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>), Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>), NSF OAC 1839201 [fnd] (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1839201)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package mets updated to version 1.2.8 with previous version 1.2.7.1 dated 2020-03-04

Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Also contains two-stage binomial modelling that can do pairwise odds-ratio dependence modelling based marginal logistic regression models. This is an alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst [aut, cre], Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>

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Package kableExtra updated to version 1.2.1 with previous version 1.1.0 dated 2019-03-16

Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>

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Package covidregionaldata updated to version 0.6.0 with previous version 0.5.0 dated 2020-07-24

Title: Subnational Data for the Covid-19 Outbreak
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://covid19.who.int>; 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>; 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>).
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>

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Package rfacebookstat updated to version 2.1.7 with previous version 2.1.1 dated 2020-05-29

Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package gtsummary updated to version 1.3.4 with previous version 1.3.3 dated 2020-08-11

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>), Joseph Larmarange [ctb] (<https://orcid.org/0000-0001-7097-700X>), Stephanie Lobaugh [ctb], Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package intmed updated to version 0.1.2 with previous version 0.1.1 dated 2020-03-01

Title: Mediation Analysis using Interventional Effects
Description: Implementing the interventional effects for mediation analysis for up to 3 mediators. The methods used are based on VanderWeele, Vansteelandt and Robins (2014) <doi:10.1097/ede.0000000000000034>, Vansteelandt and Daniel (2017) <doi:10.1097/ede.0000000000000596> and Chan and Leung (2020; unpublished manuscript, available on request from the author of this package). Linear regression, logistic regression and Poisson regression are used for continuous, binary and count mediator/outcome variables respectively.
Author: Gary Chan [aut, cre, cph]
Maintainer: Gary Chan <c.chan4@uq.edu.au>

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Package collapse updated to version 1.3.1 with previous version 1.3.0 dated 2020-08-11

Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, flexible and parsimonious to code with and programmer friendly. It is well integrated with 'dplyr', 'plm' and 'data.table'. --- Key Features: --- (1) Advanced statistical programming: A full set of fast statistical functions supporting grouped and weighted computations on vectors, matrices and data frames. Fast and programmable grouping, ordering, unique values / rows, factor generation and interactions. Fast and flexible functions for data manipulation and data object conversions. (2) Advanced aggregation: Fast and easy multi-data-type, multi-function, weighted, parallelized and fully customized data aggregation. (3) Advanced transformations: Fast (grouped) replacing and sweeping out of statistics, and (grouped, weighted) scaling / standardizing, between (averaging) and (quasi-)within (centering / demeaning) transformations, higher-dimensional centering (i.e. multiple fixed effects transformations), linear prediction and partialling-out. (4) Advanced time-computations: Fast (sequences of) lags / leads, and (lagged / leaded, iterated, quasi-, log-) differences and growth rates on (unordered) time series and panel data. Multivariate auto-, partial- and cross-correlation functions for panel data. Panel data to (ts-)array conversions. (5) List processing: (Recursive) list search / identification, extraction / subsetting, data-apply, and generalized row-binding / unlisting in 2D. (6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed) summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre], Matt Dowle [ctb], Arun Srinivasan [ctb], Simen Gaure [ctb], Dirk Eddelbuettel [ctb], R Core Team and contributors worldwide [ctb], Martyn Plummer [cph], 1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>

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Package wnl updated to version 0.6.1 with previous version 0.6.0 dated 2020-07-16

Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package mlt.docreg updated to version 1.0-6 with previous version 1.0-5 dated 2020-02-13

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package zip updated to version 2.1.1 with previous version 2.1.0 dated 2020-08-10

Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.
Author: Gábor Csárdi, Kuba Podgórski, Rich Geldreich
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package stringfish updated to version 0.14.1 with previous version 0.13.3 dated 2020-07-09

Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)
Maintainer: Travers Ching <traversc@gmail.com>

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Package stplanr updated to version 0.7.0 with previous version 0.6.2 dated 2020-07-08

Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. Enables common transport planning tasks including: downloading and cleaning transport datasets; creating geographic "desire lines" from origin-destination (OD) data; route assignment, locally and via interfaces to routing services such as <https://cyclestreets.net/>; calculation of route segment attributes such as bearing and aggregate flow; and 'travel watershed' analysis. See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Richard Ellison [aut], Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>), Barry Rowlingson [ctb] (Author of overline), Nick Bearman [ctb] (Co-author of gclip), Nikolai Berkoff [ctb] (Co-author of line2route), Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10), Mark Padgham [ctb], Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

Diff between stplanr versions 0.6.2 dated 2020-07-08 and 0.7.0 dated 2020-08-27

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More information about stplanr at CRAN
Permanent link

Package meteoland updated to version 0.9.4 with previous version 0.9.3 dated 2020-06-09

Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Cáceres [aut, cre], Nicolas Martin [aut], Víctor Granda [aut], Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>

Diff between meteoland versions 0.9.3 dated 2020-06-09 and 0.9.4 dated 2020-08-27

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More information about meteoland at CRAN
Permanent link

Package gtfsrouter updated to version 0.0.3 with previous version 0.0.1 dated 2019-03-22

Title: Routing with GTFS (General Transit Feed Specification) Data
Description: Use GTFS (General Transit Feed Specification) data for routing from nominated start and end stations, and for extracting isochrones from nominated start station.
Author: Mark Padgham [aut, cre], Marcin Stepniak [aut] (<https://orcid.org/0000-0002-6489-5443>), Alexandra Kapp [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>

Diff between gtfsrouter versions 0.0.1 dated 2019-03-22 and 0.0.3 dated 2020-08-27

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More information about gtfsrouter at CRAN
Permanent link

Package GGIR updated to version 2.1-0 with previous version 2.0-0 dated 2020-05-01

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Severine Sabia [ctb], Joan Capdevila Pujol [ctb], Jairo H Migueles [ctb], Matthew R Patterson [ctb], Dan Jackson [ctb]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>

Diff between GGIR versions 2.0-0 dated 2020-05-01 and 2.1-0 dated 2020-08-27

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Package feasts updated to version 0.1.5 with previous version 0.1.4 dated 2020-06-17

Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods, statistical summaries and graphics functions for the analysing tidy time series data. The package name 'feasts' is an acronym comprising of its key features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Di Cook [ctb], Thiyanga Talagala [ctb] (Correlation features), Leanne Chhay [ctb] (Guerrero's method)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

Diff between feasts versions 0.1.4 dated 2020-06-17 and 0.1.5 dated 2020-08-27

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New package trimetStops with initial version 0.1.0
Package: trimetStops
Title: Information on all of the TriMet Stops in the Portland Metro Area
Version: 0.1.0
Authors@R: c( person("Grayson", "White", , "graysonwhite13@gmail.com", c("aut", "cre")), person("Brendan", "Mobley", , "bmobley@reed.edu", "aut") )
Description: Information on all of the TriMet stops in the Portland Metro Area. It includes information such as the longitude, latitude, cross street, and direction of the stop. TriMet has catalogued these stops, 6880 in total.
Depends: R (>= 3.1)
License: CC0
Encoding: UTF-8
LazyData: true
URL: https://github.com/graysonwhite/trimetStops
BugReports: https://github.com/graysonwhite/trimetStops/issues
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-08-24 23:38:02 UTC; graysonwhite
Author: Grayson White [aut, cre], Brendan Mobley [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Repository: CRAN
Date/Publication: 2020-08-27 14:20:02 UTC

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New package TCIU with initial version 1.0.0
Package: TCIU
Title: Spacekime Analytics, Time Complexity and Inferential Uncertainty
Version: 1.0.0
Authors@R: c(person("Yongkai", "Qiu", role = "aut", email = "yongkai@umich.edu"), person("Zhe", "Yin", role = "aut"), person("Jinwen", "Cao", role = "aut"), person("Yupeng", "Zhang", role = "aut"), person("Yuyao", "Liu", role = "aut"), person("Rouben", "Rostamian", role = "ctb"), person("Ranjan", "Maitra", role = "ctb"), person("Daniel", "Rowe", role = "ctb"), person("Daniel", "Adrian", role = "ctb", comment = "gLRT method for complex-valued fMRI statistics"), person("Yunjie", "Guo", role = c("aut", "cre"), email = "jerryguo@umich.edu"), person("Ivo","Dinov", role = "aut", email = "statistics@umich.edu"))
URL: https://github.com/SOCR/TCIU, http://spacekime.org, http://tciu.predictive.space
BugReports: https://github.com/SOCR/TCIU/issues
Description: Provide the core functionality to transform longitudinal data to complex-time (kime) data using analytic and numerical techniques, visualize the original time-series and reconstructed kime-surfaces, perform model based (e.g., tensor-linear regression) and model-free classification and clustering methods in the book Dinov, ID and Velev, MV. (2021) "Data Science: Time Complexity, Inferential Uncertainty, and Spacekime Analytics", De Gruyter STEM Series, ISBN 978-3-11-069780-3. <https://www.degruyter.com/view/title/576646>. The package includes 18 core functions which can be separated into three groups. 1) draw longitudinal data, such as fMRI time-series, and forecast or transform the time-series data. 2) simulate real-valued time-series data, e.g., fMRI time-courses, detect the activated areas, report the corresponding p-values, and visualize the p-values in the 3D brain space. 3) Laplace transform and kimesurface reconstructions of the fMRI data.
Depends: R (>= 3.5.0)
Imports: stats, ggplot2, dplyr, tidyr, RColorBrewer, fancycut, scales, plotly, gridExtra, ggpubr, ICSNP, AnalyzeFMRI, rrcov, geometry, DT, forecast, fmri, pracma, zoo, extraDistr, parallel, foreach, spatstat, cubature, doParallel, reshape2, MultiwayRegression
Suggests: oro.nifti, magrittr, knitr
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-08-25 01:22:32 UTC; gyj99
Author: Yongkai Qiu [aut], Zhe Yin [aut], Jinwen Cao [aut], Yupeng Zhang [aut], Yuyao Liu [aut], Rouben Rostamian [ctb], Ranjan Maitra [ctb], Daniel Rowe [ctb], Daniel Adrian [ctb] (gLRT method for complex-valued fMRI statistics), Yunjie Guo [aut, cre], Ivo Dinov [aut]
Maintainer: Yunjie Guo <jerryguo@umich.edu>
Repository: CRAN
Date/Publication: 2020-08-27 14:40:03 UTC

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New package rsmatrix with initial version 0.1.0
Package: rsmatrix
Title: Matrices for Repeat-Sales Price Indexes
Version: 0.1.0
Authors@R: c( person(given = "Steve", family = "Martin", role = c("aut", "cre", "cph"), email = "stevemartin041@gmail.com") )
Description: A small package for calculating the matrices in Shiller (1991, <doi:10.1016/S1051-1377(05)80028-2>) that serve as the foundation for many repeat-sales price indexes.
Depends: R (>= 4.0)
Imports: Matrix, methods, stats
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/marberts/rsmatrix
LazyData: true
NeedsCompilation: no
Packaged: 2020-08-25 02:14:19 UTC; steve
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>
Repository: CRAN
Date/Publication: 2020-08-27 14:50:02 UTC

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New package rmdwc with initial version 0.1.1
Package: rmdwc
Type: Package
Title: Count Words, Chars and Non-Whitespace Chars in R Markdown Docs
Version: 0.1.1
Date: 2020-08-22
Authors@R: c(person("Sigbert", "Klinke", email="sigbert@hu-berlin.de", role=c("aut", "cre")))
Description: If you are using R Markdown documents then you have sometimes restrictions about the size of the documents, e.g. number of words, number of characters or non-whitespace characters. rmdcount() computes these counts with and without code chunks and returns the result as data frame.
Imports: knitr
License: GPL-3
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-08-25 06:02:47 UTC; sigbert
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Repository: CRAN
Date/Publication: 2020-08-27 14:50:07 UTC

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New package logib with initial version 0.1.0
Package: logib
Type: Package
Title: Salary Analysis by the Swiss Federal Office for Gender Equality
Version: 0.1.0
Authors@R: c( person(given = "Jonathan", family = "Chassot", email = "logib@ebg.admin.ch", role = c("aut", "cre")), person(given = "Jeremy", family = "Kolly", email = "logib@ebg.admin.ch", role = "ctb"), person(given = "Federal Office for Gender Equality of Switzerland", email = "ebg@ebg.admin.ch", role = c("cph", "fnd")) )
Maintainer: Jonathan Chassot <logib@ebg.admin.ch>
Description: Implementation of the Swiss Confederation's standard analysis model for salary analyses <https://www.ebg.admin.ch/dam/ebg/en/dokumente/lohngleichheit/infos-zu-analysen/standard-analysemodellzurueberpruefungderlohngleichheitzwischenf.pdf.download.pdf/methodological_approachformonitoringcompliancewithwageequalitybe.pdf> in R. The analysis is run at company-level and the model is intended for companies with 50 or more employees (apprentices, trainees/interns and expats are not included in the analysis). Employees with at least 100 employees are required by the Gender Equality Act to conduct an equal pay analysis. This package allows users to run the equal salary analysis in R, providing additional transparency with respect to the methodology and simple automation possibilities.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: lubridate (>= 1.7.9), readxl (>= 1.3.1)
RoxygenNote: 7.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-08-25 05:08:56 UTC; 09607938
Author: Jonathan Chassot [aut, cre], Jeremy Kolly [ctb], Federal Office for Gender Equality of Switzerland [cph, fnd]
Repository: CRAN
Date/Publication: 2020-08-27 14:50:10 UTC

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New package equatiomatic with initial version 0.1.0
Package: equatiomatic
Title: Transform Models into 'LaTeX' Equations
Version: 0.1.0
Authors@R: c( person(given = "Daniel", family = "Anderson", role = c("aut", "cre"), email = "daniela@uoregon.edu", comment = c(ORCID = "https://orcid.org/0000-0003-4699-4680")), person(given = "Andrew", family = "Heiss", role = "aut", email = "andrew@andrewheiss.com", comment = c(ORCID = "https://orcid.org/0000-0002-3948-3914")), person(given = "Joshua", family = "Rosenberg", role = "ctb", email = "jmrosenberg@utk.edu", comment = c(ORCID = "http://orcid.org/0000-0003-2170-0447")), person(given = 'Jonathan', family = 'Sidi', role = 'ctb', email = 'yonis@metrumrg.com', comment = c(ORCID = "https://orcid.org/0000-0002-4222-1819")) )
Description: The goal of 'equatiomatic' is to reduce the pain associated with writing 'LaTeX' formulas from fitted models. The primary function of the package, extract_eq(), takes a fitted model object as its input and returns the corresponding 'LaTeX' code for the model.
License: MIT + file LICENSE
Depends: R (>= 3.3.0)
Imports: broom (>= 0.7.0), stats
Suggests: texPreview, testthat (>= 2.1.0), knitr, MASS, ordinal, rmarkdown, covr
URL: https://github.com/datalorax/equatiomatic
BugReports: https://github.com/datalorax/equatiomatic/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-08-24 19:28:50 UTC; daniel
Author: Daniel Anderson [aut, cre] (<https://orcid.org/0000-0003-4699-4680>), Andrew Heiss [aut] (<https://orcid.org/0000-0002-3948-3914>), Joshua Rosenberg [ctb] (<https://orcid.org/0000-0003-2170-0447>), Jonathan Sidi [ctb] (<https://orcid.org/0000-0002-4222-1819>)
Maintainer: Daniel Anderson <daniela@uoregon.edu>
Repository: CRAN
Date/Publication: 2020-08-27 14:20:06 UTC

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New package ANOVAShiny2 with initial version 0.1.0
Package: ANOVAShiny2
Type: Package
Title: Interactive Document for Working with Analysis of Variance
Version: 0.1.0
Author: Kartikeya Bolar
Maintainer: Kartikeya Bolar <kartikeya.bolar@tapmi.edu.in>
Description: An interactive document on the topic of one-way and two-way analysis of variance using 'rmarkdown' and 'shiny' packages. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/ANOVAShiny/>.
License: GPL-2
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 4.0.0)
Imports: shiny,rmarkdown,dplyr,datasets,rhandsontable,DescTools,HH
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-08-25 13:41:28 UTC; kartikeya.bolar
Repository: CRAN
Date/Publication: 2020-08-27 15:00:02 UTC

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Package ptmixed updated to version 1.0.0 with previous version 0.5.4 dated 2020-06-13

Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed model described in Signorelli et al. (2020, <doi:10.1177/1471082X20936017>). Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre] (<https://orcid.org/0000-0002-8102-3356>), Pietro Spitali [aut], Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

Diff between ptmixed versions 0.5.4 dated 2020-06-13 and 1.0.0 dated 2020-08-27

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Package pct updated to version 0.5.0 with previous version 0.4.1 dated 2020-06-15

Title: Propensity to Cycle Tool
Description: Functions and example data to teach and increase the reproducibility of the methods and code underlying the Propensity to Cycle Tool (PCT), a research project and web application hosted at <https://www.pct.bike/>. For an academic paper on the methods, see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>

Diff between pct versions 0.4.1 dated 2020-06-15 and 0.5.0 dated 2020-08-27

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Package gprofiler2 updated to version 0.2.0 with previous version 0.1.9 dated 2020-04-23

Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>). The main tools are: (1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists; (2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces; (3) 'g:Orth' - orthology search across species; (4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>

Diff between gprofiler2 versions 0.1.9 dated 2020-04-23 and 0.2.0 dated 2020-08-27

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Package glue updated to version 1.4.2 with previous version 1.4.1 dated 2020-05-13

Title: Interpreted String Literals
Description: An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>

Diff between glue versions 1.4.1 dated 2020-05-13 and 1.4.2 dated 2020-08-27

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Package ExtremeRisks updated to version 0.0.4 with previous version 0.0.3 dated 2020-05-07

Title: Extreme Risk Measures
Description: A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations. The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2020) <arxiv:2004.04078>, Padoan and Stupfler (2020) <arxiv:2007.08944>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6>.
Author: Simone Padoan [cre, aut], Gilles Stupfler [aut], Bocconi Institute for Data Science and Analytics [fnd], French National Research [fnd] (grant ANR-19-CE40-0013-01/ExtremReg)
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>

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Package castor updated to version 1.6.3 with previous version 1.6.2 dated 2020-07-19

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package tidyr updated to version 1.1.2 with previous version 1.1.1 dated 2020-07-31

Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package TAG updated to version 0.2.1 with previous version 0.2.0 dated 2020-01-09

Title: Transformed Additive Gaussian Processes
Description: Implement the transformed additive Gaussian (TAG) process and the transformed approximately additive Gaussian (TAAG) process proposed in Lin and Joseph (2019+) <DOI:10.1080/00401706.2019.1665592>. These functions can be used to model deterministic computer experiments, obtain predictions at new inputs, and quantify the uncertainty of the predictions. This research is supported by a U.S. National Science Foundation grant DMS-1712642 and a U.S. Army Research Office grant W911NF-17-1-0007.
Author: Li-Hsiang Lin and V. Roshan Joseph
Maintainer: Li-Hsiang Lin <llin79@gatech.edu>

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Package sapfluxnetr updated to version 0.1.1 with previous version 0.1.0 dated 2020-05-11

Title: Working with 'Sapfluxnet' Project Data
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project (<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>), Rafael Poyatos [aut] (<https://orcid.org/0000-0003-0521-2523>), Victor Flo [aut] (<https://orcid.org/0000-0003-1908-4577>), Jacob Nelson [ctb] (<https://orcid.org/0000-0002-4663-2420>), Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>

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Package ptvapi updated to version 1.1.3 with previous version 1.1.2 dated 2020-06-03

Title: Access the 'Public Transport Victoria' Timetable API
Description: Access the 'Public Transport Victoria' Timetable API <https://www.ptv.vic.gov.au/footer/data-and-reporting/datasets/ptv-timetable-api/>, with results returned as familiar R data structures. Retrieve information on stops, routes, disruptions, departures, and more.
Author: David Neuzerling [aut, cre, cph]
Maintainer: David Neuzerling <david@neuzerling.com>

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Package support.BWS updated to version 0.4-2 with previous version 0.4-1 dated 2020-04-12

Title: Tools for Case 1 Best-Worst Scaling
Description: Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. For details on best-worst scaling, see Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

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Package sigminer updated to version 1.0.13 with previous version 1.0.7 dated 2020-06-17

Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>), Tao Wu [aut, ctb], Ziyu Tao [aut, ctb], Geoffrey Macintyre [ctb], Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package season updated to version 0.3.12 with previous version 0.3.11 dated 2020-05-25

Title: Seasonal Analysis of Health Data
Description: Routines for the seasonal analysis of health data, including regression models, time-stratified case-crossover, plotting functions and residual checks, see Barnett and Dobson (2010) ISBN 978-3-642-10748-1. Thanks to Yuming Guo for checking the case-crossover code.
Author: Adrian Barnett and Peter Baker
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>

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Package santoku updated to version 0.5.0 with previous version 0.4.1 dated 2020-06-16

Title: A Versatile Cutting Tool
Description: A tool for cutting data into intervals. Allows singleton intervals. Always includes the whole range of data by default. Flexible labelling. Convenience functions for cutting by quantiles etc. Handles dates and times.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

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Package RMariaDB updated to version 1.0.10 with previous version 1.0.9 dated 2020-07-03

Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB' (<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>) databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>), David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], R Consortium [fnd], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package pointblank updated to version 0.5.1 with previous version 0.5.0 dated 2020-08-12

Title: Validation of Local and Remote Data Tables
Description: Validate data in data frames, 'tibble' objects, and in database tables (e.g., 'PostgreSQL' and 'MySQL'). Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>

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More information about pointblank at CRAN
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Package hsrecombi updated to version 0.3.1 with previous version 0.3.0 dated 2020-05-28

Title: Estimation of Recombination Rate and Maternal LD in Half-Sibs
Description: Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least one sire has to be double heterozygous at the investigated pairs of SNPs. The implementation relies on paternal half-sib families. If maternal half- sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" <doi:10.3389/fgene.2018.00186>. Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" <doi:10.1534/genetics.111.137521>.
Author: Dörte Wittenburg [aut, cre]
Maintainer: Dörte Wittenburg <wittenburg@fbn-dummerstorf.de>

Diff between hsrecombi versions 0.3.0 dated 2020-05-28 and 0.3.1 dated 2020-08-27

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Package ggnewscale updated to version 0.4.3 with previous version 0.4.2 dated 2020-08-01

Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>

Diff between ggnewscale versions 0.4.2 dated 2020-08-01 and 0.4.3 dated 2020-08-27

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New package gdalcubes with initial version 0.3.1
Package: gdalcubes
Title: Earth Observation Data Cubes from Satellite Image Collections
Version: 0.3.1
Date: 2020-08-25
Authors@R: c( person(given = "Marius", family = "Appel", role = c("aut", "cre"), email = "marius.appel@uni-muenster.de", comment = c(ORCID = "0000-0001-5281-3896")), person(given = "Edzer", family = "Pebesma", role = "ctb", comment = c(ORCID = "0000-0001-8049-7069")), person(given = "Roger", family = "Bivand", role = "ctb"), person(given = "Lewis", family = "Van Winkle", role = "cph"), person(given = "Ole Christian", family = "Eidheim", role = "cph"), person(given = "Howard", family = "Hinnant", role = "cph"), person(given = "Adrian", family = "Colomitchi", role = "cph"), person(given = "Florian", family = "Dang", role = "cph"), person(given = "Paul", family = "Thompson", role = "cph"), person(given = "Tomasz", family = "Kamiński", role = "cph"), person(given = "Dropbox, Inc.", role = "cph"))
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Depends: R (>= 3.4)
Imports: Rcpp, RcppProgress, jsonlite, ncdf4
License: MIT + file LICENSE
URL: https://github.com/appelmar/gdalcubes_R
BugReports: https://github.com/appelmar/gdalcubes_R/issues/
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppProgress
Suggests: knitr, magrittr, rmarkdown, stars, magick, sf
VignetteBuilder: knitr
Copyright: file inst/COPYRIGHTS
NeedsCompilation: yes
SystemRequirements: cxx11, gdal, libgdal, libproj, netcdf4
Packaged: 2020-08-25 10:32:37 UTC; marius
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph], Dropbox, Inc. [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>
Repository: CRAN
Date/Publication: 2020-08-27 11:40:16 UTC

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Package double.truncation updated to version 1.6 with previous version 1.5 dated 2020-07-16

Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models. Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>. Parametric models from the special exponential family (SEF) are based on Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>. The parametric location-scale models are based on Dorre et al. (2020-).
Author: Takeshi Emura, Ya-Hsuan Hu, Chung-Yan Huang
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between double.truncation versions 1.5 dated 2020-07-16 and 1.6 dated 2020-08-27

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Package anytime updated to version 0.3.9 with previous version 0.3.8 dated 2020-07-24

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 BayesBP updated to version 1.1 with previous version 1.0 dated 2019-10-02

Title: Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix
Description: Smoothed lexis diagrams with Bayesian method specifically tailored to cancer incidence data. Providing to calculating slope and constructing credible interval. LC Chien et al. (2015) <doi:10.1080/01621459.2015.1042106>. LH Chien et al. (2017) <doi:10.1002/cam4.1102>.
Author: Li-Syuan Hong [aut, cre]
Maintainer: Li-Syuan Hong <lisyuan@nhri.org.tw>

Diff between BayesBP versions 1.0 dated 2019-10-02 and 1.1 dated 2020-08-27

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Package SNPassoc (with last version 1.9-2.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-08-19 1.9-2.1
2014-04-23 1.9-2
2013-11-08 1.9-1

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Package BIGDAWG (with last version 2.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-11-12 2.3
2018-02-08 2.1
2017-09-06 1.16
2017-07-19 1.14.2
2017-07-10 1.14

Permanent link
Package SQRL updated to version 0.7.3 with previous version 0.7.2 dated 2020-05-13

Title: Enhanced Database Interactivity
Description: Facilitates interaction with ODBC data sources, by remembering and hiding communication settings and supporting parameterised multi-statement SQL with embedded R.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>

Diff between SQRL versions 0.7.2 dated 2020-05-13 and 0.7.3 dated 2020-08-27

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New package nlstimedist with initial version 2.0.0
Package: nlstimedist
Type: Package
Title: Non-Linear Model Fitting of Time Distribution of Biological Phenomena
Version: 2.0.0
Authors@R: c(person( given = "Nathan", family = "Eastwood", role = c("aut", "cre", "prg", "trl", "ctr"), email = "nathan.eastwood@icloud.com"), person( given = "Nicola", family = "Steer", role = "ctb", email = "nicola.steer@plymouth.ac.uk", comment = c(ORCID = "0000-0002-6446-8601")), person( given = "Miguel", family = "Franco", role = "ctb", email = "M.Franco@plymouth.ac.uk", comment = c(ORCID = "0000-0002-7249-4981")), person( given = "Paul", family = "Ramsay", role = "ctb", email = "paul.ramsay@plymouth.ac.uk", comment = c(ORCID = "0000-0001-7631-6480")))
Description: Fit biologically meaningful distribution functions to time-sequence data (phenology), estimate parameters to draw the cumulative distribution function and probability density function and calculate standard statistical moments and percentiles. These methods are described in Steer et al. (2019) <doi:10.1111/2041-210X.13293>.
URL: https://github.com/nathaneastwood/nlstimedist
BugReports: https://github.com/nathaneastwood/nlstimedist/issues
Depends: R (>= 3.5.0)
Imports: ggplot2 (>= 2.1.0), minpack.lm (>= 1.2-0), nlstools (>= 1.0-2), poorman (>= 0.2.1), stats
Suggests: knitr, rmarkdown, tinytest
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 7.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-08-26 07:05:10 UTC; nathan
Author: Nathan Eastwood [aut, cre, prg, trl, ctr], Nicola Steer [ctb] (<https://orcid.org/0000-0002-6446-8601>), Miguel Franco [ctb] (<https://orcid.org/0000-0002-7249-4981>), Paul Ramsay [ctb] (<https://orcid.org/0000-0001-7631-6480>)
Maintainer: Nathan Eastwood <nathan.eastwood@icloud.com>
Repository: CRAN
Date/Publication: 2020-08-27 08:20:03 UTC

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Package mgcv updated to version 1.8-33 with previous version 1.8-32 dated 2020-08-19

Title: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Description: Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>

Diff between mgcv versions 1.8-32 dated 2020-08-19 and 1.8-33 dated 2020-08-27

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Package compareGroups (with last version 4.4.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-08-25 4.4.4
2020-06-25 4.4.3
2020-03-19 4.4.1
2019-09-19 4.2.0
2019-05-27 4.1.0
2018-11-02 4.0.0
2018-05-18 3.4.0
2018-04-22 3.3.4
2018-01-29 3.3.3

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Package Rsampletrees (with last version 1.0.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-03-02 1.0.3
2018-01-03 1.0.2
2017-08-29 1.0.1
2017-04-18 1.0
2015-02-02 0.1

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Package IFP (with last version 0.2.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-02-04 0.2.1
2015-06-11 0.2.0
2015-02-08 0.1.2
2015-01-10 0.1.1

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Package CollapsABEL (with last version 0.10.11) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-12-11 0.10.11
2016-04-04 0.10.8

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Package BVS (with last version 4.12.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-08-09 4.12.1
2012-05-10 4.12.0

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Package pould (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-04-15 1.0.0

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Package RTaxometrics updated to version 2.4 with previous version 2.3 dated 2017-09-09

Title: Taxometric Analysis
Description: We provide functions to perform taxometric analyses. This package contains 44 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.
Author: John Ruscio <ruscio@tcnj.edu> and Shirley Wang <shirleywang@g.harvard.edu>
Maintainer: John Ruscio <ruscio@tcnj.edu>

Diff between RTaxometrics versions 2.3 dated 2017-09-09 and 2.4 dated 2020-08-27

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Package pedquant updated to version 0.1.6 with previous version 0.1.5 dated 2020-04-09

Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for economic research and quantitative analysis. The data sources including NBS, FRED, Yahoo Finance, 163 Finance and etc.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>

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Package mixedCCA updated to version 1.3.1 with previous version 1.3.0 dated 2020-08-26

Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed Data
Description: Semi-parametric approach for sparse canonical correlation analysis which can handle mixed data types: continuous, binary and truncated continuous. Bridge functions are provided to connect Kendall's tau to latent correlation under the Gaussian copula model. The methods are described in Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007>.
Author: Grace Yoon [aut, cre] (<https://orcid.org/0000-0003-3263-1352>), Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Grace Yoon <gyoon@stat.tamu.edu>

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Permanent link

Package MARSS updated to version 3.11.1 with previous version 3.10.12 dated 2020-02-04

Title: Multivariate Autoregressive State-Space Modeling
Description: The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lectures and computer labs) at <https://nwfsc-timeseries.github.io/> See the NEWS file for update information.
Author: Eli Holmes, Eric Ward, Mark Scheuerell, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>

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Package iCARH updated to version 2.0.2.1 with previous version 2.0.2.0 dated 2020-06-16

Title: Integrative Conditional Autoregressive Horseshoe Model
Description: Implements the integrative conditional autoregressive horseshoe model discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery. BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>. The model consists in three levels: Metabolic pathways level modeling interdependencies between variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify potential associations between heterogeneous omic variables via a Horseshoe prior and experimental design level to capture experimental design conditions through a mixed-effects model. The package also provides functions to simulate data from the model, construct pathway matrices, post process and plot model parameters.
Author: Takoua Jendoubi [aut, cre], Timothy M.D. Ebbels [aut]
Maintainer: Takoua Jendoubi <t.jendoubi14@imperial.ac.uk>

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Package ecm updated to version 5.0.0 with previous version 4.5.0 dated 2020-06-27

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

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Package ores updated to version 0.3.2 with previous version 0.3.1 dated 2017-11-17

Title: Connector to the Objective Revision Evaluation Service (ORES)
Description: A connector to ORES (<https://ores.wmflabs.org/>), an AI project to provide edit scoring for content on Wikipedia and other Wikimedia projects. This lets a researcher identify if edits are likely to be reverted, damaging, or made in good faith.
Author: Os Keyes [aut, cre], Aaron Halfaker [ctb], Yuvi Panda [ctb]
Maintainer: Os Keyes <ironholds@gmail.com>

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Package labelled updated to version 2.6.0 with previous version 2.5.0 dated 2020-06-17

Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. This package provides useful functions to deal with "haven_labelled" and "haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>), Daniel Ludecke [ctb], Hadley Wickham [ctb], Michal Bojanowski [ctb], François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

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Package haplo.stats (with last version 1.8.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-08-12 1.8.2
2018-04-11 1.7.9
2016-04-05 1.7.7
2016-02-23 1.7.6
2015-08-14 1.7.1
2014-09-04 1.6.11
2013-12-06 1.6.8
2013-01-17 1.6.3
2013-01-15 1.6.1
2012-11-20 1.5.8
2012-09-28 1.5.6
2012-02-25 1.5.5
2011-12-13 1.5.2
2009-10-01 1.4.4
2009-04-28 1.4.3
2008-05-13 1.3.8
2007-06-14 1.3.1

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Package WeightIt updated to version 0.10.2 with previous version 0.10.1 dated 2020-08-12

Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>

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Package vroom updated to version 1.3.1 with previous version 1.3.0 dated 2020-08-14

Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), https://github.com/mandreyel/ [cph] (mio library), R Core Team [ctb] (localtime.c code adapted from R), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>

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Package traits updated to version 0.5.0 with previous version 0.4.2 dated 2019-06-29

Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Zachary Foster [aut], Ignasi Bartomeus [aut], David LeBauer [aut], Chris Black [aut], David Harris [aut], Rupert Collins [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rotasym updated to version 1.0.9 with previous version 1.0.8 dated 2020-07-29

Title: Tests for Rotational Symmetry on the Hypersphere
Description: Implementation of the tests for rotational symmetry on the hypersphere proposed in García-Portugués, Paindaveine and Verdebout (2020) <doi:10.1080/01621459.2019.1665527>. The package also implements the proposed distributions on the hypersphere, based on the tangent-normal decomposition, and allows for the replication of the data application considered in the paper.
Author: Eduardo García-Portugués [aut, cre] (<https://orcid.org/0000-0002-9224-4111>), Davy Paindaveine [aut], Thomas Verdebout [aut]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>

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Package ncmeta updated to version 0.3.0 with previous version 0.2.5 dated 2020-05-12

Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or servers. This package leverages and extends the lower level functions of the 'RNetCDF' package providing a consistent set of functions that all return data frames. We introduce named concepts of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the 'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library itself with only the named concepts of 'variables', 'dimensions' and 'attributes'.
Author: Michael Sumner [aut, cre], Tomas Remenyi [ctb], Ben Raymond [ctb], David Blodgett [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>

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Package fst updated to version 0.9.4 with previous version 0.9.2 dated 2020-04-01

Title: Lightning Fast Serialization of Data Frames
Description: Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and ZSTD code and copyright holder of LZ4), Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>

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Package conquer updated to version 1.0.2 with previous version 1.0.1 dated 2020-05-06

Title: Convolution-Type Smoothed Quantile Regression
Description: Fast and accurate convolution-type smoothed quantile regression. Implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Construct confidence intervals for regression coefficients using multiplier bootstrap.
Author: Xuming He [aut], Xiaoou Pan [aut, cre], Kean Ming Tan [aut], Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>

Diff between conquer versions 1.0.1 dated 2020-05-06 and 1.0.2 dated 2020-08-27

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Package bnma updated to version 1.3.0 with previous version 1.2.0 dated 2020-07-06

Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-based data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre], Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>

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Package RcppEnsmallen updated to version 0.2.14.1.1 with previous version 0.2.13.0.1 dated 2020-07-24

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 g3viz updated to version 1.1.3 with previous version 1.1.2 dated 2019-05-29

Title: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram
Description: R interface for 'g3-lollipop' JavaScript library. Visualize genetic mutation data using an interactive lollipop diagram in RStudio or your browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <g3viz.group@gmail.com>

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